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From: <nik...@us...> - 2015-11-27 17:15:36
|
Revision: 2413
http://sourceforge.net/p/jsbml/code/2413
Author: niko-rodrigue
Date: 2015-11-27 17:15:33 +0000 (Fri, 27 Nov 2015)
Log Message:
-----------
updated version number in the ant scripts + started to work on the NEWS + added the sourceforge README files
Modified Paths:
--------------
trunk/NEWS.txt
trunk/build.xml
trunk/core/build.xml
trunk/jsbml-build.properties
Added Paths:
-----------
trunk/doc/sourceforge/files/jsbml/1.1/
trunk/doc/sourceforge/files/jsbml/1.1/README.txt
trunk/doc/sourceforge/files/jsbml/1.1/modules/
trunk/doc/sourceforge/files/jsbml/1.1/modules/README.txt
Modified: trunk/NEWS.txt
===================================================================
--- trunk/NEWS.txt 2015-11-27 16:35:49 UTC (rev 2412)
+++ trunk/NEWS.txt 2015-11-27 17:15:33 UTC (rev 2413)
@@ -1,6 +1,24 @@
JSBML NEWS -- History of user-visible changes
===========================================================================
+Version 1.1 (03-12-2015)
+===========================================================================
+
+ * New Features:
+
+ - Finish to implement support for multiple version of a L3 package.
+
+ - Improvement of the maven pom files, change to the maven groud ids and
+ artifact ids, they should be stable now.
+
+ - Added some utility classes to improve support for SBML files written by
+ the cobra toolbox before the fbc package was created. The
+ CobraFormulaParser class can parse properly the Cobra gene associations
+ String into an ASTNode. The CobraUtils class contain a method to parse
+ the SBML notes into a java Properties object.
+
+
+===========================================================================
Version 1.1-beta1 (12-10-2015)
===========================================================================
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2015-11-27 16:35:49 UTC (rev 2412)
+++ trunk/build.xml 2015-11-27 17:15:33 UTC (rev 2413)
@@ -46,7 +46,7 @@
<property name="Name" value="JSBML" />
<property name="name" value="jsbml" />
- <property name="version" value="1.1-b1" />
+ <property name="version" value="1.1" />
<property name="api.version" value="1.1" />
<property name="year" value="${YEAR}" />
Modified: trunk/core/build.xml
===================================================================
--- trunk/core/build.xml 2015-11-27 16:35:49 UTC (rev 2412)
+++ trunk/core/build.xml 2015-11-27 17:15:33 UTC (rev 2413)
@@ -43,7 +43,7 @@
<property name="Name" value="JSBML"/>
<property name="name" value="jsbml"/>
- <property name="version" value="1.1-b1"/>
+ <property name="version" value="1.1"/>
<property name="api.version" value="1.1"/>
<property name="year" value="${YEAR}"/>
Added: trunk/doc/sourceforge/files/jsbml/1.1/README.txt
===================================================================
--- trunk/doc/sourceforge/files/jsbml/1.1/README.txt (rev 0)
+++ trunk/doc/sourceforge/files/jsbml/1.1/README.txt 2015-11-27 17:15:33 UTC (rev 2413)
@@ -0,0 +1,53 @@
+ J S B M L 1.1
+
+JSBML is a free, open-source programming library to help you read, write,
+manipulate, translate, and validate SBML files and data streams. It is not
+an application itself (though it does come with example programs), but
+rather a library you can embed in your own applications.
+
+This is the top-level directory of the JSBML 1.1 final release. Here you
+will find the following:
+
+ jsbml-1.1.jar -- jar file containing the classes of JSBML-1.1
+
+ jsbml-1.1-with-dependencies.jar -- jar file containing the
+ classes of JSBML-1.1 including all of the currently supported
+ SBML L3 packages and any needed dependencies libraries classes.
+
+ jsbml-1.1-full.zip -- full distribution of JSBML-1.1
+ containing the two jars file described above plus the sources and
+ documentation along with the build script to be able to compile the
+ library. Contain also the jsbml modules sources and binaries.
+
+
+Please note: some of the code for the SBML Level 3 packages reflects the current
+state of development of each packages. Many of the SBML Level 3 package
+specifications have not yet been finalized, and the package implementations
+are themselves in a state of development. The code available may be untested
+and is supplied 'as-is' for experimental development only.
+
+For more information about JSBML, please visit the JSBML website at
+
+ http://sbml.org/Software/JSBML
+
+
+Thank you for your interest in JSBML!
+
+The JSBML Team.
+
+
+ .-://///:` .:/+++++/-` .--. `---` `--
+ -/++//:---:.`://+syyyssoo+` ohhy` /hhh. -hy`
+`/++/-` ::/ohhyyssssoss- ohhh+ .yhhh. .hy`
+:++/. `:::sysoo+++++oss. ohoyh- `ohoyh. .hy`
+++//` `--:/oo+///://+os: oh//hs` :hs.yh. .hy`
+/+//. `..--:////:--:/oos. oh/`sh/ `yh-`yh. .hy`
+`////:-.......---::://///++oo- oh/ -hy. +h+ `yh. .hy`
+ .:///:::::--::::://///++oo: oh/ +hs -hy` `yh. .hy`
+`::-``..--::::::://osyyysoooo. oh/ `yh: `sh: `yh. .hy`
+:o+/` .:////oyhyyyyyyssss` oh/ :hy` /ho` `yh. .hy`
+/oo/ .///oyysoo+++oosyy- oh/ oho .hh. `yh. .hy`
+.sso: `+++oso+//////syyy` oh/ .hh-oh/ `yh. .hy`
+ :sss+-` ./oooooo//:::+syyy. oh/ /hhhs` `yh. -hy`
+ `/syssooossssssssssssyyyy/` oh/ shh- `yh. -hhooooooooooo
+ `-/+oso+/-.-:/osyyso/-` -:. .:- `--` `:::::::::::::
Added: trunk/doc/sourceforge/files/jsbml/1.1/modules/README.txt
===================================================================
--- trunk/doc/sourceforge/files/jsbml/1.1/modules/README.txt (rev 0)
+++ trunk/doc/sourceforge/files/jsbml/1.1/modules/README.txt 2015-11-27 17:15:33 UTC (rev 2413)
@@ -0,0 +1,41 @@
+ J S B M L 1.1
+
+JSBML is a free, open-source programming library to help you read, write,
+manipulate, translate, and validate SBML files and data streams. It is not
+an application itself (though it does come with example programs), but
+rather a library you can embed in your own applications.
+
+This is the top-level directory of the modules for JSBML 1.1. Here you
+will find the following:
+
+ jsbml-celldesigner-1.0.zip -- distribution for the celldesigner module
+
+ jsbml-libSBMLio-1.0.zip -- distribution for the libSBMLio module
+
+ jsbml-tidy-1.0.zip -- distribution for the tidy module
+
+For more information about JSBML, please visit the JSBML website at
+
+ http://sbml.org/Software/JSBML
+
+
+Thank you for your interest in JSBML!
+
+The JSBML Team.
+
+
+ .-://///:` .:/+++++/-` .--. `---` `--
+ -/++//:---:.`://+syyyssoo+` ohhy` /hhh. -hy`
+`/++/-` ::/ohhyyssssoss- ohhh+ .yhhh. .hy`
+:++/. `:::sysoo+++++oss. ohoyh- `ohoyh. .hy`
+++//` `--:/oo+///://+os: oh//hs` :hs.yh. .hy`
+/+//. `..--:////:--:/oos. oh/`sh/ `yh-`yh. .hy`
+`////:-.......---::://///++oo- oh/ -hy. +h+ `yh. .hy`
+ .:///:::::--::::://///++oo: oh/ +hs -hy` `yh. .hy`
+`::-``..--::::::://osyyysoooo. oh/ `yh: `sh: `yh. .hy`
+:o+/` .:////oyhyyyyyyssss` oh/ :hy` /ho` `yh. .hy`
+/oo/ .///oyysoo+++oosyy- oh/ oho .hh. `yh. .hy`
+.sso: `+++oso+//////syyy` oh/ .hh-oh/ `yh. .hy`
+ :sss+-` ./oooooo//:::+syyy. oh/ /hhhs` `yh. -hy`
+ `/syssooossssssssssssyyyy/` oh/ shh- `yh. -hhooooooooooo
+ `-/+oso+/-.-:/osyyso/-` -:. .:- `--` `:::::::::::::
Modified: trunk/jsbml-build.properties
===================================================================
--- trunk/jsbml-build.properties 2015-11-27 16:35:49 UTC (rev 2412)
+++ trunk/jsbml-build.properties 2015-11-27 17:15:33 UTC (rev 2413)
@@ -1,7 +1,7 @@
jsbml.Name=JSBML
jsbml.name=jsbml
-jsbml.version=1.1-SNAPSHOT
+jsbml.version=1.1
jsbml.api.version=1.1
jsbml.groupId=org.sbml.jsbml
jsbml.artifactId=jsbml-parent
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-27 16:35:51
|
Revision: 2412
http://sourceforge.net/p/jsbml/code/2412
Author: niko-rodrigue
Date: 2015-11-27 16:35:49 +0000 (Fri, 27 Nov 2015)
Log Message:
-----------
improved a bit the javadoc of SBMLDocument
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/SBMLDocument.java
Modified: trunk/core/src/org/sbml/jsbml/SBMLDocument.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SBMLDocument.java 2015-11-27 14:57:17 UTC (rev 2411)
+++ trunk/core/src/org/sbml/jsbml/SBMLDocument.java 2015-11-27 16:35:49 UTC (rev 2412)
@@ -941,6 +941,12 @@
/**
* Returns {@code true} if the given SBML Level 3 package is enabled within the {@link SBMLDocument}.
*
+ * <p>If the namespace was declared on the sbml element, or if any elements of this package were found while building the SBMLDocument structure,
+ * the package will be enabled.
+ * <p>For the parameter '{@code packageNameorUri}', you should use the package shortLabel or name, for example 'distrib', as given by {@link org.sbml.jsbml.ext.distrib.DistribConstants#shortLabel},
+ * this way, you don't mind about the specific package version.
+ * If you want to check for a specific package version, then you can use the namespace instead.
+ *
* @param packageURIOrName the name or URI of the package extension.
* @return {@code true} if the given SBML Level 3 package is enabled within the {@link SBMLDocument}, {@code false} otherwise.
*/
@@ -981,8 +987,9 @@
* if the package was disabled using the method {@link #disablePackage(String)} or {@code null} if this package
* was neither enabled or disabled on this {@link SBMLDocument}.
*
- * <p>This method can be used, for example, by the {@link SBMLWriter} to know if a package was really disabled
- * or if the user forgot to enable it.
+ * <p>This method can be used, for example, by the {@link SBMLWriter} to know if a package was really disabled,
+ * in which case the package elements won't be written down,
+ * or if the user forgot to enable it, in which case it will be enabled and the package elements will be written.
*
* @param packageURIOrName the name or URI of the package extension.
* @return {@code true} if the given SBML Level 3 package is enabled within the {@link SBMLDocument}, {@code false}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-27 14:57:20
|
Revision: 2411
http://sourceforge.net/p/jsbml/code/2411
Author: niko-rodrigue
Date: 2015-11-27 14:57:17 +0000 (Fri, 27 Nov 2015)
Log Message:
-----------
update the version number in the JSBML class
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/JSBML.java
Modified: trunk/core/src/org/sbml/jsbml/JSBML.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/JSBML.java 2015-11-27 14:54:26 UTC (rev 2410)
+++ trunk/core/src/org/sbml/jsbml/JSBML.java 2015-11-27 14:57:17 UTC (rev 2411)
@@ -80,7 +80,7 @@
/**
* The current version number of JSBML.
*/
- private static final String jsbmlVersion = "1.1-alpha"; // TODO: replace automatically this version number with [BUILD.NUMBER]
+ private static final String jsbmlVersion = "1.1"; // TODO: replace automatically this version number with [BUILD.NUMBER]
/**
*
*/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-27 14:54:29
|
Revision: 2410
http://sourceforge.net/p/jsbml/code/2410
Author: niko-rodrigue
Date: 2015-11-27 14:54:26 +0000 (Fri, 27 Nov 2015)
Log Message:
-----------
corrected the last failing tests + improve few toString methods
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java
trunk/core/src/org/sbml/jsbml/AbstractSBase.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
trunk/test/org/sbml/jsbml/test/PackageVersionTests.java
trunk/test/org/sbml/jsbml/test/UnregisterPackageTests.java
Modified: trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -327,10 +327,10 @@
@Override
public String toString() {
if (isSetName() && (getName().length() > 0)) {
- return name;
+ return getElementName() + ": name= " + name;
}
if (isSetId()) {
- return id;
+ return getElementName() + ": id= " + id;
}
return getElementName();
}
Modified: trunk/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -859,6 +859,7 @@
while (children.hasMoreElements()) {
TreeNode child = children.nextElement();
+
if (child instanceof AbstractSBase && ((AbstractSBase) child).getPackageName().equals(sbasePlugin.getPackageName()))
{
success &= ((AbstractSBase) child).setPackageNamespaceAndVersion(sbasePlugin.getPackageName(), packageNamespace, packageVersion);
@@ -1088,12 +1089,7 @@
SBasePlugin sbasePlugin = (SBasePlugin) newValue;
if (doc != null) {
- String packageNamespace = doc.getEnabledPackageNamespace(sbasePlugin.getPackageName());
- int packageVersion = PackageUtil.extractPackageVersion(packageNamespace);
-
- ((AbstractSBasePlugin) sbasePlugin).setNamespace(packageNamespace);
- sbasePlugin.setPackageVersion(packageVersion);
-
+ checkAndSetPackageNamespaceAndVersion(sbasePlugin, doc);
}
}
@@ -2050,6 +2046,7 @@
while (children.hasMoreElements()) {
TreeNode child = children.nextElement();
+
if (child instanceof AbstractSBase && ((AbstractSBase) child).getPackageName().equals(packageLabel)) {
success &= ((AbstractSBase) child).setPackageNamespaceAndVersion(packageLabel, namespace, packageVersion);
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -315,11 +315,12 @@
*/
@Override
public String toString() {
+
if (isSetName() && (getName().length() > 0)) {
- return name;
+ return getElementName() + ": name= " + name;
}
if (isSetId()) {
- return id;
+ return getElementName() + ": id= " + id;
}
return getElementName();
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -108,6 +108,8 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
+ setPackageVersion(-1);
+ packageName = CompConstants.shortLabel;
}
/* (non-Javadoc)
@@ -126,4 +128,18 @@
return new Port(this);
}
+ /* (non-Javadoc)
+ * @see java.lang.Object#toString()
+ */
+ @Override
+ public String toString() {
+ return "Port [id=" + getId() + ", name=" + getName()
+ + (isSetPortRef() ? ", portRef=" + getPortRef() : "")
+ + (isSetIdRef() ? ", idRef=" + getIdRef() : "")
+ + (isSetMetaIdRef() ? ", metaIdRef=" + getMetaIdRef() : "")
+ + "]";
+ }
+
+
+
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -547,8 +547,12 @@
*/
@Override
public String toString() {
- return "SBaseRef [portRef=" + portRef + ", idRef=" + idRef
- + ", unitRef=" + unitRef + ", metaIdRef=" + metaIdRef
+ return "SBaseRef ["
+ + (isSetPortRef() ? ", portRef=" + getPortRef() : "")
+ + (isSetIdRef() ? ", idRef=" + getIdRef() : "")
+ + (isSetMetaIdRef() ? ", metaIdRef=" + getMetaIdRef() : "")
+ + (isSetUnitRef() ? ", unitIdRef=" + getUnitRef() : "")
+ + (isSetSBaseRef() ? "SBaseRef child is set" : "")
+ "]";
}
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -686,7 +686,7 @@
public String toString() {
return "Group [id=" + getId() + ", name=" + getName()
+ (isSetKind()?", kind=" + getKind():"")
- + ", listOfMembers=" + listOfMembers + "]";
+ + ", memberCount=" + getMemberCount() + "]";
}
/* (non-Javadoc)
Modified: trunk/test/org/sbml/jsbml/test/PackageVersionTests.java
===================================================================
--- trunk/test/org/sbml/jsbml/test/PackageVersionTests.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/test/org/sbml/jsbml/test/PackageVersionTests.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -160,7 +160,7 @@
g2.createMemberWithIdRef("G_M4", "S1");
g2.getMember(0).setIdRef("S2");
g2.getMember("G_M2").setIdRef(cell);
- g2.createMemberConstraint("G_MC1").setDistinctAttribute("test");
+// g2.createMemberConstraint("G_MC1").setDistinctAttribute("test");
QualModelPlugin qualModel = (QualModelPlugin) m.getPlugin(QualConstants.shortLabel);
qualModel.createQualitativeSpecies("Q_QS1");
Modified: trunk/test/org/sbml/jsbml/test/UnregisterPackageTests.java
===================================================================
--- trunk/test/org/sbml/jsbml/test/UnregisterPackageTests.java 2015-11-27 13:36:43 UTC (rev 2409)
+++ trunk/test/org/sbml/jsbml/test/UnregisterPackageTests.java 2015-11-27 14:54:26 UTC (rev 2410)
@@ -25,6 +25,8 @@
import javax.xml.stream.XMLStreamException;
+import junit.framework.Assert;
+
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
@@ -436,6 +438,8 @@
CompModelPlugin comp = new CompModelPlugin(model);
+ Assert.assertFalse(CompConstants.namespaceURI_L3V1V1.equals(comp.getElementNamespace()));
+
Port port = comp.createPort();
port.setId("c");
port.setIdRef("s");
@@ -446,12 +450,17 @@
SBaseRef sbaseRefRecursive = sbaseRef.createSBaseRef();
sbaseRefRecursive.setMetaId("CMeta2");
- model.addExtension(CompConstants.namespaceURI, comp);
+ model.addExtension(CompConstants.namespaceURI_L3V1V1, comp);
assertTrue(doc.findSBase("CPortMeta1").equals(port));
assertTrue(doc.findSBase("CMeta2").equals(sbaseRefRecursive));
assertTrue(doc.findSBase("CMeta1").equals(sbaseRef));
-
+
+ assertTrue(CompConstants.namespaceURI_L3V1V1.equals(comp.getElementNamespace()));
+ assertTrue(CompConstants.namespaceURI_L3V1V1.equals(port.getNamespace()));
+ assertTrue(CompConstants.namespaceURI_L3V1V1.equals(sbaseRef.getNamespace()));
+
+
String docString = null;
try {
@@ -601,7 +610,7 @@
/**
- * Create a SBasePlugin by hand without extenddeSBase set, add it to an element and check that the ids are registered.
+ * Create a SBasePlugin by hand without extendedSBase set, add it to an element and check that the ids are registered.
*
*/
@Test public void testQual() {
@@ -621,12 +630,14 @@
qualModel.createTransition("T1");
qualModel.createTransition("T2");
- model.addPlugin(QualConstants.shortLabel, qualModel);
+ model.addPlugin(QualConstants.namespaceURI_L3V1V1, qualModel);
assertTrue(model.findUniqueNamedSBase("QS1").equals(qs1));
assertTrue(model.findUniqueNamedSBase("QS3") != null);
assertTrue(model.findUniqueNamedSBase("T2") != null);
assertTrue(doc.findSBase("QS1") != null);
+ assertTrue(qs1.getPackageVersion() == 1);
+ assertTrue(qs1.getNamespace().equals(QualConstants.namespaceURI_L3V1V1));
// cloning the whole document
SBMLDocument clonedDoc = doc.clone();
@@ -673,11 +684,11 @@
group.createMemberWithIdRef("GM2", "S2");
Member member3 = group.createMemberWithIdRef("GM3", "S1");
member3.setMetaId("GM3");
- group.createMemberConstraint("GMC1");
+ // group.createMemberConstraint("GMC1");
assertTrue(groupsModel.getGroupCount() == 1);
assertTrue(group.getMemberCount() == 3);
- assertTrue(group.getMemberConstraintCount() == 1);
+ // assertTrue(group.getMemberConstraintCount() == 1);
try {
Group g2 = groupsModel.createGroup();
@@ -692,12 +703,12 @@
} catch (IllegalArgumentException e) {
assertTrue(true);
}
- try {
- groupsModel.createGroup("GMC1");
- assertTrue("We should not be allowed to have several element with the same id inside the same model", false);
- } catch (IllegalArgumentException e) {
- assertTrue(true);
- }
+// try {
+// groupsModel.createGroup("GMC1");
+// assertTrue("We should not be allowed to have several element with the same id inside the same model", false);
+// } catch (IllegalArgumentException e) {
+// assertTrue(true);
+// }
// try {
// groupsModel.createGroup("GLMC1");
// assertTrue("We should not be allowed to have several element with the same id inside the same model", false);
@@ -728,7 +739,7 @@
assertTrue(clonedDoc.findSBase("GM3") != null);
assertTrue(clonedModel.findUniqueNamedSBase("GM3") != null);
assertTrue(clonedModel.findUniqueNamedSBase("G1") != null);
- assertTrue(clonedModel.findUniqueNamedSBase("GMC1") != null);
+// assertTrue(clonedModel.findUniqueNamedSBase("GMC1") != null);
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-27 13:36:46
|
Revision: 2409
http://sourceforge.net/p/jsbml/code/2409
Author: niko-rodrigue
Date: 2015-11-27 13:36:43 +0000 (Fri, 27 Nov 2015)
Log Message:
-----------
added the maven section to the user guide
Modified Paths:
--------------
trunk/core/doc/common/tex/literature.bib
trunk/core/doc/user_guide/JSBML_getting_started.tex
trunk/core/doc/user_guide/User_Guide.pdf
Modified: trunk/core/doc/common/tex/literature.bib
===================================================================
--- trunk/core/doc/common/tex/literature.bib 2015-11-27 10:59:35 UTC (rev 2408)
+++ trunk/core/doc/common/tex/literature.bib 2015-11-27 13:36:43 UTC (rev 2409)
@@ -701,6 +701,14 @@
year = {2015},
}
+@MISC{ApacheMaven,
+ author = {{Apache Software Foundation}},
+ title = {The {Apache} {Maven} Project},
+ howpublished = {Available on the World Wide Web at \url{http://maven.apache.org/}},
+ url = {http://maven.apache.org/},
+ year = {2015},
+}
+
@MISC{JSBMLSVN,
author = {{JSBML Team}},
title = {The {JSBML} {SVN} repository},
Modified: trunk/core/doc/user_guide/JSBML_getting_started.tex
===================================================================
--- trunk/core/doc/user_guide/JSBML_getting_started.tex 2015-11-27 10:59:35 UTC (rev 2408)
+++ trunk/core/doc/user_guide/JSBML_getting_started.tex 2015-11-27 13:36:43 UTC (rev 2409)
@@ -19,10 +19,6 @@
you have installed the JAR file on your computer, it is sufficient to add
it to your Java build and/or class path in order to use JSBML.
-\subsection{Maven dependencies}
-
-%% TODO
-
\subsection{The JSBML archive without dependencies}
\begin{table}[b]
@@ -86,6 +82,40 @@
\emph{all} to your Java build and/or class path in order to use JSBML.
+\subsection{Maven dependencies}
+
+JSBML can also be obtained through Apache Maven~\citep{ApacheMaven}.
+If you are already using Maven in your project, you can add JSBML
+as a dependency, just add the following lines into your pom.xml:
+
+\begin{example}[language=XML, title={Maven instructions to add to your pom.xml.}]
+ <repositories>
+ <repository>
+ <id>ebi-repo</id>
+ <name>The EBI repository</name>
+ <url>http://www.ebi.ac.uk/~maven/m2repo</url>
+ <releases><enabled>true</enabled></releases>
+ </repository>
+ </repositories>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml</artifactId>
+ <version>|\jsbmlversion|</version>
+ </dependency>
+ </dependencies>
+\end{example}
+
+The jsbml artifact will include jsbml-core plus all L3 packages. Like this
+there is not need to list all the packages by hand and when
+a new one is developed, you will get it without having to make too much change to your
+pom files.
+
+If you want to pick which package to include, you can list them one by one, there are
+further instructions at \url{http://sbml.org/Software/JSBML/docs/Maven_Configuration}.
+
+
\subsection{The JSBML source archive}
\label{sec:jsbml-source-archive}
@@ -94,7 +124,7 @@
not compiled into class files; you must compile them yourself. As with the
other options described above, the source distribution is available from
the JSBML area on SourceForge~\cite{JSBMLdownload}, as an archive file in
-both ZIP and compressed TAR archive formats.
+ZIP format.
Download whichever format is more convenient for you and unpack the archive
on your computer somewhere. The act of unpacking the archive will create a
@@ -321,13 +351,3 @@
example application.
-
-% JSBML also provides several modules. Two of them should ease developers to
-% interact with CellDesigner or libSBML and one module eases switching from
-% libSBML to JSBML or the other way around.
-
-% If you performed all the steps above, you should have a JSBML library, based on
-% the latest version of all classes. You can now include the created JAR file into
-% your build or class path and start using JSBML.
-
-
Modified: trunk/core/doc/user_guide/User_Guide.pdf
===================================================================
--- trunk/core/doc/user_guide/User_Guide.pdf 2015-11-27 10:59:35 UTC (rev 2408)
+++ trunk/core/doc/user_guide/User_Guide.pdf 2015-11-27 13:36:43 UTC (rev 2409)
@@ -1,800 +1,102 @@
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[truncated message content] |
|
From: <nik...@us...> - 2015-11-27 10:59:37
|
Revision: 2408
http://sourceforge.net/p/jsbml/code/2408
Author: niko-rodrigue
Date: 2015-11-27 10:59:35 +0000 (Fri, 27 Nov 2015)
Log Message:
-----------
update to the group package to support the latest specs, version 0.7 (2015-11-24). Mainly removed/commented the MemberConstraint list on the Group class.
Modified Paths:
--------------
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java
trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/BindingStatus.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -30,7 +30,6 @@
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.UniqueNamedSBase;
-import org.sbml.jsbml.util.filters.NameFilter;
/**
*
@@ -43,23 +42,27 @@
/**
* This is a collection of possible values for the {@code kind} attribute within
- * a {@link Group}. It has been defined in version 3 of the Groups proposal.
+ * a {@link Group}.
*
- * @author Clemens Wrzodek
- * @since 3.0
- * @version $Rev$
*/
public enum Kind {
/**
- * the group is a class, and its members have an <i>is-a</i> relationship to the group
+ * The group represents a class, and its members have an <i>is-a</i> relationship to the group. For example, the
+ * group could represent a type of molecule such as ATP, and the members could be species located in different
+ * compartments, thereby establishing that the species are pools of the same molecule in different locations.
*/
classification,
/**
- * the group is a collection of parts, and its members have a <i>part-of</i> relationship to the group
+ * The group represents a collection of parts, and its members have a <i>part-of</i> relationship to the group. For ex-ample,
+ * the group could represent a cellular structure, and individual compartments could be made members
+ * of the group to indicate they represent subparts of that cellular structure
*/
partonomy,
/**
- * the grouping is one of convenience, without an implied relationship
+ * The grouping is merely a collection for convenience, without an implied relationship between the members.
+ * For example, the group could be used to collect together multiple disparate components of a model—species,
+ * reactions, events—involved in a particular phenotype, and apply a common annotation rather than having to
+ * copy the same annotation to each component individually.
*/
collection
}
@@ -70,7 +73,7 @@
private static final long serialVersionUID = 2361503116934849753L;
/**
- * Defined in version 3 of the groups proposal.
+ * This attribute is used to indicate the nature of the group
*/
private Kind kind = null;
@@ -82,7 +85,7 @@
/**
*
*/
- private ListOfMemberConstraint listOfMemberConstraints = null;
+// removed as unsupported but could be added again in the future private ListOfMemberConstraint listOfMemberConstraints = null;
/**
*
@@ -105,9 +108,11 @@
if (group.isSetKind()) {
setKind(group.getKind());
}
- if (group.isSetListOfMemberConstraints()) {
- setListOfMemberConstraints(group.getListOfMemberConstraints().clone());
- }
+
+ // removed as unsupported but could be added again in the future
+ // if (group.isSetListOfMemberConstraints()) {
+// setListOfMemberConstraints(group.getListOfMemberConstraints().clone());
+// }
}
/**
@@ -214,12 +219,13 @@
position++;
}
- if (isSetListOfMemberConstraints()) {
- if (position == index) {
- return getListOfMemberConstraints();
- }
- position++;
- }
+ // removed as unsupported but could be added again in the future
+// if (isSetListOfMemberConstraints()) {
+// if (position == index) {
+// return getListOfMemberConstraints();
+// }
+// position++;
+// }
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"), index,
@@ -237,9 +243,10 @@
if (isSetListOfMembers()) {
childCount++;
}
- if (isSetListOfMemberConstraints()) {
- childCount++;
- }
+ // removed as unsupported but could be added again in the future
+// if (isSetListOfMemberConstraints()) {
+// childCount++;
+// }
return childCount;
}
@@ -453,14 +460,15 @@
return isSetListOfMembers() ? getListOfMembers().size() : 0;
}
- /**
- * Returns the number of {@link MemberConstraint}s of this {@link Group}.
- *
- * @return the number of {@link MemberConstraint}s of this {@link Group}.
- */
- public int getMemberConstraintCount() {
- return isSetListOfMemberConstraints() ? getListOfMemberConstraints().size() : 0;
- }
+ // removed as unsupported but could be added again in the future
+// /**
+// * Returns the number of {@link MemberConstraint}s of this {@link Group}.
+// *
+// * @return the number of {@link MemberConstraint}s of this {@link Group}.
+// */
+// public int getMemberConstraintCount() {
+// return isSetListOfMemberConstraints() ? getListOfMemberConstraints().size() : 0;
+// }
/**
* Returns the number of {@link Member}s of this {@link Group}.
@@ -472,15 +480,16 @@
return getMemberCount();
}
- /**
- * Returns the number of {@link MemberConstraint}s of this {@link Group}.
- *
- * @return the number of {@link MemberConstraint}s of this {@link Group}.
- * @libsbml.deprecated same as {@link #getMemberConstraintCount()}
- */
- public int getNumMemberConstraints() {
- return getMemberConstraintCount();
- }
+ // removed as unsupported but could be added again in the future
+// /**
+// * Returns the number of {@link MemberConstraint}s of this {@link Group}.
+// *
+// * @return the number of {@link MemberConstraint}s of this {@link Group}.
+// * @libsbml.deprecated same as {@link #getMemberConstraintCount()}
+// */
+// public int getNumMemberConstraints() {
+// return getMemberConstraintCount();
+// }
/**
*
@@ -506,140 +515,142 @@
public boolean isSetKind() {
return kind!=null;
}
+
+
+//
+// /**
+// * Returns {@code true}, if listOfMemberConstraints is not null.
+// *
+// * @return {@code true}, if listOfMemberConstraints is not null,
+// * otherwise {@code false}
+// */
+// public boolean isSetListOfMemberConstraints() {
+// return listOfMemberConstraints != null;
+// }
+//
+// /**
+// * Returns the listOfMemberConstraints. Creates it if it is not already existing.
+// *
+// * @return the listOfMemberConstraints
+// */
+// public ListOfMemberConstraint getListOfMemberConstraints() {
+// if (!isSetListOfMemberConstraints()) {
+// listOfMemberConstraints = new ListOfMemberConstraint(getLevel(), getVersion());
+// listOfMemberConstraints.setPackageVersion(-1);
+// // changing the ListOf package name from 'core' to 'groups'
+// listOfMemberConstraints.setPackageName(null);
+// listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
+// listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
+// registerChild(listOfMemberConstraints);
+// }
+// return listOfMemberConstraints;
+// }
+//
+// /**
+// * Sets the given {@code ListOf<MemberConstraint>}. If listOfMemberConstraints
+// * was defined before and contains some elements, they are all unset.
+// *
+// * @param listOfMemberConstraints
+// */
+// public void setListOfMemberConstraints(ListOfMemberConstraint listOfMemberConstraints) {
+// unsetListOfMemberConstraints();
+// this.listOfMemberConstraints = listOfMemberConstraints;
+//
+// if (listOfMemberConstraints != null) {
+// listOfMemberConstraints.setPackageVersion(-1);
+// // changing the ListOf package name from 'core' to 'groups'
+// listOfMemberConstraints.setPackageName(null);
+// listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
+// listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
+//
+// registerChild(this.listOfMemberConstraints);
+// }
+// }
+//
+// /**
+// * Returns {@code true}, if listOfMemberConstraints contain at least one element,
+// * otherwise {@code false}
+// *
+// * @return {@code true}, if listOfMemberConstraints contain at least one element,
+// * otherwise {@code false}
+// */
+// public boolean unsetListOfMemberConstraints() {
+// if (isSetListOfMemberConstraints()) {
+// ListOf<MemberConstraint> oldMemberConstraints = listOfMemberConstraints;
+// listOfMemberConstraints = null;
+// oldMemberConstraints.fireNodeRemovedEvent();
+// return true;
+// }
+// return false;
+// }
+//
+// /**
+// * Adds a new {@link MemberConstraint} to the listOfMemberConstraints.
+// * <p>The listOfMemberConstraints is initialized if necessary.
+// *
+// * @param memberConstraint the element to add to the list
+// * @return true (as specified by {@link java.util.Collection#add})
+// */
+// public boolean addMemberConstraint(MemberConstraint memberConstraint) {
+// return getListOfMemberConstraints().add(memberConstraint);
+// }
+//
+// /**
+// * Removes an element from the listOfMemberConstraints.
+// *
+// * @param memberConstraint the element to be removed from the list
+// * @return true if the list contained the specified element
+// * @see java.util.List#remove(Object)
+// */
+// public boolean removeMemberConstraint(MemberConstraint memberConstraint) {
+// if (isSetListOfMemberConstraints()) {
+// return getListOfMemberConstraints().remove(memberConstraint);
+// }
+// return false;
+// }
+//
+// /**
+// * Removes an element from the listOfMemberConstraints at the given index.
+// *
+// * @param i the index where to remove the {@link MemberConstraint}
+// * @throws IndexOutOfBoundsException if the listOf is not set or
+// * if the index is out of bound (index < 0 || index > list.size)
+// */
+// public void removeMemberConstraint(int i) {
+// if (!isSetListOfMemberConstraints()) {
+// throw new IndexOutOfBoundsException(Integer.toString(i));
+// }
+// getListOfMemberConstraints().remove(i);
+// }
+//
+// /**
+// * @param id
+// */
+// public void removeMemberConstraint(String id) {
+// getListOfMemberConstraints().removeFirst(new NameFilter(id));
+// }
+//
+// /**
+// * Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list
+// * @return
+// */
+// public MemberConstraint createMemberConstraint() {
+// return createMemberConstraint(null);
+// }
+//
+// /**
+// * Creates a new {@link MemberConstraint} element and adds it to the ListOfMemberConstraints list
+// * @param id
+// *
+// * @return a new {@link MemberConstraint} element
+// */
+// public MemberConstraint createMemberConstraint(String id) {
+// MemberConstraint MemberConstraint = new MemberConstraint(id, getLevel(), getVersion());
+// addMemberConstraint(MemberConstraint);
+// return MemberConstraint;
+// }
- /**
- * Returns {@code true}, if listOfMemberConstraints is not null.
- *
- * @return {@code true}, if listOfMemberConstraints is not null,
- * otherwise {@code false}
- */
- public boolean isSetListOfMemberConstraints() {
- return listOfMemberConstraints != null;
- }
- /**
- * Returns the listOfMemberConstraints. Creates it if it is not already existing.
- *
- * @return the listOfMemberConstraints
- */
- public ListOfMemberConstraint getListOfMemberConstraints() {
- if (!isSetListOfMemberConstraints()) {
- listOfMemberConstraints = new ListOfMemberConstraint(getLevel(), getVersion());
- listOfMemberConstraints.setPackageVersion(-1);
- // changing the ListOf package name from 'core' to 'groups'
- listOfMemberConstraints.setPackageName(null);
- listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
- listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
- registerChild(listOfMemberConstraints);
- }
- return listOfMemberConstraints;
- }
-
- /**
- * Sets the given {@code ListOf<MemberConstraint>}. If listOfMemberConstraints
- * was defined before and contains some elements, they are all unset.
- *
- * @param listOfMemberConstraints
- */
- public void setListOfMemberConstraints(ListOfMemberConstraint listOfMemberConstraints) {
- unsetListOfMemberConstraints();
- this.listOfMemberConstraints = listOfMemberConstraints;
-
- if (listOfMemberConstraints != null) {
- listOfMemberConstraints.setPackageVersion(-1);
- // changing the ListOf package name from 'core' to 'groups'
- listOfMemberConstraints.setPackageName(null);
- listOfMemberConstraints.setPackageName(GroupsConstants.shortLabel);
- listOfMemberConstraints.setSBaseListType(ListOf.Type.other);
-
- registerChild(this.listOfMemberConstraints);
- }
- }
-
- /**
- * Returns {@code true}, if listOfMemberConstraints contain at least one element,
- * otherwise {@code false}
- *
- * @return {@code true}, if listOfMemberConstraints contain at least one element,
- * otherwise {@code false}
- */
- public boolean unsetListOfMemberConstraints() {
- if (isSetListOfMemberConstraints()) {
- ListOf<MemberConstraint> oldMemberConstraints = listOfMemberConstraints;
- listOfMemberConstraints = null;
- oldMemberConstraints.fireNodeRemovedEvent();
- return true;
- }
- return false;
- }
-
- /**
- * Adds a new {@link MemberConstraint} to the listOfMemberConstraints.
- * <p>The listOfMemberConstraints is initialized if necessary.
- *
- * @param memberConstraint the element to add to the list
- * @return true (as specified by {@link java.util.Collection#add})
- */
- public boolean addMemberConstraint(MemberConstraint memberConstraint) {
- return getListOfMemberConstraints().add(memberConstraint);
- }
-
- /**
- * Removes an element from the listOfMemberConstraints.
- *
- * @param memberConstraint the element to be removed from the list
- * @return true if the list contained the specified element
- * @see java.util.List#remove(Object)
- */
- public boolean removeMemberConstraint(MemberConstraint memberConstraint) {
- if (isSetListOfMemberConstraints()) {
- return getListOfMemberConstraints().remove(memberConstraint);
- }
- return false;
- }
-
- /**
- * Removes an element from the listOfMemberConstraints at the given index.
- *
- * @param i the index where to remove the {@link MemberConstraint}
- * @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
- */
- public void removeMemberConstraint(int i) {
- if (!isSetListOfMemberConstraints()) {
- throw new IndexOutOfBoundsException(Integer.toString(i));
- }
- getListOfMemberConstraints().remove(i);
- }
-
- /**
- * @param id
- */
- public void removeMemberConstraint(String id) {
- getListOfMemberConstraints().removeFirst(new NameFilter(id));
- }
-
- /**
- * Creates a new MemberConstraint element and adds it to the ListOfMemberConstraints list
- * @return
- */
- public MemberConstraint createMemberConstraint() {
- return createMemberConstraint(null);
- }
-
- /**
- * Creates a new {@link MemberConstraint} element and adds it to the ListOfMemberConstraints list
- * @param id
- *
- * @return a new {@link MemberConstraint} element
- */
- public MemberConstraint createMemberConstraint(String id) {
- MemberConstraint MemberConstraint = new MemberConstraint(id, getLevel(), getVersion());
- addMemberConstraint(MemberConstraint);
- return MemberConstraint;
- }
-
-
/* (non-Javadoc)
* @see org.sbml.jsbml.element.SBase#readAttribute(String attributeName, String prefix, String value)
*/
@@ -717,10 +728,11 @@
final int prime = 31;
int result = super.hashCode();
result = prime * result + ((kind == null) ? 0 : kind.hashCode());
- result = prime
- * result
- + ((listOfMemberConstraints == null) ? 0
- : listOfMemberConstraints.hashCode());
+ // removed as unsupported but could be added again in the future
+// result = prime
+// * result
+// + ((listOfMemberConstraints == null) ? 0
+// : listOfMemberConstraints.hashCode());
result = prime * result
+ ((listOfMembers == null) ? 0 : listOfMembers.hashCode());
return result;
@@ -744,13 +756,14 @@
if (kind != other.kind) {
return false;
}
- if (listOfMemberConstraints == null) {
- if (other.listOfMemberConstraints != null) {
- return false;
- }
- } else if (!listOfMemberConstraints.equals(other.listOfMemberConstraints)) {
- return false;
- }
+ // removed as unsupported but could be added again in the future
+// if (listOfMemberConstraints == null) {
+// if (other.listOfMemberConstraints != null) {
+// return false;
+// }
+// } else if (!listOfMemberConstraints.equals(other.listOfMemberConstraints)) {
+// return false;
+// }
if (listOfMembers == null) {
if (other.listOfMembers != null) {
return false;
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -35,11 +35,13 @@
import org.sbml.jsbml.validator.SyntaxChecker;
/**
+ * This class was removed from the specifications as of version 0.7 (2015-11-24) as
+ * no software wanted to implement support for it.
+ * It might be added back in a future version of the specifications if somebody want to implement it.
*
* @author Nicolas Rodriguez
* @version $Rev$
* @since 1.0
- * @date 2013-11-14
*/
public class ListOfMemberConstraint extends ListOf<MemberConstraint> implements NamedSBase, UniqueNamedSBase {
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -28,11 +28,13 @@
import org.sbml.jsbml.UniqueNamedSBase;
/**
+ * This class was removed from the specifications as of version 0.7 (2015-11-24) as
+ * no software wanted to implement support for it.
+ * It might be added back in a future version of the specifications if somebody want to implement it.
*
* @author Nicolas Rodriguez
* @version $Rev$
* @since 1.0
- * @date 2013-11-18
*/
public class MemberConstraint extends AbstractNamedSBase implements UniqueNamedSBase {
Modified: trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/groups/src/org/sbml/jsbml/xml/parsers/GroupsParser.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -108,7 +108,9 @@
}
else if (elementName.equals("listOfMemberConstraints")) {
- return group.getListOfMemberConstraints();
+ // removed in version 0.7 of the specs but could be added again in the future
+ // return group.getListOfMemberConstraints();
+ logger.warn("Your model make use of listOfMemberConstraints which was removed in version 0.7 of the groups specification !");
}
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/BindingStatus.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/BindingStatus.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/BindingStatus.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -5,7 +5,7 @@
* This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
* for the latest version of JSBML and more information about SBML.
*
- * Copyright (C) 2009-2014 jointly by the following organizations:
+ * Copyright (C) 2009-2015 jointly by the following organizations:
* 1. The University of Tuebingen, Germany
* 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 3. The California Institute of Technology, Pasadena, CA, USA
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -41,7 +41,9 @@
*/
private String speciesTypeComponentIndex;
+ // TODO - missing the reference attribute although the whole class might be removed from the specs.
+
/**
* Creates an DenotedSpeciesTypeComponentIndex instance
*/
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -5,7 +5,7 @@
* This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
* for the latest version of JSBML and more information about SBML.
*
- * Copyright (C) 2009-2014 jointly by the following organizations:
+ * Copyright (C) 2009-2015 jointly by the following organizations:
* 1. The University of Tuebingen, Germany
* 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 3. The California Institute of Technology, Pasadena, CA, USA
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -854,7 +854,7 @@
/**
- * Initializes the default values using the namespace.
+ * Initializes the default values.
*/
public void initDefaults() {
packageName = MultiConstants.shortLabel;
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java 2015-11-26 16:32:15 UTC (rev 2407)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java 2015-11-27 10:59:35 UTC (rev 2408)
@@ -60,8 +60,7 @@
/**
*
*/
- private Boolean constant; // TODO: extends/implements the jsbml interface
- // that has the constant attribute.
+ private Boolean constant; // TODO: extends/implements the jsbml interface that has the constant attribute?
/**
*
*/
@@ -184,6 +183,7 @@
@Override
public boolean equals(Object object) {
boolean equals = super.equals(object);
+
if (equals) {
QualitativeSpecies qs = (QualitativeSpecies) object;
equals &= qs.isSetConstant() == isSetConstant();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-26 16:32:17
|
Revision: 2407
http://sourceforge.net/p/jsbml/code/2407
Author: niko-rodrigue
Date: 2015-11-26 16:32:15 +0000 (Thu, 26 Nov 2015)
Log Message:
-----------
small updates to the user guide, incorporating some of the comments from Andreas
Modified Paths:
--------------
trunk/core/doc/common/tex/literature.bib
trunk/core/doc/user_guide/JSBML_getting_started.tex
trunk/core/doc/user_guide/JSBMLdoc.cls
trunk/core/doc/user_guide/User_Guide.tex
Modified: trunk/core/doc/common/tex/literature.bib
===================================================================
--- trunk/core/doc/common/tex/literature.bib 2015-11-25 16:29:13 UTC (rev 2406)
+++ trunk/core/doc/common/tex/literature.bib 2015-11-26 16:32:15 UTC (rev 2407)
@@ -658,7 +658,7 @@
title = {Java\texttrademark},
howpublished = {Available on the World Wide Web at \url{http://www.java.com/en/download/manual.jsp}},
url = {http://www.java.com/en/download/manual.jsp},
- year = {2012},
+ year = {2015},
}
@MISC{SBMLspecs,
@@ -666,7 +666,7 @@
title = {The {SBML} Specifications},
howpublished = {Available on the World Wide Web at \url{http://sbml.org/Documents/Specifications/}},
url = {http://sbml.org/Documents/Specifications/},
- year = 2012
+ year = 2015
}
@MISC{SBMLFAQ,
@@ -674,7 +674,7 @@
title = {The {SBML} Frequently Asked Questions and Answers},
howpublished = {Available on the World Wide Web at \url{http://sbml.org/Documents/FAQ}},
url = {http://sbml.org/Documents/FAQ},
- year = 2012
+ year = 2015
}
@MISC{SBMLforums,
@@ -682,7 +682,7 @@
title = {The {SBML} discussion forums and mailing lists},
howpublished = {Available on the World Wide Web at \url{http://sbml.org/Forums/}},
url = {http://sbml.org/Forums/},
- year = 2012,
+ year = 2015
}
@MISC{JSBMLdownload,
@@ -690,7 +690,7 @@
title = {The {JSBML} Downloads},
howpublished = {Available on the World Wide Web at \url{http://sourceforge.net/projects/jsbml/files/}},
url = {http://sourceforge.net/projects/jsbml/files/},
- year = {2012},
+ year = 2015,
}
@MISC{ApacheAnt,
@@ -698,23 +698,23 @@
title = {The {Apache} {Ant} Project},
howpublished = {Available on the World Wide Web at \url{http://ant.apache.org/}},
url = {http://ant.apache.org/},
- year = {2012},
+ year = {2015},
}
@MISC{JSBMLSVN,
author = {{JSBML Team}},
title = {The {JSBML} {SVN} repository},
- howpublished = {Available on the World Wide Web at \url{http://sourceforge.net/scm/?type=svn&group_id=279608}},
- url = {http://sourceforge.net/scm/?type=svn&group_id=279608},
- year = {2012},
+ howpublished = {Available on the World Wide Web at \url{https://sourceforge.net/p/jsbml/code}},
+ url = {https://sourceforge.net/p/jsbml/code},
+ year = {2015},
}
@MISC{unitontology,
author = {George Gkoutos},
title = {{The Ontology of Units of Measurement}},
- howpublished = {Available on the World Wide Web at \url{http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit}},
- url = {http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit},
- year = {2012},
+ howpublished = {Available on the World Wide Web at \url{http://www.obofoundry.org/ontology/uo.html}},
+ url = {http://www.obofoundry.org/ontology/uo.html},
+ year = {2015},
}
@MISC{log4j,
@@ -722,7 +722,7 @@
title = {log4j},
howpublished = {Available on the World Wide Web at \url{http://logging.apache.org/log4j/1.2/}},
url = {http://logging.apache.org/log4j/1.2/},
- year = {2010},
+ year = {2015},
}
@MISC{tomcat,
@@ -730,15 +730,15 @@
title = {{Apache Tomcat}},
howpublished = {Available on the World Wide Web at \url{http://tomcat.apache.org/}},
url = {http://tomcat.apache.org/},
- year = {2012},
+ year = {2015},
}
@MISC{logViewersWebpage,
author = {{Wikipedia Foundation}},
- title = {Log4j Log Viewers},
- howpublished = {Available on the World Wide Web at \url{http://en.wikipedia.org/wiki/Log4j#Log_Viewers}},
- url = {http://en.wikipedia.org/wiki/Log4j#Log_Viewers},
- year = {2012},
+ title = {Chainsaw log viewer with some alternatives},
+ howpublished = {Available on the World Wide Web at \url{https://en.wikipedia.org/wiki/Chainsaw_(log_file_viewer)}},
+ url = {https://en.wikipedia.org/wiki/Chainsaw_(log_file_viewer)},
+ year = {2015},
}
@MISC{libSBMLwebsite,
@@ -746,7 +746,7 @@
title = {{libSBML}},
howpublished = {Available on the World Wide Web at \url{http://sbml.org/Software/libSBML}},
url = {http://sbml.org/Software/libSBML},
- year = {2012},
+ year = {2015},
}
@MISC{graphvizWebsite,
@@ -756,7 +756,7 @@
title = {{Graphviz} -- Graph Visualization Software},
howpublished = {Available on the World Wide Web at \url{http://www.graphviz.org/}},
url = {http://www.graphviz.org/},
- year = {2012},
+ year = {2015},
}
@MISC{junitWebsite,
@@ -764,5 +764,5 @@
title = {{JUnit.org}},
howpublished = {Available on the World Wide Web at \url{http://www.junit.org}},
url = {http://www.junit.org},
- year = {2012},
+ year = {2015},
}
Modified: trunk/core/doc/user_guide/JSBML_getting_started.tex
===================================================================
--- trunk/core/doc/user_guide/JSBML_getting_started.tex 2015-11-25 16:29:13 UTC (rev 2406)
+++ trunk/core/doc/user_guide/JSBML_getting_started.tex 2015-11-26 16:32:15 UTC (rev 2407)
@@ -19,7 +19,10 @@
you have installed the JAR file on your computer, it is sufficient to add
it to your Java build and/or class path in order to use JSBML.
+\subsection{Maven dependencies}
+%% TODO
+
\subsection{The JSBML archive without dependencies}
\begin{table}[b]
@@ -32,9 +35,8 @@
\toprule
\textbf{\sffamily Library name} & \textbf{Purpose} & \textbf{Source URL} \\
\midrule
- biojava-1.7-ontology.jar
- & A stripped-down version of biojava-1.7
- containing mostly ontology-related classes~\citep{Holland2008}.
+ biojava3-ontology-3.1.0.jar
+ & biojava3 ontology-related classes~\citep{Holland2008}.
\index{Ontology}
& \href{http://biojava.org}{biojava.org} \\
@@ -43,19 +45,15 @@
run the tests in the \code{tests} folder.
& \href{http://www.junit.org}{www.junit.org} \\
- stax2-api-3.0.3.jar
+ stax2-api-3.1.4.jar
& Used for reading and writing XML.
& \href{http://docs.codehaus.org/display/WSTX/StAX2}{docs.codehaus.org/display/WSTX/StAX2} \\
- stax-api-1.0.1.jar
+ woodstox-core-5.0.1.jar
& Used for reading and writing XML.
- & \href{http://stax.codehaus.org}{stax.codehaus.org} \\
-
- woodstox-core-lgpl-4.0.9.jar
- & Used for reading and writing XML.
& \href{http://woodstox.codehaus.org}{woodstox.codehaus.org} \\
- staxmate-2.0.0.jar
+ staxmate-2.3.0.jar
& Used for reading and writing XML. Provides a more user-friendly StAX
interface.
& \href{http://staxmate.codehaus.org}{staxmate.codehaus.org} \\
@@ -70,7 +68,7 @@
Dec. 2010), containing classes for date manipulation.
& \href{http://jigsaw.w3.org}{jigsaw.w3.org} \\
- log4j-1.2.8.jar
+ log4j-1.2.17.jar
& Library for logging errors and other diagnostics.
& \href{http://logging.apache.org/log4j}{logging.apache.org/log4j} \\
@@ -101,7 +99,7 @@
Download whichever format is more convenient for you and unpack the archive
on your computer somewhere. The act of unpacking the archive will create a
folder on your computer named after the distribution version; for
-example, this may be ``\code{jsbml-1.0}''. Next, you will need to compile
+example, this may be ``\code{jsbml-}\jsbmlversion''. Next, you will need to compile
the Java source code. JSBML comes with a \emph{build file} (i.e., scripted
instructions in a specialized format) for Apache Ant~\citep{ApacheAnt};
you can use other approaches for compiling the JSBML classes and
@@ -112,7 +110,7 @@
\begin{example}[style=bash, title={Compiling JSBML with Ant; this example
uses Bash shell syntax.}]
-cd jsbml-1.0
+cd jsbml-|\jsbmlversion|
ant compile
\end{example}
@@ -137,13 +135,13 @@
The fourth approach to obtaining a copy of JSBML is to retrieve it directly
from the Subversion repository~\cite{JSBMLSVN}. Here is an example of how
-to retrieve the latest version of the core JSBML sources:
+to retrieve the latest version of the JSBML sources:
\newcommand{\dirname}{\code{\emph{\color{winered}jsbml}}\xspace}
\begin{example}[style=bash, title={Downloading the latest JSBML
sources from the JSBML project's Subversion repository.}]
-svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/core |\dirname|
+svn co https://svn.code.sf.net/p/jsbml/code/trunk |\dirname|
cd |\dirname|
\end{example}
@@ -170,7 +168,10 @@
because the different parsers in JSBML are registered automatically using
Java annotations. To configure the annotation processor in Eclipse, follow
the instructions found on the web page
-\url{https://code.google.com/p/spi/wiki/EclipseSettings}.
+\url{https://code.google.com/p/spi/wiki/EclipseSettings}. If you checkout
+the full trunk (and not just the core), you can find a folder dev, which
+contains a README.txt file that has also these instructions and further
+important information.
Finally, you can run the \code{ParserManager} class to check that the list of
parsers are not empty and that they contain the parsers you need.
@@ -208,7 +209,7 @@
\begin{example}[style=bash, title={Downloading the latest JSBML extensions
source folder from the project's Subversion repository.}]
-svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/extensions extensions
+svn co https://svn.code.sf.net/p/jsbml/code/trunk/extensions jsbml-extensions
\end{example}
Each of the extensions has its own Ant build script, located in a file
@@ -224,6 +225,7 @@
\subsubsection{JSBML Modules}
\label{sec:jsbml-modules}
+%% TODO - add few words about the tidy writer module
JSBML currently provides five additional modules. Each provides features
for task-specific purposes. Binary versions of the modules can be found at
@@ -250,7 +252,7 @@
listed in the first column of \tab{tab:jsbml-modules}:
\begin{example}[style=bash, title={Obtaining a JSBML module.}]
-svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/modules/|\modulename| |\modulename|
+svn co https://svn.code.sf.net/p/jsbml/code/trunk/modules/|\modulename| |\modulename|
\end{example}
(In other words, if you would like to obtain both the Android and libSBML
@@ -311,7 +313,7 @@
\begin{example}[style=bash, title={Retrieving the \emph{SBML Bar Graph}
example application.}]
-svn co https://jsbml.svn.sourceforge.net/svnroot/jsbml/trunk/examples/sbmlbargraph sbmlbargraph
+svn co https://svn.code.sf.net/p/jsbml/code/trunk/examples/sbmlbargraph sbmlbargraph
\end{example}
Finally, please read the ``\code{README.txt}'' file in the freshly-obtained
Modified: trunk/core/doc/user_guide/JSBMLdoc.cls
===================================================================
--- trunk/core/doc/user_guide/JSBMLdoc.cls 2015-11-25 16:29:13 UTC (rev 2406)
+++ trunk/core/doc/user_guide/JSBMLdoc.cls 2015-11-26 16:32:15 UTC (rev 2407)
@@ -28,7 +28,8 @@
%% It would be so nice to be able to put the CVS/RCS 'Date' tag in the
%% \filedate below. Unfortunately, LaTeX will barf on the resulting string.
-\def\filedate{2012/04/06}
+\def\filedate{2015/12/01}
+\def\jsbmlversion{1.1}
\NeedsTeXFormat{LaTeX2e}
Modified: trunk/core/doc/user_guide/User_Guide.tex
===================================================================
--- trunk/core/doc/user_guide/User_Guide.tex 2015-11-25 16:29:13 UTC (rev 2406)
+++ trunk/core/doc/user_guide/User_Guide.tex 2015-11-26 16:32:15 UTC (rev 2407)
@@ -36,7 +36,7 @@
\title{\textls[20]{User Guide for JSBML}}
-\version{1.0 \\[0.5em]{\normalsize Document version: 24 October 2014}}
+\version{1.1 \\[0.5em]{\normalsize Document version: 01 December 2015}}
\newcommand{\where}[1]{\,\textsuperscript{#1}}
\newcommand{\divider}[1]{\multicolumn{3}{c}{\emph{#1}:}}
@@ -102,7 +102,7 @@
Before you can use JSBML, you will need to obtain a copy of the library.
\sec{sec:obtaining-jsbml} below describes different ways of doing
this, and explains which additional libraries you may need. JSBML also
-requires the use of a Java Runtime Environment (JRE) version~1.5 or
+requires the use of a Java Runtime Environment (JRE) version~1.6 or
later~\cite{JavaDownloadURL}. \index{Java Runtime Environment (JRE)} In the
rest of this document, we assume that you have already installed a suitable
JRE or Java Development Kit (JDK), and know how to configure the Java class
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <lea...@us...> - 2015-11-25 16:29:17
|
Revision: 2406
http://sourceforge.net/p/jsbml/code/2406
Author: leandrohw
Date: 2015-11-25 16:29:13 +0000 (Wed, 25 Nov 2015)
Log Message:
-----------
Fixed problem with org.sbml.jsbml.ext.arrays.test.CompilerTest.testVectorMinus
Modified Paths:
--------------
trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java
trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/ArraysJUnitTests.java
trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java
trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/VoteModel.xml
Added Paths:
-----------
trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/and.xml
trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/example04.xml
trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/toggleSwitch.xml
Modified: trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java
===================================================================
--- trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java 2015-11-23 09:10:55 UTC (rev 2405)
+++ trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java 2015-11-25 16:29:13 UTC (rev 2406)
@@ -3169,19 +3169,23 @@
plus(negValues);
ASTNode plus = getNode();
- ASTNode minus = new ASTNode(ASTNode.Type.MINUS);
- if(plus.getChildCount() > 0) {
- minus.addChild(plus.getChild(0));
+ setNode(plus);
+ if(useId)
+ {
+ ASTNode minus = new ASTNode(ASTNode.Type.MINUS);
+ if(plus.getChildCount() > 0) {
+ minus.addChild(plus.getChild(0));
- for(int i = 1; i < plus.getChildCount(); i++)
- {
- if(plus.getChild(i).getType() == ASTNode.Type.MINUS && plus.getChild(i).getChildCount() == 1)
+ for(int i = 1; i < plus.getChildCount(); i++)
{
- minus.addChild(plus.getChild(i).getChild(0));
+ if(plus.getChild(i).getType() == ASTNode.Type.MINUS && plus.getChild(i).getChildCount() == 1)
+ {
+ minus.addChild(plus.getChild(i).getChild(0));
+ }
}
+
+ setNode(minus);
}
-
- setNode(minus);
}
return dummy;
}
@@ -3688,11 +3692,11 @@
double result = 0;
node.getChildren().clear();
-
+
if (! node.getType().equals(ASTNode.Type.PLUS)) {
node.setType(ASTNode.Type.PLUS);
}
-
+
if (values.size() > 0) {
for (int i = 0; i < values.size(); ++i) {
ASTNode value = values.get(i);
Modified: trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/ArraysJUnitTests.java
===================================================================
--- trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/ArraysJUnitTests.java 2015-11-23 09:10:55 UTC (rev 2405)
+++ trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/ArraysJUnitTests.java 2015-11-25 16:29:13 UTC (rev 2406)
@@ -35,6 +35,6 @@
*/
@RunWith(value=Suite.class)
@SuiteClasses(value={ArrayExtensionTest.class, ArraysWriteTest.class, MathTest.class, ArraysValidationTest.class,
- CompilerTest.class})
+ CompilerTest.class, FlatteningTest.class})
public class ArraysJUnitTests {
}
Modified: trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java
===================================================================
--- trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java 2015-11-23 09:10:55 UTC (rev 2405)
+++ trunk/extensions/arrays/test/org/sbml/jsbml/ext/arrays/test/FlatteningTest.java 2015-11-25 16:29:13 UTC (rev 2406)
@@ -60,6 +60,42 @@
*/
public class FlatteningTest {
+
+ @Test
+ public void sizeZeroTest() {
+ try {
+ SBMLDocument document = new SBMLDocument(3,1);
+
+ Model model = document.createModel();
+
+ Species spec = model.createSpecies("s");
+
+ Parameter param = model.createParameter("n");
+
+ param.setConstant(true);
+
+ param.setValue(0);
+
+ ArraysSBasePlugin arraysSBasePlugin = new ArraysSBasePlugin(spec);
+
+ spec.addExtension(ArraysConstants.shortLabel, arraysSBasePlugin);
+
+ Dimension dim = arraysSBasePlugin.createDimension("i");
+
+ dim.setArrayDimension(0);
+
+ dim.setSize("n");
+
+ SBMLDocument flattened = ArraysFlattening.convert(document);
+
+ assertTrue(flattened.getModel().getSpeciesCount() == 0);
+
+ } catch (SBMLException e) {
+ assertTrue(false);
+ e.printStackTrace();
+ }
+ }
+
/**
*
*/
@@ -538,12 +574,12 @@
inda.setReferencedAttribute("species");
inda.setArrayDimension(0);
inda.setMath(ASTNode.parseFormula("j"));
-
+
Index impa = arraysSBasePlugina.createIndex();
impa.setReferencedAttribute("id");
impa.setArrayDimension(0);
impa.setMath(ASTNode.parseFormula("j"));
-
+
SpeciesReference b = r.createProduct(B);
b.setId("b");
ArraysSBasePlugin arraysSBasePluginb = new ArraysSBasePlugin(b);
@@ -559,7 +595,7 @@
impb.setReferencedAttribute("id");
impb.setArrayDimension(0);
impb.setMath(ASTNode.parseFormula("j"));
-
+
SBMLWriter.write(doc, System.out, ' ', (short) 2);
System.out.println("\n-------------------------------------------");
SBMLDocument flattened = ArraysFlattening.convert(doc);
@@ -712,11 +748,11 @@
SBMLDocument doc;
try {
doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/VoteModel.xml"));
- SBMLWriter.write(doc, System.out, ' ', (short) 2);
- SBMLDocument flattened = ArraysFlattening.convert(doc);
+ //SBMLWriter.write(doc, System.out, ' ', (short) 2);
+ //SBMLDocument flattened = ArraysFlattening.convert(doc);
+ //SBMLWriter.write(flattened, System.out, ' ', (short) 2);
+ ArraysFlattening.convert(doc);
- SBMLWriter.write(flattened, System.out, ' ', (short) 2);
-
} catch (XMLStreamException e) {
assertTrue(false);
}
@@ -749,29 +785,96 @@
doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/layoutTest.xml"));
SBMLWriter.write(doc, System.out, ' ', (short) 2);
SBMLDocument flattened = ArraysFlattening.convert(doc);
-
+
SBMLWriter.write(flattened, System.out, ' ', (short) 2);
} catch (XMLStreamException e) {
assertTrue(false);
}
-
+
}
+
+// @Test
+// public void testMetaIdRef() {
+// SBMLDocument doc;
+// try {
+// doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/xyz.xml"));
+// SBMLWriter.write(doc, System.out, ' ', (short) 2);
+// SBMLDocument flattened = ArraysFlattening.convert(doc);
+//
+// SBMLWriter.write(flattened, System.out, ' ', (short) 2);
+//
+// } catch (XMLStreamException e) {
+// assertTrue(false);
+// }
+//
+// }
+
+ @Test
+ public void getmodel() {
+ SBMLDocument doc;
+ try {
+ doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/example04.xml"));
+ SBMLWriter.write(doc, System.out, ' ', (short) 2);
+ SBMLDocument flattened = ArraysFlattening.convert(doc);
+
+ SBMLWriter.write(flattened, System.out, ' ', (short) 2);
+
+ } catch (XMLStreamException e) {
+ assertTrue(false);
+ }
+
+ }
+
+// @Test
+// public void testASTNodeType()
+// {
+// SBMLDocument doc = new SBMLDocument(3,1);
+// Model model = doc.createModel("foo");
+// FunctionDefinition function = model.createFunctionDefinition("uniform");
+// Constraint c = model.createConstraint();
+// try {
+// function.setMath(ASTNode.parseFormula("lambda(a,b,(a+b)/2)"));
+// c.setMath(ASTNode.parseFormula("uniform(0,1) > 0.5"));
+// }
+// catch (ParseException e1) {
+// assertTrue(false);
+// }
+// System.out.println(c.getMath().toString());
+// doc = ArraysFlattening.convert(model.getSBMLDocument());
+// assertTrue(c.getMath().getType() == doc.getModel().getConstraint(0).getMath().getType());
+// }
@Test
- public void testMetaIdRef() {
+ public void testTime() {
SBMLDocument doc;
try {
- doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/xyz.xml"));
+ doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/and.xml"));
SBMLWriter.write(doc, System.out, ' ', (short) 2);
SBMLDocument flattened = ArraysFlattening.convert(doc);
-
+
SBMLWriter.write(flattened, System.out, ' ', (short) 2);
} catch (XMLStreamException e) {
assertTrue(false);
}
-
+
}
+
+ @Test
+ public void toggleTime() {
+ SBMLDocument doc;
+ try {
+ doc = SBMLReader.read(ArraysWriteTest.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/arrays/toggleSwitch.xml"));
+ SBMLWriter.write(doc, System.out, ' ', (short) 2);
+ SBMLDocument flattened = ArraysFlattening.convert(doc);
+
+ SBMLWriter.write(flattened, System.out, ' ', (short) 2);
+
+ } catch (XMLStreamException e) {
+ assertTrue(false);
+ }
+
+ }
}
Modified: trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/VoteModel.xml
===================================================================
--- trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/VoteModel.xml 2015-11-23 09:10:55 UTC (rev 2405)
+++ trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/VoteModel.xml 2015-11-25 16:29:13 UTC (rev 2406)
@@ -1,6 +1,6 @@
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="3" arrays:required="true" fbc:required="false" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" comp:required="true" xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1" version="1" layout:required="false">
- <model id="VoteModel" metaid="iBioSim4">
+<model id="VoteModel" metaid="iBioSim4">
<listOfFunctionDefinitions>
<functionDefinition id="uniform" name="Uniform distribution">
<math xmlns="http://www.w3.org/1998/Math/MathML">
Added: trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/and.xml
===================================================================
--- trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/and.xml (rev 0)
+++ trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/and.xml 2015-11-25 16:29:13 UTC (rev 2406)
@@ -0,0 +1,564 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" level="3" arrays:required="true" fbc:required="false" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" comp:required="true" xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1" version="1" layout:required="false">
+ <model id="and" metaid="iBioSim46">
+ <comp:listOfPorts xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1">
+ <comp:port comp:idRef="Cell" sboTerm="SBO:0000601" comp:id="compartment__Cell"/>
+ <comp:port comp:idRef="CI" sboTerm="SBO:0000601" comp:id="output__CI"/>
+ <comp:port comp:idRef="Degradation_CI" sboTerm="SBO:0000601" comp:id="Degradation_CI"/>
+ <comp:port comp:idRef="GFP" sboTerm="SBO:0000601" comp:id="output__GFP"/>
+ <comp:port comp:idRef="Degradation_GFP" sboTerm="SBO:0000601" comp:id="Degradation_GFP"/>
+ <comp:port comp:idRef="LacI" sboTerm="SBO:0000600" comp:id="input__LacI"/>
+ <comp:port comp:idRef="Degradation_LacI" sboTerm="SBO:0000601" comp:id="Degradation_LacI"/>
+ <comp:port comp:idRef="TetR" sboTerm="SBO:0000600" comp:id="input__TetR"/>
+ <comp:port comp:idRef="Degradation_TetR" sboTerm="SBO:0000601" comp:id="Degradation_TetR"/>
+ </comp:listOfPorts>
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="iBioSim">
+ <layout:dimensions layout:width="1070" layout:height="425" layout:depth="0"/>
+ <layout:listOfAdditionalGraphicalObjects>
+ <layout:generalGlyph layout:reference="event0" layout:id="Glyph__event0">
+ <layout:boundingBox>
+ <layout:position layout:x="12.5" layout:y="0"/>
+ <layout:dimensions layout:width="75" layout:height="25"/>
+ </layout:boundingBox>
+ <layout:listOfReferenceGlyphs>
+ <layout:referenceGlyph layout:id="Glyph__event0__product__TetR" layout:role="product" layout:glyph="Glyph__TetR">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="50" layout:y="12.5"/>
+ <layout:end layout:x="50" layout:y="91.4775390625"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:referenceGlyph>
+ </layout:listOfReferenceGlyphs>
+ </layout:generalGlyph>
+ <layout:generalGlyph layout:reference="event1" layout:id="Glyph__event1">
+ <layout:boundingBox>
+ <layout:position layout:x="142.5" layout:y="0"/>
+ <layout:dimensions layout:width="75" layout:height="25"/>
+ </layout:boundingBox>
+ <layout:listOfReferenceGlyphs>
+ <layout:referenceGlyph layout:id="Glyph__event1__product__LacI" layout:role="product" layout:glyph="Glyph__LacI">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="180" layout:y="12.5"/>
+ <layout:end layout:x="180" layout:y="91.4775390625"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:referenceGlyph>
+ </layout:listOfReferenceGlyphs>
+ </layout:generalGlyph>
+ </layout:listOfAdditionalGraphicalObjects>
+ <layout:listOfCompartmentGlyphs>
+ <layout:compartmentGlyph layout:id="Glyph__Cell" layout:compartment="Cell">
+ <layout:boundingBox>
+ <layout:position layout:x="0" layout:y="0"/>
+ <layout:dimensions layout:width="1070" layout:height="425"/>
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ </layout:listOfCompartmentGlyphs>
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="Glyph__CI" layout:species="CI">
+ <layout:boundingBox>
+ <layout:position layout:x="65" layout:y="159.4326171875"/>
+ <layout:dimensions layout:width="100" layout:height="30"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="Glyph__GFP" layout:species="GFP">
+ <layout:boundingBox>
+ <layout:position layout:x="65" layout:y="242.3876953125"/>
+ <layout:dimensions layout:width="100" layout:height="30"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="Glyph__LacI" layout:species="LacI">
+ <layout:boundingBox>
+ <layout:position layout:x="130" layout:y="76.4775390625"/>
+ <layout:dimensions layout:width="100" layout:height="30"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="Glyph__TetR" layout:species="TetR">
+ <layout:boundingBox>
+ <layout:position layout:x="0" layout:y="76.4775390625"/>
+ <layout:dimensions layout:width="100" layout:height="30"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ </layout:listOfSpeciesGlyphs>
+ <layout:listOfReactionGlyphs>
+ <layout:reactionGlyph layout:id="Glyph__CI__repression__GFP">
+ <layout:boundingBox>
+ <layout:position layout:x="115" layout:y="257.3876953125"/>
+ <layout:dimensions layout:width="0" layout:height="0"/>
+ </layout:boundingBox>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__CI__repression__GFP" layout:role="product" layout:speciesGlyph="Glyph__GFP">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="115" layout:y="174.4326171875"/>
+ <layout:end layout:x="115" layout:y="257.3876953125"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ <layout:reactionGlyph layout:id="Glyph__LacI__repression__CI">
+ <layout:boundingBox>
+ <layout:position layout:x="115" layout:y="174.4326171875"/>
+ <layout:dimensions layout:width="0" layout:height="0"/>
+ </layout:boundingBox>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__LacI__repression__CI" layout:role="product" layout:speciesGlyph="Glyph__CI">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="180" layout:y="91.4775390625"/>
+ <layout:end layout:x="115" layout:y="174.4326171875"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ <layout:reactionGlyph layout:id="Glyph__TetR__repression__CI">
+ <layout:boundingBox>
+ <layout:position layout:x="115" layout:y="174.4326171875"/>
+ <layout:dimensions layout:width="0" layout:height="0"/>
+ </layout:boundingBox>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="ReferenceGlyph__TetR__repression__CI" layout:role="product" layout:speciesGlyph="Glyph__CI">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="50" layout:y="91.4775390625"/>
+ <layout:end layout:x="115" layout:y="174.4326171875"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ <layout:listOfTextGlyphs>
+ <layout:textGlyph layout:graphicalObject="Glyph__Cell" layout:id="TextGlyph__Cell" layout:text="Cell">
+ <layout:boundingBox>
+ <layout:position layout:x="0" layout:y="0"/>
+ <layout:dimensions layout:width="1070" layout:height="425"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="Glyph__CI" layout:id="TextGlyph__CI" layout:text="CI">
+ <layout:boundingBox>
+ <layout:position layout:x="65" layout:y="159.4326171875"/>
+ <layout:dimensions layout:width="100" layout:height="30"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="Glyph__GFP" layout:id="TextGlyph__GFP" layout:text="GFP">
+ <layout:boundingBox>
+ <layout:position layout:x="65" layout:y="242.3876953125"/>
+ <layout:dimensions layout:width="100" layout:height="30"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="Glyph__LacI" layout:id="TextGlyph__LacI" layout:text="LacI">
+ <layout:boundingBox>
+ <layout:position layout:x="130" layout:y="76.4775390625"/>
+ <layout:dimensions layout:width="100" layout:height="30"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="Glyph__TetR" layout:id="TextGlyph__TetR" layout:text="TetR">
+ <layout:boundingBox>
+ <layout:position layout:x="0" layout:y="76.4775390625"/>
+ <layout:dimensions layout:width="100" layout:height="30"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="Glyph__event0" layout:id="TextGlyph__event0" layout:text="event0">
+ <layout:boundingBox>
+ <layout:position layout:x="12.5" layout:y="0"/>
+ <layout:dimensions layout:width="75" layout:height="25"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:graphicalObject="Glyph__event1" layout:id="TextGlyph__event1" layout:text="event1">
+ <layout:boundingBox>
+ <layout:position layout:x="142.5" layout:y="0"/>
+ <layout:dimensions layout:width="75" layout:height="25"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfCompartments>
+ <compartment id="Cell" constant="true" spatialDimensions="3" size="1"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species id="CI" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim31" boundaryCondition="false" compartment="Cell"/>
+ <species id="GFP" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim32" boundaryCondition="false" compartment="Cell"/>
+ <species id="LacI" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim33" boundaryCondition="true" compartment="Cell"/>
+ <species id="TetR" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim34" boundaryCondition="true" compartment="Cell"/>
+ <species id="Promoter_GFP" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim35" boundaryCondition="false" sboTerm="SBO:0000590" compartment="Cell"/>
+ <species id="P1" constant="false" initialAmount="4" hasOnlySubstanceUnits="true" metaid="iBioSim36" boundaryCondition="false" sboTerm="SBO:0000590" compartment="Cell"/>
+ <species id="P3" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim37" boundaryCondition="false" sboTerm="SBO:0000590" compartment="Cell"/>
+ <species id="P3_mRNA" constant="false" initialAmount="0" hasOnlySubstanceUnits="true" metaid="iBioSim38" boundaryCondition="false" sboTerm="SBO:0000250" compartment="Cell"/>
+ <species id="P2" constant="false" initialAmount="2" hasOnlySubstanceUnits="true" metaid="iBioSim39" boundaryCondition="false" sboTerm="SBO:0000590" compartment="Cell"/>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter id="ko_r" constant="true" name="Reverse RNAP binding rate" metaid="iBioSim2" value="1"/>
+ <parameter id="nr" constant="true" name="Initial RNAP count" metaid="iBioSim7" value="30"/>
+ <parameter id="np" constant="true" name="Stoichiometry of production" metaid="iBioSim8" value="10"/>
+ <parameter id="kr_r" constant="true" name="Reverse repression binding rate" metaid="iBioSim9" value="1"/>
+ <parameter id="ka_f" constant="true" name="Forward activation binding rate" metaid="iBioSim10" value="0.0033"/>
+ <parameter id="kecdiff" constant="true" name="Extracellular diffusion rate" metaid="iBioSim11" value="1"/>
+ <parameter id="ko" constant="true" name="Open complex production rate" metaid="iBioSim12" value="0.05"/>
+ <parameter id="kmdiff_f" constant="true" name="Forward membrane diffusion rate" metaid="iBioSim13" value="1"/>
+ <parameter id="kecd" constant="true" name="Extracellular degradation rate" metaid="iBioSim14" value="0.005"/>
+ <parameter id="kc_r" constant="true" name="Reverse complex formation rate" metaid="iBioSim15" value="1"/>
+ <parameter id="kr_f" constant="true" name="Forward repression binding rate" metaid="iBioSim16" value="0.5"/>
+ <parameter id="ka_r" constant="true" name="Reverse activation binding rate" metaid="iBioSim17" value="1"/>
+ <parameter id="nc" constant="true" name="Stoichiometry of binding" metaid="iBioSim18" value="2"/>
+ <parameter id="kao_r" constant="true" name="Reverse activated RNAP binding rate" metaid="iBioSim19" value="1"/>
+ <parameter id="kd" constant="true" name="Degradation rate" metaid="iBioSim20" value="0.0075"/>
+ <parameter id="kb" constant="true" name="Basal production rate" metaid="iBioSim21" value="0.0001"/>
+ <parameter id="ng" constant="true" name="Initial promoter count" metaid="iBioSim22" value="2"/>
+ <parameter id="ka" constant="true" name="Activated production rate" metaid="iBioSim23" value="0.255"/>
+ <parameter id="kao_f" constant="true" name="Forward activated RNAP binding rate" metaid="iBioSim24" value="1"/>
+ <parameter id="kmdiff_r" constant="true" name="Reverse membrane diffusion rate" metaid="iBioSim25" value="0.01"/>
+ <parameter id="ko_f" constant="true" name="Forward RNAP binding rate" metaid="iBioSim26" value="0.033"/>
+ <parameter id="kc_f" constant="true" name="Forward complex formation rate" metaid="iBioSim27" value="0.05"/>
+ <parameter id="High" constant="true" metaid="iBioSim28" value="60"/>
+ <parameter id="HighTime" constant="true" metaid="iBioSim29" value="2000"/>
+ <parameter id="HighTime2" constant="true" metaid="iBioSim30" value="4000"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction id="Degradation_CI" metaid="iBioSim40" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="Cell">
+ <listOfReactants>
+ <speciesReference constant="true" species="CI" stoichiometry="1"/>
+ </listOfReactants>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> kd </ci>
+ <ci> CI </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="Degradation_GFP" metaid="iBioSim41" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="Cell">
+ <listOfReactants>
+ <speciesReference constant="true" species="GFP" stoichiometry="1"/>
+ </listOfReactants>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> kd </ci>
+ <ci> GFP </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="Degradation_LacI" metaid="iBioSim42" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="Cell">
+ <listOfReactants>
+ <speciesReference constant="true" species="LacI" stoichiometry="1"/>
+ </listOfReactants>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> kd </ci>
+ <ci> LacI </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="Degradation_TetR" metaid="iBioSim43" reversible="false" sboTerm="SBO:0000179" fast="false" compartment="Cell">
+ <listOfReactants>
+ <speciesReference constant="true" species="TetR" stoichiometry="1"/>
+ </listOfReactants>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <ci> kd </ci>
+ <ci> TetR </ci>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="Production_Promoter_GFP" metaid="iBioSim3" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="Cell">
+ <listOfProducts>
+ <speciesReference constant="true" species="GFP" stoichiometry="10"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="Promoter_GFP" sboTerm="SBO:0000598"/>
+ <modifierSpeciesReference species="CI" sboTerm="SBO:0000020"/>
+ </listOfModifiers>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <apply>
+ <times/>
+ <apply>
+ <times/>
+ <ci> Promoter_GFP </ci>
+ <ci> ko </ci>
+ </apply>
+ <apply>
+ <divide/>
+ <ci> ko_f </ci>
+ <ci> ko_r </ci>
+ </apply>
+ </apply>
+ <ci> nr </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <apply>
+ <plus/>
+ <cn type="integer"> 1 </cn>
+ <apply>
+ <times/>
+ <apply>
+ <divide/>
+ <ci> ko_f </ci>
+ <ci> ko_r </ci>
+ </apply>
+ <ci> nr </ci>
+ </apply>
+ </apply>
+ <apply>
+ <power/>
+ <apply>
+ <times/>
+ <apply>
+ <divide/>
+ <ci> kr_f </ci>
+ <ci> kr_r </ci>
+ </apply>
+ <ci> CI </ci>
+ </apply>
+ <ci> nc_CI_r </ci>
+ </apply>
+ </apply>
+ </apply>
+ </math>
+ <listOfLocalParameters>
+ <localParameter id="nc_CI_r" value="3"/>
+ </listOfLocalParameters>
+ </kineticLaw>
+ </reaction>
+ <reaction id="Production_P1" metaid="iBioSim4" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="Cell">
+ <listOfProducts>
+ <speciesReference constant="true" species="CI" stoichiometry="10"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="P1" sboTerm="SBO:0000598"/>
+ <modifierSpeciesReference species="LacI" sboTerm="SBO:0000020"/>
+ </listOfModifiers>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <apply>
+ <times/>
+ <apply>
+ <times/>
+ <ci> P1 </ci>
+ <ci> ko </ci>
+ </apply>
+ <apply>
+ <divide/>
+ <ci> ko_f </ci>
+ <ci> ko_r </ci>
+ </apply>
+ </apply>
+ <ci> nr </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <apply>
+ <plus/>
+ <cn type="integer"> 1 </cn>
+ <apply>
+ <times/>
+ <apply>
+ <divide/>
+ <ci> ko_f </ci>
+ <ci> ko_r </ci>
+ </apply>
+ <ci> nr </ci>
+ </apply>
+ </apply>
+ <apply>
+ <power/>
+ <apply>
+ <times/>
+ <apply>
+ <divide/>
+ <ci> kr_f </ci>
+ <ci> kr_r </ci>
+ </apply>
+ <ci> LacI </ci>
+ </apply>
+ <ci> nc </ci>
+ </apply>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="Production_P3" metaid="iBioSim5" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="Cell">
+ <listOfProducts>
+ <speciesReference constant="true" species="P3_mRNA" stoichiometry="10"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="P3" sboTerm="SBO:0000598"/>
+ </listOfModifiers>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <apply>
+ <times/>
+ <apply>
+ <times/>
+ <ci> P3 </ci>
+ <ci> ko </ci>
+ </apply>
+ <apply>
+ <divide/>
+ <ci> ko_f </ci>
+ <ci> ko_r </ci>
+ </apply>
+ </apply>
+ <ci> nr </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <cn type="integer"> 1 </cn>
+ <apply>
+ <times/>
+ <apply>
+ <divide/>
+ <ci> ko_f </ci>
+ <ci> ko_r </ci>
+ </apply>
+ <ci> nr </ci>
+ </apply>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ <reaction id="Production_P2" metaid="iBioSim6" reversible="false" sboTerm="SBO:0000589" fast="false" compartment="Cell">
+ <listOfProducts>
+ <speciesReference constant="true" species="CI" stoichiometry="10"/>
+ </listOfProducts>
+ <listOfModifiers>
+ <modifierSpeciesReference species="P2" sboTerm="SBO:0000598"/>
+ <modifierSpeciesReference species="TetR" sboTerm="SBO:0000020"/>
+ </listOfModifiers>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <apply>
+ <times/>
+ <apply>
+ <times/>
+ <apply>
+ <times/>
+ <ci> P2 </ci>
+ <ci> ko </ci>
+ </apply>
+ <apply>
+ <divide/>
+ <ci> ko_f </ci>
+ <ci> ko_r </ci>
+ </apply>
+ </apply>
+ <ci> nr </ci>
+ </apply>
+ <apply>
+ <plus/>
+ <apply>
+ <plus/>
+ <cn type="integer"> 1 </cn>
+ <apply>
+ <times/>
+ <apply>
+ <divide/>
+ <ci> ko_f </ci>
+ <ci> ko_r </ci>
+ </apply>
+ <ci> nr </ci>
+ </apply>
+ </apply>
+ <apply>
+ <power/>
+ <apply>
+ <times/>
+ <apply>
+ <divide/>
+ <ci> kr_f </ci>
+ <ci> kr_r </ci>
+ </apply>
+ <ci> TetR </ci>
+ </apply>
+ <ci> nc </ci>
+ </apply>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ <listOfEvents>
+ <event id="event0" metaid="iBioSim44" useValuesFromTriggerTime="true">
+ <trigger persistent="false" initialValue="true">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <geq/>
+ <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
+ <ci> HighTime </ci>
+ </apply>
+ </math>
+ </trigger>
+ <listOfEventAssignments>
+ <eventAssignment variable="TetR">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> High </ci>
+ </math>
+ </eventAssignment>
+ </listOfEventAssignments>
+ </event>
+ <event id="event1" metaid="iBioSim45" useValuesFromTriggerTime="true">
+ <trigger persistent="false" initialValue="true">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <geq/>
+ <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> t </csymbol>
+ <ci> HighTime2 </ci>
+ </apply>
+ </math>
+ </trigger>
+ <listOfEventAssignments>
+ <eventAssignment variable="LacI">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> High </ci>
+ </math>
+ </eventAssignment>
+ </listOfEventAssignments>
+ </event>
+ </listOfEvents>
+ </model>
+</sbml>
\ No newline at end of file
Added: trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/example04.xml
===================================================================
--- trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/example04.xml (rev 0)
+++ trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/example04.xml 2015-11-25 16:29:13 UTC (rev 2406)
@@ -0,0 +1,317 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version1" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" arrays:required="true" comp:required="true" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" version="1" fbc:required="false">
+ <model metaid="iBioSim8" id="example04">
+ <layout:listOfLayouts xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <layout:layout layout:id="iBioSim">
+ <layout:dimensions layout:height="360" layout:depth="0" layout:width="620"/>
+ <layout:listOfAdditionalGraphicalObjects>
+ <layout:generalGlyph layout:id="Glyph__k" layout:reference="k">
+ <layout:boundingBox>
+ <layout:position layout:x="375" layout:y="300"/>
+ <layout:dimensions layout:height="30" layout:width="30"/>
+ </layout:boundingBox>
+ <layout:listOfReferenceGlyphs>
+ <layout:referenceGlyph layout:id="Glyph__k__product__r" layout:role="product" layout:glyph="Glyph__r">
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="163" layout:y="59"/>
+ <layout:end layout:x="389" layout:y="248"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:referenceGlyph>
+ </layout:listOfReferenceGlyphs>
+ </layout:generalGlyph>
+ </layout:listOfAdditionalGraphicalObjects>
+ <layout:listOfCompartmentGlyphs>
+ <layout:compartmentGlyph layout:id="Glyph__Cell" layout:compartment="Cell">
+ <layout:boundingBox>
+ <layout:position layout:x="160" layout:y="80"/>
+ <layout:dimensions layout:height="280" layout:width="460"/>
+ </layout:boundingBox>
+ </layout:compartmentGlyph>
+ </layout:listOfCompartmentGlyphs>
+ <layout:listOfSpeciesGlyphs>
+ <layout:speciesGlyph layout:id="Glyph__B" layout:species="B">
+ <layout:boundingBox>
+ <layout:position layout:x="190" layout:y="270"/>
+ <layout:dimensions layout:height="30" layout:width="100"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="Glyph__A" layout:species="A">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="layout:species">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ <layout:boundingBox>
+ <layout:position layout:x="190" layout:y="190"/>
+ <layout:dimensions layout:height="30" layout:width="100"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ <layout:speciesGlyph layout:id="Glyph__C" layout:species="C">
+ <layout:boundingBox>
+ <layout:position layout:x="439" layout:y="232"/>
+ <layout:dimensions layout:height="30" layout:width="100"/>
+ </layout:boundingBox>
+ </layout:speciesGlyph>
+ </layout:listOfSpeciesGlyphs>
+ <layout:listOfReactionGlyphs>
+ <layout:reactionGlyph layout:id="Glyph__r" layout:reaction="r">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="layout:reaction">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ <layout:boundingBox>
+ <layout:position layout:x="374" layout:y="233"/>
+ <layout:dimensions layout:height="30" layout:width="30"/>
+ </layout:boundingBox>
+ <layout:listOfSpeciesReferenceGlyphs>
+ <layout:speciesReferenceGlyph layout:id="Glyph__r__substrate__B" layout:role="substrate" layout:speciesGlyph="Glyph__B">
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="layout:id">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="240" layout:y="285"/>
+ <layout:end layout:x="389" layout:y="248"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="Glyph__r__substrate__A" layout:role="substrate" layout:speciesGlyph="Glyph__A">
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="layout:speciesGlyph">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="layout:id">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="240" layout:y="205"/>
+ <layout:end layout:x="389" layout:y="248"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ <layout:speciesReferenceGlyph layout:id="Glyph__r__product__C" layout:role="product" layout:speciesGlyph="Glyph__C">
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="layout:id">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ <layout:curve>
+ <layout:listOfCurveSegments>
+ <layout:curveSegment xsi:type="LineSegment">
+ <layout:start layout:x="389" layout:y="248"/>
+ <layout:end layout:x="489" layout:y="247"/>
+ </layout:curveSegment>
+ </layout:listOfCurveSegments>
+ </layout:curve>
+ </layout:speciesReferenceGlyph>
+ </layout:listOfSpeciesReferenceGlyphs>
+ </layout:reactionGlyph>
+ </layout:listOfReactionGlyphs>
+ <layout:listOfTextGlyphs>
+ <layout:textGlyph layout:id="TextGlyph__Cell" layout:text="Cell[n]" layout:graphicalObject="Glyph__Cell">
+ <layout:boundingBox>
+ <layout:position layout:x="160" layout:y="80"/>
+ <layout:dimensions layout:height="280" layout:width="460"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph__k" layout:text="k" layout:graphicalObject="Glyph__k">
+ <layout:boundingBox>
+ <layout:position layout:x="375" layout:y="300"/>
+ <layout:dimensions layout:height="30" layout:width="30"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph__B" layout:text="B[n]" layout:graphicalObject="Glyph__B">
+ <layout:boundingBox>
+ <layout:position layout:x="190" layout:y="270"/>
+ <layout:dimensions layout:height="30" layout:width="100"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph__A" layout:text="A[n]" layout:graphicalObject="Glyph__A">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="layout:graphicalObject">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ <layout:boundingBox>
+ <layout:position layout:x="190" layout:y="190"/>
+ <layout:dimensions layout:height="30" layout:width="100"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph__C" layout:text="C[n]" layout:graphicalObject="Glyph__C">
+ <layout:boundingBox>
+ <layout:position layout:x="439" layout:y="232"/>
+ <layout:dimensions layout:height="30" layout:width="100"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ <layout:textGlyph layout:id="TextGlyph__r" layout:text="r[n]" layout:graphicalObject="Glyph__r">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="layout:graphicalObject">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ <layout:boundingBox>
+ <layout:position layout:x="374" layout:y="233"/>
+ <layout:dimensions layout:height="30" layout:width="30"/>
+ </layout:boundingBox>
+ </layout:textGlyph>
+ </layout:listOfTextGlyphs>
+ </layout:layout>
+ </layout:listOfLayouts>
+ <listOfCompartments>
+ <compartment constant="true" id="Cell" size="1" spatialDimensions="3">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ </compartment>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" constant="false" metaid="iBioSim3" hasOnlySubstanceUnits="true" initialAmount="0" compartment="Cell" id="B">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="compartment">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ </species>
+ <species boundaryCondition="false" constant="false" metaid="iBioSim4" hasOnlySubstanceUnits="true" initialAmount="0" compartment="Cell" id="A">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="compartment">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ </species>
+ <species boundaryCondition="false" constant="false" metaid="iBioSim5" hasOnlySubstanceUnits="true" initialAmount="0" compartment="Cell" id="C">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="compartment">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ </species>
+ </listOfSpecies>
+ <listOfParameters>
+ <parameter constant="false" id="k" metaid="iBioSim1" value="1"/>
+ <parameter constant="true" id="n" metaid="iBioSim2" value="5"/>
+ </listOfParameters>
+ <listOfReactions>
+ <reaction compartment="Cell" fast="false" id="r" metaid="iBioSim6" reversible="false">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="compartment">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ <listOfReactants>
+ <speciesReference stoichiometry="1" constant="true" species="B">
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="species">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ </speciesReference>
+ <speciesReference stoichiometry="1" constant="true" species="A">
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="species">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ </speciesReference>
+ </listOfReactants>
+ <listOfProducts>
+ <speciesReference stoichiometry="1" constant="true" species="C">
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="species">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ </speciesReference>
+ </listOfProducts>
+ <kineticLaw>
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <apply>
+ <times/>
+ <ci> k </ci>
+ <apply>
+ <selector/>
+ <ci> A </ci>
+ <ci> d0 </ci>
+ </apply>
+ </apply>
+ <apply>
+ <selector/>
+ <ci> B </ci>
+ <ci> d0 </ci>
+ </apply>
+ </apply>
+ </math>
+ </kineticLaw>
+ </reaction>
+ </listOfReactions>
+ </model>
+</sbml>
\ No newline at end of file
Added: trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/toggleSwitch.xml
===================================================================
--- trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/toggleSwitch.xml (rev 0)
+++ trunk/extensions/arrays/test/org/sbml/jsbml/xml/test/data/arrays/toggleSwitch.xml 2015-11-25 16:29:13 UTC (rev 2406)
@@ -0,0 +1,1611 @@
+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" layout:required="false" xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:comp="http://www.sbml.org/sbml/level3/version1/comp/version1" level="3" arrays:required="true" comp:required="true" xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1" version="1" fbc:required="false">
+ <model metaid="iBioSim55" id="toggleSwitch">
+ <listOfCompartments>
+ <compartment constant="true" id="Cell_Interior" size="1" metaid="iBioSim2" spatialDimensions="3">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ <arrays:dimension arrays:arrayDimension="1" arrays:id="d1" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ </compartment>
+ <compartment constant="true" id="Exterior" size="1" metaid="iBioSim3" spatialDimensions="3"/>
+ </listOfCompartments>
+ <listOfSpecies>
+ <species boundaryCondition="false" constant="false" metaid="iBioSim4" hasOnlySubstanceUnits="true" initialAmount="0" compartment="Cell_Interior" id="LacI">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ <arrays:dimension arrays:arrayDimension="1" arrays:id="d1" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:index arrays:arrayDimension="0" arrays:referencedAttribute="compartment">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d0 </ci>
+ </math>
+ </arrays:index>
+ <arrays:index arrays:arrayDimension="1" arrays:referencedAttribute="compartment">
+ <math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> d1 </ci>
+ </math>
+ </arrays:index>
+ </arrays:listOfIndices>
+ </species>
+ <species boundaryCondition="false" constant="false" metaid="iBioSim5" hasOnlySubstanceUnits="true" initialAmount="0" compartment="Cell_Interior" id="IPTG">
+ <arrays:listOfDimensions xmlns:arrays="http://www.sbml.org/sbml/level3/version1/arrays/version1">
+ <arrays:dimension arrays:arrayDimension="0" arrays:id="d0" arrays:size="n"/>
+ <arrays:dimension arrays:arrayDimension="1" arrays:id="d1" arrays:size="n"/>
+ </arrays:listOfDimensions>
+ <arrays:listOfIndices xmlns:arrays="http://www.sbml.org/sbml/level3/ver...
[truncated message content] |
|
From: <and...@us...> - 2015-11-23 09:10:57
|
Revision: 2405
http://sourceforge.net/p/jsbml/code/2405
Author: andreas-draeger
Date: 2015-11-23 09:10:55 +0000 (Mon, 23 Nov 2015)
Log Message:
-----------
Updated keyword property.
Modified Paths:
--------------
trunk/examples/test/src/org/sbml/jsbml/test/RecursiveSBMLDocumentExploration.java
Property Changed:
----------------
trunk/examples/test/src/org/sbml/jsbml/test/RecursiveSBMLDocumentExploration.java
Modified: trunk/examples/test/src/org/sbml/jsbml/test/RecursiveSBMLDocumentExploration.java
===================================================================
--- trunk/examples/test/src/org/sbml/jsbml/test/RecursiveSBMLDocumentExploration.java 2015-11-23 09:09:55 UTC (rev 2404)
+++ trunk/examples/test/src/org/sbml/jsbml/test/RecursiveSBMLDocumentExploration.java 2015-11-23 09:10:55 UTC (rev 2405)
@@ -1,6 +1,6 @@
/*
- * $Id: RecursiveSBMLDocumentExploration.java 10:00:04 draeger $
- * $URL: RecursiveSBMLDocumentExploration.java $
+ * $Id$
+ * $URL$
* ----------------------------------------------------------------------------
* This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
* for the latest version of JSBML and more information about SBML.
Property changes on: trunk/examples/test/src/org/sbml/jsbml/test/RecursiveSBMLDocumentExploration.java
___________________________________________________________________
Modified: svn:keywords
## -0,0 +1 ##
+Id URL Rev
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <and...@us...> - 2015-11-23 09:09:56
|
Revision: 2404
http://sourceforge.net/p/jsbml/code/2404
Author: andreas-draeger
Date: 2015-11-23 09:09:55 +0000 (Mon, 23 Nov 2015)
Log Message:
-----------
Added new example for recursively traversing SBML documents.
Added Paths:
-----------
trunk/examples/test/src/org/sbml/jsbml/test/RecursiveSBMLDocumentExploration.java
Added: trunk/examples/test/src/org/sbml/jsbml/test/RecursiveSBMLDocumentExploration.java
===================================================================
--- trunk/examples/test/src/org/sbml/jsbml/test/RecursiveSBMLDocumentExploration.java (rev 0)
+++ trunk/examples/test/src/org/sbml/jsbml/test/RecursiveSBMLDocumentExploration.java 2015-11-23 09:09:55 UTC (rev 2404)
@@ -0,0 +1,83 @@
+/*
+ * $Id: RecursiveSBMLDocumentExploration.java 10:00:04 draeger $
+ * $URL: RecursiveSBMLDocumentExploration.java $
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2015 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+package org.sbml.jsbml.test;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
+
+import javax.swing.tree.TreeNode;
+import javax.xml.stream.XMLStreamException;
+
+import org.sbml.jsbml.SBMLReader;
+import org.sbml.jsbml.SBase;
+
+
+/**
+ * @author Andreas Dräger
+ * @version $Rev$
+ * @since 1.1
+ * @date 23.11.2015
+ */
+public class RecursiveSBMLDocumentExploration {
+
+ /**
+ * @param args must be the absolute or relative path to one file.
+ * @throws IOException
+ * @throws XMLStreamException
+ */
+ public static void main(String[] args) throws XMLStreamException, IOException {
+ Set<SBase> setOfSBase = traverse(SBMLReader.read(new File(args[0])));
+ for (SBase sbase : setOfSBase) {
+ System.out.println(sbase.toString());
+ }
+ }
+
+ /**
+ * Recursively traverses all children of the given {@link SBase}.
+ *
+ * @param sbase
+ * @return
+ */
+ public static Set<SBase> traverse(SBase sbase) {
+ Set<SBase> setOfSBase = new HashSet<SBase>();
+ traverse(sbase, setOfSBase);
+ return setOfSBase;
+ }
+
+ /**
+ * More efficient private method that does not create new sets each time.
+ *
+ * @param sbase
+ * @param setOfSBase
+ */
+ private static void traverse(SBase sbase, Set<SBase> setOfSBase) {
+ setOfSBase.add(sbase);
+ for (int i = 0; i < sbase.getChildCount(); i++) {
+ TreeNode child = sbase.getChildAt(i);
+ if (child instanceof SBase) {
+ traverse((SBase) child, setOfSBase);
+ }
+ }
+ }
+
+}
Property changes on: trunk/examples/test/src/org/sbml/jsbml/test/RecursiveSBMLDocumentExploration.java
___________________________________________________________________
Added: svn:keywords
\ No newline at end of property
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-17 17:00:24
|
Revision: 2403
http://sourceforge.net/p/jsbml/code/2403
Author: niko-rodrigue
Date: 2015-11-17 17:00:21 +0000 (Tue, 17 Nov 2015)
Log Message:
-----------
removed some debug outputs or comments
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/AbstractSBase.java
trunk/core/test/org/sbml/jsbml/test/PerformanceTest.java
trunk/test/org/sbml/jsbml/test/PackageVersionTests.java
Modified: trunk/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-11-17 13:13:46 UTC (rev 2402)
+++ trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-11-17 17:00:21 UTC (rev 2403)
@@ -2173,8 +2173,6 @@
parentPackageVersion = parentPlugin.getPackageVersion();
}
- System.out.println("setPackageVersion - packageVersion = " + packageVersion + ", parentPackageVersion = " + parentPackageVersion);
-
if (packageVersion != -1 && parentPackageVersion != -1 && packageVersion != parentPackageVersion) {
if (parentPlugin != null) {
throw new LevelVersionError(parentPlugin, this);
Modified: trunk/core/test/org/sbml/jsbml/test/PerformanceTest.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/test/PerformanceTest.java 2015-11-17 13:13:46 UTC (rev 2402)
+++ trunk/core/test/org/sbml/jsbml/test/PerformanceTest.java 2015-11-17 17:00:21 UTC (rev 2403)
@@ -25,7 +25,9 @@
import java.io.File;
import java.io.FileFilter;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.Calendar;
+import java.util.List;
import javax.xml.stream.XMLStreamException;
@@ -41,6 +43,9 @@
*/
public class PerformanceTest {
+ private static final double THRESHOLD = 1;
+ private static final List<String> modelLongerThanThresholdList = new ArrayList<String>();
+
/**
* Test class used to check the jsbml speed to read and write SBML models.
*
@@ -146,12 +151,20 @@
System.out.println("Reading: " + nbSecondsRead + " seconds.");
System.out.println("Writing: " + nbSecondsWrite + " seconds.");
+ if (nbSeconds > THRESHOLD) {
+ modelLongerThanThresholdList.add(fileName);
+ }
+
if (files.length == 1)
{
System.out.println((int)nbMilliseconds);
}
}
+ if (modelLongerThanThresholdList.size() > 0) {
+ System.out.println("Models longer than '" + THRESHOLD + "' secondes: " + modelLongerThanThresholdList);
+ }
+
if (files.length > 1)
{
double globalNbMilliseconds = globalEnd - globalInit;
@@ -163,6 +176,7 @@
System.out.println((int)globalNbMilliseconds);
}
+
}
}
Modified: trunk/test/org/sbml/jsbml/test/PackageVersionTests.java
===================================================================
--- trunk/test/org/sbml/jsbml/test/PackageVersionTests.java 2015-11-17 13:13:46 UTC (rev 2402)
+++ trunk/test/org/sbml/jsbml/test/PackageVersionTests.java 2015-11-17 17:00:21 UTC (rev 2403)
@@ -170,10 +170,7 @@
tr1.createOutput("Q_O1");
qualModel.createTransition("Q_T2", new Input("Q_I2"), new Output("Q_O2"));
- // check and fix package version and namespaces
- // TODO - update when jsbml will be fixed to set properly package version and namespace -
- // now the fix is done in SBMLCoreParser#processEndDocument when reading a file
- // PackageUtil.checkPackages(doc, true, true);
+ // check package version and namespaces
System.out.println("Checking packages:");
PackageUtil.checkPackages(doc, false, false);
}
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-17 13:13:48
|
Revision: 2402
http://sourceforge.net/p/jsbml/code/2402
Author: niko-rodrigue
Date: 2015-11-17 13:13:46 +0000 (Tue, 17 Nov 2015)
Log Message:
-----------
second and last batch of packages updates to remove the setNamepace that is not necessary any more
Modified Paths:
--------------
trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java
trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/Dimension.java
trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/Index.java
trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java
trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribInput.java
trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java
trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java
trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java
trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java
trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynElement.java
trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java
trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynSBasePlugin.java
trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/SpatialComponent.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Dimensions.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/LayoutModelPlugin.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Point.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/AbstractRenderPlugin.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/ColorDefinition.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/LocalRenderInformation.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/Polygon.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderCurve.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderGroup.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderLayoutPlugin.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderListOfLayoutsPlugin.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderPoint.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/Style.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/Transformation.java
trunk/extensions/req/src/org/sbml/jsbml/ext/req/ChangedMath.java
trunk/extensions/req/src/org/sbml/jsbml/ext/req/ReqSBasePlugin.java
Modified: trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java
===================================================================
--- trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -156,7 +156,6 @@
public ListOf<Index> getListOfIndices() {
if (!isSetListOfIndices()) {
listOfIndices = new ListOf<Index>();
- listOfIndices.setNamespace(ArraysConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfIndices.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'arrays'
listOfIndices.setPackageName(null);
@@ -181,8 +180,6 @@
this.listOfIndices = listOfIndices;
if (listOfIndices != null) {
- listOfIndices.unsetNamespace();
- listOfIndices.setNamespace(ArraysConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfIndices.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'arrays'
listOfIndices.setPackageName(null);
@@ -363,7 +360,6 @@
public ListOf<Dimension> getListOfDimensions() {
if (!isSetListOfDimensions()) {
listOfDimensions = new ListOf<Dimension>();
- listOfDimensions.setNamespace(ArraysConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDimensions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'arrays'
listOfDimensions.setPackageName(null);
@@ -388,8 +384,6 @@
this.listOfDimensions = listOfDimensions;
if (listOfDimensions != null) {
- listOfDimensions.unsetNamespace();
- listOfDimensions.setNamespace(ArraysConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDimensions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'arrays'
listOfDimensions.setPackageName(null);
Modified: trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/Dimension.java
===================================================================
--- trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/Dimension.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/Dimension.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -154,7 +154,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(ArraysConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = ArraysConstants.shortLabel;
arrayDimension = -1;
Modified: trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/Index.java
===================================================================
--- trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/Index.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/Index.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -111,7 +111,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(ArraysConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = ArraysConstants.shortLabel;
Modified: trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java
===================================================================
--- trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribFunctionDefinitionPlugin.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -131,11 +131,6 @@
}
@Override
- public String getElementNamespace() {
- return DistribConstants.namespaceURI;
- }
-
- @Override
public String getPackageName() {
return DistribConstants.shortLabel;
}
@@ -145,12 +140,7 @@
return DistribConstants.shortLabel;
}
- @Override
- public String getURI() {
- return DistribConstants.namespaceURI; // TODO - update to return a stored String that can change
- }
-
@Override
public int getChildCount() {
int count = 0;
@@ -198,5 +188,11 @@
return false;
}
+ @Override
+ public String getURI() {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
Modified: trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribInput.java
===================================================================
--- trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribInput.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribInput.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -127,7 +127,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(DistribConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = DistribConstants.shortLabel;
}
Modified: trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java
===================================================================
--- trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DistribSBasePlugin.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -139,11 +139,6 @@
@Override
- public String getElementNamespace() {
- return DistribConstants.namespaceURI_L3V1V1; // TODO - change to return a String attribute that can be changed
- }
-
- @Override
public String getPackageName() {
return DistribConstants.shortLabel;
}
@@ -155,7 +150,7 @@
@Override
public String getURI() {
- return DistribConstants.namespaceURI; // TODO - change to return a String attribute that can be changed
+ return getElementNamespace();
}
Modified: trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java
===================================================================
--- trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -165,7 +165,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(DistribConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = DistribConstants.shortLabel;
}
@@ -246,7 +245,6 @@
public ListOf<DistribInput> getListOfDistribInputs() {
if (!isSetListOfDistribInputs()) {
listOfDistribInputs = new ListOf<DistribInput>();
- listOfDistribInputs.setNamespace(DistribConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDistribInputs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'distrib'
listOfDistribInputs.setPackageName(null);
@@ -270,8 +268,6 @@
this.listOfDistribInputs = listOfDistribInputs;
if (listOfDistribInputs != null) {
- listOfDistribInputs.unsetNamespace();
- listOfDistribInputs.setNamespace(DistribConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDistribInputs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'distrib'
listOfDistribInputs.setPackageName(null);
Modified: trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java
===================================================================
--- trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/Uncertainty.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -116,7 +116,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(DistribConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = DistribConstants.shortLabel;
}
Modified: trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java
===================================================================
--- trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynCompartmentPlugin.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -94,7 +94,6 @@
public ListOf<SpatialComponent> getListOfSpatialComponents() {
if (listOfSpatialComponents == null) {
listOfSpatialComponents = new ListOf<SpatialComponent>();
- listOfSpatialComponents.setNamespace(DynConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpatialComponents.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'dyn'
listOfSpatialComponents.setPackageName(null);
@@ -131,7 +130,6 @@
this.listOfSpatialComponents = listOfSpatialComponents;
if ((this.listOfSpatialComponents != null)) {
- listOfSpatialComponents.setNamespace(DynConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpatialComponents.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'dyn'
listOfSpatialComponents.setPackageName(null);
Modified: trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynElement.java
===================================================================
--- trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynElement.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynElement.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -62,7 +62,6 @@
* Initializes custom Class attributes
* */
private void initDefaults() {
- setNamespace(DynConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = DynConstants.shortLabel;
idRef = null;
Modified: trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java
===================================================================
--- trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynEventPlugin.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -160,7 +160,6 @@
public ListOf<DynElement> getListOfDynElements() {
if (listOfDynElements == null) {
listOfDynElements = new ListOf<DynElement>();
- listOfDynElements.setNamespace(DynConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDynElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'dyn'
listOfDynElements.setPackageName(null);
@@ -194,7 +193,6 @@
this.listOfDynElements = listOfDynElements;
if (this.listOfDynElements != null) {
- listOfDynElements.setNamespace(DynConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDynElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'dyn'
listOfDynElements.setPackageName(null);
Modified: trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynSBasePlugin.java
===================================================================
--- trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynSBasePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/DynSBasePlugin.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -54,7 +54,6 @@
* */
public DynSBasePlugin() {
super();
- elementNamespace = DynConstants.namespaceURI; // TODO - removed once the mechanism are in place to set package version and namespace
}
/**
@@ -77,10 +76,16 @@
*/
public DynSBasePlugin(SBase extendedSBase) {
super(extendedSBase);
- elementNamespace = DynConstants.namespaceURI; // TODO - removed once the mechanism are in place to set package version and namespace
}
/**
+ * Initializes custom Class attributes
+ * */
+ private void initDefaults() {
+ setPackageVersion(-1);
+ }
+
+ /**
* Returns the value of CBO
*
* @return the value of CBO
Modified: trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/SpatialComponent.java
===================================================================
--- trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/SpatialComponent.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/SpatialComponent.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -64,9 +64,8 @@
* Initializes custom Class attributes
* */
private void initDefaults() {
- setNamespace(DynConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
- packageName = DynConstants.namespaceURI;
+ packageName = DynConstants.shortLabel;
variable = null;
spatialIndex = null;
}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/BoundingBox.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -279,7 +279,6 @@
*
*/
private void init() {
- setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Curve.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -229,10 +229,11 @@
*
*/
private void initDefaults() {
- setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
- listOfCurveSegments.setNamespace(LayoutConstants.namespaceURI);
+ // changing the ListOf package name from 'core' to 'layout'
+ listOfCurveSegments.setPackageName(null);
+ listOfCurveSegments.setPackageName(LayoutConstants.shortLabel);
listOfCurveSegments.setSBaseListType(ListOf.Type.other);
registerChild(listOfCurveSegments);
}
@@ -272,8 +273,13 @@
public void setListOfCurveSegments(ListOf<CurveSegment> listOfCurveSegments) {
unsetListOfCurveSegments();
this.listOfCurveSegments = listOfCurveSegments;
- if ((this.listOfCurveSegments != null) && (this.listOfCurveSegments.getSBaseListType() != ListOf.Type.other)) {
- this.listOfCurveSegments.setSBaseListType(ListOf.Type.other);
+ if (this.listOfCurveSegments != null) {
+ listOfCurveSegments.setPackageVersion(-1);
+ // changing the ListOf package name from 'core' to 'layout'
+ listOfCurveSegments.setPackageName(null);
+ listOfCurveSegments.setPackageName(LayoutConstants.shortLabel);
+ listOfCurveSegments.setSBaseListType(ListOf.Type.other);
+
}
registerChild(this.listOfCurveSegments);
}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -248,7 +248,6 @@
*
*/
private void initDefaults() {
- setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Dimensions.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Dimensions.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Dimensions.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -155,7 +155,6 @@
*
*/
private void initDefaults() {
- setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -144,7 +144,6 @@
public ListOf<GraphicalObject> getListOfSubGlyphs() {
if (!isSetListOfSubGlyphs()) {
listOfSubGlyphs = new ListOfWithName<GraphicalObject>(getLevel(), getVersion(), LayoutConstants.listOfSubGlyphs);
- listOfSubGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSubGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfSubGlyphs.setPackageName(null);
@@ -177,8 +176,6 @@
{
if ((listOfSubGlyphs instanceof ListOfWithName<?>) && (listOfSubGlyphs.getElementName().equals(LayoutConstants.listOfSubGlyphs))) {
this.listOfSubGlyphs = listOfSubGlyphs;
- listOfSubGlyphs.unsetNamespace();
- listOfSubGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSubGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfSubGlyphs.setPackageName(null);
@@ -565,7 +562,6 @@
public ListOf<ReferenceGlyph> getListOfReferenceGlyphs() {
if (!isSetListOfReferenceGlyphs()) {
listOfReferenceGlyphs = new ListOf<ReferenceGlyph>();
- listOfReferenceGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfReferenceGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfReferenceGlyphs.setPackageName(null);
@@ -662,8 +658,6 @@
if (listOfReferenceGlyph != null)
{
- listOfReferenceGlyphs.unsetNamespace();
- listOfReferenceGlyphs.setPackageName(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfReferenceGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfReferenceGlyphs.setPackageName(null);
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GraphicalObject.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -137,7 +137,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
}
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -706,7 +706,6 @@
if (!isSetListOfAdditionalGraphicalObjects()) {
listOfAdditionalGraphicalObjects = new ListOfWithName<GraphicalObject>(LayoutConstants.listOfAdditionalGraphicalObjects);
listOfAdditionalGraphicalObjects.setSBaseListType(ListOf.Type.other);
- listOfAdditionalGraphicalObjects.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfAdditionalGraphicalObjects.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfAdditionalGraphicalObjects.setPackageName(null);
@@ -724,7 +723,6 @@
if (!isSetListOfCompartmentGlyphs()) {
listOfCompartmentGlyphs = ListOf.newInstance(this, CompartmentGlyph.class);
listOfCompartmentGlyphs.setSBaseListType(ListOf.Type.other);
- listOfCompartmentGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCompartmentGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfCompartmentGlyphs.setPackageName(null);
@@ -742,7 +740,6 @@
if (!isSetListOfReactionGlyphs()) {
listOfReactionGlyphs = ListOf.newInstance(this, ReactionGlyph.class);
listOfReactionGlyphs.setSBaseListType(ListOf.Type.other);
- listOfReactionGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfReactionGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfReactionGlyphs.setPackageName(null);
@@ -760,7 +757,6 @@
if (!isSetListOfSpeciesGlyphs()) {
listOfSpeciesGlyphs = ListOf.newInstance(this, SpeciesGlyph.class);
listOfSpeciesGlyphs.setSBaseListType(ListOf.Type.other);
- listOfSpeciesGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfSpeciesGlyphs.setPackageName(null);
@@ -778,7 +774,6 @@
if (!isSetListOfTextGlyphs()) {
listOfTextGlyphs = ListOf.newInstance(this, TextGlyph.class);
listOfTextGlyphs.setSBaseListType(ListOf.Type.other);
- listOfTextGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfTextGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfTextGlyphs.setPackageName(null);
@@ -950,7 +945,6 @@
*
*/
private void initDefault() {
- setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
}
@@ -1358,8 +1352,6 @@
if (!registerDone) {
listOfAdditionalGraphicalObjects = additionalGraphicalObjects;
- listOfAdditionalGraphicalObjects.unsetNamespace();
- listOfAdditionalGraphicalObjects.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfAdditionalGraphicalObjects.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfAdditionalGraphicalObjects.setPackageName(null);
@@ -1382,8 +1374,6 @@
listOfCompartmentGlyphs = compartmentGlyphs;
if (listOfCompartmentGlyphs != null) {
- listOfCompartmentGlyphs.unsetNamespace();
- listOfCompartmentGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCompartmentGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfCompartmentGlyphs.setPackageName(null);
@@ -1405,8 +1395,6 @@
listOfReactionGlyphs = reactionGlyphs;
if (listOfReactionGlyphs != null) {
- listOfReactionGlyphs.unsetNamespace();
- listOfReactionGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfReactionGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfReactionGlyphs.setPackageName(null);
@@ -1428,8 +1416,6 @@
listOfSpeciesGlyphs = speciesGlyphs;
if (listOfSpeciesGlyphs != null) {
- listOfSpeciesGlyphs.unsetNamespace();
- listOfSpeciesGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfSpeciesGlyphs.setPackageName(null);
@@ -1450,8 +1436,6 @@
listOfTextGlyphs = textGlyphs;
if (listOfTextGlyphs != null) {
- listOfTextGlyphs.unsetNamespace();
- listOfTextGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfTextGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfTextGlyphs.setPackageName(null);
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/LayoutModelPlugin.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/LayoutModelPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/LayoutModelPlugin.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -76,7 +76,6 @@
*/
public LayoutModelPlugin(Model model) {
super(model);
- setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
createListOfLayout();
}
@@ -138,7 +137,6 @@
*/
private ListOf<Layout> createListOfLayout() {
listOfLayouts = new ListOf<Layout>();
- listOfLayouts.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfLayouts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfLayouts.setPackageName(null);
@@ -330,8 +328,6 @@
this.listOfLayouts = listOfLayouts;
if (listOfLayouts != null) {
- listOfLayouts.unsetNamespace();
- listOfLayouts.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfLayouts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfLayouts.setPackageName(null);
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Point.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Point.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Point.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -189,7 +189,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/ReactionGlyph.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -263,7 +263,6 @@
public ListOf<SpeciesReferenceGlyph> getListOfSpeciesReferenceGlyphs() {
if (!isSetListOfSpeciesReferencesGlyphs()) {
listOfSpeciesReferencesGlyphs = new ListOf<SpeciesReferenceGlyph>();
- listOfSpeciesReferencesGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesReferencesGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfSpeciesReferencesGlyphs.setPackageName(null);
@@ -401,8 +400,6 @@
listOfSpeciesReferencesGlyphs = listOfSpeciesReferencesGlyph;
if (listOfSpeciesReferencesGlyphs != null) {
- listOfSpeciesReferencesGlyph.unsetNamespace();
- listOfSpeciesReferencesGlyphs.setNamespace(LayoutConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesReferencesGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfSpeciesReferencesGlyphs.setPackageName(null);
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/AbstractRenderPlugin.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/AbstractRenderPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/AbstractRenderPlugin.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -119,7 +119,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
versionMajor = 0;
versionMinor = 0;
}
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/ColorDefinition.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/ColorDefinition.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/ColorDefinition.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -141,7 +141,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = RenderConstants.shortLabel;
}
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/GlobalRenderInformation.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -187,7 +187,6 @@
public ListOf<Style> getListOfStyles() {
if (!isSetListOfStyles()) {
listOfStyles = new ListOf<Style>(getLevel(), getVersion());
- listOfStyles.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfStyles.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfStyles.setPackageName(null);
@@ -207,8 +206,6 @@
this.listOfStyles = listOfStyles;
if (listOfStyles != null) {
- listOfStyles.unsetNamespace();
- listOfStyles.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfStyles.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfStyles.setPackageName(null);
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientBase.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -184,7 +184,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = RenderConstants.shortLabel;
spreadMethod = Spread.PAD;
@@ -304,7 +303,6 @@
public ListOf<GradientStop> getListOfGradientStops() {
if (!isSetListOfGradientStops()) {
listOfGradientStops = new ListOf<GradientStop>(getLevel(), getVersion());
- listOfGradientStops.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGradientStops.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfGradientStops.setPackageName(null);
@@ -323,8 +321,6 @@
this.listOfGradientStops = listOfGradientStops;
if (listOfGradientStops != null) {
- listOfGradientStops.unsetNamespace();
- listOfGradientStops.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGradientStops.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfGradientStops.setPackageName(null);
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/GradientStop.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -118,7 +118,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = RenderConstants.shortLabel;
}
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/LocalRenderInformation.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/LocalRenderInformation.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/LocalRenderInformation.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -187,7 +187,6 @@
public ListOf<LocalStyle> getListOfLocalStyles() {
if (!isSetListOfLocalStyles()) {
listOfLocalStyles = new ListOf<LocalStyle>(getLevel(), getVersion());
- listOfLocalStyles.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfLocalStyles.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfLocalStyles.setPackageName(null);
@@ -206,8 +205,6 @@
this.listOfLocalStyles = listOfLocalStyles;
if (listOfLocalStyles != null) {
- listOfLocalStyles.unsetNamespace();
- listOfLocalStyles.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfLocalStyles.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfLocalStyles.setPackageName(null);
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/Polygon.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/Polygon.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/Polygon.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -129,7 +129,6 @@
public ListOf<RenderPoint> getListOfElements() {
if (!isSetListOfElements()) {
listOfElements = new ListOf<RenderPoint>(getLevel(), getVersion());
- listOfElements.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfElements.setPackageName(null);
@@ -164,8 +163,6 @@
this.listOfElements = listOfElements;
if (listOfElements != null) {
- listOfElements.unsetNamespace();
- listOfElements.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfElements.setPackageName(null);
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderCurve.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderCurve.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderCurve.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -271,7 +271,6 @@
public ListOf<RenderPoint> getListOfElements() {
if (!isSetListOfElements()) {
listOfElements = new ListOf<RenderPoint>(getLevel(), getVersion());
- listOfElements.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfElements.setPackageName(null);
@@ -290,8 +289,6 @@
this.listOfElements = listOfElements;
if (listOfElements != null) {
- listOfElements.unsetNamespace();
- listOfElements.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfElements.setPackageName(null);
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderGroup.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderGroup.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderGroup.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -842,7 +842,6 @@
public ListOf<Transformation2D> getListOfElements() {
if (!isSetListOfElements()) {
listOfElements = new ListOf<Transformation2D>();
- listOfElements.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfElements.setPackageName(null);
@@ -866,8 +865,6 @@
this.listOfElements = listOfElements;
if (listOfElements != null) {
- listOfElements.unsetNamespace();
- listOfElements.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfElements.setPackageName(null);
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderInformationBase.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -168,7 +168,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = RenderConstants.shortLabel;
backgroundColor = new Color(0, 0, 0);
@@ -469,7 +468,6 @@
public ListOf<ColorDefinition> getListOfColorDefinitions() {
if (!isSetListOfColorDefinitions()) {
listOfColorDefinitions = new ListOf<ColorDefinition>(getLevel(), getVersion());
- listOfColorDefinitions.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfColorDefinitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfColorDefinitions.setPackageName(null);
@@ -488,8 +486,6 @@
this.listOfColorDefinitions = listOfColorDefinitions;
if (listOfColorDefinitions != null) {
- listOfColorDefinitions.unsetNamespace();
- listOfColorDefinitions.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfColorDefinitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfColorDefinitions.setPackageName(null);
@@ -569,7 +565,6 @@
public ListOf<GradientBase> getListOfGradientDefinitions() {
if (!isSetListOfGradientDefinitions()) {
listOfGradientDefinitions = new ListOf<GradientBase>(getLevel(), getVersion());
- listOfGradientDefinitions.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGradientDefinitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfGradientDefinitions.setPackageName(null);
@@ -588,8 +583,6 @@
listOfGradientDefinitions = listOfGradientDefintions;
if (listOfGradientDefintions != null) {
- listOfGradientDefintions.unsetNamespace();
- listOfGradientDefintions.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGradientDefintions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfGradientDefintions.setPackageName(null);
@@ -722,7 +715,6 @@
public ListOf<LineEnding> getListOfLineEndings() {
if (!isSetListOfLineEndings()) {
listOfLineEndings = new ListOf<LineEnding>(getLevel(), getVersion());
- listOfLineEndings.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfLineEndings.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfLineEndings.setPackageName(null);
@@ -742,8 +734,6 @@
this.listOfLineEndings = listOfLineEndings;
if (listOfLineEndings != null) {
- listOfLineEndings.unsetNamespace();
- listOfLineEndings.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfLineEndings.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfLineEndings.setPackageName(null);
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderLayoutPlugin.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderLayoutPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderLayoutPlugin.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -139,7 +139,6 @@
public ListOf<LocalRenderInformation> getListOfLocalRenderInformation() {
if (!isSetListOfLocalRenderInformation()) {
listOfLocalRenderInformation = new ListOf<LocalRenderInformation>();
- listOfLocalRenderInformation.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfLocalRenderInformation.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfLocalRenderInformation.setPackageName(null);
@@ -170,8 +169,6 @@
this.listOfLocalRenderInformation = listOfLocalRenderInformation;
if (listOfLocalRenderInformation != null) {
- listOfLocalRenderInformation.unsetNamespace();
- listOfLocalRenderInformation.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfLocalRenderInformation.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfLocalRenderInformation.setPackageName(null);
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderListOfLayoutsPlugin.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderListOfLayoutsPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderListOfLayoutsPlugin.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -152,7 +152,6 @@
public ListOf<GlobalRenderInformation> getListOfGlobalRenderInformation() {
if (!isSetListOfGlobalRenderInformation()) {
listOfGlobalRenderInformation = new ListOf<GlobalRenderInformation>();
- listOfGlobalRenderInformation.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGlobalRenderInformation.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfGlobalRenderInformation.setPackageName(null);
@@ -219,12 +218,8 @@
*/
public void setListOfGlobalRenderInformation(ListOf<GlobalRenderInformation> listOfGlobalRenderInformation) {
unsetListOfGlobalRenderInformation();
- this.listOfGlobalRenderInformation = listOfGlobalRenderInformation;
if (listOfGlobalRenderInformation != null) {
- listOfGlobalRenderInformation.unsetNamespace();
- listOfGlobalRenderInformation = new ListOf<GlobalRenderInformation>();
- listOfGlobalRenderInformation.setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGlobalRenderInformation.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'render'
listOfGlobalRenderInformation.setPackageName(null);
@@ -234,6 +229,8 @@
if (isSetExtendedSBase()) {
extendedSBase.registerChild(this.listOfGlobalRenderInformation);
}
+
+ this.listOfGlobalRenderInformation = listOfGlobalRenderInformation;
}
/**
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderPoint.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderPoint.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderPoint.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -170,7 +170,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = RenderConstants.shortLabel;
z = 0d;
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/Style.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/Style.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/Style.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -208,7 +208,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = RenderConstants.shortLabel;
roleList = null;
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/Transformation.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/Transformation.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/Transformation.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -85,7 +85,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(RenderConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = RenderConstants.shortLabel;
}
Modified: trunk/extensions/req/src/org/sbml/jsbml/ext/req/ChangedMath.java
===================================================================
--- trunk/extensions/req/src/org/sbml/jsbml/ext/req/ChangedMath.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/req/src/org/sbml/jsbml/ext/req/ChangedMath.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -179,7 +179,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(ReqConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = ReqConstants.shortLabel;
}
Modified: trunk/extensions/req/src/org/sbml/jsbml/ext/req/ReqSBasePlugin.java
===================================================================
--- trunk/extensions/req/src/org/sbml/jsbml/ext/req/ReqSBasePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
+++ trunk/extensions/req/src/org/sbml/jsbml/ext/req/ReqSBasePlugin.java 2015-11-17 13:13:46 UTC (rev 2402)
@@ -100,7 +100,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(ReqConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
@@ -169,7 +168,6 @@
if (!isSetListOfChangedMaths()) {
listOfChangedMaths = new ListOf<ChangedMath>();
- listOfChangedMaths.setNamespace(ReqConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfChangedMaths.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'req'
listOfChangedMaths.setPackageName(null);
@@ -195,8 +193,6 @@
this.listOfChangedMaths = listOfChangedMaths;
if (listOfChangedMaths != null) {
- listOfChangedMaths.unsetNamespace();
- listOfChangedMaths.setNamespace(ReqConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfChangedMaths.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'req'
listOfChangedMaths.setPackageName(null);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-17 11:57:15
|
Revision: 2401
http://sourceforge.net/p/jsbml/code/2401
Author: niko-rodrigue
Date: 2015-11-17 11:57:12 +0000 (Tue, 17 Nov 2015)
Log Message:
-----------
first batch of packages updates to remove the setNamepace that is not necessary any more
Modified Paths:
--------------
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ModelDefinition.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsModelPlugin.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Member.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/CompartmentReference.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/InSpeciesTypeBond.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSimpleSpeciesReferencePlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/PossibleSpeciesFeatureValue.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureChange.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureValue.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/InteriorPoint.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/OrdinalMapping.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParameterType.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/PolygonObject.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledField.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialParameterPlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialPoints.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SpatialSpeciesPlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/TransformationComponent.java
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/AbstractNamedSBaseRef.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -135,7 +135,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = CompConstants.shortLabel;
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -308,7 +308,6 @@
} else {
listOfPorts = new ListOf<Port>();
}
- listOfPorts.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfPorts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfPorts.setPackageName(null);
@@ -335,7 +334,6 @@
} else {
listOfSubmodels = new ListOf<Submodel>();
}
- listOfSubmodels.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSubmodels.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfSubmodels.setPackageName(null);
@@ -568,7 +566,6 @@
if ((this.listOfPorts != null)) {
this.listOfPorts.setSBaseListType(ListOf.Type.other);
listOfPorts.unsetNamespace();
- listOfPorts.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfPorts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfPorts.setPackageName(null);
@@ -590,8 +587,6 @@
this.listOfSubmodels = listOfSubmodels;
if ((this.listOfSubmodels != null)) {
this.listOfSubmodels.setSBaseListType(ListOf.Type.other);
- listOfSubmodels.unsetNamespace();
- listOfSubmodels.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSubmodels.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfSubmodels.setPackageName(null);
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -141,7 +141,6 @@
} else {
listOfExternalModelDefinitions = new ListOf<ExternalModelDefinition>();
}
- listOfExternalModelDefinitions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfExternalModelDefinitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfExternalModelDefinitions.setPackageName(null);
@@ -243,8 +242,6 @@
this.listOfExternalModelDefinitions = listOfExternalModelDefinitions;
if (listOfExternalModelDefinitions != null) {
- listOfExternalModelDefinitions.unsetNamespace();
- listOfExternalModelDefinitions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfExternalModelDefinitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfExternalModelDefinitions.setPackageName(null);
@@ -431,7 +428,6 @@
} else {
listOfModelDefinitions = new ListOf<ModelDefinition>();
}
- listOfModelDefinitions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfModelDefinitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfModelDefinitions.setPackageName(null);
@@ -459,8 +455,6 @@
this.listOfModelDefinitions = listOfModelDefinitions;
if (listOfModelDefinitions != null) {
- listOfModelDefinitions.unsetNamespace();
- listOfModelDefinitions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfModelDefinitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfModelDefinitions.setPackageName(null);
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -344,7 +344,6 @@
} else {
listOfReplacedElements = new ListOf<ReplacedElement>();
}
- listOfReplacedElements.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfReplacedElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfReplacedElements.setPackageName(null);
@@ -379,8 +378,6 @@
this.listOfReplacedElements = listOfReplacedElements;
if (listOfReplacedElements != null) {
- listOfReplacedElements.unsetNamespace();
- listOfReplacedElements.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfReplacedElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfReplacedElements.setPackageName(null);
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Deletion.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -120,7 +120,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/* (non-Javadoc)
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ModelDefinition.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ModelDefinition.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ModelDefinition.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -100,7 +100,6 @@
*/
public void init()
{
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = CompConstants.shortLabel;
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Port.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -108,7 +108,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/* (non-Javadoc)
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedBy.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -89,7 +89,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/ReplacedElement.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -109,7 +109,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/SBaseRef.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -139,7 +139,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = CompConstants.shortLabel;
}
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -162,7 +162,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = CompConstants.shortLabel;
}
@@ -452,7 +451,6 @@
public ListOf<Deletion> getListOfDeletions() {
if (!isSetListOfDeletions()) {
listOfDeletions = new ListOf<Deletion>(getLevel(), getVersion());
- listOfDeletions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDeletions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfDeletions.setPackageName(null);
@@ -479,8 +477,6 @@
if ((listOfDeletions != null)) {
listOfDeletions.setSBaseListType(ListOf.Type.other);
- listOfDeletions.unsetNamespace();
- listOfDeletions.setNamespace(CompConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDeletions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfDeletions.setPackageName(null);
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -763,7 +763,6 @@
this.listOfFluxBounds = listOfFluxBounds;
if (listOfFluxBounds != null) {
- listOfFluxBounds.unsetNamespace();
listOfFluxBounds.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'fbc'
listOfFluxBounds.setPackageName(null);
@@ -787,7 +786,6 @@
this.listOfGeneProducts = listOfGeneProducts;
if (listOfGeneProducts != null) {
- listOfGeneProducts.unsetNamespace();
listOfGeneProducts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'fbc'
listOfGeneProducts.setPackageName(null);
@@ -813,7 +811,7 @@
*
* @param listOfObjectives
*/
- public void setListOfObjectives(ListOf<Objective> listOfObjectives) { // TODO - fix the listOfObjectives methods
+ public void setListOfObjectives(ListOf<Objective> listOfObjectives) {
if (listOfObjectives instanceof ListOfObjectives) {
setListOfObjectives((ListOfObjectives) listOfObjectives);
} else {
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -28,6 +28,7 @@
/**
* Unlike other SBML {@link ListOf} classes, {@link ListOfObjectives} adds an additional
* required attribute activeObjective.
+ *
* @author Nicolas Rodriguez
* @since 1.0
* @version $Rev$
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -261,7 +261,6 @@
public ListOf<Member> getListOfMembers() {
if (!isSetListOfMembers()) {
listOfMembers = new ListOf<Member>();
- listOfMembers.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfMembers.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfMembers.setPackageName(null);
@@ -297,8 +296,6 @@
this.listOfMembers = listOfMembers;
if (listOfMembers != null) {
- listOfMembers.unsetNamespace();
- listOfMembers.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfMembers.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfMembers.setPackageName(null);
@@ -489,7 +486,6 @@
*
*/
private void initDefaults() {
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = GroupsConstants.shortLabel;
setPackageVersion(-1);
}
@@ -529,7 +525,6 @@
public ListOfMemberConstraint getListOfMemberConstraints() {
if (!isSetListOfMemberConstraints()) {
listOfMemberConstraints = new ListOfMemberConstraint(getLevel(), getVersion());
- listOfMemberConstraints.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfMemberConstraints.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfMemberConstraints.setPackageName(null);
@@ -551,8 +546,6 @@
this.listOfMemberConstraints = listOfMemberConstraints;
if (listOfMemberConstraints != null) {
- listOfMemberConstraints.unsetNamespace();
- listOfMemberConstraints.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfMemberConstraints.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfMemberConstraints.setPackageName(null);
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsModelPlugin.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/GroupsModelPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -221,7 +221,6 @@
if (!isSetListOfGroups()) {
listOfGroups = new ListOf<Group>();
- listOfGroups.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGroups.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfGroups.setPackageName(null);
@@ -294,7 +293,6 @@
*
*/
private void initDefaults() {
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
}
@@ -325,7 +323,6 @@
this.listOfGroups = listOfGroups;
if (listOfGroups != null) {
- listOfGroups.setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGroups.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'groups'
listOfGroups.setPackageName(null);
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/ListOfMemberConstraint.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -77,7 +77,6 @@
super();
setPackageVersion(-1);
packageName = GroupsConstants.shortLabel;
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/**
@@ -88,7 +87,6 @@
super(level, version);
setPackageVersion(-1);
packageName = GroupsConstants.shortLabel;
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/**
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Member.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Member.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Member.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -65,7 +65,6 @@
*
*/
private void initDefaults() {
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = GroupsConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/MemberConstraint.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -180,7 +180,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(GroupsConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = GroupsConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/CompartmentReference.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/CompartmentReference.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/CompartmentReference.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -161,8 +161,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- // TODO - removed once the mechanism are in place to set package version and namespace
- setNamespace(MultiConstants.namespaceURI);
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/DenotedSpeciesTypeComponentIndex.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -88,7 +88,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/InSpeciesTypeBond.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/InSpeciesTypeBond.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/InSpeciesTypeBond.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -139,7 +139,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -107,7 +107,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
@@ -116,7 +115,7 @@
*/
@Override
public String getPackageName() {
- return MultiConstants.packageName;
+ return MultiConstants.shortLabel;
}
@@ -180,7 +179,6 @@
public ListOf<CompartmentReference> getListOfCompartmentReferences() {
if (listOfCompartmentReferences == null) {
listOfCompartmentReferences = new ListOf<CompartmentReference>();
- listOfCompartmentReferences.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCompartmentReferences.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfCompartmentReferences.setPackageName(null);
@@ -208,8 +206,6 @@
this.listOfCompartmentReferences = listOfCompartmentReferences;
if (listOfCompartmentReferences != null) {
- listOfCompartmentReferences.unsetNamespace();
- listOfCompartmentReferences.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCompartmentReferences.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfCompartmentReferences.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiModelPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -95,7 +95,6 @@
*/
public MultiModelPlugin(Model model) {
super(model);
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/**
@@ -136,7 +135,6 @@
public ListOf<SpeciesType> getListOfSpeciesTypes() {
if (listOfSpeciesTypes == null) {
listOfSpeciesTypes = new ListOf<SpeciesType>();
- listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypes.setPackageName(null);
@@ -234,8 +232,6 @@
this.listOfSpeciesTypes = listOfSpeciesTypes;
if (listOfSpeciesTypes != null) {
- listOfSpeciesTypes.unsetNamespace();
- listOfSpeciesTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypes.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSimpleSpeciesReferencePlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSimpleSpeciesReferencePlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSimpleSpeciesReferencePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -93,7 +93,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -94,7 +94,6 @@
*/
public MultiSpeciesPlugin(Species species) {
super(species);
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
@@ -148,7 +147,6 @@
public ListOf<OutwardBindingSite> getListOfOutwardBindingSites() {
if (listOfOutwardBindingSites == null) {
listOfOutwardBindingSites = new ListOf<OutwardBindingSite>();
- listOfOutwardBindingSites.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfOutwardBindingSites.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfOutwardBindingSites.setPackageName(null);
@@ -175,8 +173,6 @@
this.listOfOutwardBindingSites = listOfOutwardBindingSites;
if (listOfOutwardBindingSites != null) {
- listOfOutwardBindingSites.unsetNamespace();
- listOfOutwardBindingSites.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfOutwardBindingSites.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfOutwardBindingSites.setPackageName(null);
@@ -333,7 +329,6 @@
public ListOf<SpeciesFeature> getListOfSpeciesFeatures() {
if (listOfSpeciesFeatures == null) {
listOfSpeciesFeatures = new ListOf<SpeciesFeature>();
- listOfSpeciesFeatures.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatures.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatures.setPackageName(null);
@@ -360,8 +355,6 @@
this.listOfSpeciesFeatures = listOfSpeciesFeatures;
if (listOfSpeciesFeatures != null) {
- listOfSpeciesFeatures.unsetNamespace();
- listOfSpeciesFeatures.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatures.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatures.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -94,7 +94,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
@@ -173,7 +172,6 @@
public ListOf<SpeciesTypeComponentMapInProduct> getListOfSpeciesTypeComponentMapInProducts() {
if (listOfSpeciesTypeComponentMapInProducts == null) {
listOfSpeciesTypeComponentMapInProducts = new ListOf<SpeciesTypeComponentMapInProduct>();
- listOfSpeciesTypeComponentMapInProducts.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeComponentMapInProducts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeComponentMapInProducts.setPackageName(null);
@@ -200,8 +198,6 @@
this.listOfSpeciesTypeComponentMapInProducts = listOfSpeciesTypeComponentMapInProducts;
if (listOfSpeciesTypeComponentMapInProducts != null) {
- listOfSpeciesTypeComponentMapInProducts.unsetNamespace();
- listOfSpeciesTypeComponentMapInProducts.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeComponentMapInProducts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeComponentMapInProducts.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/OutwardBindingSite.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -92,7 +92,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/PossibleSpeciesFeatureValue.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/PossibleSpeciesFeatureValue.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/PossibleSpeciesFeatureValue.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -147,7 +147,6 @@
*
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -163,7 +163,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
@@ -261,7 +260,6 @@
public ListOf<SpeciesFeatureValue> getListOfSpeciesFeatureValues() {
if (listOfSpeciesFeatureValues == null) {
listOfSpeciesFeatureValues = new ListOf<SpeciesFeatureValue>();
- listOfSpeciesFeatureValues.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureValues.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureValues.setPackageName(null);
@@ -286,8 +284,6 @@
this.listOfSpeciesFeatureValues = listOfSpeciesFeatureValues;
if (listOfSpeciesFeatureValues != null) {
- listOfSpeciesFeatureValues.unsetNamespace();
- listOfSpeciesFeatureValues.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureValues.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureValues.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureChange.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureChange.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureChange.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -136,7 +136,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -155,7 +155,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
@@ -245,7 +244,6 @@
public ListOf<PossibleSpeciesFeatureValue> getListOfPossibleSpeciesFeatureValues() {
if (listOfPossibleSpeciesFeatureValues == null) {
listOfPossibleSpeciesFeatureValues = new ListOf<PossibleSpeciesFeatureValue>();
- listOfPossibleSpeciesFeatureValues.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfPossibleSpeciesFeatureValues.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfPossibleSpeciesFeatureValues.setPackageName(null);
@@ -270,8 +268,6 @@
this.listOfPossibleSpeciesFeatureValues = listOfPossibleSpeciesFeatureValues;
if (listOfPossibleSpeciesFeatureValues != null) {
- listOfPossibleSpeciesFeatureValues.unsetNamespace();
- listOfPossibleSpeciesFeatureValues.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfPossibleSpeciesFeatureValues.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfPossibleSpeciesFeatureValues.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureValue.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureValue.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureValue.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -89,7 +89,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -568,7 +568,6 @@
public ListOf<InSpeciesTypeBond> getListOfInSpeciesTypeBonds() {
if (listOfInSpeciesTypeBonds == null) {
listOfInSpeciesTypeBonds = new ListOf<InSpeciesTypeBond>();
- listOfInSpeciesTypeBonds.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfInSpeciesTypeBonds.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfInSpeciesTypeBonds.setPackageName(null);
@@ -590,7 +589,6 @@
public ListOf<SpeciesFeatureType> getListOfSpeciesFeatureTypes() {
if (listOfSpeciesFeatureTypes == null) {
listOfSpeciesFeatureTypes = new ListOf<SpeciesFeatureType>();
- listOfSpeciesFeatureTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureTypes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureTypes.setPackageName(null);
@@ -612,7 +610,6 @@
public ListOf<SpeciesTypeComponentIndex> getListOfSpeciesTypeComponentIndexes() {
if (listOfSpeciesTypeComponentIndexes == null) {
listOfSpeciesTypeComponentIndexes = new ListOf<SpeciesTypeComponentIndex>();
- listOfSpeciesTypeComponentIndexes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeComponentIndexes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeComponentIndexes.setPackageName(null);
@@ -634,7 +631,6 @@
public ListOf<SpeciesTypeInstance> getListOfSpeciesTypeInstances() {
if (listOfSpeciesTypeInstances == null) {
listOfSpeciesTypeInstances = new ListOf<SpeciesTypeInstance>();
- listOfSpeciesTypeInstances.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeInstances.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeInstances.setPackageName(null);
@@ -861,7 +857,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
@@ -1204,8 +1199,6 @@
unsetListOfInSpeciesTypeBonds();
this.listOfInSpeciesTypeBonds = listOfInSpeciesTypeBonds;
if (listOfInSpeciesTypeBonds != null) {
- listOfInSpeciesTypeBonds.unsetNamespace();
- listOfInSpeciesTypeBonds.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfInSpeciesTypeBonds.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfInSpeciesTypeBonds.setPackageName(null);
@@ -1228,8 +1221,6 @@
unsetListOfSpeciesFeatureTypes();
this.listOfSpeciesFeatureTypes = listOfSpeciesFeatureTypes;
if (listOfSpeciesFeatureTypes != null) {
- listOfSpeciesFeatureTypes.unsetNamespace();
- listOfSpeciesFeatureTypes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureTypes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureTypes.setPackageName(null);
@@ -1253,8 +1244,6 @@
this.listOfSpeciesTypeComponentIndexes = listOfSpeciesTypeComponentIndexes;
if (listOfSpeciesTypeComponentIndexes != null) {
- listOfSpeciesTypeComponentIndexes.unsetNamespace();
- listOfSpeciesTypeComponentIndexes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeComponentIndexes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeComponentIndexes.setPackageName(null);
@@ -1277,8 +1266,6 @@
unsetListOfSpeciesTypeInstances();
this.listOfSpeciesTypeInstances = listOfSpeciesTypeInstances;
if (listOfSpeciesTypeInstances != null) {
- listOfSpeciesTypeInstances.unsetNamespace();
- listOfSpeciesTypeInstances.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesTypeInstances.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesTypeInstances.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -164,7 +164,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
@@ -278,7 +277,6 @@
public ListOf<DenotedSpeciesTypeComponentIndex> getListOfDenotedSpeciesTypeComponentIndexes() {
if (listOfDenotedSpeciesTypeComponentIndexes == null) {
listOfDenotedSpeciesTypeComponentIndexes = new ListOf<DenotedSpeciesTypeComponentIndex>();
- listOfDenotedSpeciesTypeComponentIndexes.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDenotedSpeciesTypeComponentIndexes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfDenotedSpeciesTypeComponentIndexes.setPackageName(null);
@@ -302,8 +300,6 @@
unsetListOfDenotedSpeciesTypeComponentIndexes();
listOfDenotedSpeciesTypeComponentIndexes = listOfDenotedSpeciesTypeComponentIndices;
if (listOfDenotedSpeciesTypeComponentIndices != null) {
- listOfDenotedSpeciesTypeComponentIndices.unsetNamespace();
- listOfDenotedSpeciesTypeComponentIndices.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfDenotedSpeciesTypeComponentIndices.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfDenotedSpeciesTypeComponentIndices.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -117,7 +117,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
@@ -226,7 +225,6 @@
public ListOf<SpeciesFeatureChange> getListOfSpeciesFeatureChanges() {
if (listOfSpeciesFeatureChanges == null) {
listOfSpeciesFeatureChanges = new ListOf<SpeciesFeatureChange>();
- listOfSpeciesFeatureChanges.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureChanges.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureChanges.setPackageName(null);
@@ -250,8 +248,6 @@
unsetListOfSpeciesFeatureChanges();
this.listOfSpeciesFeatureChanges = listOfSpeciesFeatureChanges;
if (listOfSpeciesFeatureChanges != null) {
- listOfSpeciesFeatureChanges.unsetNamespace();
- listOfSpeciesFeatureChanges.setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfSpeciesFeatureChanges.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfSpeciesFeatureChanges.setPackageName(null);
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeInstance.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -152,7 +152,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(MultiConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
packageName = MultiConstants.shortLabel;
setPackageVersion(-1);
}
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -579,7 +579,6 @@
this.listOfQualitativeSpecies = listOfQualitativeSpecies;
if (listOfQualitativeSpecies != null) {
- listOfQualitativeSpecies.unsetNamespace();
listOfQualitativeSpecies.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfQualitativeSpecies.setPackageName(null);
@@ -603,7 +602,6 @@
this.listOfTransitions = listOfTransitions;
if (listOfTransitions != null) {
- listOfTransitions.unsetNamespace();
listOfTransitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfTransitions.setPackageName(null);
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -666,7 +666,6 @@
listOfFunctionTerms = loft;
if (listOfFunctionTerms != null) {
- listOfFunctionTerms.unsetNamespace();
listOfFunctionTerms.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfFunctionTerms.setPackageName(null);
@@ -685,7 +684,6 @@
listOfInputs = loi;
if (listOfInputs != null) {
- listOfInputs.unsetNamespace();
listOfInputs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfInputs.setPackageName(null);
@@ -705,7 +703,6 @@
listOfOutputs = loo;
if (listOfOutputs != null) {
- listOfOutputs.unsetNamespace();
listOfOutputs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfOutputs.setPackageName(null);
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialNamedSBase.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -117,7 +117,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = SpatialConstants.shortLabel;
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AbstractSpatialSBasePlugin.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -73,7 +73,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/* (non-Javadoc)
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticVolume.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -120,7 +120,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = SpatialConstants.shortLabel;
}
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -25,14 +25,12 @@
import java.util.Collection;
import java.util.List;
import java.util.Map;
-import java.util.regex.Pattern;
import javax.swing.tree.TreeNode;
import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.PropertyUndefinedError;
-import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.util.filters.NameFilter;
/**
@@ -340,7 +338,6 @@
if (!isSetListOfCSGNodes()) {
listOfCSGNodes = new ListOf<CSGNode>(getLevel(),
getVersion());
- listOfCSGNodes.setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCSGNodes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'spatial'
listOfCSGNodes.setPackageName(null);
@@ -363,7 +360,6 @@
this.listOfCSGNodes = listOfCSGNodes;
if (listOfCSGNodes != null) {
- listOfCSGNodes.setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCSGNodes.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'spatial'
listOfCSGNodes.setPackageName(null);
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java 2015-11-17 11:57:12 UTC (rev 2401)
@@ -139,7 +139,6 @@
if (!isSetListOfCSGObjects()) {
listOfCSGObjects = new ListOf<CSGObject>(getLevel(),
getVersion());
- listOfCSGObjects.setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCSGObjects.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'spatial'
listOfCSGObjects.setPackageName(null);
@@ -162,8 +161,6 @@
this.listOfCSGObjects = listOfCSGObjects;
if (listOfCSGObjects != null) {
- listOfCSGObjects.unsetNamespace();
- listOfCSGObjects.setNamespace(SpatialConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfCSGObjects.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'spatial'
listOfCSGObjects.setPackageName(null);
@@ -242,13 +239,6 @@
}
- /*
- * TODO: if the ID is mandatory for CSGObject objects,
- * one should also add this methods
- */
- //public void removeCSGObject(String id) {
- // getListOfCSGObjects().removeFirst(new NameFilter(id));
- //}
/**
* Creates a new CSGObject element and adds it to the ListOfCSGObjects list
* @return
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-11-16 16:54:14 UTC (rev 2400)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CoordinateReference.java 2015-...
[truncated message content] |
|
From: <nik...@us...> - 2015-11-16 16:54:16
|
Revision: 2400
http://sourceforge.net/p/jsbml/code/2400
Author: niko-rodrigue
Date: 2015-11-16 16:54:14 +0000 (Mon, 16 Nov 2015)
Log Message:
-----------
mechanism to set the package version and namespace mostly done, need more testing + adapted qual and fbc so that I could test the changes + put GeneProductAssociation and GeneProductRef as UniqueNamedSBase so that their ids are registered in the model
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/AbstractSBase.java
trunk/core/src/org/sbml/jsbml/LevelVersionError.java
trunk/core/src/org/sbml/jsbml/SBMLDocument.java
trunk/core/src/org/sbml/jsbml/SBase.java
trunk/core/src/org/sbml/jsbml/xml/parsers/PackageUtil.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/AbstractFBCSBasePlugin.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxBound.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxObjective.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductAssociation.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductRef.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/FunctionTerm.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Input.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Output.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java
trunk/test/org/sbml/jsbml/test/PackageVersionTests.java
Modified: trunk/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -47,6 +47,7 @@
import org.sbml.jsbml.xml.XMLNode;
import org.sbml.jsbml.xml.XMLTriple;
import org.sbml.jsbml.xml.parsers.PackageParser;
+import org.sbml.jsbml.xml.parsers.PackageUtil;
import org.sbml.jsbml.xml.parsers.ParserManager;
/**
@@ -356,6 +357,7 @@
((AbstractSBasePlugin) sbasePlugin).setExtendedSBase(this);
}
+ // the package namespace and version will be set in firePropertyChange
firePropertyChange(TreeNodeChangeEvent.addExtension, null, sbasePlugin);
} else {
throw new IllegalArgumentException(MessageFormat.format(
@@ -773,6 +775,104 @@
throw new LevelVersionError(this, sbase);
}
+ /**
+ * Checks whether or not the given {@link SBase} has the same package
+ * version configuration than this element or the SBMLDocument. If the package namespace and version combination
+ * for the given {@code sbase} is not yet defined, this method sets it to the
+ * identical values as it is for the current object or the SBMLDocument.
+ *
+ * @param sbase
+ * the element to be checked.
+ * @return {@code true} if the given {@code sbase} and this object
+ * have the same package configuration.
+ * @throws LevelVersionError
+ * In case the given {@link SBase} has a different, but defined
+ * package version combination than this current {@link SBase}, an
+ * {@link LevelVersionError} is thrown. This method is only
+ * package-wide visible because it is not intended to be a
+ * <i>real</i> check, rather than to indicate potential errors.
+ */
+ protected boolean checkAndSetPackageNamespaceAndVersion(SBase sbase) {
+ String expectedPackageNamespace = "";
+ int expectedPackageVersion = -1;
+ String packageLabel = sbase.getPackageName();
+
+ if (packageLabel.equals("core")) {
+ return true;
+ }
+
+ if (getPackageName().equals(sbase.getPackageName())) {
+ expectedPackageNamespace = getNamespace();
+ expectedPackageVersion = getPackageVersion();
+ } else if (isSetPlugin(packageLabel)) {
+ SBasePlugin parentSBasePlugin = getPlugin(packageLabel);
+ expectedPackageNamespace = parentSBasePlugin.getElementNamespace();
+ expectedPackageVersion = parentSBasePlugin.getPackageVersion();
+ }
+
+ if (expectedPackageVersion == sbase.getPackageVersion() &&
+ expectedPackageNamespace != null && expectedPackageNamespace.equals(sbase.getNamespace())) {
+ return true;
+ } else {
+ return ((AbstractSBase) sbase).setPackageNamespaceAndVersion(packageLabel, expectedPackageNamespace, expectedPackageVersion);
+ }
+ }
+
+ /**
+ * Checks whether or not the given {@link SBasePlugin} has the same package
+ * configuration than the SBMLDocument. If the package namespace and version combination
+ * for the given {@code sbasePlugin} is not yet defined, this method sets it to the
+ * identical values as it is for the current SBMLDocument.
+ *
+ * @param sbasePlugin
+ * the element to be checked.
+ * @return {@code true} if the given {@code sbase} and this object
+ * have the same package configuration.
+ * @throws LevelVersionError
+ * In case the given {@link SBase} has a different, but defined
+ * package version combination than this current {@link SBase}, an
+ * {@link LevelVersionError} is thrown. This method is only
+ * package-wide visible because it is not intended to be a
+ * <i>real</i> check, rather than to indicate potential errors.
+ */
+ protected boolean checkAndSetPackageNamespaceAndVersion(SBasePlugin sbasePlugin, SBMLDocument doc) {
+
+ if (doc != null) {
+ String packageNamespace = doc.getEnabledPackageNamespace(sbasePlugin.getPackageName());
+
+ if (packageNamespace == null) {
+ return false;
+ }
+
+ int packageVersion = PackageUtil.extractPackageVersion(packageNamespace);
+
+ if (packageVersion == sbasePlugin.getPackageVersion() &&
+ packageNamespace != null && packageNamespace.equals(sbasePlugin.getElementNamespace()))
+ {
+ return true;
+ } else {
+ sbasePlugin.setPackageVersion(packageVersion);
+ ((AbstractSBasePlugin) sbasePlugin).setNamespace(packageNamespace);
+
+ boolean success = true;
+ Enumeration<TreeNode> children = children();
+
+ while (children.hasMoreElements()) {
+ TreeNode child = children.nextElement();
+ if (child instanceof AbstractSBase && ((AbstractSBase) child).getPackageName().equals(sbasePlugin.getPackageName()))
+ {
+ success &= ((AbstractSBase) child).setPackageNamespaceAndVersion(sbasePlugin.getPackageName(), packageNamespace, packageVersion);
+ }
+ }
+
+ return success;
+ }
+ }
+
+ return true;
+ }
+
+
/* (non-Javadoc)
* @see java.lang.Object#clone()
*/
@@ -982,6 +1082,20 @@
// the parent need to be set as well (would be done, if we call the registerChild method)
if ((newValue != null) && (newValue instanceof SBasePlugin)) {
((AbstractTreeNode) newValue).setParent(this);
+
+ // set the proper package namespace and version
+ SBMLDocument doc = getSBMLDocument();
+ SBasePlugin sbasePlugin = (SBasePlugin) newValue;
+
+ if (doc != null) {
+ String packageNamespace = doc.getEnabledPackageNamespace(sbasePlugin.getPackageName());
+ int packageVersion = PackageUtil.extractPackageVersion(packageNamespace);
+
+ ((AbstractSBasePlugin) sbasePlugin).setNamespace(packageNamespace);
+ sbasePlugin.setPackageVersion(packageVersion);
+
+ }
+
}
if ((oldValue != null) && (oldValue instanceof SBasePlugin)) {
@@ -1592,6 +1706,14 @@
public boolean isSetNotes() {
return notesXMLNode != null;
}
+
+ /* (non-Javadoc)
+ * @see org.sbml.jsbml.SBase#isSetPackageVErsion()
+ */
+ @Override
+ public boolean isSetPackageVErsion() {
+ return packageVersion != -1;
+ }
/* (non-Javadoc)
* @see org.sbml.jsbml.SBase#isSetParentSBMLObject()
@@ -1708,7 +1830,7 @@
return false;
}
- if ((sbase != null) && checkLevelAndVersionCompatibility(sbase)) {
+ if ((sbase != null) && checkLevelAndVersionCompatibility(sbase) && checkAndSetPackageNamespaceAndVersion(sbase)) {
SBMLDocument doc = getSBMLDocument();
if (doc != null) {
/*
@@ -1754,8 +1876,6 @@
sbase.getElementName()));
}
- // TODO - set package version and namespace if needed
-
/*
* Now, we can add all previous listeners. The next change will
* be fired after registering all ids.
@@ -1784,7 +1904,8 @@
private void registerChild(SBasePlugin sbasePlugin) {
// Could/Should be used by the method #firePropertyChange
- // TODO - set package version and namespace if needed
+ // set package version and namespace if needed
+ checkAndSetPackageNamespaceAndVersion(sbasePlugin, getSBMLDocument());
int childCount = sbasePlugin.getChildCount();
@@ -1910,6 +2031,36 @@
return false;
}
+ /**
+ * Sets recursively the package namespace and version.
+ *
+ * @param packageLabel the short label of the package
+ * @param namespace the namespace of the package
+ * @param packageVersion the package version
+ * @return
+ */
+ boolean setPackageNamespaceAndVersion(String packageLabel, String namespace, int packageVersion) {
+
+ if (packageLabel.equals(getPackageName())) {
+ setNamespace(namespace);
+ setPackageVersion(packageVersion);
+
+ boolean success = true;
+ Enumeration<TreeNode> children = children();
+
+ while (children.hasMoreElements()) {
+ TreeNode child = children.nextElement();
+ if (child instanceof AbstractSBase && ((AbstractSBase) child).getPackageName().equals(packageLabel)) {
+ success &= ((AbstractSBase) child).setPackageNamespaceAndVersion(packageLabel, namespace, packageVersion);
+ }
+ }
+ return success;
+
+ }
+
+ return false;
+ }
+
/* (non-Javadoc)
* @see org.sbml.jsbml.SBase#setMetaId(java.lang.String)
*/
@@ -2009,8 +2160,29 @@
public void setPackageVersion(int packageVersion) {
int oldPackageVersion = this.packageVersion;
- // TODO - add some checks to see if it agree with the package version of the parent
- // either SBase or SBasePlugin, if the parent belong to a different package ??
+ SBase parent = getParent();
+ SBasePlugin parentPlugin = null;
+
+ if ((parent != null) && (parent != this)) {
+ int parentPackageVersion = -1;
+
+ if (parent.getPackageName().equals(packageName)) {
+ parentPackageVersion = parent.getPackageVersion();
+ } else if (parent.isSetPlugin(packageName)) {
+ parentPlugin = parent.getPlugin(packageName);
+ parentPackageVersion = parentPlugin.getPackageVersion();
+ }
+
+ System.out.println("setPackageVersion - packageVersion = " + packageVersion + ", parentPackageVersion = " + parentPackageVersion);
+
+ if (packageVersion != -1 && parentPackageVersion != -1 && packageVersion != parentPackageVersion) {
+ if (parentPlugin != null) {
+ throw new LevelVersionError(parentPlugin, this);
+ } else {
+ throw new LevelVersionError(parent, this);
+ }
+ }
+ }
this.packageVersion = packageVersion;
firePropertyChange(TreeNodeChangeEvent.packageVersion, oldPackageVersion, packageVersion);
Modified: trunk/core/src/org/sbml/jsbml/LevelVersionError.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/LevelVersionError.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/core/src/org/sbml/jsbml/LevelVersionError.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -23,6 +23,7 @@
import java.text.MessageFormat;
+import org.sbml.jsbml.ext.SBasePlugin;
import org.sbml.jsbml.util.Message;
/**
@@ -61,6 +62,13 @@
* element and version in second argument.
*/
public static final String VERSION_MISMATCH_MSG = "Version mismatch between {0} in Version {1,number,integer} and {2} in Version {3,number,integer}.";
+ /**
+ * Message to display in cases that two objects do not have identical
+ * package version attributes. Requires the following replacement arguments: Class
+ * name of first element, package version in first element, class name of second
+ * element and package version in second argument.
+ */
+ public static final String PACKAGE_VERSION_MISMATCH_MSG = "Package '{4}' Version mismatch between {0} in Version {1,number,integer} and {2} in Version {3,number,integer}.";
/**
* Creates an error message if the level fields of both elements are not
@@ -72,7 +80,7 @@
*/
public static String levelMismatchMessage(SBase element1, SBase element2) {
if (element1.getLevel() != element2.getLevel()) {
- return MessageFormat.format(VERSION_MISMATCH_MSG, element1
+ return MessageFormat.format(LEVEL_MISMATCH_MSG, element1
.getElementName(), element1.getLevel(), element2
.getElementName(), element2.getLevel());
}
@@ -97,7 +105,34 @@
}
/**
+ * Creates an error message showing the different package versions of the given SBase elements.
*
+ * @param element1
+ * @param element2
+ * @return an error message showing the different package versions.
+ */
+ public static String packageVersionMismatchMessage(SBase element1, SBase element2) {
+ return MessageFormat.format(PACKAGE_VERSION_MISMATCH_MSG, element1
+ .getElementName(), element1.getPackageVersion(), element2
+ .getElementName(), element2.getPackageVersion(),
+ element1.getPackageName());
+ }
+
+ /**
+ * Creates an error message showing the different package versions of the given SBase elements.
+ *
+ * @param element1
+ * @param element2
+ * @return an error message showing the different package versions.
+ */
+ public static String packageVersionMismatchMessage(SBasePlugin element1, SBase element2) {
+ return MessageFormat.format(PACKAGE_VERSION_MISMATCH_MSG, element1.getClass().getSimpleName(),
+ element1.getPackageVersion(), element2.getElementName(), element2.getPackageVersion(),
+ element1.getPackageName());
+ }
+
+ /**
+ *
* @param sbase
*/
public LevelVersionError(SBase sbase) {
@@ -145,10 +180,29 @@
message.setMessage(levelMismatchMessage(element1, element2));
} else if (element1.getVersion() != element2.getVersion()) {
message.setMessage(versionMismatchMessage(element1, element2));
+ } else if (element1.getPackageVersion() != element2.getPackageVersion()) {
+ message.setMessage(packageVersionMismatchMessage(element1, element2));
}
setMessage(message);
}
+ /**
+ *
+ * @param element1
+ * @param element2
+ */
+ public LevelVersionError(SBasePlugin element1, SBase element2) {
+ super();
+ Message message = new Message();
+
+ if (element1.getPackageVersion() != element2.getPackageVersion()) {
+ message.setMessage(packageVersionMismatchMessage(element1, element2));
+ }
+ setMessage(message);
+ }
+
+
+
/* (non-Javadoc)
* @see org.sbml.jsbml.SBMLError#toString()
*/
Modified: trunk/core/src/org/sbml/jsbml/SBMLDocument.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SBMLDocument.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/core/src/org/sbml/jsbml/SBMLDocument.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -579,7 +579,7 @@
if (packageParser != null) {
String packageURI = packageURIOrName;
- // if the shorLabel has been used, getting the last namespace in the list of namespaces // TODO - add a getDefaultNamspace() to PackageParser
+ // if the shorLabel has been used, getting the last namespace in the list of namespaces // TODO - add a getDefaultNamespace() to PackageParser
// TODO - add a getPackageShortLabel() to PackageParser, so that a proper name can be used for packages ? Might be confusing getPackageDisplayName() might be better.
if (packageURI.equals(packageParser.getPackageName())) {
packageURI = packageParser.getPackageNamespaces().get(packageParser.getPackageNamespaces().size() - 1);
@@ -714,6 +714,35 @@
}
/**
+ * Return the package namespace enabled on this SBMLDocument or null if the package
+ * is not enabled.
+ *
+ * @param packageNameorUri the name or URI of the package extension.
+ * @return the package namespace enabled on this SBMLDocument or null if the package
+ * is not enabled.
+ */
+ public String getEnabledPackageNamespace(String packageURIOrName) {
+
+ if (enabledPackageMap.containsKey(packageURIOrName)) {
+ return packageURIOrName;
+ }
+
+ // Get the package URI is needed
+ PackageParser packageParser = ParserManager.getManager().getPackageParser(packageURIOrName);
+
+ if (packageParser != null) {
+
+ for (String packageNamespaceUri : packageParser.getPackageNamespaces()) {
+ if (enabledPackageMap.containsKey(packageNamespaceUri)) {
+ return packageNamespaceUri;
+ }
+ }
+ }
+
+ return null;
+ }
+
+ /**
* Returns the i<sup>th</sup> error or warning encountered during consistency checking.
*
* @param i - the index of the {@link SBMLError} to get
Modified: trunk/core/src/org/sbml/jsbml/SBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SBase.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/core/src/org/sbml/jsbml/SBase.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -790,7 +790,15 @@
*/
public boolean isSetNotes();
+
/**
+ * Returns {@code true} if the package version is not equals to '-1'.
+ *
+ * @return {@code true} if the package version is not equals to '-1'.
+ */
+ public boolean isSetPackageVErsion();
+
+ /**
* Check whether this {@link SBase} has been linked to a parent within the
* hierarchical SBML data structure.
*
Modified: trunk/core/src/org/sbml/jsbml/xml/parsers/PackageUtil.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/parsers/PackageUtil.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/core/src/org/sbml/jsbml/xml/parsers/PackageUtil.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -308,7 +308,7 @@
* @param namespace
* @return
*/
- private static int extractPackageVersion(String namespace) {
+ public static int extractPackageVersion(String namespace) {
int versionIndex = namespace.lastIndexOf("version");
if (versionIndex == -1) {
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/AbstractFBCSBasePlugin.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/AbstractFBCSBasePlugin.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/AbstractFBCSBasePlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -43,7 +43,6 @@
public AbstractFBCSBasePlugin() {
super();
setPackageVersion(-1);
- elementNamespace = FBCConstants.namespaceURI; // TODO - removed once the mechanism are in place to set package version and namespace
}
/**
@@ -61,7 +60,6 @@
public AbstractFBCSBasePlugin(SBase sbase) {
super(sbase);
setPackageVersion(-1);
- elementNamespace = FBCConstants.namespaceURI; // TODO - removed once the mechanism are in place to set package version and namespace
}
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -387,7 +387,6 @@
public ListOf<FluxBound> getListOfFluxBounds() {
if (!isSetListOfFluxBounds()) {
listOfFluxBounds = new ListOf<FluxBound>();
- listOfFluxBounds.setNamespace(FBCConstants.namespaceURI_L3V1V1); // TODO - removed once the mechanism are in place to set package version and namespace
listOfFluxBounds.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'fbc'
listOfFluxBounds.setPackageName(null);
@@ -409,7 +408,6 @@
public ListOf<GeneProduct> getListOfGeneProducts() {
if (!isSetListOfGeneProducts()) {
listOfGeneProducts = new ListOf<GeneProduct>();
- listOfGeneProducts.setNamespace(FBCConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGeneProducts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'fbc'
listOfGeneProducts.setPackageName(null);
@@ -766,7 +764,6 @@
if (listOfFluxBounds != null) {
listOfFluxBounds.unsetNamespace();
- listOfFluxBounds.setNamespace(FBCConstants.namespaceURI_L3V1V1); // TODO - removed once the mechanism are in place to set package version and namespace
listOfFluxBounds.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'fbc'
listOfFluxBounds.setPackageName(null);
@@ -791,7 +788,6 @@
if (listOfGeneProducts != null) {
listOfGeneProducts.unsetNamespace();
- listOfGeneProducts.setNamespace(FBCConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfGeneProducts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'fbc'
listOfGeneProducts.setPackageName(null);
@@ -817,7 +813,7 @@
*
* @param listOfObjectives
*/
- public void setListOfObjectives(ListOf<Objective> listOfObjectives) {
+ public void setListOfObjectives(ListOf<Objective> listOfObjectives) { // TODO - fix the listOfObjectives methods
if (listOfObjectives instanceof ListOfObjectives) {
setListOfObjectives((ListOfObjectives) listOfObjectives);
} else {
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxBound.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxBound.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxBound.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -328,7 +328,6 @@
*/
@Deprecated
public void initDefaults() {
- setNamespace(FBCConstants.namespaceURI_L3V1V1); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = FBCConstants.shortLabel;
}
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxObjective.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxObjective.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FluxObjective.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -219,7 +219,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(FBCConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = FBCConstants.shortLabel;
}
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProduct.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -170,7 +170,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(FBCConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = FBCConstants.shortLabel;
}
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductAssociation.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductAssociation.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductAssociation.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -26,6 +26,7 @@
import javax.swing.tree.TreeNode;
import org.sbml.jsbml.AbstractNamedSBase;
+import org.sbml.jsbml.UniqueNamedSBase;
/**
* Introduced to FBC in version 2.
@@ -35,7 +36,7 @@
* @since 1.1
* @date 06.03.2015
*/
-public class GeneProductAssociation extends AbstractNamedSBase {
+public class GeneProductAssociation extends AbstractNamedSBase implements UniqueNamedSBase {
/**
* Generated serial version identifier.
@@ -59,7 +60,6 @@
*
*/
private void initDefaults() {
- setNamespace(FBCConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = FBCConstants.shortLabel;
}
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductRef.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductRef.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/GeneProductRef.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -23,6 +23,7 @@
import java.util.Map;
import org.sbml.jsbml.AbstractNamedSBase;
+import org.sbml.jsbml.UniqueNamedSBase;
/**
* Introduced to FBC in version 2.
@@ -32,7 +33,7 @@
* @since 1.1
* @date 06.03.2015
*/
-public class GeneProductRef extends AbstractNamedSBase implements Association {
+public class GeneProductRef extends AbstractNamedSBase implements Association, UniqueNamedSBase {
/**
* Generated serial version identifier.
@@ -112,7 +113,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(FBCConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = FBCConstants.shortLabel;
}
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/ListOfObjectives.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -85,7 +85,6 @@
*
*/
private void initDefaults() {
- setNamespace(FBCConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = FBCConstants.shortLabel;
setSBaseListType(ListOf.Type.other);
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -266,7 +266,6 @@
*
*/
private void initDefaults() {
- setNamespace(FBCConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = FBCConstants.shortLabel;
}
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -370,7 +370,6 @@
*
*/
private void initDefaults() {
- setNamespace(FBCConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = FBCConstants.shortLabel;
}
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/FunctionTerm.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/FunctionTerm.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/FunctionTerm.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -112,7 +112,6 @@
* Initializes the default values using the namespace.
*/
public void initDefaults() {
- setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = QualConstants.shortLabel;
}
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Input.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Input.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Input.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -159,7 +159,6 @@
*
*/
public void initDefaults() {
- setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = QualConstants.shortLabel;
qualitativeSpecies = null;
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Output.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Output.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Output.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -160,7 +160,6 @@
*
*/
public void initDefaults() {
- setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = QualConstants.shortLabel;
qualitativeSpecies = null;
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualModelPlugin.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -112,7 +112,6 @@
*/
public QualModelPlugin(Model model) {
super(model);
- setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
}
/**
@@ -354,7 +353,6 @@
public ListOf<QualitativeSpecies> getListOfQualitativeSpecies() {
if (!isSetListOfQualitativeSpecies()) {
listOfQualitativeSpecies = new ListOf<QualitativeSpecies>();
- listOfQualitativeSpecies.setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfQualitativeSpecies.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfQualitativeSpecies.setPackageName(null);
@@ -374,7 +372,6 @@
public ListOf<Transition> getListOfTransitions() {
if (!isSetListOfTransitions()) {
listOfTransitions = new ListOf<Transition>();
- listOfTransitions.setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfTransitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfTransitions.setPackageName(null);
@@ -583,7 +580,6 @@
if (listOfQualitativeSpecies != null) {
listOfQualitativeSpecies.unsetNamespace();
- listOfQualitativeSpecies.setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfQualitativeSpecies.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfQualitativeSpecies.setPackageName(null);
@@ -608,7 +604,6 @@
if (listOfTransitions != null) {
listOfTransitions.unsetNamespace();
- listOfTransitions.setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfTransitions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfTransitions.setPackageName(null);
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/QualitativeSpecies.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -285,7 +285,6 @@
*
*/
public void initDefaults() {
- setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = QualConstants.shortLabel;
compartment = null;
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -436,7 +436,6 @@
if (!isSetListOfFunctionTerms()) {
listOfFunctionTerms = new ListOf<FunctionTerm>(getLevel(), getVersion());
listOfFunctionTerms.setSBaseListType(ListOf.Type.other);
- listOfFunctionTerms.setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfFunctionTerms.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfFunctionTerms.setPackageName(null);
@@ -453,7 +452,6 @@
if (!isSetListOfInputs()) {
listOfInputs = new ListOf<Input>(getLevel(), getVersion());
listOfInputs.setSBaseListType(ListOf.Type.other);
- listOfInputs.setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfInputs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfInputs.setPackageName(null);
@@ -470,7 +468,6 @@
if (!isSetListOfOutputs()) {
listOfOutputs = new ListOf<Output>(getLevel(), getVersion());
listOfOutputs.setSBaseListType(ListOf.Type.other);
- listOfOutputs.setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfOutputs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfOutputs.setPackageName(null);
@@ -509,7 +506,6 @@
*
*/
public void initDefaults() {
- setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
setPackageVersion(-1);
packageName = QualConstants.shortLabel;
listOfFunctionTerms = null;
@@ -671,7 +667,6 @@
if (listOfFunctionTerms != null) {
listOfFunctionTerms.unsetNamespace();
- listOfFunctionTerms.setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfFunctionTerms.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfFunctionTerms.setPackageName(null);
@@ -691,7 +686,6 @@
if (listOfInputs != null) {
listOfInputs.unsetNamespace();
- listOfInputs.setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfInputs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfInputs.setPackageName(null);
@@ -712,7 +706,6 @@
if (listOfOutputs != null) {
listOfOutputs.unsetNamespace();
- listOfOutputs.setNamespace(QualConstants.namespaceURI); // TODO - removed once the mechanism are in place to set package version and namespace
listOfOutputs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'qual'
listOfOutputs.setPackageName(null);
Modified: trunk/test/org/sbml/jsbml/test/PackageVersionTests.java
===================================================================
--- trunk/test/org/sbml/jsbml/test/PackageVersionTests.java 2015-11-12 13:37:58 UTC (rev 2399)
+++ trunk/test/org/sbml/jsbml/test/PackageVersionTests.java 2015-11-16 16:54:14 UTC (rev 2400)
@@ -33,6 +33,7 @@
import org.sbml.jsbml.FunctionDefinition;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
+import org.sbml.jsbml.Reaction;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.SBMLWriter;
@@ -49,10 +50,16 @@
import org.sbml.jsbml.ext.dyn.DynConstants;
import org.sbml.jsbml.ext.dyn.DynEventPlugin;
import org.sbml.jsbml.ext.dyn.SpatialKind;
+import org.sbml.jsbml.ext.fbc.And;
import org.sbml.jsbml.ext.fbc.FBCConstants;
import org.sbml.jsbml.ext.fbc.FBCModelPlugin;
+import org.sbml.jsbml.ext.fbc.FBCReactionPlugin;
import org.sbml.jsbml.ext.fbc.FluxBound;
+import org.sbml.jsbml.ext.fbc.GeneProduct;
+import org.sbml.jsbml.ext.fbc.GeneProductAssociation;
+import org.sbml.jsbml.ext.fbc.GeneProductRef;
import org.sbml.jsbml.ext.fbc.Objective;
+import org.sbml.jsbml.ext.fbc.Or;
import org.sbml.jsbml.ext.groups.Group;
import org.sbml.jsbml.ext.groups.GroupsConstants;
import org.sbml.jsbml.ext.groups.GroupsModelPlugin;
@@ -63,6 +70,7 @@
import org.sbml.jsbml.ext.qual.Transition;
import org.sbml.jsbml.ext.req.ReqConstants;
import org.sbml.jsbml.xml.parsers.PackageUtil;
+import org.sbml.jsbml.xml.stax.SBMLReader;
/**
*
@@ -165,9 +173,9 @@
// check and fix package version and namespaces
// TODO - update when jsbml will be fixed to set properly package version and namespace -
// now the fix is done in SBMLCoreParser#processEndDocument when reading a file
- PackageUtil.checkPackages(doc, true, true);
+ // PackageUtil.checkPackages(doc, true, true);
System.out.println("Checking packages:");
- PackageUtil.checkPackages(doc, false, true);
+ PackageUtil.checkPackages(doc, false, false);
}
@@ -208,7 +216,121 @@
}
}
+
/**
+ * Checks that package version and namespace are set properly for FBC version 2.
+ */
+ @Test public void testFbcPackageVersion2() {
+
+ doc = new SBMLDocument(3, 1);
+ m = doc.createModel("test");
+
+ // using the namespace to create the plugin so that the test is valid even when there is a version 3 or more of fbc
+ FBCModelPlugin fbcModel = ((FBCModelPlugin) m.getPlugin(FBCConstants.namespaceURI_L3V1V2));
+
+ Assert.assertTrue(fbcModel.getPackageVersion() == 2);
+ Assert.assertTrue(fbcModel.getPackageName().equals(FBCConstants.shortLabel));
+ Assert.assertTrue(fbcModel.getElementNamespace().equals(FBCConstants.namespaceURI_L3V1V2));
+
+ fbcModel.createObjective("fbc_O1");
+
+ ListOf<Objective> objectives = fbcModel.getListOfObjectives();
+
+ Assert.assertTrue(objectives.getPackageVersion() == 2);
+ Assert.assertTrue(objectives.getPackageName().equals(FBCConstants.shortLabel));
+ Assert.assertTrue(objectives.getNamespace().equals(FBCConstants.namespaceURI_L3V1V2));
+
+ for (Objective objective : objectives) {
+ Assert.assertTrue(objective.getPackageVersion() == 2);
+ Assert.assertTrue(objective.getPackageName().equals(FBCConstants.shortLabel));
+ Assert.assertTrue(objective.getNamespace().equals(FBCConstants.namespaceURI_L3V1V2));
+ }
+
+ fbcModel.createGeneProduct("fbc_GP1");
+ fbcModel.createGeneProduct("fbc_GP2");
+ fbcModel.createGeneProduct("fbc_GP3");
+
+ ListOf<GeneProduct> geneProducts = fbcModel.getListOfGeneProducts();
+
+ Assert.assertTrue(geneProducts.getPackageVersion() == 2);
+ Assert.assertTrue(geneProducts.getPackageName().equals(FBCConstants.shortLabel));
+ Assert.assertTrue(geneProducts.getNamespace().equals(FBCConstants.namespaceURI_L3V1V2));
+
+ for (GeneProduct geneProduct : geneProducts) {
+ Assert.assertTrue(geneProduct.getPackageVersion() == 2);
+ Assert.assertTrue(geneProduct.getPackageName().equals(FBCConstants.shortLabel));
+ Assert.assertTrue(geneProduct.getNamespace().equals(FBCConstants.namespaceURI_L3V1V2));
+ }
+
+ Reaction r1 = m.createReaction("R1");
+
+ FBCReactionPlugin fbcReaction = (FBCReactionPlugin) r1.getPlugin("fbc");
+
+ GeneProductAssociation gpa = fbcReaction.createGeneProductAssociation("fbc_GPA1");
+
+ Or association = new Or();
+ association.addAssociation(new GeneProductRef("fbc_GPR1"));
+
+ And and = new And();
+ and.addAssociation(new GeneProductRef("fbc_GPR2"));
+ and.addAssociation(new GeneProductRef("fbc_GPR3"));
+ association.addAssociation(and);
+
+ gpa.setAssociation(association);
+
+ Assert.assertTrue(and.getPackageVersion() == 2);
+ Assert.assertTrue(and.getPackageName().equals(FBCConstants.shortLabel));
+ Assert.assertTrue(and.getNamespace().equals(FBCConstants.namespaceURI_L3V1V2));
+
+ System.out.println("Checking packages for FBC v2 SBMLDocument:");
+ PackageUtil.checkPackages(doc, false, false);
+ System.out.println("Checking packages for FBC v2 SBMLDocument done.");
+
+
+ SBMLDocument newDoc = new SBMLDocument(3, 1);
+ Model clonedModel = m.clone();
+ newDoc.setModel(clonedModel);
+
+ Assert.assertFalse(newDoc.isPackageEnabled("fbc"));
+
+ Assert.assertTrue(clonedModel.findNamedSBase("fbc_GPR2") != null);
+ Assert.assertTrue(clonedModel.findNamedSBase("fbc_GPR2").getPackageVersion() == 2);
+ Assert.assertTrue(clonedModel.findNamedSBase("fbc_GPR2").getNamespace().equals(FBCConstants.namespaceURI_L3V1V2));
+
+
+ try {
+ String docStr = new SBMLWriter().writeSBMLToString(newDoc);
+
+ Assert.assertTrue(newDoc.isPackageEnabled("fbc"));
+
+ SBMLDocument doc3 = new SBMLReader().readSBMLFromString(docStr);
+
+ Assert.assertTrue(doc3.isPackageEnabled("fbc"));
+
+ Model m3 = doc3.getModel();
+
+ Assert.assertTrue(m3.findNamedSBase("fbc_GPR1") != null);
+ Assert.assertTrue(m3.findNamedSBase("fbc_GPR1").getPackageVersion() == 2);
+ Assert.assertTrue(m3.findNamedSBase("fbc_GPR1").getNamespace().equals(FBCConstants.namespaceURI_L3V1V2));
+
+ Assert.assertTrue(m3.findNamedSBase("fbc_GPA1") != null);
+ Assert.assertTrue(m3.findNamedSBase("fbc_GPA1").getPackageVersion() == 2);
+ Assert.assertTrue(m3.findNamedSBase("fbc_GPA1").getNamespace().equals(FBCConstants.namespaceURI_L3V1V2));
+
+ System.out.println("Checking packages for FBC v2 SBMLDocument cloned + read/write:");
+ PackageUtil.checkPackages(doc3, false, false);
+ System.out.println("Checking packages for FBC v2 SBMLDocument done.");
+
+
+ } catch (SBMLException e) {
+ e.printStackTrace();
+ } catch (XMLStreamException e) {
+ e.printStackTrace();
+ }
+ }
+
+
+ /**
* Checks that package version and namespace are set properly after cloning the Model element
* only and writing the new SBMLDocument to String or XML.
*
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <and...@us...> - 2015-11-12 13:38:01
|
Revision: 2399
http://sourceforge.net/p/jsbml/code/2399
Author: andreas-draeger
Date: 2015-11-12 13:37:58 +0000 (Thu, 12 Nov 2015)
Log Message:
-----------
* Solved some of the TODOs in the UnitsCompilier for better use of generic types.
* Corrected a few JavaDoc entries in CobraFormulaParser
* Updated third-party libraries in the build script for the CellDesigner module.
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java
trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java
trunk/modules/celldesigner/build.xml
Modified: trunk/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java 2015-11-11 14:30:20 UTC (rev 2398)
+++ trunk/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java 2015-11-12 13:37:58 UTC (rev 2399)
@@ -122,7 +122,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> and(List<ASTNode2> values) throws SBMLException {
- ASTNode2Value<Boolean> value = (ASTNode2Value<Boolean>) dimensionless();
+ ASTNode2Value<Boolean> value = dimensionless(Boolean.class);
boolean val = true;
for (ASTNode2 v : values) {
val &= v.compile(this).toBoolean();
@@ -452,8 +452,8 @@
*/
@Override
// TODO: Specify specific type T i.e. ASTNode2Value<String>
- public <T> ASTNode2Value<?> delay(String delayName, ASTNode2 x, ASTNode2 delay)
- throws SBMLException {
+ public <T> ASTNode2Value<?> delay(String delayName, ASTNode2 x, ASTNode2 delay)
+ throws SBMLException {
/*
* This represents a delay function. The delay function has the form
* delay(x, d), taking two MathML expressions as arguments. Its value is
@@ -485,15 +485,15 @@
/**
* Creates a dimensionless unit definition object encapsulated in an
- * ASTNode2Value.
+ * {@link ASTNode2Value}.
+ * @param type The type of the dimensionless value, e.g., Boolean.class etc.
*
* @return
*/
- // TODO: Specify type generic type T i.e. ASTNode2Value<?>
- private <T> ASTNode2Value dimensionless() {
+ private <T> ASTNode2Value<T> dimensionless(Class<T> type) {
UnitDefinition ud = new UnitDefinition(level, version);
ud.addUnit(Unit.Kind.DIMENSIONLESS);
- return new ASTNode2Value(ud, this);
+ return new ASTNode2Value<T>(ud, this);
}
/* (non-Javadoc)
@@ -501,8 +501,8 @@
*/
@Override
public <T> ASTNode2Value<Boolean> eq(ASTNode2 left, ASTNode2 right) throws SBMLException {
- // TODO: Specify type T i.e. ASTNode2Value<Boolean>
- ASTNode2Value v = dimensionless(), leftvalue, rightvalue;
+ ASTNode2Value<Boolean> v = dimensionless(Boolean.class);
+ ASTNode2Value<?> leftvalue, rightvalue;
leftvalue = left.compile(this);
rightvalue = right.compile(this);
unifyUnits(leftvalue, rightvalue);
@@ -572,7 +572,7 @@
@Override
public <T> ASTNode2Value<Double> frac(int numerator, int denominator) {
ASTNode2Value<Double> value = new ASTNode2Value<Double>(
- new UnitDefinition(level, version), this);
+ new UnitDefinition(level, version), this);
value.setValue(((double) numerator) / ((double) denominator));
return value;
}
@@ -586,14 +586,14 @@
ASTLambdaFunctionNode lambda = (ASTLambdaFunctionNode) function.getMath().toASTNode2();
HashMap<String, ASTNode2Value<?>> argValues = new HashMap<String, ASTNode2Value<?>>();
for (int i = 0; i < args.size(); i++) {
- // TODO: Check getChildAt() method ...
+ // TODO: Check getChildAt() method ...
argValues.put(lambda.getChildAt(i).compile(this).toString(), args
.get(i).compile(this));
}
try {
namesToUnits = argValues;
- // TODO: Check getChildAt() method ...
+ // TODO: Check getChildAt() method ...
ASTNode2Value value = lambda.getChildAt(lambda.getChildCount() - 1).compile(this);
namesToUnits.clear();
return value;
@@ -618,8 +618,8 @@
*/
@Override
public <T> ASTNode2Value<Boolean> geq(ASTNode2 left, ASTNode2 right) throws SBMLException {
- // TODO: Specify type T i.e. ASTNode2Value<Boolean>
- ASTNode2Value v = dimensionless(), leftvalue, rightvalue;
+ ASTNode2Value<Boolean> v = dimensionless(Boolean.class);
+ ASTNode2Value<?> leftvalue, rightvalue;
leftvalue = left.compile(this);
rightvalue = right.compile(this);
unifyUnits(leftvalue, rightvalue);
@@ -647,7 +647,7 @@
*/
@Override
public <T> ASTNode2Value<Double> getConstantE() {
- ASTNode2Value<Double> v = (ASTNode2Value<Double>) dimensionless();
+ ASTNode2Value<Double> v = dimensionless(Double.class);
v.setValue(Math.E);
return v;
}
@@ -657,7 +657,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> getConstantFalse() {
- ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
+ ASTNode2Value<Boolean> v = dimensionless(Boolean.class);
v.setValue(false);
return v;
}
@@ -667,7 +667,7 @@
*/
@Override
public <T> ASTNode2Value<Double> getConstantPi() {
- ASTNode2Value<Double> v = (ASTNode2Value<Double>) dimensionless();
+ ASTNode2Value<Double> v = dimensionless(Double.class);
v.setValue(Math.PI);
return v;
}
@@ -677,7 +677,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> getConstantTrue() {
- ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
+ ASTNode2Value<Boolean> v = dimensionless(Boolean.class);
v.setValue(true);
return v;
}
@@ -705,8 +705,8 @@
*/
@Override
public <T> ASTNode2Value<Boolean> gt(ASTNode2 left, ASTNode2 right) throws SBMLException {
- // TODO: Specify type T i.e. ASTNode2Value<Boolean>
- ASTNode2Value v = dimensionless(), leftvalue, rightvalue;
+ ASTNode2Value<Boolean> v = dimensionless(Boolean.class);
+ ASTNode2Value<?> leftvalue, rightvalue;
leftvalue = left.compile(this);
rightvalue = right.compile(this);
unifyUnits(leftvalue, rightvalue);
@@ -743,8 +743,9 @@
* @see org.sbml.jsbml.ASTNodeCompiler#lessEqual(org.sbml.jsbml.ASTNode2Value, org.sbml.jsbml.ASTNode2Value)
*/
@Override
- public ASTNode2Value<?> leq(ASTNode2 left, ASTNode2 right) throws SBMLException {
- ASTNode2Value v = dimensionless(), leftvalue, rightvalue;
+ public ASTNode2Value<Boolean> leq(ASTNode2 left, ASTNode2 right) throws SBMLException {
+ ASTNode2Value<Boolean> v = dimensionless(Boolean.class);
+ ASTNode2Value<?> leftvalue, rightvalue;
leftvalue = left.compile(this);
rightvalue = right.compile(this);
unifyUnits(leftvalue, rightvalue);
@@ -795,8 +796,9 @@
*/
@Override
// TODO: Specify generic type T i.e. ASTNode2Value<?>
- public <T> ASTNode2Value<?> lt(ASTNode2 left, ASTNode2 right) throws SBMLException {
- ASTNode2Value<?> v = (ASTNode2Value<?>) dimensionless(), leftvalue, rightvalue;
+ public <T> ASTNode2Value<Boolean> lt(ASTNode2 left, ASTNode2 right) throws SBMLException {
+ ASTNode2Value<Boolean> v = dimensionless(Boolean.class);
+ ASTNode2Value<?> leftvalue, rightvalue;
leftvalue = left.compile(this);
rightvalue = right.compile(this);
unifyUnits(leftvalue, rightvalue);
@@ -849,9 +851,9 @@
* @see org.sbml.jsbml.ASTNodeCompiler#notEqual(org.sbml.jsbml.ASTNode2Value, org.sbml.jsbml.ASTNode2Value)
*/
@Override
- // TODO: Specify type T i.e. ASTNode2Value<Boolean>
- public ASTNode2Value<?> neq(ASTNode2 left, ASTNode2 right) throws SBMLException {
- ASTNode2Value<?> v = (ASTNode2Value<?>) dimensionless(), leftvalue, rightvalue;
+ public ASTNode2Value<Boolean> neq(ASTNode2 left, ASTNode2 right) throws SBMLException {
+ ASTNode2Value<Boolean> v = dimensionless(Boolean.class);
+ ASTNode2Value<?> leftvalue, rightvalue;
leftvalue = left.compile(this);
rightvalue = right.compile(this);
unifyUnits(leftvalue, rightvalue);
@@ -864,7 +866,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> not(ASTNode2 value) throws SBMLException {
- ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
+ ASTNode2Value<Boolean> v = dimensionless(Boolean.class);
v.setValue(!value.compile(this).toBoolean());
return v;
}
@@ -874,7 +876,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> or(List<ASTNode2> values) throws SBMLException {
- ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
+ ASTNode2Value<Boolean> v = dimensionless(Boolean.class);
v.setValue(false);
for (ASTNode2 value : values) {
if (value.compile(this).toBoolean()) {
@@ -968,7 +970,6 @@
*
* @param left
* @param right
- * @return
*/
private void unifyUnits(ASTNode2Value left, ASTNode2Value right)
throws SBMLException {
@@ -1050,7 +1051,7 @@
throws SBMLException {
if (exponent instanceof ASTCnNumberNode) {
checkForDimensionlessOrInvalidUnits(((ASTCnNumberNode)exponent)
- .getUnitsInstance());
+ .getUnitsInstance());
}
return pow(base.compile(this), exponent.compile(this));
@@ -1078,7 +1079,7 @@
if (!Double.isNaN(exp)) {
return root(exp, base);
}
- // TODO:
+ // TODO:
return new ASTNode2Value(this);
}
@@ -1116,8 +1117,8 @@
public <T> ASTNode2Value<Double> root(ASTNode2 rootExponent, ASTNode2 radiant)
throws SBMLException {
if (rootExponent instanceof ASTCnNumberNode) {
- if (!(rootExponent instanceof ASTCnIntegerNode
- || rootExponent instanceof ASTCnRationalNode)) {
+ if (!(rootExponent instanceof ASTCnIntegerNode
+ || rootExponent instanceof ASTCnRationalNode)) {
checkForDimensionlessOrInvalidUnits(((ASTCnNumberNode)rootExponent)
.getUnitsInstance());
}
@@ -1326,7 +1327,7 @@
*/
@Override
public <T> ASTNode2Value<Boolean> xor(List<ASTNode2> values) throws SBMLException {
- ASTNode2Value<Boolean> value = (ASTNode2Value<Boolean>) dimensionless();
+ ASTNode2Value<Boolean> value = dimensionless(Boolean.class);
boolean v = false;
for (int i = 0; i < values.size(); i++) {
if (values.get(i).compile(this).toBoolean()) {
@@ -1362,7 +1363,7 @@
*/
@Override
public <T> ASTNode2Value<?> function(T functionDefinitionName,
- List<ASTNode2> args) throws SBMLException {
+ List<ASTNode2> args) throws SBMLException {
// TODO Auto-generated method stub
return null;
}
Modified: trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java 2015-11-11 14:30:20 UTC (rev 2398)
+++ trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java 2015-11-12 13:37:58 UTC (rev 2399)
@@ -11,7 +11,7 @@
* 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 3. The California Institute of Technology, Pasadena, CA, USA
* 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
+ * 5. The Babraham Institute, Cambridge, UK
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
@@ -37,14 +37,14 @@
* "(8639_AT1) || (26_AT1) || (314_AT2) || (314_AT1)".
* <p>
* Support almost the same syntax as defined in <a href="http://sbml.org/Software/libSBML/docs/java-api/org/sbml/libsbml/libsbml.html#parseL3Formula(java.lang.String)">
- * the LibSBML L3 parser</a>.
+ * the LibSBML L3 parser</a>.
* <p>One of the main differences is that ID are allowed to start by a number so that ID like that '8639_AT1' are recognised as ID.
- *
+ *
* <p>The things not supported for now are the units associated with numbers.
*
* <p>
* Parsing of the various MathML functions and constants are all
- * case-sensitive by default: names such as
+ * case-sensitive by default: names such as
* <code>Cos</code> and <code>COS</code> are not parsed as the MathML cosine
* operator, <code><cos></code>.
*
@@ -81,8 +81,8 @@
<p>
- * In the table above, <em>operand</em> implies the construct is an operand,
- * <em>prefix</em> implies the operation is applied to the following arguments,
+ * In the table above, <em>operand</em> implies the construct is an operand,
+ * <em>prefix</em> implies the operation is applied to the following arguments,
* <em>unary</em> implies there is one argument, and <em>binary</em> implies there are
* two arguments. The values in the <b>Precedence</b> column show how the
* order of different types of operation are determined. For example, the
@@ -106,7 +106,7 @@
* functions added in SBML Level 2 and Level 3:
<p>
- * <table border="0" width="95%"
+ * <table border="0" width="95%"
class="centered text-table normal-font alt-row-colors">
<tr>
<th align="left" width="60">Name</th>
@@ -115,8 +115,8 @@
<th align="left" width="90">Argument Constraints</th>
<th align="left" width="90">Result constraints</th>
</tr>
-<tr><td><code>abs</code></td>
- <td><em>x</em></td>
+<tr><td><code>abs</code></td>
+ <td><em>x</em></td>
<td>Absolute value of <em>x</em>.</td>
<td></td>
<td></td>
@@ -470,16 +470,16 @@
*
* <p>The default behavior is to be case sensitive, meaning
* '{@code cos}' would be recognized as the mathematical <a href="http://www.w3.org/TR/MathML2/chapter4.html#contm.trig">cosinus</a> but
- * '{@code Cos}', '{@code cOs}' or any other alternatives would be recognized
+ * '{@code Cos}', '{@code cOs}' or any other alternatives would be recognized
* as a name and read as a 'ci' element. If you pass {@code false} to this method
* all the different versions of {@code cos} would be recognized as the mathematical
- * <a href="http://www.w3.org/TR/MathML2/chapter4.html#contm.trig">cosinus</a>.
+ * <a href="http://www.w3.org/TR/MathML2/chapter4.html#contm.trig">cosinus</a>.
*
- * @param caseSensitive boolean to define if the parser should be case sensitive or not.
+ * @param caseSensitive boolean to define if the parser should be case sensitive or not.
*/
public void setCaseSensitive(boolean caseSensitive)
{
- this.ignoreCase = !caseSensitive;
+ ignoreCase = !caseSensitive;
}
private void checkSize(ArrayList < ASTNode > arguments, int i) throws ParseException
@@ -516,44 +516,44 @@
}
}
-/**
- * Returns a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
- *
- * <p/> The formula produced for 'a % b' or modulo(a, b) is 'piecewise(floor(a/b), gt(a/b, 0), ceil(a/b))'
- *
- * @param leftChild
- * @param rightChild
- * @return a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
- * @see http://sbml.org/Documents/FAQ#Why_can.27t_I_use_the_.3Crem.3E_operator_in_SBML_MathML.3F
- */
+ /**
+ * Returns a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
+ *
+ * <p/> The formula produced for 'a % b' or modulo(a, b) is 'piecewise(floor(a/b), gt(a/b, 0), ceil(a/b))'
+ *
+ * @param leftChild
+ * @param rightChild
+ * @return a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
+ * @see "http://sbml.org/Documents/FAQ#Why_can.27t_I_use_the_.3Crem.3E_operator_in_SBML_MathML.3F"
+ */
private ASTNode createModulo(ASTNode leftChild, ASTNode rightChild)
{
- ASTNode node = new ASTNode(ASTNode.Type.FUNCTION_PIECEWISE);
+ ASTNode node = new ASTNode(ASTNode.Type.FUNCTION_PIECEWISE);
- ASTNode floorNode = new ASTNode(ASTNode.Type.FUNCTION_FLOOR);
- ASTNode aDividedByB = new ASTNode(ASTNode.Type.DIVIDE);
- aDividedByB.addChild(leftChild);
- aDividedByB.addChild(rightChild);
+ ASTNode floorNode = new ASTNode(ASTNode.Type.FUNCTION_FLOOR);
+ ASTNode aDividedByB = new ASTNode(ASTNode.Type.DIVIDE);
+ aDividedByB.addChild(leftChild);
+ aDividedByB.addChild(rightChild);
- floorNode.addChild(aDividedByB);
- node.addChild(floorNode);
+ floorNode.addChild(aDividedByB);
+ node.addChild(floorNode);
- ASTNode greaterThan = new ASTNode(ASTNode.Type.RELATIONAL_GT);
- greaterThan.addChild(aDividedByB.clone());
- greaterThan.addChild(new ASTNode(0));
+ ASTNode greaterThan = new ASTNode(ASTNode.Type.RELATIONAL_GT);
+ greaterThan.addChild(aDividedByB.clone());
+ greaterThan.addChild(new ASTNode(0));
- node.addChild(greaterThan);
+ node.addChild(greaterThan);
- ASTNode ceilNode = new ASTNode(ASTNode.Type.FUNCTION_CEILING);
- ceilNode.addChild(aDividedByB.clone());
+ ASTNode ceilNode = new ASTNode(ASTNode.Type.FUNCTION_CEILING);
+ ceilNode.addChild(aDividedByB.clone());
- node.addChild(ceilNode);
+ node.addChild(ceilNode);
- return node;
+ return node;
}
final public Token string() throws ParseException {
- Token t;
+ Token t;
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case LOG:
t = jj_consume_token(LOG);
@@ -566,19 +566,24 @@
jj_consume_token(-1);
throw new ParseException();
}
- {if (true) return t;}
+ {if (true) {
+ return t;
+ }}
throw new Error("Missing return statement in function");
}
+ @Override
final public ASTNode parse() throws ParseException {
- ASTNode node = null;
+ ASTNode node = null;
node = expression();
- {if (true) return node;}
+ {if (true) {
+ return node;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode expression() throws ParseException {
- ASTNode value = null;
+ ASTNode value = null;
value = termLevel2();
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case 0:
@@ -592,236 +597,252 @@
jj_consume_token(-1);
throw new ParseException();
}
- {if (true) return value;}
+ {if (true) {
+ return value;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel2() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
- Token t;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
+ Token t;
leftChild = termLevel3();
label_1:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case BOOLEAN_LOGIC:
- ;
- break;
- default:
- jj_la1[2] = jj_gen;
- break label_1;
- }
- t = jj_consume_token(BOOLEAN_LOGIC);
- rightChild = termLevel3();
- // TODO - do we want to ignore the case for those cases ?
- String s = t.image;
- Type type = null;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case BOOLEAN_LOGIC:
+ ;
+ break;
+ default:
+ jj_la1[2] = jj_gen;
+ break label_1;
+ }
+ t = jj_consume_token(BOOLEAN_LOGIC);
+ rightChild = termLevel3();
+ // TODO - do we want to ignore the case for those cases ?
+ String s = t.image;
+ Type type = null;
- if (s.equalsIgnoreCase("or") || s.equalsIgnoreCase("||"))
- {
- type = ASTNode.Type.LOGICAL_OR;
+ if (s.equalsIgnoreCase("or") || s.equalsIgnoreCase("||"))
+ {
+ type = ASTNode.Type.LOGICAL_OR;
+ }
+ else if (s.equalsIgnoreCase("and") || s.equalsIgnoreCase("&&"))
+ {
+ type = ASTNode.Type.LOGICAL_AND;
+ }
+ else if (s.equalsIgnoreCase("xor"))
+ {
+ type = ASTNode.Type.LOGICAL_XOR;
+ }
+ node = new ASTNode(type);
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
}
- else if (s.equalsIgnoreCase("and") || s.equalsIgnoreCase("&&"))
- {
- type = ASTNode.Type.LOGICAL_AND;
- }
- else if (s.equalsIgnoreCase("xor"))
- {
- type = ASTNode.Type.LOGICAL_XOR;
- }
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
- {if (true) return leftChild;}
+ {if (true) {
+ return leftChild;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel3() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
- Token t;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
+ Token t;
leftChild = termLevel4();
label_2:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case COMPARISON:
- ;
- break;
- default:
- jj_la1[3] = jj_gen;
- break label_2;
- }
- t = jj_consume_token(COMPARISON);
- rightChild = termLevel4();
- String s = t.image;
- Type type = null;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case COMPARISON:
+ ;
+ break;
+ default:
+ jj_la1[3] = jj_gen;
+ break label_2;
+ }
+ t = jj_consume_token(COMPARISON);
+ rightChild = termLevel4();
+ String s = t.image;
+ Type type = null;
- if (s.equalsIgnoreCase("<"))
- {
- type = ASTNode.Type.RELATIONAL_LT;
+ if (s.equalsIgnoreCase("<"))
+ {
+ type = ASTNode.Type.RELATIONAL_LT;
+ }
+ else if (s.equalsIgnoreCase(">"))
+ {
+ type = ASTNode.Type.RELATIONAL_GT;
+ }
+ else if (s.equalsIgnoreCase("=="))
+ {
+ type = ASTNode.Type.RELATIONAL_EQ;
+ }
+ else if (s.equalsIgnoreCase("!="))
+ {
+ type = ASTNode.Type.RELATIONAL_NEQ;
+ }
+ else if (s.equalsIgnoreCase(">="))
+ {
+ type = ASTNode.Type.RELATIONAL_GEQ;
+ }
+ else if (s.equalsIgnoreCase("<="))
+ {
+ type = ASTNode.Type.RELATIONAL_LEQ;
+ }
+ node = new ASTNode(type);
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
}
- else if (s.equalsIgnoreCase(">"))
- {
- type = ASTNode.Type.RELATIONAL_GT;
- }
- else if (s.equalsIgnoreCase("=="))
- {
- type = ASTNode.Type.RELATIONAL_EQ;
- }
- else if (s.equalsIgnoreCase("!="))
- {
- type = ASTNode.Type.RELATIONAL_NEQ;
- }
- else if (s.equalsIgnoreCase(">="))
- {
- type = ASTNode.Type.RELATIONAL_GEQ;
- }
- else if (s.equalsIgnoreCase("<="))
- {
- type = ASTNode.Type.RELATIONAL_LEQ;
- }
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
- {if (true) return leftChild;}
+ {if (true) {
+ return leftChild;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel4() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
leftChild = termLevel5();
label_3:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- case MINUS:
- ;
- break;
- default:
- jj_la1[4] = jj_gen;
- break label_3;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case PLUS:
+ case MINUS:
+ ;
+ break;
+ default:
+ jj_la1[4] = jj_gen;
+ break label_3;
+ }
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case PLUS:
+ jj_consume_token(PLUS);
+ rightChild = termLevel5();
+ node = new ASTNode('+');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ break;
+ case MINUS:
+ jj_consume_token(MINUS);
+ rightChild = termLevel5();
+ node = new ASTNode('-');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ break;
+ default:
+ jj_la1[5] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
}
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- jj_consume_token(PLUS);
- rightChild = termLevel5();
- node = new ASTNode('+');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case MINUS:
- jj_consume_token(MINUS);
- rightChild = termLevel5();
- node = new ASTNode('-');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- default:
- jj_la1[5] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- {if (true) return leftChild;}
+ {if (true) {
+ return leftChild;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel5() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
leftChild = termLevel6();
label_4:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- case DIVIDE:
- case MODULO:
- ;
- break;
- default:
- jj_la1[6] = jj_gen;
- break label_4;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case TIMES:
+ case DIVIDE:
+ case MODULO:
+ ;
+ break;
+ default:
+ jj_la1[6] = jj_gen;
+ break label_4;
+ }
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case TIMES:
+ jj_consume_token(TIMES);
+ rightChild = termLevel6();
+ node = new ASTNode('*');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ break;
+ case DIVIDE:
+ jj_consume_token(DIVIDE);
+ rightChild = termLevel6();
+ Integer left, right;
+ left = getInteger(leftChild);
+ right = getInteger(rightChild);
+ // TODO - check if libsbml behave the same way
+ if (left != null && right != null) // Node transformed into a ASTNode.Type.RATIONAL number if both left and right are integer
+ {
+ node = new ASTNode();
+ node.setValue(left, right);
+ leftChild = node;
+ }
+ else
+ {
+ node = new ASTNode('/');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ }
+ break;
+ case MODULO:
+ jj_consume_token(MODULO);
+ rightChild = termLevel6();
+ node = createModulo(leftChild, rightChild);
+ leftChild = node;
+ break;
+ default:
+ jj_la1[7] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
}
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- jj_consume_token(TIMES);
- rightChild = termLevel6();
- node = new ASTNode('*');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case DIVIDE:
- jj_consume_token(DIVIDE);
- rightChild = termLevel6();
- Integer left, right;
- left = getInteger(leftChild);
- right = getInteger(rightChild);
- // TODO - check if libsbml behave the same way
- if (left != null && right != null) // Node transformed into a ASTNode.Type.RATIONAL number if both left and right are integer
- {
- node = new ASTNode();
- node.setValue(left, right);
- leftChild = node;
- }
- else
- {
- node = new ASTNode('/');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
- break;
- case MODULO:
- jj_consume_token(MODULO);
- rightChild = termLevel6();
- node = createModulo(leftChild, rightChild);
- leftChild = node;
- break;
- default:
- jj_la1[7] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
- }
- {if (true) return leftChild;}
+ {if (true) {
+ return leftChild;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel6() throws ParseException {
- ASTNode node = null;
+ ASTNode node = null;
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case MINUS:
jj_consume_token(MINUS);
node = termLevel7();
- ASTNode uiMinus = new ASTNode('-');
- uiMinus.addChild(node);
- {if (true) return uiMinus;}
+ ASTNode uiMinus = new ASTNode('-');
+ uiMinus.addChild(node);
+ {if (true) {
+ return uiMinus;
+ }}
break;
case NOT:
jj_consume_token(NOT);
node = termLevel7();
- ASTNode not = new ASTNode(Type.LOGICAL_NOT);
- not.addChild(node);
- {if (true) return not;}
+ ASTNode not = new ASTNode(Type.LOGICAL_NOT);
+ not.addChild(node);
+ {if (true) {
+ return not;
+ }}
break;
case OPEN_PAR:
case LEFT_BRACES:
case LOG:
case STRING:
node = termLevel7();
- {if (true) return node;}
+ {if (true) {
+ return node;
+ }}
break;
default:
jj_la1[8] = jj_gen;
@@ -832,267 +853,283 @@
}
final private ASTNode termLevel7() throws ParseException {
- ASTNode rightChild;
- ASTNode leftChild;
- ASTNode node = null;
+ ASTNode rightChild;
+ ASTNode leftChild;
+ ASTNode node = null;
leftChild = termLevel8();
label_5:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case POWER:
- ;
- break;
- default:
- jj_la1[9] = jj_gen;
- break label_5;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case POWER:
+ ;
+ break;
+ default:
+ jj_la1[9] = jj_gen;
+ break label_5;
+ }
+ jj_consume_token(POWER);
+ rightChild = termLevel8();
+ node = new ASTNode(Type.POWER);
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
}
- jj_consume_token(POWER);
- rightChild = termLevel8();
- node = new ASTNode(Type.POWER);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
- {if (true) return leftChild;}
+ {if (true) {
+ return leftChild;
+ }}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel8() throws ParseException, NumberFormatException {
- Token t;
- double d;
- int i;
- ASTNode node = new ASTNode();
- ASTNode vector = null;
- ASTNode child, furtherChild;
- String s;
- String vals [ ];
- ArrayList < ASTNode > arguments = new ArrayList < ASTNode > ();
+ Token t;
+ double d;
+ int i;
+ ASTNode node = new ASTNode();
+ ASTNode vector = null;
+ ASTNode child, furtherChild;
+ String s;
+ String vals [ ];
+ ArrayList < ASTNode > arguments = new ArrayList < ASTNode > ();
if (jj_2_1(2)) {
t = string();
jj_consume_token(OPEN_PAR);
child = termLevel2();
label_6:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SPLITTER:
- ;
- break;
- default:
- jj_la1[10] = jj_gen;
- break label_6;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case SPLITTER:
+ ;
+ break;
+ default:
+ jj_la1[10] = jj_gen;
+ break label_6;
+ }
+ jj_consume_token(SPLITTER);
+ furtherChild = termLevel2();
+ arguments.add(furtherChild);
}
- jj_consume_token(SPLITTER);
- furtherChild = termLevel2();
- arguments.add(furtherChild);
+ jj_consume_token(CLOSE_PAR);
+ s = t.image;
+ Type type = null;
+ if (ignoreCase)
+ {
+ s = s.toLowerCase();
}
- jj_consume_token(CLOSE_PAR);
- s = t.image;
- Type type = null;
- if (ignoreCase)
- {
- s = s.toLowerCase();
- }
- if (stringToType.containsKey(s))
- {
- type = ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
- }
- if (s.equals("pow") || s.equals("power"))
- {
- checkSize(arguments, 1);
- node.addChild(child);
- }
- else if (s.equals("sqr"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- node.addChild(new ASTNode(2));
- }
- else if (s.equals("sqrt"))
- {
- checkSize(arguments, 0);
- node.addChild(new ASTNode(2));
- node.addChild(child);
- }
- else if (s.equals("not"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- type = Type.LOGICAL_NOT;
- }
- else if (s.equals("ln"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- type = Type.FUNCTION_LN;
- }
- else if (s.equals("lambda"))
- {
- node.addChild(child);
- type = Type.LAMBDA;
- }
- else if (s.equals("piecewise"))
- {
- type = ASTNode.Type.FUNCTION_PIECEWISE;
- node.addChild(child);
- type = Type.FUNCTION_PIECEWISE;
- }
- else if (s.equals("modulo") || s.equals("mod"))
- {
- checkSize(arguments, 1);
- ASTNode rightChild = arguments.get(0);
- arguments.clear();
- node = createModulo(child, rightChild);
- {if (true) return node;}
- }
- else
- {
- node.addChild(child);
- }
- if (type != null)
- {
- node.setType(type);
- // TODO - should we set the name of the ASTNode for FUNCTION, ...
- }
- else
- {
- node.setName(s);
- }
- for (ASTNode argument : arguments)
- {
- node.addChild(argument);
- }
- {if (true) return node;}
+ if (stringToType.containsKey(s))
+ {
+ type = ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
+ }
+ if (s.equals("pow") || s.equals("power"))
+ {
+ checkSize(arguments, 1);
+ node.addChild(child);
+ }
+ else if (s.equals("sqr"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(child);
+ node.addChild(new ASTNode(2));
+ }
+ else if (s.equals("sqrt"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(new ASTNode(2));
+ node.addChild(child);
+ }
+ else if (s.equals("not"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(child);
+ type = Type.LOGICAL_NOT;
+ }
+ else if (s.equals("ln"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(child);
+ type = Type.FUNCTION_LN;
+ }
+ else if (s.equals("lambda"))
+ {
+ node.addChild(child);
+ type = Type.LAMBDA;
+ }
+ else if (s.equals("piecewise"))
+ {
+ type = ASTNode.Type.FUNCTION_PIECEWISE;
+ node.addChild(child);
+ type = Type.FUNCTION_PIECEWISE;
+ }
+ else if (s.equals("modulo") || s.equals("mod"))
+ {
+ checkSize(arguments, 1);
+ ASTNode rightChild = arguments.get(0);
+ arguments.clear();
+ node = createModulo(child, rightChild);
+ {if (true) {
+ return node;
+ }}
+ }
+ else
+ {
+ node.addChild(child);
+ }
+ if (type != null)
+ {
+ node.setType(type);
+ // TODO - should we set the name of the ASTNode for FUNCTION, ...
+ }
+ else
+ {
+ node.setName(s);
+ }
+ for (ASTNode argument : arguments)
+ {
+ node.addChild(argument);
+ }
+ {if (true) {
+ return node;
+ }}
} else {
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case OPEN_PAR:
jj_consume_token(OPEN_PAR);
node = termLevel2();
jj_consume_token(CLOSE_PAR);
- {if (true) return node;}
+ {if (true) {
+ return node;
+ }}
break;
default:
jj_la1[14] = jj_gen;
if (jj_2_2(4)) {
t = jj_consume_token(STRING);
- ASTNode selector = new ASTNode();
- selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
- selector.addChild(new ASTNode(t.image));
+ ASTNode selector = new ASTNode();
+ selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
+ selector.addChild(new ASTNode(t.image));
label_7:
- while (true) {
- jj_consume_token(LEFT_BRACKET);
- node = termLevel2();
- selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[11] = jj_gen;
- break label_7;
+ while (true) {
+ jj_consume_token(LEFT_BRACKET);
+ node = termLevel2();
+ selector.addChild(node);
+ jj_consume_token(RIGHT_BRACKET);
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACKET:
+ ;
+ break;
+ default:
+ jj_la1[11] = jj_gen;
+ break label_7;
+ }
}
- }
- {if (true) return selector;}
+ {if (true) {
+ return selector;
+ }}
} else if (jj_2_3(2)) {
jj_consume_token(LEFT_BRACES);
node = termLevel2();
- ASTNode selector = new ASTNode();
- vector = new ASTNode();
- boolean isSelector = false;
- selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
- vector.setType(ASTNode.Type.VECTOR);
- vector.addChild(node);
+ ASTNode selector = new ASTNode();
+ vector = new ASTNode();
+ boolean isSelector = false;
+ selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
+ vector.setType(ASTNode.Type.VECTOR);
+ vector.addChild(node);
label_8:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SPLITTER:
- ;
- break;
- default:
- jj_la1[12] = jj_gen;
- break label_8;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case SPLITTER:
+ ;
+ break;
+ default:
+ jj_la1[12] = jj_gen;
+ break label_8;
+ }
+ jj_consume_token(SPLITTER);
+ node = termLevel2();
+ vector.addChild(node);
}
- jj_consume_token(SPLITTER);
- node = termLevel2();
- vector.addChild(node);
- }
jj_consume_token(RIGHT_BRACES);
- selector.addChild(vector);
+ selector.addChild(vector);
label_9:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[13] = jj_gen;
- break label_9;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACKET:
+ ;
+ break;
+ default:
+ jj_la1[13] = jj_gen;
+ break label_9;
+ }
+ jj_consume_token(LEFT_BRACKET);
+ node = termLevel2();
+ isSelector = true;
+ selector.addChild(node);
+ jj_consume_token(RIGHT_BRACKET);
}
- jj_consume_token(LEFT_BRACKET);
- node = termLevel2();
- isSelector = true;
- selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- }
- {if (true) return isSelector ? selector : vector;}
+ {if (true) {
+ return isSelector ? selector : vector;
+ }}
} else {
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case LEFT_BRACES:
jj_consume_token(LEFT_BRACES);
- vector = new ASTNode();
- vector.setType(ASTNode.Type.VECTOR);
+ vector = new ASTNode();
+ vector.setType(ASTNode.Type.VECTOR);
jj_consume_token(RIGHT_BRACES);
- {if (true) return vector;}
+ {if (true) {
+ return vector;
+ }}
break;
case STRING:
t = jj_consume_token(STRING);
- s = t.image;
- if (ignoreCase)
- {
- s = s.toLowerCase();
- }
- // TODO - should we set the name of the ASTNode
- if (s.equalsIgnoreCase("true")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Type.CONSTANT_TRUE);
- }
- else if (s.equalsIgnoreCase("false")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Type.CONSTANT_FALSE);
- }
- else if (s.equals("pi"))
- {
- node = new ASTNode(Type.CONSTANT_PI);
- }
- else if (s.equals("avogadro"))
- {
- node = new ASTNode(Type.NAME_AVOGADRO);
- }
- else if (s.equals("time")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Type.NAME_TIME);
- }
- else if (s.equals("exponentiale"))
- {
- node = new ASTNode(Type.CONSTANT_E);
- }
- else if (s.equals("-infinity") || s.equals("-INF"))
- {
- node = new ASTNode(Double.NEGATIVE_INFINITY);
- }
- else if (s.equals("infinity") || s.equals("INF"))
- {
- node = new ASTNode(Double.POSITIVE_INFINITY);
- }
- else if (s.equals("NotANumber") || s.equals("NaN")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Double.NaN);
- }
- else
- {
- node = new ASTNode(s);
- }
- {if (true) return node;}
+ s = t.image;
+ if (ignoreCase)
+ {
+ s = s.toLowerCase();
+ }
+ // TODO - should we set the name of the ASTNode
+ if (s.equalsIgnoreCase("true")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Type.CONSTANT_TRUE);
+ }
+ else if (s.equalsIgnoreCase("false")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Type.CONSTANT_FALSE);
+ }
+ else if (s.equals("pi"))
+ {
+ node = new ASTNode(Type.CONSTANT_PI);
+ }
+ else if (s.equals("avogadro"))
+ {
+ node = new ASTNode(Type.NAME_AVOGADRO);
+ }
+ else if (s.equals("time")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Type.NAME_TIME);
+ }
+ else if (s.equals("exponentiale"))
+ {
+ node = new ASTNode(Type.CONSTANT_E);
+ }
+ else if (s.equals("-infinity") || s.equals("-INF"))
+ {
+ node = new ASTNode(Double.NEGATIVE_INFINITY);
+ }
+ else if (s.equals("infinity") || s.equals("INF"))
+ {
+ node = new ASTNode(Double.POSITIVE_INFINITY);
+ }
+ else if (s.equals("NotANumber") || s.equals("NaN")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Double.NaN);
+ }
+ else
+ {
+ node = new ASTNode(s);
+ }
+ {if (true) {
+ return node;
+ }}
break;
default:
jj_la1[15] = jj_gen;
@@ -1127,38 +1164,54 @@
}
private boolean jj_3R_28() {
- if (jj_scan_token(MODULO)) return true;
+ if (jj_scan_token(MODULO)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_22() {
- if (jj_scan_token(MINUS)) return true;
+ if (jj_scan_token(MINUS)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_31() {
- if (jj_scan_token(POWER)) return true;
+ if (jj_scan_token(POWER)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_14() {
- if (jj_scan_token(BOOLEAN_LOGIC)) return true;
+ if (jj_scan_token(BOOLEAN_LOGIC)) {
+ return true;
+ }
return false;
}
private boolean jj_3_3() {
- if (jj_scan_token(LEFT_BRACES)) return true;
- if (jj_3R_12()) return true;
+ if (jj_scan_token(LEFT_BRACES)) {
+ return true;
+ }
+ if (jj_3R_12()) {
+ return true;
+ }
return false;
}
private boolean jj_3R_34() {
- if (jj_scan_token(STRING)) return true;
+ if (jj_scan_token(STRING)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_29() {
- if (jj_3R_30()) return true;
+ if (jj_3R_30()) {
+ return true;
+ }
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1168,7 +1221,9 @@
}
private boolean jj_3R_12() {
- if (jj_3R_13()) return true;
+ if (jj_3R_13()) {
+ return true;
+ }
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1181,24 +1236,32 @@
Token xsp;
xsp = jj_scanpos;
if (jj_3R_21()) {
- jj_scanpos = xsp;
- if (jj_3R_22()) return true;
+ jj_scanpos = xsp;
+ if (jj_3R_22()) {
+ return true;
+ }
}
return false;
}
private boolean jj_3R_21() {
- if (jj_scan_token(PLUS)) return true;
+ if (jj_scan_token(PLUS)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_16() {
- if (jj_scan_token(COMPARISON)) return true;
+ if (jj_scan_token(COMPARISON)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_15() {
- if (jj_3R_17()) return true;
+ if (jj_3R_17()) {
+ return true;
+ }
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1208,7 +1271,9 @@
}
private boolean jj_3R_13() {
- if (jj_3R_15()) return true;
+ if (jj_3R_15()) {
+ return true;
+ }
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1218,25 +1283,39 @@
}
private boolean jj_3R_11() {
- if (jj_scan_token(LEFT_BRACKET)) return true;
- if (jj_3R_12()) return true;
- if (jj_scan_token(RIGHT_BRACKET)) return true;
+ if (jj_scan_token(LEFT_BRACKET)) {
+ return true;
+ }
+ if (jj_3R_12()) {
+ return true;
+ }
+ if (jj_scan_token(RIGHT_BRACKET)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_33() {
- if (jj_scan_token(LEFT_BRACES)) return true;
- if (jj_scan_token(RIGHT_BRACES)) return true;
+ if (jj_scan_token(LEFT_BRACES)) {
+ return true;
+ }
+ if (jj_scan_token(RIGHT_BRACES)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_27() {
- if (jj_scan_token(DIVIDE)) return true;
+ if (jj_scan_token(DIVIDE)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_25() {
- if (jj_3R_29()) return true;
+ if (jj_3R_29()) {
+ return true;
+ }
return false;
}
@@ -1244,8 +1323,10 @@
Token xsp;
xsp = jj_scanpos;
if (jj_scan_token(23)) {
- jj_scanpos = xsp;
- if (jj_scan_token(24)) return true;
+ jj_scanpos = xsp;
+ if (jj_scan_token(24)) {
+ return true;
+ }
}
return false;
}
@@ -1254,34 +1335,44 @@
Token xsp;
xsp = jj_scanpos;
if (jj_3_1()) {
- jj_scanpos = xsp;
- if (jj_3R_32()) {
- jj_scanpos = xsp;
- if (jj_3_2()) {
- jj_scanpos = xsp;
- if (jj_3_3()) {
- jj_scanpos = xsp;
- if (jj_3R_33()) {
- jj_scanpos = xsp;
- if (jj_3R_34()) return true;
+ jj_scanpos = xsp;
+ if (jj_3R_32()) {
+ jj_scanpos = xsp;
+ if (jj_3_2()) {
+ jj_scanpos = xsp;
+ if (jj_3_3()) {
+ jj_scanpos = xsp;
+ if (jj_3R_33()) {
+ jj_scanpos = xsp;
+ if (jj_3R_34()) {
+ return true;
+ }
+ }
+ }
+ }
+ }
}
- }
- }
- }
- }
return false;
}
private boolean jj_3_1() {
- if (jj_3R_10()) return true;
- if (jj_scan_token(OPEN_PAR)) return true;
+ if (jj_3R_10()) {
+ return true;
+ }
+ if (jj_scan_token(OPEN_PAR)) {
+ return true;
+ }
return false;
}
private boolean jj_3_2() {
- if (jj_scan_token(STRING)) return true;
+ if (jj_scan_token(STRING)) {
+ return true;
+ }
Token xsp;
- if (jj_3R_11()) return true;
+ if (jj_3R_11()) {
+ return true;
+ }
while (true) {
xsp = jj_scanpos;
if (jj_3R_11()) { jj_scanpos = xsp; break; }
@@ -1290,13 +1381,19 @@
}
private boolean jj_3R_26() {
- if (jj_scan_token(TIMES)) return true;
+ if (jj_scan_token(TIMES)) {
+ return true;
+ }
return false;
}
private boolean jj_3R_24() {
- if (jj_scan_token(NOT)) return true;
- if (jj_3R_29()) return true;
+ if (jj_scan_token(NOT)) {
+ return true;
+ }
+ if (jj_3R_29()) {
+ return true;
+ }
return false;
}
@@ -1304,23 +1401,31 @@
Token xsp;
xsp = jj_scanpos;
if (jj_3R_26()) {
- jj_scanpos = xsp;
- if (jj_3R_27()) {
- jj_scanpos = xsp;
- if (jj_3R_28()) return true;
+ jj_scanpos = xsp;
+ if (jj_3R_27()) {
+ jj_scanpos = xsp;
+ if (jj_3R_28()) {
+ return true;
+ }
+ }
}
- }
return false;
}
private boolean jj_3R_32() {
- if (jj_scan_token(OPEN_PAR)) return true;
- if (jj_3R_12()) return true;
+ if (jj_scan_token(OPEN_PAR)) {
+ return true;
+ }
+ if (jj_3R_12()) {
+ return true;
+ }
return false;
}
private boolean jj_3R_17() {
- if (jj_3R_19()) return true;
+ if (jj_3R_19()) {
+ return true;
+ }
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1333,18 +1438,24 @@
Token xsp;
xsp = jj_scanpos;
if (jj_3R_23()) {
- jj_scanpos = xsp;
- if (jj_3R_24()) {
- jj_scanpos = xsp;
- if (jj_3R_25()) return true;
+ jj_scanpos = xsp;
+ if (jj_3R_24()) {
+ jj_scanpos = xsp;
+ if (jj_3R_25()) {
+ return true;
+ }
+ }
}
- }
return false;
}
private boolean jj_3R_23() {
- if (jj_scan_token(MINUS)) return true;
- if (jj_3R_29()) return true;
+ if (jj_scan_token(MINUS)) {
+ return true;
+ }
+ if (jj_3R_29()) {
+ return true;
+ }
return false;
}
@@ -1362,18 +1473,18 @@
final private int[] jj_la1 = new int[16];
static private int[] jj_la1_0;
static {
- jj_la1_init_0();
- }
- private static void jj_la1_init_0() {
- jj_la1_0 = new int[] {0x1800000,0x8000001,0x40000,0x20000,0xa0,0xa0,0x700,0x700,0x1c02880,0x40,0x10,0x8000,0x10,0x8000,0x800,0x1002000,};
- }
+ jj_la1_init_0();
+ }
+ private static void jj_la1_init_0() {
+ jj_la1_0 = new int[] {0x1800000,0x8000001,0x40000,0x20000,0xa0,0xa0,0x700,0x700,0x1c02880,0x40,0x10,0x8000,0x10,0x8000,0x800,0x1002000,};
+ }
final private JJCalls[] jj_2_rtns = new JJCalls[3];
private boolean jj_rescan = false;
private int jj_gc = 0;
/** Constructor with InputStream. */
public CobraFormulaParser(java.io.InputStream stream) {
- this(stream, null);
+ this(stream, null);
}
/** Constructor with InputStream and supplied encoding */
public CobraFormulaParser(java.io.InputStream stream, String encoding) {
@@ -1382,23 +1493,33 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 16; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 16; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
/** Reinitialise. */
+ @Override
public void ReInit(java.io.InputStream stream) {
- ReInit(stream, null);
+ ReInit(stream, null);
}
/** Reinitialise. */
+ @Override
public void ReInit(java.io.InputStream stream, String encoding) {
try { jj_input_stream.ReInit(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); }
token_source.ReInit(jj_input_stream);
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 16; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 16; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
/** Constructor. */
@@ -1408,19 +1529,28 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 16; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 16; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
/** Reinitialise. */
+ @Override
public void ReInit(java.io.Reader stream) {
jj_input_stream.ReInit(stream, 1, 1);
token_source.ReInit(jj_input_stream);
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 16; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 16; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
/** Constructor with generated Token Manager. */
@@ -1429,8 +1559,12 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 16; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 16; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
/** Reinitialise. */
@@ -1439,14 +1573,21 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 16; i++) jj_la1[i] = -1;
- for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
+ for (int i = 0; i < 16; i++) {
+ jj_la1[i] = -1;
+ }
+ for (int i = 0; i < jj_2_rtns.length; i++) {
+ jj_2_rtns[i] = new JJCalls();
+ }
}
private Token jj_consume_token(int kind) throws ParseException {
Token oldToken;
- if ((oldToken = token).next != null) token = token.next;
- else token = token.next = token_source.getNextToken();
+ if ((oldToken = token).next != null) {
+ token = token.next;
+ } else {
+ token = token.next = token_source.getNextToken();
+ }
jj_ntk = -1;
if (token.kind == kind) {
jj_gen++;
@@ -1455,7 +1596,9 @@
for (int i = 0; i < jj_2_rtns.length; i++) {
JJCalls c = jj_2_rtns[i];
while (c != null) {
- if (c.gen < jj_gen) c.first = null;
+ if (c.gen < jj_gen) {
+ c.first = null;
+ }
c = c.next;
}
}
@@ -1483,38 +1626,51 @@
if (jj_rescan) {
int i = 0; Token tok = token;
while (tok != null && tok != jj_scanpos) { i++; tok = tok.next; }
- if (tok != null) jj_add_error_token(kind, i);
+ if (tok != null) {
+ jj_add_error_token(kind, i);
+ }
}
- if (jj_scanpos.kind != kind) return true;
- if (jj_la == 0 && jj_scanpos == jj_lastpos) throw jj_ls;
+ if (jj_scanpos.kind != kind) {
+ return true;
+ }
+ if (jj_la == 0 && jj_scanpos == jj_lastpos) {
+ throw jj_ls;
+ }
return false;
}
-/** Get the next Token. */
+ /** Get the next Token. */
final public Token getNextToken() {
- if (token.next != null) token = token.next;
- else token = token.next = token_source.getNextToken();
+ if (token.next != null) {
+ token = token.next;
+ } else {
+ token = token.next = token_source.getNextToken();
+ }
jj_ntk = -1;
jj_gen++;
return token;
}
-/** Get the specific Token. */
+ /** Get the specific Token. */
final public Token getToken(int index) {
Token t = token;
for (int i = 0; i < index; i++) {
- if (t.next != null) t = t.next;
- else t = t.next = token_source.getNextToken();
+ if (t.next != null) {
+ t = t.next;
+ } else {
+ t = t.next = token_source.getNextToken();
+ }
}
return t;
}
private int jj_ntk() {
- if ((jj_nt=token.next) == null)
+ if ((jj_nt=token.next) == null) {
return (jj_ntk = (token.next=token_source.getNextToken()).kind);
- else
+ } else {
return (jj_ntk = jj_nt.kind);
+ }
}
private java.util.List<int[]> jj_expentries = new java.util.ArrayList<int[]>();
@@ -1524,7 +1680,9 @@
private int jj_endpos;
private void jj_add_error_token(int kind, int pos) {
- if (pos >= 100) return;
+ if (pos >= 100) {
+ return;
+ }
if (pos == jj_endpos + 1) {
jj_lasttokens[jj_endpos++] = kind;
} else if (jj_endpos != 0) {
@@ -1544,7 +1702,9 @@
break jj_entries_loop;
}
}
- if (pos != 0) jj_lasttokens[(jj_endpos = pos) - 1] = kind;
+ if (pos != 0) {
+ jj_lasttokens[(jj_endpos = pos) - 1] = kind;
+ }
}
}
@@ -1593,19 +1753,19 @@
private void jj_rescan_token() {
jj_rescan = true;
for (int i = 0; i < 3; i++) {
- try {
- JJCalls p = jj_2_rtns[i];
- do {
- if (p.gen > jj_gen) {
- jj_la = p.arg; jj_lastpos = jj_scanpos = p.first;
- switch (i) {
+ try {
+ JJCalls p = jj_2_rtns[i];
+ do {
+ if (p.gen > jj_gen) {
+ jj_la = p.arg; jj_lastpos = jj_scanpos = p.first;
+ switch (i) {
case 0: jj_3_1(); break;
case 1: jj_3_2(); break;
case 2: jj_3_3(); break;
+ }
}
- }
- p = p.next;
- } while (p != null);
+ p = p.next;
+ } while (p != null);
} catch(LookaheadSuccess ls) { }
}
jj_rescan = false;
Modified: trunk/modules/celldesigner/build.xml
===================================================================
--- trunk/modules/celldesigner/build.xml 2015-11-11 14:30:20 UTC (rev 2398)
+++ trunk/modules/celldesigner/build.xml 2015-11-12 13:37:58 UTC (rev 2399)
@@ -614,9 +614,9 @@
<zipfileset excludes="META-INF/**, **/package-info.class, **/package.html, **/*.java" src="${jsbml.dir}/core/lib/jigsaw-dateParser.jar"/>
<zipfileset excludes="META-INF/**, **/package-info.class, **/package.html, **/*.java" src="${jsbml.dir}/core/lib/log4j-1.2.8.jar"/>
<zipfileset excludes="META-INF/**, **/package-info.class, **/package.html, **/*.java" src="${jsbml.dir}/core/lib/stax-api-1.0.1.jar"/>
- <zipfileset excludes="META-INF/**, **/package-info.class, **/package.html, **/*.java" src="${jsbml.dir}/core/lib/stax2-api-3.0.3.jar"/>
- <zipfileset excludes="META-INF/**, **/package-info.class, **/package.html, **/*.java" src="${jsbml.dir}/core/lib/staxmate-2.0.0.jar"/>
- <zipfileset excludes="META-INF/**, **/package-info.class, **/package.html, **/*.java" src="${jsbml.dir}/core/lib/woodstox-core-lgpl-4.0.9.jar"/>
+ <zipfileset excludes="META-INF/**, **/package-info.class, **/package.html, **/*.java" src="${jsbml.dir}/core/lib/stax2-api-3.1.4.jar"/>
+ <zipfileset excludes="META-INF/**, **/package-info.class, **/package.html, **/*.java" src="${jsbml.dir}/core/lib/staxmate-2.3.0.jar"/>
+ <zipfileset excludes="META-INF/**, **/package-info.class, **/package.html, **/*.java" src="${jsbml.dir}/core/l...
[truncated message content] |
|
From: <nik...@us...> - 2015-11-11 14:30:22
|
Revision: 2398
http://sourceforge.net/p/jsbml/code/2398
Author: niko-rodrigue
Date: 2015-11-11 14:30:20 +0000 (Wed, 11 Nov 2015)
Log Message:
-----------
added more information in the main pom file like license, developers contact and scm location. Those are part of the requirements to add a library to maven central.
Modified Paths:
--------------
trunk/pom.xml
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2015-11-10 13:27:08 UTC (rev 2397)
+++ trunk/pom.xml 2015-11-11 14:30:20 UTC (rev 2398)
@@ -30,10 +30,35 @@
<artifactId>jsbml-parent</artifactId>
<version>1.1-b1</version>
<packaging>pom</packaging>
+ <description>JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams.</description>
+ <url>http://www.sbml.org/Software/JSBML</url>
+
+ <licenses>
+ <license>
+ <name>LGPL License</name>
+ <url>http://opensource.org/licenses/LGPL-2.1</url>
+ </license>
+ </licenses>
+
+ <developers>
+ <developer>
+ <name>JSBML team</name>
+ <email>jsb...@ca...</email>
+ <organization>SBML Team</organization>
+ <organizationUrl>http://www.sbml.org</organizationUrl>
+ </developer>
+ </developers>
+ <scm>
+ <connection>scm:svn:http://svn.code.sf.net/p/jsbml/code/trunk</connection>
+ <developerConnection>scm:svn:https://use...@sv.../p/jsbml/code/trunk</developerConnection>
+ <url>https://sourceforge.net/p/jsbml/code/HEAD/tree/trunk/</url>
+ </scm>
+
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+ <jsbml.version>${project.version}</jsbml.version>
</properties>
<build>
@@ -42,20 +67,20 @@
<testSourceDirectory>test</testSourceDirectory>
<resources>
<resource>
- <directory>resources</directory>
+ <directory>resources</directory>
</resource>
</resources>
<testResources>
<testResource>
- <directory>test</directory>
+ <directory>test</directory>
</testResource>
</testResources>
<extensions>
<extension>
- <groupId>org.apache.maven.wagon</groupId>
- <artifactId>wagon-ssh</artifactId>
- <version>2.4</version>
+ <groupId>org.apache.maven.wagon</groupId>
+ <artifactId>wagon-ssh</artifactId>
+ <version>2.4</version>
</extension>
</extensions>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-10 13:27:10
|
Revision: 2397
http://sourceforge.net/p/jsbml/code/2397
Author: niko-rodrigue
Date: 2015-11-10 13:27:08 +0000 (Tue, 10 Nov 2015)
Log Message:
-----------
some more corrections to be able to generate the test jar files. To have all maven tests succesful in core, we need to move/remove/correct few more classes.
Modified Paths:
--------------
trunk/build.xml
trunk/core/pom.xml
trunk/extensions/distrib/pom.xml
trunk/extensions/layout/test/org/sbml/jsbml/ext/layout/test/LayoutExtentionTest.java
trunk/extensions/pom.xml
trunk/pom.xml
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/build.xml 2015-11-10 13:27:08 UTC (rev 2397)
@@ -126,6 +126,8 @@
<fileset dir="${simulation.core.dir}/lib/ext-lib/" includes="*.jar"/>
</path>
+ <property name="maven.repo.url" value="file:///homes/maven/public_html/m2repo"/>
+ <!-- local test instance url file:///homes/maven/public_html/m2repo -->
</target>
@@ -735,8 +737,10 @@
<arg value="deploy:deploy-file"/>
<arg value="-DpomFile=./dev/maven/pom.xml"/>
<arg value="-Dfile=./dev/maven/jsbml-pom.jar"/>
+ <arg value="-Durl=${maven.repo.url}"/>
</exec>
+ <!-- mvn test jar:test-jar to generate the test jar files to be able to run the tests in a new project -->
</target>
Modified: trunk/core/pom.xml
===================================================================
--- trunk/core/pom.xml 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/core/pom.xml 2015-11-10 13:27:08 UTC (rev 2397)
@@ -61,12 +61,6 @@
<testResource>
<directory>test</directory>
</testResource>
- <testResource>
- <directory>resources</directory>
- </testResource>
- <testResource>
- <directory>src</directory>
- </testResource>
</testResources>
<extensions>
@@ -78,7 +72,7 @@
</extensions>
<plugins>
- <plugin>
+ <plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
Modified: trunk/extensions/distrib/pom.xml
===================================================================
--- trunk/extensions/distrib/pom.xml 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/extensions/distrib/pom.xml 2015-11-10 13:27:08 UTC (rev 2397)
@@ -35,4 +35,14 @@
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>jsbml-distrib</artifactId>
<packaging>jar</packaging>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.sbml.jsbml.modules</groupId>
+ <artifactId>jsbml-tidy</artifactId>
+ <version>${project.version}</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
</project>
Modified: trunk/extensions/layout/test/org/sbml/jsbml/ext/layout/test/LayoutExtentionTest.java
===================================================================
--- trunk/extensions/layout/test/org/sbml/jsbml/ext/layout/test/LayoutExtentionTest.java 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/extensions/layout/test/org/sbml/jsbml/ext/layout/test/LayoutExtentionTest.java 2015-11-10 13:27:08 UTC (rev 2397)
@@ -25,6 +25,7 @@
import java.io.File;
import java.io.IOException;
+import java.io.InputStream;
import javax.xml.stream.XMLStreamException;
@@ -46,6 +47,7 @@
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
import org.sbml.jsbml.ext.layout.TextGlyph;
+import org.sbml.jsbml.xml.test.SBML_L2V1Test;
/**
*
@@ -69,16 +71,15 @@
static {
final SBMLReader reader = new SBMLReader();
- final String LAYOUT = System.getProperty("user.dir") + "/extensions/layout/test/org/sbml/jsbml/xml/test/data/layout/Layout_Example_1.xml";
+ final InputStream fileStream = SBML_L2V1Test.class.getResourceAsStream("/org/sbml/jsbml/xml/test/data/layout/Layout_Example_1.xml");
final String LAYOUT_NS = "http://www.sbml.org/sbml/level3/version1/layout/version1";
try {
- doc = reader.readSBML(new File(LAYOUT));
+ doc = reader.readSBMLFromStream(fileStream);
} catch (XMLStreamException e) {
e.printStackTrace();
- } catch (IOException e) {
- e.printStackTrace();
- }
+ }
+
layoutModel = (LayoutModelPlugin) doc.getModel().getExtension(LAYOUT_NS);
}
Modified: trunk/extensions/pom.xml
===================================================================
--- trunk/extensions/pom.xml 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/extensions/pom.xml 2015-11-10 13:27:08 UTC (rev 2397)
@@ -36,31 +36,6 @@
<relativePath>../</relativePath>
</parent>
- <build>
- <sourceDirectory>${basedir}/src/</sourceDirectory>
- <!--
- <testSourceDirectory>${basedir}/test/</testSourceDirectory>
- -->
- <resources>
- <resource>
- <directory>${basedir}/resources/</directory>
- </resource>
- </resources>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-surefire-plugin</artifactId>
- <version>2.5</version>
- <configuration>
- <skipTests>true</skipTests>
- <systemPropertyVariables>
- <user.dir>${basedir}/../../</user.dir>
- </systemPropertyVariables>
- </configuration>
- </plugin>
- </plugins>
- </build>
-
<dependencies>
<dependency>
<groupId>org.sbml.jsbml</groupId>
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2015-11-10 13:23:25 UTC (rev 2396)
+++ trunk/pom.xml 2015-11-10 13:27:08 UTC (rev 2397)
@@ -24,23 +24,44 @@
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
-
- <groupId>org.sbml.jsbml</groupId>
- <artifactId>jsbml-parent</artifactId>
- <version>1.1-b1</version>
- <packaging>pom</packaging>
-
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
- </properties>
-
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml-parent</artifactId>
+ <version>1.1-b1</version>
+ <packaging>pom</packaging>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+ </properties>
+
<build>
+
+ <sourceDirectory>src</sourceDirectory>
+ <testSourceDirectory>test</testSourceDirectory>
+ <resources>
+ <resource>
+ <directory>resources</directory>
+ </resource>
+ </resources>
+ <testResources>
+ <testResource>
+ <directory>test</directory>
+ </testResource>
+ </testResources>
+
+ <extensions>
+ <extension>
+ <groupId>org.apache.maven.wagon</groupId>
+ <artifactId>wagon-ssh</artifactId>
+ <version>2.4</version>
+ </extension>
+ </extensions>
+
<plugins>
-
-<!-- properties file not used at the moment
-
+
+ <!-- properties file not used at the moment
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
@@ -60,8 +81,7 @@
</execution>
</executions>
</plugin>
- </plugins>
--->
+ -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
@@ -113,12 +133,12 @@
</build>
- <modules>
- <module>core</module>
- <module>extensions</module>
- <module>modules</module>
- </modules>
-
+ <modules>
+ <module>core</module>
+ <module>extensions</module>
+ <module>modules</module>
+ </modules>
+
<repositories>
<repository>
<id>local-repo</id>
@@ -126,21 +146,21 @@
</repository>
</repositories>
- <distributionManagement>
- <repository>
+ <distributionManagement>
+ <repository>
<id>local-repo-deploy</id>
<name>Test Maven2 repository</name>
<url>file:///var/www/html/repo</url>
</repository>
- <snapshotRepository>
+ <snapshotRepository>
+ <id>jsbmlmavenrepotest.sourceforge.net</id>
+ <name>JSBML Maven2 SNAPSHOT repository</name>
+ <url>scp://shell.sourceforge.net/home/project-web/jsbmlmavenrepotest/htdocs/snapshotRepository</url>
+ </snapshotRepository>
+ </distributionManagement>
+
+ <!-- <repository>
<id>jsbmlmavenrepotest.sourceforge.net</id>
- <name>JSBML Maven2 SNAPSHOT repository</name>
- <url>scp://shell.sourceforge.net/home/project-web/jsbmlmavenrepotest/htdocs/snapshotRepository</url>
- </snapshotRepository>
- </distributionManagement>
-
-<!-- <repository>
- <id>jsbmlmavenrepotest.sourceforge.net</id>
<name>JSBML Maven2 repository</name>
<url>scp://shell.sourceforge.net/home/project-web/jsbmlmavenrepotest/htdocs/releaseRepository</url>
</repository>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-10 13:23:28
|
Revision: 2396
http://sourceforge.net/p/jsbml/code/2396
Author: niko-rodrigue
Date: 2015-11-10 13:23:25 +0000 (Tue, 10 Nov 2015)
Log Message:
-----------
added some missing test files + corrected few tests from the new ASTNode2
Modified Paths:
--------------
trunk/core/test/org/sbml/jsbml/math/test/ASTCiFunctionNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTCnNumberNodeTest.java
trunk/core/test/org/sbml/jsbml/math/test/ASTNodeFormulaToStringTest.java
Added Paths:
-----------
trunk/core/test/org/sbml/jsbml/math/compiler/
trunk/core/test/org/sbml/jsbml/math/compiler/resources/
trunk/core/test/org/sbml/jsbml/math/compiler/resources/NaN.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/abs.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/and.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/apply.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccos.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccosh.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccsc.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccsch.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsec.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsech.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsin.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsinh.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/arctan.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/arctanh.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/boolean-false.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/boolean-true.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/ceil.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/ci-number.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/cos.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/cosh.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/csc.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/csch.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-avogadro.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-delay.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-time.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/divide.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/e.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/eq.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/exp.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/exponential.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/factorial.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/floor.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/geq.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/gt.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/infinity.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/integer.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/lambda.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/leq.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/ln.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/log.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/lt.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/minus-infinity.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/minus.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/neq.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/not.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/or.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/package-info.java
trunk/core/test/org/sbml/jsbml/math/compiler/resources/pi.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/piecewise.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/plus.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/power.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/rational.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/real.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/root.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/sec.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/sech.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/sin.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/sinh.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/tan.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/tanh.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/times.xml
trunk/core/test/org/sbml/jsbml/math/compiler/resources/xor.xml
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/NaN.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/NaN.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/NaN.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <notanumber/>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/abs.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/abs.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/abs.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <abs/>
+ <cn type="integer"> -5 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/and.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/and.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/and.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <and/>
+ <true/>
+ <false/>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/apply.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/apply.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/apply.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <and/>
+ <true/>
+ <false/>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccos.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccos.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccos.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <arccos/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccosh.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccosh.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccosh.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <arccosh/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccsc.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccsc.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccsc.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <arccsc/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccsch.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccsch.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/arccsch.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <arccsch/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsec.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsec.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsec.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <arcsec/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsech.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsech.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsech.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <arcsech/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsin.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsin.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsin.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <arcsin/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsinh.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsinh.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/arcsinh.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <arcsinh/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/arctan.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/arctan.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/arctan.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <arctan/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/arctanh.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/arctanh.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/arctanh.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <arctanh/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/boolean-false.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/boolean-false.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/boolean-false.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <false/>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/boolean-true.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/boolean-true.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/boolean-true.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <true/>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/ceil.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/ceil.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/ceil.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <ceiling/>
+ <cn type="integer"> -5 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/ci-number.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/ci-number.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/ci-number.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <ci> tau2 </ci>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/cos.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/cos.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/cos.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <cos/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/cosh.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/cosh.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/cosh.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <cosh/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/csc.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/csc.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/csc.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <csc/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/csch.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/csch.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/csch.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <csch/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-avogadro.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-avogadro.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-avogadro.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/avogadro"> avogadro </csymbol>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-delay.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-delay.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-delay.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/delay"> delay </csymbol>
+ <ci> x </ci>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-time.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-time.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/csymbol-time.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/divide.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/divide.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/divide.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <divide/>
+ <cn type="integer"> 1 </cn>
+ <cn type="integer"> 1 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/e.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/e.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/e.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <exponentiale/>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/eq.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/eq.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/eq.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <eq/>
+ <true/>
+ <false/>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/exp.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/exp.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/exp.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <exp/>
+ <cn type="integer"> -5 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/exponential.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/exponential.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/exponential.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <cn type="e-notation"> 7 <sep/> 2 </cn>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/factorial.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/factorial.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/factorial.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <factorial/>
+ <cn type="integer"> 5 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/floor.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/floor.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/floor.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <floor/>
+ <cn type="integer"> 5 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/geq.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/geq.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/geq.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <geq/>
+ <true/>
+ <false/>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/gt.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/gt.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/gt.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <gt/>
+ <true/>
+ <false/>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/infinity.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/infinity.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/infinity.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <infinity/>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/integer.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/integer.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/integer.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <cn type="integer"> 10 </cn>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/lambda.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/lambda.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/lambda.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,16 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <lambda>
+ <bvar>
+ <ci> x </ci>
+ </bvar>
+ <bvar>
+ <ci> y </ci>
+ </bvar>
+ <apply>
+ <plus/>
+ <ci> x </ci>
+ <ci> y </ci>
+ </apply>
+ </lambda>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/leq.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/leq.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/leq.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <leq/>
+ <true/>
+ <false/>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/ln.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/ln.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/ln.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <ln/>
+ <exponentiale/>
+ <cn type="integer"> 1 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/log.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/log.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/log.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <log/>
+ <cn type="integer"> 1 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/lt.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/lt.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/lt.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <lt/>
+ <true/>
+ <false/>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/minus-infinity.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/minus-infinity.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/minus-infinity.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <minus/>
+ <infinity/>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/minus.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/minus.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/minus.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <minus/>
+ <cn type="integer"> 1 </cn>
+ <cn type="integer"> 1 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/neq.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/neq.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/neq.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <neq/>
+ <true/>
+ <false/>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/not.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/not.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/not.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <not/>
+ <true/>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/or.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/or.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/or.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <or/>
+ <true/>
+ <false/>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/package-info.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/package-info.java (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/package-info.java 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,27 @@
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ * Copyright (C) 2009-2014 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ * 6. The University of Toronto, Toronto, ON, Canada
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+/**
+ * @author Victor Kofia
+ * @version $Rev$
+ * @since 1.0
+ * @date Aug 8, 2014
+ */
+package org.sbml.jsbml.math.compiler.resources;
\ No newline at end of file
Property changes on: trunk/core/test/org/sbml/jsbml/math/compiler/resources/package-info.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: svn:keywords
## -0,0 +1 ##
+Author Date Id Rev URL
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/pi.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/pi.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/pi.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <pi/>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/piecewise.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/piecewise.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/piecewise.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,20 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <piecewise>
+ <piece>
+ <cn type="integer"> 0 </cn>
+ <apply>
+ <geq/>
+ <ci> x </ci>
+ <cn type="integer"> 10 </cn>
+ </apply>
+ </piece>
+ <otherwise>
+ <apply>
+ <plus/>
+ <cn type="integer"> 2 </cn>
+ <cn type="integer"> 28 </cn>
+ </apply>
+ </otherwise>
+ </piecewise>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/plus.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/plus.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/plus.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <plus/>
+ <cn type="integer"> 1 </cn>
+ <cn type="integer"> 1 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/power.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/power.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/power.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <power/>
+ <cn type="integer"> 2 </cn>
+ <cn type="integer"> 5 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/rational.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/rational.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/rational.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <cn type="rational"> 1 <sep/> 2 </cn>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/real.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/real.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/real.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,4 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <cn type="real"> 10 </cn>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/root.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/root.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/root.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,10 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <root/>
+ <degree>
+ <cn type="integer"> 4 </cn>
+ </degree>
+ <cn type="integer"> 10000 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/sec.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/sec.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/sec.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <sec/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/sech.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/sech.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/sech.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <sech/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/sin.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/sin.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/sin.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <sin/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/sinh.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/sinh.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/sinh.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <sinh/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/tan.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/tan.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/tan.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <tan/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/tanh.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/tanh.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/tanh.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,7 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <tanh/>
+ <cn type="integer"> 2 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/times.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/times.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/times.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <times/>
+ <cn type="integer"> 1 </cn>
+ <cn type="integer"> 1 </cn>
+ </apply>
+</math>
\ No newline at end of file
Added: trunk/core/test/org/sbml/jsbml/math/compiler/resources/xor.xml
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/compiler/resources/xor.xml (rev 0)
+++ trunk/core/test/org/sbml/jsbml/math/compiler/resources/xor.xml 2015-11-10 13:23:25 UTC (rev 2396)
@@ -0,0 +1,8 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+ <apply>
+ <xor/>
+ <true/>
+ <false/>
+ </apply>
+</math>
\ No newline at end of file
Modified: trunk/core/test/org/sbml/jsbml/math/test/ASTCiFunctionNodeTest.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/test/ASTCiFunctionNodeTest.java 2015-11-09 16:32:05 UTC (rev 2395)
+++ trunk/core/test/org/sbml/jsbml/math/test/ASTCiFunctionNodeTest.java 2015-11-10 13:23:25 UTC (rev 2396)
@@ -193,7 +193,7 @@
/**
* Test method for {@link org.sbml.jsbml.math.ASTCiFunctionNode#toFormula()}.
*/
- @Test
+ /* @Test
public final void testToFormula() {
// TODO: This test case might not be consistent with how real SBML elements
// are manipulated. Verify.
@@ -222,7 +222,8 @@
assertTrue(ci.toFormula().equals("pow3()"));
}
-
+*/
+
/**
* Test method for {@link org.sbml.jsbml.math.ASTCiFunctionNode#toFormula()}.
*/
Modified: trunk/core/test/org/sbml/jsbml/math/test/ASTCnNumberNodeTest.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/test/ASTCnNumberNodeTest.java 2015-11-09 16:32:05 UTC (rev 2395)
+++ trunk/core/test/org/sbml/jsbml/math/test/ASTCnNumberNodeTest.java 2015-11-10 13:23:25 UTC (rev 2396)
@@ -28,6 +28,8 @@
import org.junit.Test;
import org.junit.rules.ExpectedException;
import org.sbml.jsbml.ASTNode.Type;
+import org.sbml.jsbml.Assignment;
+import org.sbml.jsbml.AssignmentRule;
import org.sbml.jsbml.Constraint;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.PropertyUndefinedError;
@@ -88,7 +90,9 @@
*/
@Test
public void testDeriveUnit() {
+ AssignmentRule rule = new AssignmentRule(3, 1);
ASTCnNumberNode<Integer> number = new ASTCnNumberNode<Integer>();
+ number.setParentSBMLObject(rule);
number.setUnits(Unit.Kind.COULOMB.getName());
UnitDefinition unitDefinition = number.deriveUnit();
assertTrue(unitDefinition.getUnitCount() == 1);
Modified: trunk/core/test/org/sbml/jsbml/math/test/ASTNodeFormulaToStringTest.java
===================================================================
--- trunk/core/test/org/sbml/jsbml/math/test/ASTNodeFormulaToStringTest.java 2015-11-09 16:32:05 UTC (rev 2395)
+++ trunk/core/test/org/sbml/jsbml/math/test/ASTNodeFormulaToStringTest.java 2015-11-10 13:23:25 UTC (rev 2396)
@@ -29,10 +29,12 @@
import org.junit.BeforeClass;
import org.junit.Test;
import org.sbml.jsbml.ASTNode;
+import org.sbml.jsbml.text.parser.FormulaParser;
import org.sbml.jsbml.text.parser.FormulaParserLL3;
import org.sbml.jsbml.text.parser.ParseException;
import org.sbml.jsbml.util.compilers.FormulaCompiler;
import org.sbml.jsbml.util.compilers.FormulaCompilerLibSBML;
+import org.sbml.jsbml.util.compilers.LibSBMLFormulaCompiler;
/**
* Tests related to {@link ASTNode#toFormula()} and {@link ASTNode#toFormula(FormulaCompiler)}.
@@ -46,11 +48,17 @@
/**
*
*/
- final static FormulaCompiler defaultFormulaCompiler = new FormulaCompiler();
+ final static FormulaCompiler oldFormulaCompiler = new FormulaCompiler();
/**
*
*/
final static FormulaCompiler formulaCompilerLibsbml = new FormulaCompilerLibSBML();
+
+ /**
+ *
+ */
+ final static FormulaCompiler formulaCompilerOldLibsbml = new LibSBMLFormulaCompiler();
+
/**
*
@@ -78,7 +86,7 @@
*/
@BeforeClass public static void init() {
try {
- relationalAnd = ASTNode.parseFormula("x and y");
+ relationalAnd = ASTNode.parseFormula("x and y", new FormulaParser(new StringReader("")));
relationalAnd2 = ASTNode.parseFormula("x && y", new FormulaParserLL3(new StringReader("")));
relationalAnd3 = ASTNode.parseFormula("and(x, y)", new FormulaParserLL3(new StringReader("")));
logicalEq = ASTNode.parseFormula("x == y");
@@ -97,15 +105,20 @@
String formula = relationalAnd.toFormula();
- assertTrue(formula.equals("x and y"));
+ assertTrue(formula.equals("x && y"));
formula = relationalAnd.toFormula(formulaCompilerLibsbml);
assertTrue(formula.equals("x && y"));
- formula = relationalAnd.toFormula(defaultFormulaCompiler);
+ formula = relationalAnd.toFormula(oldFormulaCompiler);
- assertTrue(formula.equals("x and y"));
+ assertTrue(formula.equals("x && y"));
+
+ formula = relationalAnd.toFormula(formulaCompilerOldLibsbml);
+
+ assertTrue(formula.equals("and(x, y)"));
+
}
/**
@@ -115,15 +128,15 @@
String formula = relationalAnd2.toFormula();
- assertTrue(formula.equals("x and y"));
+ assertTrue(formula.equals("x && y"));
formula = relationalAnd2.toFormula(formulaCompilerLibsbml);
assertTrue(formula.equals("x && y"));
- formula = relationalAnd2.toFormula(defaultFormulaCompiler);
+ formula = relationalAnd2.toFormula(oldFormulaCompiler);
- assertTrue(formula.equals("x and y"));
+ assertTrue(formula.equals("x && y"));
}
/**
@@ -133,15 +146,15 @@
String formula = relationalAnd3.toFormula();
- assertTrue(formula.equals("x and y"));
+ assertTrue(formula.equals("x && y"));
formula = relationalAnd3.toFormula(formulaCompilerLibsbml);
assertTrue(formula.equals("x && y"));
- formula = relationalAnd3.toFormula(defaultFormulaCompiler);
+ formula = relationalAnd3.toFormula(oldFormulaCompiler);
- assertTrue(formula.equals("x and y"));
+ assertTrue(formula.equals("x && y"));
}
@@ -156,13 +169,17 @@
formula = logicalEq.toFormula(formulaCompilerLibsbml);
- assertTrue(formula.equals("eq(x, y)"));
+ assertTrue(formula.equals("x == y"));
- formula = logicalEq.toFormula(defaultFormulaCompiler);
+ formula = logicalEq.toFormula(oldFormulaCompiler);
assertTrue(formula.equals("x == y"));
- }
+ formula = logicalEq.toFormula(formulaCompilerOldLibsbml);
+
+ assertTrue(formula.equals("eq(x, y)"));
+}
+
/**
*
*/
@@ -176,7 +193,7 @@
assertTrue(formula.equals("x+y")); // TODO - add a space for this compiler ??!
- formula = simplePlus.toFormula(defaultFormulaCompiler);
+ formula = simplePlus.toFormula(oldFormulaCompiler);
assertTrue(formula.equals("x+y"));
}
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|
|
From: <nik...@us...> - 2015-11-09 16:32:07
|
Revision: 2395
http://sourceforge.net/p/jsbml/code/2395
Author: niko-rodrigue
Date: 2015-11-09 16:32:05 +0000 (Mon, 09 Nov 2015)
Log Message:
-----------
added a pseudo jar file to be able to add a maven artifact that regroup all the jsbml dependencies. Let see what people think about it.
Modified Paths:
--------------
trunk/build.xml
Added Paths:
-----------
trunk/dev/maven/
trunk/dev/maven/jsbml-pom.jar
trunk/dev/maven/pom.xml
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2015-11-09 14:31:49 UTC (rev 2394)
+++ trunk/build.xml 2015-11-09 16:32:05 UTC (rev 2395)
@@ -728,6 +728,16 @@
<arg value="deploy"/>
</exec>
+ <!-- deploy a pseudo jar file to be able to have all dependencies defined in one go ? -->
+ <!-- mvn deploy:deploy-file -DpomFile=./dev/maven/pom.xml -Dfile=./dev/maven/jsbml-pom.jar -->
+
+ <exec executable="mvn">
+ <arg value="deploy:deploy-file"/>
+ <arg value="-DpomFile=./dev/maven/pom.xml"/>
+ <arg value="-Dfile=./dev/maven/jsbml-pom.jar"/>
+ </exec>
+
+
</target>
<!-- =================================================================== -->
Added: trunk/dev/maven/jsbml-pom.jar
===================================================================
(Binary files differ)
Index: trunk/dev/maven/jsbml-pom.jar
===================================================================
--- trunk/dev/maven/jsbml-pom.jar 2015-11-09 14:31:49 UTC (rev 2394)
+++ trunk/dev/maven/jsbml-pom.jar 2015-11-09 16:32:05 UTC (rev 2395)
Property changes on: trunk/dev/maven/jsbml-pom.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/dev/maven/pom.xml
===================================================================
--- trunk/dev/maven/pom.xml (rev 0)
+++ trunk/dev/maven/pom.xml 2015-11-09 16:32:05 UTC (rev 2395)
@@ -0,0 +1,207 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+ $Id: pom.xml 2394 2015-11-09 14:31:49Z niko-rodrigue $
+ $URL: svn+ssh://nik...@sv.../p/jsbml/code/trunk/pom.xml $
+
+ This file is part of JSBML. Please visit http://sbml.org/Software/JSBML
+ for the latest version of JSBML and more information about SBML.
+
+ Copyright (C) 2009-2015 jointly by the following organizations:
+ 1. The University of Tuebingen, Germany
+ 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ 3. The California Institute of Technology, Pasadena, CA, USA
+ 4. The University of California, San Diego, La Jolla, CA, USA
+ 5. The Babraham Institute, Cambridge, UK
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation. A copy of the license agreement is provided
+ in the file named "LICENSE.txt" included with this software distribution
+ and also available online as http://sbml.org/Software/JSBML/License.
+
+ Version: $Rev: 2394 $
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml</artifactId>
+ <version>1.1-b1</version>
+ <packaging>jar</packaging>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+ </properties>
+
+ <dependencyManagement>
+ <dependencies>
+ <dependency>
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml-core</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-arrays</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-comp</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-distrib</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-dyn</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-fbc</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-groups</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-layout</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-multi</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-qual</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-render</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-req</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-spatial</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.modules</groupId>
+ <artifactId>jsbml-tidy</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+ </dependencyManagement>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml-core</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-arrays</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-comp</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-distrib</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-dyn</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-fbc</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-groups</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-layout</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-multi</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-qual</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-render</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-req</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-spatial</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.sbml.jsbml.modules</groupId>
+ <artifactId>jsbml-tidy</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+ <distributionManagement>
+ <repository>
+ <id>local-repo-deploy</id>
+ <name>Test Maven2 repository</name>
+ <url>file:///var/www/html/repo</url>
+ </repository>
+ <snapshotRepository>
+ <id>jsbmlmavenrepotest.sourceforge.net</id>
+ <name>JSBML Maven2 SNAPSHOT repository</name>
+ <url>scp://shell.sourceforge.net/home/project-web/jsbmlmavenrepotest/htdocs/snapshotRepository</url>
+ </snapshotRepository>
+ </distributionManagement>
+
+ <!-- <repository>
+ <id>jsbmlmavenrepotest.sourceforge.net</id>
+ <name>JSBML Maven2 repository</name>
+ <url>scp://shell.sourceforge.net/home/project-web/jsbmlmavenrepotest/htdocs/releaseRepository</url>
+ </repository>
+ -->
+
+</project>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-09 14:31:51
|
Revision: 2394
http://sourceforge.net/p/jsbml/code/2394
Author: niko-rodrigue
Date: 2015-11-09 14:31:49 +0000 (Mon, 09 Nov 2015)
Log Message:
-----------
corrected few javadoc error in core + added an option so that the javadoc task do not fail when there are errors + added some maven related task in the ant build file
Modified Paths:
--------------
trunk/build.xml
trunk/core/pom.xml
trunk/core/src/org/sbml/jsbml/ASTNode.java
trunk/core/src/org/sbml/jsbml/CVTerm.java
trunk/core/src/org/sbml/jsbml/JSBML.java
trunk/pom.xml
Property Changed:
----------------
trunk/core/
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2015-11-09 13:35:03 UTC (rev 2393)
+++ trunk/build.xml 2015-11-09 14:31:49 UTC (rev 2394)
@@ -694,8 +694,43 @@
</target>
+ <!-- =================================================================== -->
+ <!-- Install jsbml in the local repo -->
+ <!-- =================================================================== -->
+ <target
+ name="maven-install"
+ description="Install jsbml localy"
+ depends="init"
+ >
+ <!-- mvn javadoc:jar source:jar install
+ -->
+ <exec executable="mvn">
+ <arg value="javadoc:jar"/>
+ <arg value="source:jar"/>
+ <arg value="install"/>
+ </exec>
+ </target>
+
<!-- =================================================================== -->
+ <!-- Deploy jsbml in a remote repo -->
+ <!-- =================================================================== -->
+ <target
+ name="maven-deploy"
+ description="Deploy jsbml remotely"
+ depends="init"
+ >
+ <!-- mvn javadoc:jar source:jar deploy
+ -->
+ <exec executable="mvn">
+ <arg value="javadoc:jar"/>
+ <arg value="source:jar"/>
+ <arg value="deploy"/>
+ </exec>
+
+ </target>
+
+ <!-- =================================================================== -->
<!-- Cleans everything -->
<!-- =================================================================== -->
<target
Index: trunk/core
===================================================================
--- trunk/core 2015-11-09 13:35:03 UTC (rev 2393)
+++ trunk/core 2015-11-09 14:31:49 UTC (rev 2394)
Property changes on: trunk/core
___________________________________________________________________
Modified: svn:ignore
## -9,3 +9,4 ##
.apt_generated
.factorypath
.settings
+target
Modified: trunk/core/pom.xml
===================================================================
--- trunk/core/pom.xml 2015-11-09 13:35:03 UTC (rev 2393)
+++ trunk/core/pom.xml 2015-11-09 14:31:49 UTC (rev 2394)
@@ -47,7 +47,7 @@
<directory>dist</directory>
<outputDirectory>dist/classes</outputDirectory>
- <finalName>${artifactId}-${version}</finalName>
+ <finalName>${project.artifactId}-${project.version}</finalName>
<testOutputDirectory>dist/test-classes</testOutputDirectory>
<sourceDirectory>src</sourceDirectory>
<scriptSourceDirectory>scripts</scriptSourceDirectory>
Modified: trunk/core/src/org/sbml/jsbml/ASTNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-11-09 13:35:03 UTC (rev 2393)
+++ trunk/core/src/org/sbml/jsbml/ASTNode.java 2015-11-09 14:31:49 UTC (rev 2394)
@@ -985,7 +985,7 @@
*
* <p> You can change this behaviour by using the {@link FormulaParserLL3#setCaseSensitive(boolean)}
* method and using the {@link ASTNode#parseFormula(String, IFormulaParser)} method instead of this one:
-<p><pre><blockquote>
+<p><blockquote><pre>
FormulaParserLL3 caseSensitiveParser = new FormulaParserLL3(new StringReader(""));
caseInsensitiveParser.setCaseSensitive(false);
ASTNode n = ASTNode.parseFormula("Cos(x)", caseInsensitiveParser);
@@ -993,10 +993,10 @@
*
* <p> This method has a different behaviour since JSBML-1.0 compare to JSBML-0.8. There is a different
* operator precedence, the parsing is now case sensitive for mathML elements and boolean operators are
- * now differently interpreted: '&&' and '||' are used instead of 'and' and 'or'.<br>
+ * now differently interpreted: '&&' and '||' are used instead of 'and' and 'or'.<br>
* If you want to use the parser used in JSBML-0.8, you can do that by using the {@link FormulaParser}
* parser class and using the {@link ASTNode#parseFormula(String, IFormulaParser)} method instead of this one:
-<p><pre><blockquote>
+<p><blockquote><pre>
FormulaParser oldParser = new FormulaParser(new StringReader(""));
ASTNode n = ASTNode.parseFormula("x and y", oldParser);
@@ -1039,14 +1039,14 @@
*
* <p>For example, you can change the behaviour of the {@link FormulaParserLL3} class by using the
* {@link FormulaParserLL3#setCaseSensitive(boolean)} method:
-<p><pre><blockquote>
+<p><blockquote><pre>
FormulaParserLL3 caseSensitiveParser = new FormulaParserLL3(new StringReader(""));
caseInsensitiveParser.setCaseSensitive(false);
ASTNode n = ASTNode.parseFormula("Cos(x)", caseInsensitiveParser);
</pre></blockquote></p>
*
* <p> You can as well use the {@link FormulaParser} class to get the same parsing behaviour as in JSBML-0.8:
-<p><pre><blockquote>
+<p><blockquote><pre>
FormulaParser oldParser = new FormulaParser(new StringReader(""));
ASTNode n = ASTNode.parseFormula("x and y", oldParser);
Modified: trunk/core/src/org/sbml/jsbml/CVTerm.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/CVTerm.java 2015-11-09 13:35:03 UTC (rev 2393)
+++ trunk/core/src/org/sbml/jsbml/CVTerm.java 2015-11-09 14:31:49 UTC (rev 2394)
@@ -1258,7 +1258,7 @@
* @param i the index where to remove the {@link CVTerm}.
* @return the specified element if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or if the index is
- * out of bound ({@code (i < 0) || (i > listOfNestedCVTerms)}).
+ * out of bound ({@code (i < 0) || (i > listOfNestedCVTerms)}).
*/
public CVTerm removeNestedCVTerm(int i) {
if (!isSetListOfNestedCVTerms()) {
@@ -1286,7 +1286,7 @@
* @param i the index of the {@link CVTerm} element to get.
* @return an element from the listOfNestedCVTerms at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public CVTerm getNestedCVTerm(int i) {
if (!isSetListOfNestedCVTerms()) {
Modified: trunk/core/src/org/sbml/jsbml/JSBML.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/JSBML.java 2015-11-09 13:35:03 UTC (rev 2393)
+++ trunk/core/src/org/sbml/jsbml/JSBML.java 2015-11-09 14:31:49 UTC (rev 2394)
@@ -285,18 +285,18 @@
*
* <p> You can change this behaviour by using the {@link FormulaParserLL3#setCaseSensitive(boolean)}
* method and using the {@link ASTNode#parseFormula(String, IFormulaParser)} method instead of this one:
-<p><pre><blockquote>
+<p><pre>
FormulaParserLL3 caseSensitiveParser = new FormulaParserLL3(new StringReader(""));
caseInsensitiveParser.setCaseSensitive(false);
ASTNode n = ASTNode.parseFormula("Cos(x)", caseInsensitiveParser);
-</pre></blockquote></p>
+</pre></p>
*
* <p> This method has a different behaviour since JSBML-1.0 compare to JSBML-0.8. There is a different
* operator precedence, the parsing is now case sensitive for mathML elements and boolean operators are
- * now differently interpreted: '&&' and '||' are used instead of 'and' and 'or'.<br>
+ * now differently interpreted: '&&' and '||' are used instead of 'and' and 'or'.<br>
* If you want to use the parser used in JSBML-0.8, you can do that by using the {@link FormulaParser}
* parser class and using the {@link ASTNode#parseFormula(String, IFormulaParser)} method instead of this one:
-<p><pre><blockquote>
+<p><blockquote><pre>
FormulaParser oldParser = new FormulaParser(new StringReader(""));
ASTNode n = ASTNode.parseFormula("x and y", oldParser);
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2015-11-09 13:35:03 UTC (rev 2393)
+++ trunk/pom.xml 2015-11-09 14:31:49 UTC (rev 2394)
@@ -105,6 +105,7 @@
<head>Last modified:</head>
</tag>
</tags>
+ <failOnError>false</failOnError>
</configuration>
</plugin>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-09 13:35:05
|
Revision: 2393
http://sourceforge.net/p/jsbml/code/2393
Author: niko-rodrigue
Date: 2015-11-09 13:35:03 +0000 (Mon, 09 Nov 2015)
Log Message:
-----------
further javadoc corrections to allow all of the maven javadoc jars to be generated + added the encoding in the parent pom file
Modified Paths:
--------------
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java
trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/package-info.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java
trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/package-info.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderGroup.java
trunk/extensions/render/src/org/sbml/jsbml/ext/render/package-info.java
trunk/extensions/req/src/org/sbml/jsbml/ext/req/ReqSBasePlugin.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/package-info.java
trunk/pom.xml
Property Changed:
----------------
trunk/
trunk/extensions/arrays/
trunk/extensions/comp/
trunk/extensions/distrib/
trunk/extensions/dyn/
trunk/extensions/fbc/
trunk/extensions/groups/
trunk/extensions/layout/
trunk/extensions/multi/
trunk/extensions/qual/
trunk/extensions/render/
trunk/extensions/req/
trunk/extensions/spatial/
Index: trunk
===================================================================
--- trunk 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk
___________________________________________________________________
Modified: svn:ignore
## -8,3 +8,4 ##
.factorypath
.settings
jsbmlTestResults.txt
+target
Index: trunk/extensions/arrays
===================================================================
--- trunk/extensions/arrays 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/arrays 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/arrays
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Index: trunk/extensions/comp
===================================================================
--- trunk/extensions/comp 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/comp 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/comp
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Index: trunk/extensions/distrib
===================================================================
--- trunk/extensions/distrib 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/distrib 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/distrib
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Index: trunk/extensions/dyn
===================================================================
--- trunk/extensions/dyn 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/dyn 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/dyn
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Index: trunk/extensions/fbc
===================================================================
--- trunk/extensions/fbc 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/fbc 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/fbc
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Index: trunk/extensions/groups
===================================================================
--- trunk/extensions/groups 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/groups 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/groups
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Index: trunk/extensions/layout
===================================================================
--- trunk/extensions/layout 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/layout 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/layout
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,5 ##
.apt_generated
.factorypath
.settings
+target
+layoutTestResults.txt
Index: trunk/extensions/multi
===================================================================
--- trunk/extensions/multi 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/multi 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/multi
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiCompartmentPlugin.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -334,7 +334,7 @@
* @param i the index of the {@link CompartmentReference} element to get.
* @return an element from the listOfCompartmentReferences at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public CompartmentReference getCompartmentReference(int i) {
if (!isSetListOfCompartmentReferences()) {
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesPlugin.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -273,7 +273,7 @@
* @param i the index of the {@link OutwardBindingSite} element to get.
* @return an element from the listOfOutwardBindingSites at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public OutwardBindingSite getOutwardBindingSite(int i) {
if (!isSetListOfOutwardBindingSites()) {
@@ -487,7 +487,7 @@
* @param i the index of the {@link SpeciesFeature} element to get.
* @return an element from the listOfSpeciesFeatures at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public SpeciesFeature getSpeciesFeature(int i) {
if (!isSetListOfSpeciesFeatures()) {
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/MultiSpeciesReferencePlugin.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -298,7 +298,7 @@
* @param i the index of the {@link SpeciesTypeComponentMapInProduct} element to get.
* @return an element from the listOfSpeciesTypeComponentMapInProducts at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public SpeciesTypeComponentMapInProduct getSpeciesTypeComponentMapInProduct(int i) {
if (!isSetListOfSpeciesTypeComponentMapInProducts()) {
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeature.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -380,7 +380,7 @@
* @param i the index of the {@link SpeciesFeatureValue} element to get.
* @return an element from the listOfSpeciesFeatureValues at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public SpeciesFeatureValue getSpeciesFeatureValue(int i) {
if (!isSetListOfSpeciesFeatureValues()) {
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesFeatureType.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -393,7 +393,7 @@
* @param i the index of the {@link PossibleSpeciesFeatureValue} element to get.
* @return an element from the listOfPossibleSpeciesFeatureValues at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public PossibleSpeciesFeatureValue getPossibleSpeciesFeatureValue(int i) {
if (!isSetListOfPossibleSpeciesFeatureValues()) {
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesType.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -35,20 +35,22 @@
/**
*
- * <p/>The element SpeciesType, which is part of SBML Level 2 Version 4 specification, is not part
+ * <p>The element SpeciesType, which is part of SBML Level 2 Version 4 specification, is not part
* of SBML Level 3 Version 1 Core any more. Instead, it will be defined in the multi package. The
* SpeciesType element carries not only the basic attributes which it had in SBML Level 2 Version 4
* (metaid, id, name), but is also extended for the needs of describing multi-component entities
* with the attribute bindingSite and for the needs of multistate entities by linking it to a list of
- * StateFeatures
- * <p/>A species type can be used to describe a component of a supra-macromolecular assembly,
+ * StateFeatures</p>
+ *
+ * <p>A species type can be used to describe a component of a supra-macromolecular assembly,
* but also a domain of a macromolecule. Such a domain can be a portion of the macromolecule,
* a non-connex set of atoms forming a functional domain, or just a conceptual construct suiting
* the needs of the modeler. The type of component can be specified by referring terms from the
* subbranch functional entity of the <a href="http://biomodels.net/sbo/">Systems Biology Ontology</a>
* through the optional sboTerm attribute. The following table provides typical examples of
- * component or domains (the list is absolutely not complete).
+ * component or domains (the list is absolutely not complete).</p>
* <table>
+ * <caption>Typical examples of components or domains</caption>
* <tr>
* <th> SBO identifier </th><th> Definition </th>
* </tr><tr>
@@ -520,7 +522,7 @@
* @param i the index of the {@link InSpeciesTypeBond} element to get.
* @return an element from the listOfInSpeciesTypeBonds at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public InSpeciesTypeBond getInSpeciesTypeBond(int i) {
if (!isSetListOfInSpeciesTypeBonds()) {
@@ -703,7 +705,7 @@
* @param i the index of the {@link SpeciesFeatureType} element to get.
* @return an element from the listOfSpeciesFeatureTypes at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public SpeciesFeatureType getSpeciesFeatureType(int i) {
if (!isSetListOfSpeciesFeatureTypes()) {
@@ -746,7 +748,7 @@
* @param i the index of the {@link SpeciesTypeComponentIndex} element to get.
* @return an element from the listOfSpeciesTypeComponentIndexes at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public SpeciesTypeComponentIndex getSpeciesTypeComponentIndex(int i) {
if (!isSetListOfSpeciesTypeComponentIndexes()) {
@@ -789,7 +791,7 @@
* @param i the index of the {@link SpeciesTypeInstance} element to get.
* @return an element from the listOfSpeciesTypeInstances at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public SpeciesTypeInstance getSpeciesTypeInstance(int i) {
if (!isSetListOfSpeciesTypeInstances()) {
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentIndex.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -396,7 +396,7 @@
* @param i the index of the {@link DenotedSpeciesTypeComponentIndex} element to get.
* @return an element from the listOfDenotedSpeciesTypeComponentIndexes at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public DenotedSpeciesTypeComponentIndex getDenotedSpeciesTypeComponentIndex(int i) {
if (!isSetListOfDenotedSpeciesTypeComponentIndexes()) {
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/SpeciesTypeComponentMapInProduct.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -374,7 +374,7 @@
* @param i the index of the {@link SpeciesFeatureChange} element to get.
* @return an element from the listOfSpeciesFeatureChanges at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public SpeciesFeatureChange getSpeciesFeatureChange(int i) {
if (!isSetListOfSpeciesFeatureChanges()) {
Modified: trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/package-info.java
===================================================================
--- trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/package-info.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/multi/src/org/sbml/jsbml/ext/multi/package-info.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -29,7 +29,7 @@
* "http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Multistate_and_Multicomponent_Species_Proposal"
* > proposal by Nicolas Le Novère and Anika Oellrich</a>. There is only few
* classes from the proposal and it need to be completed.
- * <p><img title="JSBML" alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
+ * <p><img alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
*
* @version $Rev$
* @since 1.0
Index: trunk/extensions/qual
===================================================================
--- trunk/extensions/qual 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/qual 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/qual
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/Transition.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -38,9 +38,9 @@
* <p>
* In logical models a {@link Transition} is used to specify the logical rule associated with a
* {@link QualitativeSpecies} (that appears as an {@link Output} of this {@link Transition}).
- * For example, the rule if A > 1 : B = 2 would be encapsulated as a {@link Transition} with
+ * For example, the rule if A > 1 : B = 2 would be encapsulated as a {@link Transition} with
* {@link QualitativeSpecies} "A" as an {@link Input} and "B" as an {@link Output}; the
- * if A > 1 rule being encoded by the math element of a {@link FunctionTerm} with the resultLevel
+ * if A > 1 rule being encoded by the math element of a {@link FunctionTerm} with the resultLevel
* attribute having a value "2".
* <p>
* In Petri net models a {@link Transition} is interpreted, using the common Petri net semantics, as events
Modified: trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/package-info.java
===================================================================
--- trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/package-info.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/qual/src/org/sbml/jsbml/ext/qual/package-info.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -28,7 +28,7 @@
* The current version of the package follow the <a href=
* "http://sbml.org/images/6/61/SBML-L3-qual-proposal_2.1.pdf"
* >proposal by S. Keating</a>
- * <p><img title="JSBML" alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
+ * <p><img alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
*
*
* @version $Rev$
Index: trunk/extensions/render
===================================================================
--- trunk/extensions/render 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/render 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/render
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderGroup.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderGroup.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/RenderGroup.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -944,7 +944,7 @@
* @param i the index where to remove the {@link Transformation2D}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public Transformation2D removeElement(int i) {
if (!isSetListOfElements()) {
@@ -1037,7 +1037,7 @@
* @param i the index of the {@link Transformation2D} element to get.
* @return an element from the listOfElements at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public Transformation2D getElement(int i) {
if (!isSetListOfElements()) {
Modified: trunk/extensions/render/src/org/sbml/jsbml/ext/render/package-info.java
===================================================================
--- trunk/extensions/render/src/org/sbml/jsbml/ext/render/package-info.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/render/src/org/sbml/jsbml/ext/render/package-info.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -38,7 +38,7 @@
* engineering class at the University of Tuebingen, Germany, in the summer
* semester 2012, supervised by Johannes Eichner and Andreas Dräger.
* </p>
- * <p><img title="JSBML" alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
+ * <p><img alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
*
* @author Alexander Diamantikos
* @author Jakob Matthes
Index: trunk/extensions/req
===================================================================
--- trunk/extensions/req 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/req 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/req
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Modified: trunk/extensions/req/src/org/sbml/jsbml/ext/req/ReqSBasePlugin.java
===================================================================
--- trunk/extensions/req/src/org/sbml/jsbml/ext/req/ReqSBasePlugin.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/req/src/org/sbml/jsbml/ext/req/ReqSBasePlugin.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -255,7 +255,7 @@
*
* @param i - the index where to remove the {@link ChangedMath}
* @throws IndexOutOfBoundsException - if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeChangedMath(int i) {
if (!isSetListOfChangedMaths()) {
Index: trunk/extensions/spatial
===================================================================
--- trunk/extensions/spatial 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/spatial 2015-11-09 13:35:03 UTC (rev 2393)
Property changes on: trunk/extensions/spatial
___________________________________________________________________
Modified: svn:ignore
## -7,3 +7,4 ##
.apt_generated
.factorypath
.settings
+target
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AnalyticGeometry.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -183,7 +183,7 @@
*
* @param i the index where to remove the {@link AnalyticVolume}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeAnalyticVolume(int i) {
if (!isSetListOfAnalyticVolumes()) {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGSetOperator.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -425,7 +425,7 @@
*
* @param i the index where to remove the {@link CSGNode}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeCSGNode(int i) {
if (!isSetListOfCSGNodes()) {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/CSGeometry.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -229,7 +229,7 @@
*
* @param i the index where to remove the {@link CSGObject}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeCSGObject(int i) {
if (!isSetListOfCSGObjects()) {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Domain.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -285,7 +285,7 @@
*
* @param i the index where to remove the {@link InteriorPoint}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeInteriorPoint(int i) {
if (!isSetListOfInteriorPoints()) {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/Geometry.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -359,7 +359,7 @@
*
* @param i the index where to remove the {@link SampledField}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeSampledField(int i) {
if (!isSetListOfSampledFields()) {
@@ -505,7 +505,7 @@
*
* @param i the index where to remove the {@link GeometryDefinition}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeGeometryDefinition(int i) {
if (!isSetListOfGeometryDefinitions()) {
@@ -719,7 +719,7 @@
*
* @param i the index where to remove the {@link AdjacentDomains}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeAdjacentDomain(int i) {
if (!isSetListOfAdjacentDomains()) {
@@ -865,7 +865,7 @@
*
* @param i the index where to remove the {@link DomainType}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeDomainType(int i) {
if (!isSetListOfDomainTypes()) {
@@ -1010,7 +1010,7 @@
*
* @param i the index where to remove the {@link Domain}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeDomain(int i) {
if (!isSetListOfDomains()) {
@@ -1155,7 +1155,7 @@
*
* @param i the index where to remove the {@link CoordinateComponent}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeCoordinateComponent(int i) {
if (!isSetListOfCoordinateComponents()) {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/MixedGeometry.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -243,7 +243,7 @@
*
* @param i the index where to remove the {@link GeometryDefinition}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeGeometryDefinition(int i) {
if (!isSetListOfGeometryDefinitions()) {
@@ -454,7 +454,7 @@
*
* @param i the index where to remove the {@link OrdinalMapping}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeOrdinalMapping(int i) {
if (!isSetListOfOrdinalMappings()) {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/ParametricGeometry.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -230,7 +230,7 @@
*
* @param i the index where to remove the {@link ParametricObject}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeParametricObject(int i) {
if (!isSetListOfParametricObjects()) {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/SampledFieldGeometry.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -291,7 +291,7 @@
*
* @param i the index where to remove the {@link SampledVolume}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public void removeSampledVolume(int i) {
if (!isSetListOfSampledVolumes()) {
Modified: trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/package-info.java
===================================================================
--- trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/package-info.java 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/extensions/spatial/src/org/sbml/jsbml/ext/spatial/package-info.java 2015-11-09 13:35:03 UTC (rev 2393)
@@ -28,7 +28,7 @@
* The current version of the package follow the <a href=
* "http://sbml.org/images/1/15/SBMLSpatialProposal_2011_04_20.pdf"
* >proposal by J.C. Schaff</a>
- * <p><img title="JSBML" alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
+ * <p><img alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
*
* @author Alex Thomas
* @author Andreas Dräger
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2015-11-06 17:43:00 UTC (rev 2392)
+++ trunk/pom.xml 2015-11-09 13:35:03 UTC (rev 2393)
@@ -31,6 +31,11 @@
<version>1.1-b1</version>
<packaging>pom</packaging>
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+ </properties>
+
<build>
<plugins>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-06 17:43:02
|
Revision: 2392
http://sourceforge.net/p/jsbml/code/2392
Author: niko-rodrigue
Date: 2015-11-06 17:43:00 +0000 (Fri, 06 Nov 2015)
Log Message:
-----------
more update to the pom to be able to deploy the jar files all in one go. Deploy seems to work fine now. Corrected many javadoc errors as maven seems to be very picky about it, much more than the standart javadoc
Modified Paths:
--------------
trunk/core/pom.xml
trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/package-info.java
trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java
trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/package-info.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/package-info.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/package-info.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java
trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/package-info.java
trunk/extensions/pom.xml
trunk/extensions/spatial/pom.xml
trunk/modules/pom.xml
trunk/modules/tidy/pom.xml
trunk/pom.xml
Modified: trunk/core/pom.xml
===================================================================
--- trunk/core/pom.xml 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/core/pom.xml 2015-11-06 17:43:00 UTC (rev 2392)
@@ -24,7 +24,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.sbml.jsbml</groupId>
- <artifactId>core</artifactId>
+ <artifactId>jsbml-core</artifactId>
<description>JSBML</description>
<packaging>jar</packaging>
@@ -59,8 +59,14 @@
</resources>
<testResources>
<testResource>
- <directory>test/org/sbml/jsbml/xml/test</directory>
+ <directory>test</directory>
</testResource>
+ <testResource>
+ <directory>resources</directory>
+ </testResource>
+ <testResource>
+ <directory>src</directory>
+ </testResource>
</testResources>
<extensions>
@@ -72,88 +78,7 @@
</extensions>
<plugins>
- <!--
- <plugin>
-
-
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>buildnumber-maven-plugin</artifactId>
- <version>1.2</version>
- <executions>
- <execution>
- <phase>validate</phase>
- <goals>
- <goal>create</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <doCheck>false</doCheck>
- <doUpdate>false</doUpdate>
- <revisionOnScmFailure>unknownbuild</revisionOnScmFailure>
- </configuration>
-
- </plugin>
- -->
- <!--
- <plugin>
- <artifactId>maven-compiler-plugin</artifactId>
- <configuration>
- <source>1.6</source>
- <target>1.6</target>
- </configuration>
- </plugin>
- -->
- <plugin>
- <artifactId>maven-antrun-plugin</artifactId>
- <executions>
- <execution>
- <phase>process-resources</phase>
- <configuration>
- <tasks>
- <property name="version" value="${version}"/>
- <property name="name" value="${artifactId}-ant"/>
- <ant antfile="build.xml" target="jar"/>
- </tasks>
- </configuration>
- <goals>
- <goal>run</goal>
- </goals>
- </execution>
- </executions>
- <dependencies>
- <dependency>
- <groupId>com.sun</groupId>
- <artifactId>tools</artifactId>
- <version>1.7.0</version>
- <scope>system</scope>
- <systemPath>${java.home}/../lib/tools.jar</systemPath>
- </dependency>
- </dependencies>
- </plugin>
- <!-- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>build-helper-maven-plugin</artifactId>
- <version>1.3</version>
- <executions>
- <execution>
- <id>add-jar</id>
- <phase>package</phase>
- <goals>
- <goal>attach-artifact</goal>
- </goals>
- <configuration>
- <artifacts>
- <artifact>
- <file>build/${artifactId}-${version}-ant.jar</file>
- <type>jar</type>
- </artifact>
- </artifacts>
- </configuration>
- </execution>
- </executions>
- </plugin> -->
- <plugin>
+ <plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
@@ -163,31 +88,7 @@
<argLine>-Dfile.encoding=UTF-8 -DDATA_FOLDER=${project.basedir}/test/org/sbml/jsbml/xml/test/data/ -ea</argLine>
</configuration>
</plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-eclipse-plugin</artifactId>
- <version>2.9</version>
- <configuration>
- <workspace>${basedir}</workspace>
- <workspaceCodeStylesURL>http://http://jsbmlmavenrepotest.sourceforge.net/codetemplates.xml</workspaceCodeStylesURL>
- </configuration>
- </plugin>
- <!--
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-site-plugin</artifactId>
- <version>3.3</version>
- <dependencies>
- <dependency>
- <groupId>org.apache.maven.wagon</groupId>
- <artifactId>wagon-ssh</artifactId>
- <version>2.4</version>
- </dependency>
- </dependencies>
- </plugin>
- -->
</plugins>
-
</build>
<repositories>
@@ -278,6 +179,7 @@
</dependency>
</dependencies>
+ <!--
<distributionManagement>
<repository>
<id>jsbmlmavenrepotest.sourceforge.net</id>
@@ -290,6 +192,7 @@
<url>scp://shell.sourceforge.net/home/project-web/jsbmlmavenrepotest/htdocs/snapshotRepository</url>
</snapshotRepository>
</distributionManagement>
+-->
<!--
To deploy to EBI:
Modified: trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java
===================================================================
--- trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/ArraysSBasePlugin.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -266,7 +266,7 @@
* @param i the index where to remove the {@link Index}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public Index removeIndex(int i) {
if (!isSetListOfIndices()) {
@@ -291,7 +291,7 @@
* @param i the index of the {@link Index} element to get.
* @return an element from the listOfIndices at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public Index getIndex(int i) {
if (!isSetListOfIndices()) {
@@ -483,7 +483,7 @@
* @param i the index where to remove the {@link Dimension}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public Dimension removeDimension(int i) {
if (!isSetListOfDimensions()) {
@@ -518,7 +518,7 @@
* @param i the dimension of the {@link Dimension} element to get.
* @return an element from the listOfDimensions at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > 2).
+ * if the index is out of bound (index < 0 || index > 2)
*/
public Dimension getDimension(int i) {
if (!isSetListOfDimensions()) {
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompModelPlugin.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -487,7 +487,7 @@
*
* @param i the index where to remove the {@link Port}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public void removePort(int i) {
if (!isSetListOfPorts()) {
@@ -516,7 +516,7 @@
*
* @param i the index where to remove the {@link Submodel}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public void removeSubmodel(int i) {
if (!isSetListOfSubmodels()) {
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBMLDocumentPlugin.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -306,7 +306,7 @@
*
* @param i the index where to remove the {@link ExternalModelDefinition}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public void removeExternalModelDefinition(int i) {
if (!isSetListOfExternalModelDefinitions()) {
@@ -522,7 +522,7 @@
*
* @param i the index where to remove the {@link ModelDefinition}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public void removeModelDefinition(int i) {
if (!isSetListOfModelDefinitions()) {
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/CompSBasePlugin.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -439,7 +439,7 @@
*
* @param i the index of the element to be removed
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public void removeReplacedElement(int i) {
if (!isSetListOfReplacedElements()) {
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/Submodel.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -537,7 +537,7 @@
*
* @param i the index where to remove the {@link Deletion}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public void removeDeletion(int i) {
if (!isSetListOfDeletions()) {
Modified: trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/package-info.java
===================================================================
--- trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/package-info.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/comp/src/org/sbml/jsbml/ext/comp/package-info.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -30,7 +30,7 @@
* "http://identifiers.org/combine.specifications/sbml.level-3.version-1.comp.version-1.release-3"
* >version 1 release 3</a>.
*
- * <p><img title="JSBML" alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
+ * <p><img alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
*
* @author Nicolas Rodriguez
* @version $Rev$
Modified: trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java
===================================================================
--- trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/distrib/src/org/sbml/jsbml/ext/distrib/DrawFromDistribution.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -348,7 +348,7 @@
* @param i the index where to remove the {@link DistribInput}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public DistribInput removeDistribInput(int i) {
if (!isSetListOfDistribInputs()) {
@@ -386,7 +386,7 @@
* @param i the index of the {@link DistribInput} element to get.
* @return an element from the listOfDistribInputs at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public DistribInput getDistribInput(int i) {
if (!isSetListOfDistribInputs()) {
Modified: trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/package-info.java
===================================================================
--- trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/package-info.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/package-info.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -29,7 +29,7 @@
* The current version of the package follow the <a href=
* "http://sourceforge.net/p/sbml/code/HEAD/tree/trunk/specifications/sbml-level-3/version-1/dyn/spec/sbml-dyn-v1-rel0.1.pdf?format=raw"
* >proposal by AUTHORS</a>
- * <p><img title="JSBML" alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
+ * <p><img alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
*
* @author Harold Gómez
* @since 1.0
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/FBCModelPlugin.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -317,7 +317,7 @@
*
* @param i the index where to get the {@link FluxBound}
* @throws IndexOutOfBoundsException
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
* @return an element from the listOfFluxBounds at the given index.
* @deprecated Only defined in FBC version 1.
*/
@@ -346,7 +346,7 @@
* @param i the index of the {@link GeneProduct} element to get.
* @return an element from the listOfGeneProducts at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public GeneProduct getGeneProduct(int i) {
if (!isSetListOfGeneProducts()) {
@@ -477,7 +477,7 @@
*
* @param i the index where to get the {@link Objective}
* @throws IndexOutOfBoundsException
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
* @return an element from the listOfObjectives at the given index.
*/
public Objective getObjective(int i) {
@@ -651,7 +651,7 @@
*
* @param i the index where to remove the {@link FluxBound}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
* @deprecated Only defined in FBC version 1.
*/
@Deprecated
@@ -682,7 +682,7 @@
* @param i the index where to remove the {@link GeneProduct}.
* @return the specified element if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public GeneProduct removeGeneProduct(int i) {
if (!isSetListOfGeneProducts()) {
@@ -710,7 +710,7 @@
*
* @param i the index where to remove the {@link Objective}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public void removeObjective(int i) {
if (!isSetListOfObjectives()) {
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/LogicalOperator.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -186,7 +186,7 @@
* @param i the index of the {@link Association} element to get.
* @return an element from the listOfAssociations at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public Association getAssociation(int i) {
if (!isSetListOfAssociations()) {
@@ -323,7 +323,7 @@
* @param i the index where to remove the {@link Association}.
* @return the specified element if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public Association removeAssociation(int i) {
if (!isSetListOfAssociations()) {
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/Objective.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -439,7 +439,7 @@
*
* @param i the index where to remove the {@link FluxObjective}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public void removeFluxObjective(int i) {
if (!isSetListOfFluxObjectives()) {
@@ -454,7 +454,7 @@
*
* @param id the id of the {@link FluxObjective} to remove.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public void removeFluxObjective(String id) {
getListOfFluxObjectives().removeFirst(new NameFilter(id));
Modified: trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/package-info.java
===================================================================
--- trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/package-info.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/fbc/src/org/sbml/jsbml/ext/fbc/package-info.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -29,7 +29,7 @@
* "http://identifiers.org/combine.specifications/sbml.level-3.version-1.fbc.version-1.release-1"
* >version 1 release 1</a> specifications.
*
- * <p><img title="JSBML" alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
+ * <p><img alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
*
* @author Nicolas Rodriguez
* @version $Rev$
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/Group.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -422,7 +422,7 @@
* @param i the index of the {@link Member} element to get.
* @return an element from the listOfMembers at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public Member getMember(int i) {
if (!isSetListOfMembers()) {
@@ -610,7 +610,7 @@
*
* @param i the index where to remove the {@link MemberConstraint}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public void removeMemberConstraint(int i) {
if (!isSetListOfMemberConstraints()) {
Modified: trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/package-info.java
===================================================================
--- trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/package-info.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/groups/src/org/sbml/jsbml/ext/groups/package-info.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -28,7 +28,7 @@
* The current version of the package follow the <a href=
* "http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Groups_Proposal_(2009-10)"
* >proposal by M. Hucka</a>
- * <p><img title="JSBML" alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
+ * <p><img alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
*
* @version $Rev$
* @since 1.0
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/CurveSegment.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -31,7 +31,7 @@
/**
* Parent class to {@link LineSegment} and {@link CubicBezier}.
*
- * @author Sebastian Fr&oum;hlich
+ * @author Sebastian Fröhlich
* @author Nicolas Rodriguez
* @since 1.0
* @version $Rev$
@@ -40,7 +40,7 @@
/**
*
- * @author Sebastian Fr&oum;hlich
+ * @author Sebastian Fröhlich
* @author Nicolas Rodriguez
* @version $Rev$
* @since 1.0
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/GeneralGlyph.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -164,7 +164,7 @@
* the listOfAdditionalGraphicalObjects (which may only contain {@link GraphicalObject} or {@link GeneralGlyph}s),
* the listOfSubGlyphs may contain any derived class, such as for example {@link TextGlyph} elements.
*
- * Sets the given ListOf<{@link GraphicalObject}>. If listOfSubGlyphs
+ * Sets the given ListOf<{@link GraphicalObject}>. If listOfSubGlyphs
* was defined before and contains some elements, they are all unset.
*
* @param listOfSubGlyphs
@@ -239,7 +239,7 @@
*
* @param i the index where to remove the {@link GraphicalObject}
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size)
+ * if the index is out of bound (index < 0 || index > list.size)
*/
public void removeSubGlyph(int i) {
if (!isSetListOfSubGlyphs()) {
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/Layout.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -659,7 +659,7 @@
* @param i the index of the {@link CompartmentGlyph} element to get.
* @return an element from the listOfCompartmentGlyphs at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public CompartmentGlyph getCompartmentGlyph(int i) {
if (!isSetListOfCompartmentGlyphs()) {
@@ -1048,7 +1048,7 @@
* @param i the index where to remove the {@link CompartmentGlyph}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public CompartmentGlyph removeCompartmentGlyph(int i) {
if (!isSetListOfCompartmentGlyphs()) {
@@ -1091,7 +1091,7 @@
* @param i the index where to remove the {@link GeneralGlyph}.
* @return the removed object
* @throws IndexOutOfBoundsException if the listOf is not set or if the index
- * is out of bound (index < 0 || index > list.size).
+ * is out of bound (index < 0 || index > list.size).
* @throws ClassCastException if the additional graphical object at the given
* index is not an instance of {@link GeneralGlyph}. Note that the element is
* still removed, but an exception will be thrown. The element will not be
@@ -1126,7 +1126,7 @@
* @param i the index where to remove the {@link ReactionGlyph}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public ReactionGlyph removeReactionGlyph(int i) {
if (!isSetListOfReactionGlyphs()) {
@@ -1208,7 +1208,7 @@
* @param i the index where to remove the {@link SpeciesGlyph}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public SpeciesGlyph removeSpeciesGlyph(int i) {
if (!isSetListOfSpeciesGlyphs()) {
@@ -1250,7 +1250,7 @@
* @param i the index where to remove the {@link TextGlyph}.
* @return the specified element, if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or
- * if the index is out of bound (index < 0 || index > list.size).
+ * if the index is out of bound (index < 0 || index > list.size).
*/
public TextGlyph removeTextGlyph(int i) {
if (!isSetListOfTextGlyphs()) {
Modified: trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/package-info.java
===================================================================
--- trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/package-info.java 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/layout/src/org/sbml/jsbml/ext/layout/package-info.java 2015-11-06 17:43:00 UTC (rev 2392)
@@ -32,7 +32,7 @@
* href="http://otto.bioquant.uni-heidelberg.de/sbml/">Layout proposal by Gauges
* et al.</a> as an annotation in SBMl level 2
* </p>
- * <p><img title="JSBML" alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
+ * <p><img alt="JSBML" height="54" src="http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">
*
* @author Nicolas Rodriguez
* @author Sebastian Fröhlich
Modified: trunk/extensions/pom.xml
===================================================================
--- trunk/extensions/pom.xml 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/pom.xml 2015-11-06 17:43:00 UTC (rev 2392)
@@ -64,7 +64,7 @@
<dependencies>
<dependency>
<groupId>org.sbml.jsbml</groupId>
- <artifactId>core</artifactId>
+ <artifactId>jsbml-core</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
Modified: trunk/extensions/spatial/pom.xml
===================================================================
--- trunk/extensions/spatial/pom.xml 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/extensions/spatial/pom.xml 2015-11-06 17:43:00 UTC (rev 2392)
@@ -36,56 +36,5 @@
<artifactId>jsbml-spatial</artifactId>
<packaging>jar</packaging>
- <build>
- <plugins>
- <plugin>
- <artifactId>maven-antrun-plugin</artifactId>
- <executions>
- <execution>
- <phase>process-resources</phase>
- <configuration>
- <tasks>
- <ant antfile="build.xml" target="jar"/>
- </tasks>
- </configuration>
- <goals>
- <goal>run</goal>
- </goals>
- </execution>
- </executions>
- <dependencies>
- <dependency>
- <groupId>com.sun</groupId>
- <artifactId>tools</artifactId>
- <version>1.7.0</version>
- <scope>system</scope>
- <systemPath>${java.home}/../lib/tools.jar</systemPath>
- </dependency>
- </dependencies>
- </plugin>
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>build-helper-maven-plugin</artifactId>
- <version>1.3</version>
- <executions>
- <execution>
- <id>add-jar</id>
- <phase>package</phase>
- <goals>
- <goal>attach-artifact</goal>
- </goals>
- <configuration>
- <artifacts>
- <artifact>
- <file>build/${artifactId}-${version}-with-dependencies.jar</file>
- <type>jar</type>
- </artifact>
- </artifacts>
- </configuration>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
</project>
Modified: trunk/modules/pom.xml
===================================================================
--- trunk/modules/pom.xml 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/modules/pom.xml 2015-11-06 17:43:00 UTC (rev 2392)
@@ -72,8 +72,8 @@
<dependencies>
<dependency>
- <groupId>org.sbml.jsbml.core</groupId>
- <artifactId>jsbml_core</artifactId>
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>jsbml-core</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
@@ -85,9 +85,9 @@
</dependencies>
<modules>
- <module>android</module>
+ <!-- <module>android</module>
<module>celldesigner</module>
- <module>libSBMLio</module>
+ <module>libSBMLio</module> cellDesigner and libSBML are dependencies that are not on maven -->
<module>tidy</module>
</modules>
Modified: trunk/modules/tidy/pom.xml
===================================================================
--- trunk/modules/tidy/pom.xml 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/modules/tidy/pom.xml 2015-11-06 17:43:00 UTC (rev 2392)
@@ -36,30 +36,6 @@
<artifactId>jsbml-tidy</artifactId>
<packaging>jar</packaging>
- <build>
- <plugins>
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>properties-maven-plugin</artifactId>
- <version>1.0-alpha-2</version>
- <executions>
- <execution>
- <id>tidy</id>
- <phase>initialize</phase>
- <goals>
- <goal>read-project-properties</goal>
- </goals>
- <configuration>
- <files>
- <file>tidy-build.properties</file>
- </files>
- </configuration>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
-
<dependencies>
<dependency>
<groupId>net.sf.jtidy</groupId>
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2015-11-06 11:48:57 UTC (rev 2391)
+++ trunk/pom.xml 2015-11-06 17:43:00 UTC (rev 2392)
@@ -31,9 +31,11 @@
<version>1.1-b1</version>
<packaging>pom</packaging>
-<!--
<build>
<plugins>
+
+<!-- properties file not used at the moment
+
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>properties-maven-plugin</artifactId>
@@ -54,13 +56,88 @@
</executions>
</plugin>
</plugins>
+-->
+
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-javadoc-plugin</artifactId>
+ <version>2.10.3</version>
+ <configuration>
+ <stylesheetfile>${basedir}/stylesheetfile.css</stylesheetfile>
+ <links>
+ <link>http://docs.oracle.com/javase/6/docs/api/</link>
+ <link>http://www.biojava.org/docs/api17</link> <!-- TODO update -->
+ </links>
+ <tags>
+ <tag>
+ <name>sbml.deprecated</name>
+ <placement>a</placement>
+ <head>Deprecated in SBML since:</head>
+ </tag>
+ <tag>
+ <name>libsbml.deprecated</name>
+ <placement>a</placement>
+ <head>Note: this method is kept here as it exist in libSBML.</head>
+ </tag>
+ <tag>
+ <name>jsbml.note</name>
+ <placement>a</placement>
+ <head>Note:</head>
+ </tag>
+ <tag>
+ <name>jsbml.warning</name>
+ <placement>a</placement>
+ <head>Warning:</head>
+ </tag>
+ <tag>
+ <name>doc.note</name>
+ <placement>a</placement>
+ <head>Documentation note:</head>
+ </tag>
+ <tag>
+ <name>date</name>
+ <placement>a</placement>
+ <head>Last modified:</head>
+ </tag>
+ </tags>
+ </configuration>
+ </plugin>
+
+ </plugins>
</build>
--->
+
<modules>
<module>core</module>
<module>extensions</module>
<module>modules</module>
</modules>
+ <repositories>
+ <repository>
+ <id>local-repo</id>
+ <url>http://localhost/repo</url>
+ </repository>
+ </repositories>
+
+ <distributionManagement>
+ <repository>
+ <id>local-repo-deploy</id>
+ <name>Test Maven2 repository</name>
+ <url>file:///var/www/html/repo</url>
+ </repository>
+ <snapshotRepository>
+ <id>jsbmlmavenrepotest.sourceforge.net</id>
+ <name>JSBML Maven2 SNAPSHOT repository</name>
+ <url>scp://shell.sourceforge.net/home/project-web/jsbmlmavenrepotest/htdocs/snapshotRepository</url>
+ </snapshotRepository>
+ </distributionManagement>
+
+<!-- <repository>
+ <id>jsbmlmavenrepotest.sourceforge.net</id>
+ <name>JSBML Maven2 repository</name>
+ <url>scp://shell.sourceforge.net/home/project-web/jsbmlmavenrepotest/htdocs/releaseRepository</url>
+ </repository>
+-->
+
</project>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-06 11:48:59
|
Revision: 2391
http://sourceforge.net/p/jsbml/code/2391
Author: niko-rodrigue
Date: 2015-11-06 11:48:57 +0000 (Fri, 06 Nov 2015)
Log Message:
-----------
updated some of the pom files to reflect the changes for the group and artifact ids
Modified Paths:
--------------
trunk/extensions/arrays/pom.xml
trunk/extensions/pom.xml
trunk/extensions/render/pom.xml
trunk/pom.xml
Modified: trunk/extensions/arrays/pom.xml
===================================================================
--- trunk/extensions/arrays/pom.xml 2015-11-03 17:13:47 UTC (rev 2390)
+++ trunk/extensions/arrays/pom.xml 2015-11-06 11:48:57 UTC (rev 2391)
@@ -35,4 +35,13 @@
<groupId>org.sbml.jsbml.ext</groupId>
<artifactId>jsbml-arrays</artifactId>
<packaging>jar</packaging>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-comp</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
</project>
Modified: trunk/extensions/pom.xml
===================================================================
--- trunk/extensions/pom.xml 2015-11-03 17:13:47 UTC (rev 2390)
+++ trunk/extensions/pom.xml 2015-11-06 11:48:57 UTC (rev 2391)
@@ -63,8 +63,8 @@
<dependencies>
<dependency>
- <groupId>org.sbml.jsbml.core</groupId>
- <artifactId>jsbml_core</artifactId>
+ <groupId>org.sbml.jsbml</groupId>
+ <artifactId>core</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
Modified: trunk/extensions/render/pom.xml
===================================================================
--- trunk/extensions/render/pom.xml 2015-11-03 17:13:47 UTC (rev 2390)
+++ trunk/extensions/render/pom.xml 2015-11-06 11:48:57 UTC (rev 2391)
@@ -38,8 +38,8 @@
<dependencies>
<dependency>
- <groupId>org.sbml.jsbml.ext.layout</groupId>
- <artifactId>jsbml_ext_layout</artifactId>
+ <groupId>org.sbml.jsbml.ext</groupId>
+ <artifactId>jsbml-layout</artifactId>
<version>1.1-b1</version>
</dependency>
</dependencies>
Modified: trunk/pom.xml
===================================================================
--- trunk/pom.xml 2015-11-03 17:13:47 UTC (rev 2390)
+++ trunk/pom.xml 2015-11-06 11:48:57 UTC (rev 2391)
@@ -31,6 +31,7 @@
<version>1.1-b1</version>
<packaging>pom</packaging>
+<!--
<build>
<plugins>
<plugin>
@@ -54,6 +55,7 @@
</plugin>
</plugins>
</build>
+-->
<modules>
<module>core</module>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-11-03 17:13:49
|
Revision: 2390
http://sourceforge.net/p/jsbml/code/2390
Author: niko-rodrigue
Date: 2015-11-03 17:13:47 +0000 (Tue, 03 Nov 2015)
Log Message:
-----------
added a new utility class that contain a method to read Cobra notes into a java Properties object
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/xml/XMLNode.java
Added Paths:
-----------
trunk/core/src/org/sbml/jsbml/util/CobraUtil.java
Added: trunk/core/src/org/sbml/jsbml/util/CobraUtil.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/util/CobraUtil.java (rev 0)
+++ trunk/core/src/org/sbml/jsbml/util/CobraUtil.java 2015-11-03 17:13:47 UTC (rev 2390)
@@ -0,0 +1,124 @@
+/*
+ * $Id$
+ * $URL$
+ * ----------------------------------------------------------------------------
+ * This file is part of JSBML. Please visit <http://sbml.org/Software/JSBML>
+ * for the latest version of JSBML and more information about SBML.
+ *
+ * Copyright (C) 2009-2014 jointly by the following organizations:
+ * 1. The University of Tuebingen, Germany
+ * 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
+ * 3. The California Institute of Technology, Pasadena, CA, USA
+ * 4. The University of California, San Diego, La Jolla, CA, USA
+ * 5. The Babraham Institute, Cambridge, UK
+ *
+ * This library is free software; you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation. A copy of the license agreement is provided
+ * in the file named "LICENSE.txt" included with this software distribution
+ * and also available online as <http://sbml.org/Software/JSBML/License>.
+ * ----------------------------------------------------------------------------
+ */
+
+package org.sbml.jsbml.util;
+
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.SBase;
+import org.sbml.jsbml.xml.XMLNode;
+
+
+/**
+ * Contains some useful methods to manipulate 'COBRA SBML'
+ *
+ *
+ * @author Nicolas Rodriguez
+ * @version $Rev$
+ * @since 1.1
+ */
+public class CobraUtil {
+
+ private static Logger logger = Logger.getLogger(CobraUtil.class);
+
+ /**
+ * Parses the notes of the given {@link SBase} element.
+ *
+ *<p>The notes are expecting to have some 'p' elements with
+ * a content of the form 'KEY: VALUE'. The key will be used for the property
+ * name and the value will be the property value. The key is inserted even is the value
+ * is an empty String.
+ *
+ * <p>Below are examples for a species and a reaction:
+ *
+ * <pre>
+ <body xmlns="http://www.w3.org/1999/xhtml">
+ <p>FORMULA: H4N</p>
+ <p>CHARGE: 1</p>
+ <p>HEPATONET_1.0_ABBREVIATION: HC00765</p>
+ <p>EHMN_ABBREVIATION: C01342</p>
+ <p>INCHI: InChI=1S/H3N/h1H3/p+1</p>
+ </body>
+</pre>
+
+<pre>
+ <body xmlns="http://www.w3.org/1999/xhtml">
+ <p>GENE_ASSOCIATION: 1594.1</p>
+ <p>SUBSYSTEM: Vitamin D metabolism</p>
+ <p>EC Number: </p>
+ <p>Confidence Level: 4</p>
+ <p>AUTHORS: PMID:14671156,PMID:9333115</p>
+ <p>NOTES: based on Vitamins, G.F.M. Ball,2004, Blackwell publishing, 1st ed (book) pg.196 IT</p>
+ </body>
+</pre>
+
+ * @param sbase
+ * @return a {@link Properties} object that store all the KEY/VALUE pair found in the notes. If the given {@link SBase}
+ * has no notes or if the notes are not of the expected format, an empty {@link Properties} object is returned.
+ */
+ public static Properties parseCobraNotes(SBase sbase) {
+ Properties props = new Properties();
+
+ if (sbase.isSetNotes()) {
+ XMLNode notes = sbase.getNotes();
+ // just in case no body element is present
+ XMLNode parent = notes;
+
+ // Getting the body element
+ XMLNode body = notes.getChildElement("body", null);
+
+ if (body != null) {
+ parent = body;
+ }
+
+ // Getting the all the p elements (only direct child of 'parent')
+ List<XMLNode> pNodes = parent.getChildElements("p", null);
+
+ for (XMLNode pNode : pNodes) {
+ if (pNode.getChildCount() > 0) {
+ String content = pNode.getChild(0).getCharacters();
+ String key = "", value = "";
+
+ int firstColonIndex = content.indexOf(':');
+
+ if (firstColonIndex != -1) {
+ key = content.substring(0, firstColonIndex);
+ value = content.substring(firstColonIndex + 1).trim();
+
+ props.setProperty(key, value);
+ } else if (logger.isDebugEnabled()) {
+ logger.debug("The content of one of the 'p' element does not seems to respect the expected pattern (KEY: VALUE), found '" + content + "'");
+ }
+ } // else if (logger.isDebugEnabled()) {
+ // logger.debug("The content of one of the 'p' element does not seems to respect the expected pattern (KEY: VALUE), found no children !");
+ //}
+ }
+ }
+
+ return props;
+ }
+
+ // TODO - XMLNode writeCobraNotes(Properties props)
+
+}
Property changes on: trunk/core/src/org/sbml/jsbml/util/CobraUtil.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
Added: svn:keywords
## -0,0 +1 ##
+Author Date Id Rev URL
\ No newline at end of property
Added: svn:eol-style
## -0,0 +1 ##
+native
\ No newline at end of property
Modified: trunk/core/src/org/sbml/jsbml/xml/XMLNode.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/xml/XMLNode.java 2015-10-28 10:35:08 UTC (rev 2389)
+++ trunk/core/src/org/sbml/jsbml/xml/XMLNode.java 2015-11-03 17:13:47 UTC (rev 2390)
@@ -645,7 +645,8 @@
*
* @param elementName - The local name of the elements to match on. The special value "*" matches all local names.
* @param elementURI - The namespace URI of the elements to match on. The special value "*" matches all namespaces.
- * @return the first direct child of this {@link XMLNode} with the given local name and namespace.
+ * @return the first direct child of this {@link XMLNode} with the given local name and namespace or null
+ * if no match found.
*/
public XMLNode getChildElement(String elementName, String elementURI)
{
@@ -687,7 +688,7 @@
* - The namespace URI of the elements to match on. The special value
* "*" matches all namespaces.
* @return all the direct children of this {@link XMLNode} with the given
- * local name and namespace.
+ * local name and namespace or an empty List if not match were found.
*/
public List<XMLNode> getChildElements(String elementName, String elementURI)
{
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nik...@us...> - 2015-10-28 10:35:10
|
Revision: 2389
http://sourceforge.net/p/jsbml/code/2389
Author: niko-rodrigue
Date: 2015-10-28 10:35:08 +0000 (Wed, 28 Oct 2015)
Log Message:
-----------
modified the CobraFormulaParser to be able to parse properly the Cobra gene associations String. I removed the parsing of numbers as most ids look like numbers and we want only String on those formulas.
Modified Paths:
--------------
trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java
trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.jj
trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParserConstants.java
trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParserTokenManager.java
Modified: trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java 2015-10-20 15:57:25 UTC (rev 2388)
+++ trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.java 2015-10-28 10:35:08 UTC (rev 2389)
@@ -11,7 +11,7 @@
* 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 3. The California Institute of Technology, Pasadena, CA, USA
* 4. The University of California, San Diego, La Jolla, CA, USA
- * 5. The Babraham Institute, Cambridge, UK
+ * 5. The Babraham Institute, Cambridge, UK
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
@@ -37,14 +37,14 @@
* "(8639_AT1) || (26_AT1) || (314_AT2) || (314_AT1)".
* <p>
* Support almost the same syntax as defined in <a href="http://sbml.org/Software/libSBML/docs/java-api/org/sbml/libsbml/libsbml.html#parseL3Formula(java.lang.String)">
- * the LibSBML L3 parser</a>.
+ * the LibSBML L3 parser</a>.
* <p>One of the main differences is that ID are allowed to start by a number so that ID like that '8639_AT1' are recognised as ID.
- *
+ *
* <p>The things not supported for now are the units associated with numbers.
*
* <p>
* Parsing of the various MathML functions and constants are all
- * case-sensitive by default: names such as
+ * case-sensitive by default: names such as
* <code>Cos</code> and <code>COS</code> are not parsed as the MathML cosine
* operator, <code><cos></code>.
*
@@ -81,8 +81,8 @@
<p>
- * In the table above, <em>operand</em> implies the construct is an operand,
- * <em>prefix</em> implies the operation is applied to the following arguments,
+ * In the table above, <em>operand</em> implies the construct is an operand,
+ * <em>prefix</em> implies the operation is applied to the following arguments,
* <em>unary</em> implies there is one argument, and <em>binary</em> implies there are
* two arguments. The values in the <b>Precedence</b> column show how the
* order of different types of operation are determined. For example, the
@@ -106,7 +106,7 @@
* functions added in SBML Level 2 and Level 3:
<p>
- * <table border="0" width="95%"
+ * <table border="0" width="95%"
class="centered text-table normal-font alt-row-colors">
<tr>
<th align="left" width="60">Name</th>
@@ -115,8 +115,8 @@
<th align="left" width="90">Argument Constraints</th>
<th align="left" width="90">Result constraints</th>
</tr>
-<tr><td><code>abs</code></td>
- <td><em>x</em></td>
+<tr><td><code>abs</code></td>
+ <td><em>x</em></td>
<td>Absolute value of <em>x</em>.</td>
<td></td>
<td></td>
@@ -470,16 +470,16 @@
*
* <p>The default behavior is to be case sensitive, meaning
* '{@code cos}' would be recognized as the mathematical <a href="http://www.w3.org/TR/MathML2/chapter4.html#contm.trig">cosinus</a> but
- * '{@code Cos}', '{@code cOs}' or any other alternatives would be recognized
+ * '{@code Cos}', '{@code cOs}' or any other alternatives would be recognized
* as a name and read as a 'ci' element. If you pass {@code false} to this method
* all the different versions of {@code cos} would be recognized as the mathematical
- * <a href="http://www.w3.org/TR/MathML2/chapter4.html#contm.trig">cosinus</a>.
+ * <a href="http://www.w3.org/TR/MathML2/chapter4.html#contm.trig">cosinus</a>.
*
- * @param caseSensitive boolean to define if the parser should be case sensitive or not.
+ * @param caseSensitive boolean to define if the parser should be case sensitive or not.
*/
public void setCaseSensitive(boolean caseSensitive)
{
- ignoreCase = !caseSensitive;
+ this.ignoreCase = !caseSensitive;
}
private void checkSize(ArrayList < ASTNode > arguments, int i) throws ParseException
@@ -516,44 +516,44 @@
}
}
- /**
- * Returns a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
- *
- * <p/> The formula produced for 'a % b' or modulo(a, b) is 'piecewise(floor(a/b), gt(a/b, 0), ceil(a/b))'
- *
- * @param leftChild
- * @param rightChild
- * @return a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
- * @see "http://sbml.org/Documents/FAQ#Why_can.27t_I_use_the_.3Crem.3E_operator_in_SBML_MathML.3F"
- */
+/**
+ * Returns a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
+ *
+ * <p/> The formula produced for 'a % b' or modulo(a, b) is 'piecewise(floor(a/b), gt(a/b, 0), ceil(a/b))'
+ *
+ * @param leftChild
+ * @param rightChild
+ * @return a piecewise {@link ASTNode} representing the modulo operation between the left and right child given.
+ * @see http://sbml.org/Documents/FAQ#Why_can.27t_I_use_the_.3Crem.3E_operator_in_SBML_MathML.3F
+ */
private ASTNode createModulo(ASTNode leftChild, ASTNode rightChild)
{
- ASTNode node = new ASTNode(ASTNode.Type.FUNCTION_PIECEWISE);
+ ASTNode node = new ASTNode(ASTNode.Type.FUNCTION_PIECEWISE);
- ASTNode floorNode = new ASTNode(ASTNode.Type.FUNCTION_FLOOR);
- ASTNode aDividedByB = new ASTNode(ASTNode.Type.DIVIDE);
- aDividedByB.addChild(leftChild);
- aDividedByB.addChild(rightChild);
+ ASTNode floorNode = new ASTNode(ASTNode.Type.FUNCTION_FLOOR);
+ ASTNode aDividedByB = new ASTNode(ASTNode.Type.DIVIDE);
+ aDividedByB.addChild(leftChild);
+ aDividedByB.addChild(rightChild);
- floorNode.addChild(aDividedByB);
- node.addChild(floorNode);
+ floorNode.addChild(aDividedByB);
+ node.addChild(floorNode);
- ASTNode greaterThan = new ASTNode(ASTNode.Type.RELATIONAL_GT);
- greaterThan.addChild(aDividedByB.clone());
- greaterThan.addChild(new ASTNode(0));
+ ASTNode greaterThan = new ASTNode(ASTNode.Type.RELATIONAL_GT);
+ greaterThan.addChild(aDividedByB.clone());
+ greaterThan.addChild(new ASTNode(0));
- node.addChild(greaterThan);
+ node.addChild(greaterThan);
- ASTNode ceilNode = new ASTNode(ASTNode.Type.FUNCTION_CEILING);
- ceilNode.addChild(aDividedByB.clone());
+ ASTNode ceilNode = new ASTNode(ASTNode.Type.FUNCTION_CEILING);
+ ceilNode.addChild(aDividedByB.clone());
- node.addChild(ceilNode);
+ node.addChild(ceilNode);
- return node;
+ return node;
}
final public Token string() throws ParseException {
- Token t;
+ Token t;
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case LOG:
t = jj_consume_token(LOG);
@@ -566,24 +566,19 @@
jj_consume_token(-1);
throw new ParseException();
}
- {if (true) {
- return t;
- }}
+ {if (true) return t;}
throw new Error("Missing return statement in function");
}
- @Override
final public ASTNode parse() throws ParseException {
- ASTNode node = null;
+ ASTNode node = null;
node = expression();
- {if (true) {
- return node;
- }}
+ {if (true) return node;}
throw new Error("Missing return statement in function");
}
final private ASTNode expression() throws ParseException {
- ASTNode value = null;
+ ASTNode value = null;
value = termLevel2();
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case 0:
@@ -597,255 +592,236 @@
jj_consume_token(-1);
throw new ParseException();
}
- {if (true) {
- return value;
- }}
+ {if (true) return value;}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel2() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
- Token t;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
+ Token t;
leftChild = termLevel3();
label_1:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case BOOLEAN_LOGIC:
- ;
- break;
- default:
- jj_la1[2] = jj_gen;
- break label_1;
- }
- t = jj_consume_token(BOOLEAN_LOGIC);
- rightChild = termLevel3();
- // TODO - do we want to ignore the case for those cases ?
- String s = t.image;
- Type type = null;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case BOOLEAN_LOGIC:
+ ;
+ break;
+ default:
+ jj_la1[2] = jj_gen;
+ break label_1;
+ }
+ t = jj_consume_token(BOOLEAN_LOGIC);
+ rightChild = termLevel3();
+ // TODO - do we want to ignore the case for those cases ?
+ String s = t.image;
+ Type type = null;
- if (s.equalsIgnoreCase("or") || s.equalsIgnoreCase("||"))
- {
- type = ASTNode.Type.LOGICAL_OR;
- }
- else if (s.equalsIgnoreCase("and") || s.equalsIgnoreCase("&&"))
- {
- type = ASTNode.Type.LOGICAL_AND;
- }
- else if (s.equalsIgnoreCase("xor"))
- {
- type = ASTNode.Type.LOGICAL_XOR;
- }
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
+ if (s.equalsIgnoreCase("or") || s.equalsIgnoreCase("||"))
+ {
+ type = ASTNode.Type.LOGICAL_OR;
}
- {if (true) {
- return leftChild;
- }}
+ else if (s.equalsIgnoreCase("and") || s.equalsIgnoreCase("&&"))
+ {
+ type = ASTNode.Type.LOGICAL_AND;
+ }
+ else if (s.equalsIgnoreCase("xor"))
+ {
+ type = ASTNode.Type.LOGICAL_XOR;
+ }
+ node = new ASTNode(type);
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ }
+ {if (true) return leftChild;}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel3() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
- Token t;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
+ Token t;
leftChild = termLevel4();
label_2:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case COMPARISON:
- ;
- break;
- default:
- jj_la1[3] = jj_gen;
- break label_2;
- }
- t = jj_consume_token(COMPARISON);
- rightChild = termLevel4();
- String s = t.image;
- Type type = null;
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case COMPARISON:
+ ;
+ break;
+ default:
+ jj_la1[3] = jj_gen;
+ break label_2;
+ }
+ t = jj_consume_token(COMPARISON);
+ rightChild = termLevel4();
+ String s = t.image;
+ Type type = null;
- if (s.equalsIgnoreCase("<"))
- {
- type = ASTNode.Type.RELATIONAL_LT;
- }
- else if (s.equalsIgnoreCase(">"))
- {
- type = ASTNode.Type.RELATIONAL_GT;
- }
- else if (s.equalsIgnoreCase("=="))
- {
- type = ASTNode.Type.RELATIONAL_EQ;
- }
- else if (s.equalsIgnoreCase("!="))
- {
- type = ASTNode.Type.RELATIONAL_NEQ;
- }
- else if (s.equalsIgnoreCase(">="))
- {
- type = ASTNode.Type.RELATIONAL_GEQ;
- }
- else if (s.equalsIgnoreCase("<="))
- {
- type = ASTNode.Type.RELATIONAL_LEQ;
- }
- node = new ASTNode(type);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
+ if (s.equalsIgnoreCase("<"))
+ {
+ type = ASTNode.Type.RELATIONAL_LT;
}
- {if (true) {
- return leftChild;
- }}
+ else if (s.equalsIgnoreCase(">"))
+ {
+ type = ASTNode.Type.RELATIONAL_GT;
+ }
+ else if (s.equalsIgnoreCase("=="))
+ {
+ type = ASTNode.Type.RELATIONAL_EQ;
+ }
+ else if (s.equalsIgnoreCase("!="))
+ {
+ type = ASTNode.Type.RELATIONAL_NEQ;
+ }
+ else if (s.equalsIgnoreCase(">="))
+ {
+ type = ASTNode.Type.RELATIONAL_GEQ;
+ }
+ else if (s.equalsIgnoreCase("<="))
+ {
+ type = ASTNode.Type.RELATIONAL_LEQ;
+ }
+ node = new ASTNode(type);
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ }
+ {if (true) return leftChild;}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel4() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
leftChild = termLevel5();
label_3:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- case MINUS:
- ;
- break;
- default:
- jj_la1[4] = jj_gen;
- break label_3;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case PLUS:
- jj_consume_token(PLUS);
- rightChild = termLevel5();
- node = new ASTNode('+');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case MINUS:
- jj_consume_token(MINUS);
- rightChild = termLevel5();
- node = new ASTNode('-');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- default:
- jj_la1[5] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case PLUS:
+ case MINUS:
+ ;
+ break;
+ default:
+ jj_la1[4] = jj_gen;
+ break label_3;
}
- {if (true) {
- return leftChild;
- }}
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case PLUS:
+ jj_consume_token(PLUS);
+ rightChild = termLevel5();
+ node = new ASTNode('+');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ break;
+ case MINUS:
+ jj_consume_token(MINUS);
+ rightChild = termLevel5();
+ node = new ASTNode('-');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ break;
+ default:
+ jj_la1[5] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
+ }
+ {if (true) return leftChild;}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel5() throws ParseException {
- ASTNode rightChild = null;
- ASTNode leftChild;
- ASTNode node = null;
+ ASTNode rightChild = null;
+ ASTNode leftChild;
+ ASTNode node = null;
leftChild = termLevel6();
label_4:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- case DIVIDE:
- case MODULO:
- ;
- break;
- default:
- jj_la1[6] = jj_gen;
- break label_4;
- }
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case TIMES:
- jj_consume_token(TIMES);
- rightChild = termLevel6();
- node = new ASTNode('*');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- break;
- case DIVIDE:
- jj_consume_token(DIVIDE);
- rightChild = termLevel6();
- Integer left, right;
- left = getInteger(leftChild);
- right = getInteger(rightChild);
- // TODO - check if libsbml behave the same way
- if (left != null && right != null) // Node transformed into a ASTNode.Type.RATIONAL number if both left and right are integer
- {
- node = new ASTNode();
- node.setValue(left, right);
- leftChild = node;
- }
- else
- {
- node = new ASTNode('/');
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
- }
- break;
- case MODULO:
- jj_consume_token(MODULO);
- rightChild = termLevel6();
- node = createModulo(leftChild, rightChild);
- leftChild = node;
- break;
- default:
- jj_la1[7] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
- }
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case TIMES:
+ case DIVIDE:
+ case MODULO:
+ ;
+ break;
+ default:
+ jj_la1[6] = jj_gen;
+ break label_4;
}
- {if (true) {
- return leftChild;
- }}
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case TIMES:
+ jj_consume_token(TIMES);
+ rightChild = termLevel6();
+ node = new ASTNode('*');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ break;
+ case DIVIDE:
+ jj_consume_token(DIVIDE);
+ rightChild = termLevel6();
+ Integer left, right;
+ left = getInteger(leftChild);
+ right = getInteger(rightChild);
+ // TODO - check if libsbml behave the same way
+ if (left != null && right != null) // Node transformed into a ASTNode.Type.RATIONAL number if both left and right are integer
+ {
+ node = new ASTNode();
+ node.setValue(left, right);
+ leftChild = node;
+ }
+ else
+ {
+ node = new ASTNode('/');
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ }
+ break;
+ case MODULO:
+ jj_consume_token(MODULO);
+ rightChild = termLevel6();
+ node = createModulo(leftChild, rightChild);
+ leftChild = node;
+ break;
+ default:
+ jj_la1[7] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
+ }
+ {if (true) return leftChild;}
throw new Error("Missing return statement in function");
}
final private ASTNode termLevel6() throws ParseException {
- ASTNode node = null;
+ ASTNode node = null;
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case MINUS:
jj_consume_token(MINUS);
node = termLevel7();
- ASTNode uiMinus = new ASTNode('-');
- uiMinus.addChild(node);
- {if (true) {
- return uiMinus;
- }}
+ ASTNode uiMinus = new ASTNode('-');
+ uiMinus.addChild(node);
+ {if (true) return uiMinus;}
break;
case NOT:
jj_consume_token(NOT);
node = termLevel7();
- ASTNode not = new ASTNode(Type.LOGICAL_NOT);
- not.addChild(node);
- {if (true) {
- return not;
- }}
+ ASTNode not = new ASTNode(Type.LOGICAL_NOT);
+ not.addChild(node);
+ {if (true) return not;}
break;
- case INTEGER:
- case NUMBER:
- case EXPNUMBER:
case OPEN_PAR:
case LEFT_BRACES:
case LOG:
case STRING:
node = termLevel7();
- {if (true) {
- return node;
- }}
+ {if (true) return node;}
break;
default:
jj_la1[8] = jj_gen;
@@ -856,326 +832,273 @@
}
final private ASTNode termLevel7() throws ParseException {
- ASTNode rightChild;
- ASTNode leftChild;
- ASTNode node = null;
+ ASTNode rightChild;
+ ASTNode leftChild;
+ ASTNode node = null;
leftChild = termLevel8();
label_5:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case POWER:
+ ;
+ break;
+ default:
+ jj_la1[9] = jj_gen;
+ break label_5;
+ }
+ jj_consume_token(POWER);
+ rightChild = termLevel8();
+ node = new ASTNode(Type.POWER);
+ node.addChild(leftChild);
+ node.addChild(rightChild);
+ leftChild = node;
+ }
+ {if (true) return leftChild;}
+ throw new Error("Missing return statement in function");
+ }
+
+ final private ASTNode termLevel8() throws ParseException, NumberFormatException {
+ Token t;
+ double d;
+ int i;
+ ASTNode node = new ASTNode();
+ ASTNode vector = null;
+ ASTNode child, furtherChild;
+ String s;
+ String vals [ ];
+ ArrayList < ASTNode > arguments = new ArrayList < ASTNode > ();
+ if (jj_2_1(2)) {
+ t = string();
+ jj_consume_token(OPEN_PAR);
+ child = termLevel2();
+ label_6:
while (true) {
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case POWER:
+ case SPLITTER:
;
break;
default:
- jj_la1[9] = jj_gen;
- break label_5;
+ jj_la1[10] = jj_gen;
+ break label_6;
}
- jj_consume_token(POWER);
- rightChild = termLevel8();
- node = new ASTNode(Type.POWER);
- node.addChild(leftChild);
- node.addChild(rightChild);
- leftChild = node;
+ jj_consume_token(SPLITTER);
+ furtherChild = termLevel2();
+ arguments.add(furtherChild);
}
- {if (true) {
- return leftChild;
- }}
- throw new Error("Missing return statement in function");
- }
-
- final private ASTNode termLevel8() throws ParseException, NumberFormatException {
- Token t;
- double d;
- int i;
- ASTNode node = new ASTNode();
- ASTNode vector = null;
- ASTNode child, furtherChild;
- String s;
- String vals [ ];
- ArrayList < ASTNode > arguments = new ArrayList < ASTNode > ();
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case INTEGER:
- t = jj_consume_token(INTEGER);
- i = Integer.parseInt(t.image); // Could use StringTools.parseXXX methods here but not doing so allow to support different locale ??
- node.setValue(i);
- {if (true) {
- return node;
- }}
- break;
- case NUMBER:
- t = jj_consume_token(NUMBER);
- d = Double.parseDouble(t.image);
- node.setValue(d);
- {if (true) {
- return node;
- }}
- break;
- case EXPNUMBER:
- t = jj_consume_token(EXPNUMBER);
- s = t.image;
- vals = s.toLowerCase().split("e");
- if (vals [ 1 ].startsWith("+"))
- {
- i = Integer.parseInt(vals [ 1 ].substring(1));
- }
- else
- {
- i = Integer.parseInt(vals [ 1 ]);
- }
- node.setValue(Double.parseDouble(vals [ 0 ]), i);
- {if (true) {
- return node;
- }}
- break;
- default:
- jj_la1[14] = jj_gen;
- if (jj_2_1(2)) {
- t = string();
+ jj_consume_token(CLOSE_PAR);
+ s = t.image;
+ Type type = null;
+ if (ignoreCase)
+ {
+ s = s.toLowerCase();
+ }
+ if (stringToType.containsKey(s))
+ {
+ type = ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
+ }
+ if (s.equals("pow") || s.equals("power"))
+ {
+ checkSize(arguments, 1);
+ node.addChild(child);
+ }
+ else if (s.equals("sqr"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(child);
+ node.addChild(new ASTNode(2));
+ }
+ else if (s.equals("sqrt"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(new ASTNode(2));
+ node.addChild(child);
+ }
+ else if (s.equals("not"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(child);
+ type = Type.LOGICAL_NOT;
+ }
+ else if (s.equals("ln"))
+ {
+ checkSize(arguments, 0);
+ node.addChild(child);
+ type = Type.FUNCTION_LN;
+ }
+ else if (s.equals("lambda"))
+ {
+ node.addChild(child);
+ type = Type.LAMBDA;
+ }
+ else if (s.equals("piecewise"))
+ {
+ type = ASTNode.Type.FUNCTION_PIECEWISE;
+ node.addChild(child);
+ type = Type.FUNCTION_PIECEWISE;
+ }
+ else if (s.equals("modulo") || s.equals("mod"))
+ {
+ checkSize(arguments, 1);
+ ASTNode rightChild = arguments.get(0);
+ arguments.clear();
+ node = createModulo(child, rightChild);
+ {if (true) return node;}
+ }
+ else
+ {
+ node.addChild(child);
+ }
+ if (type != null)
+ {
+ node.setType(type);
+ // TODO - should we set the name of the ASTNode for FUNCTION, ...
+ }
+ else
+ {
+ node.setName(s);
+ }
+ for (ASTNode argument : arguments)
+ {
+ node.addChild(argument);
+ }
+ {if (true) return node;}
+ } else {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case OPEN_PAR:
jj_consume_token(OPEN_PAR);
- child = termLevel2();
- label_6:
+ node = termLevel2();
+ jj_consume_token(CLOSE_PAR);
+ {if (true) return node;}
+ break;
+ default:
+ jj_la1[14] = jj_gen;
+ if (jj_2_2(4)) {
+ t = jj_consume_token(STRING);
+ ASTNode selector = new ASTNode();
+ selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
+ selector.addChild(new ASTNode(t.image));
+ label_7:
while (true) {
+ jj_consume_token(LEFT_BRACKET);
+ node = termLevel2();
+ selector.addChild(node);
+ jj_consume_token(RIGHT_BRACKET);
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACKET:
+ ;
+ break;
+ default:
+ jj_la1[11] = jj_gen;
+ break label_7;
+ }
+ }
+ {if (true) return selector;}
+ } else if (jj_2_3(2)) {
+ jj_consume_token(LEFT_BRACES);
+ node = termLevel2();
+ ASTNode selector = new ASTNode();
+ vector = new ASTNode();
+ boolean isSelector = false;
+ selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
+ vector.setType(ASTNode.Type.VECTOR);
+ vector.addChild(node);
+ label_8:
+ while (true) {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
case SPLITTER:
;
break;
default:
- jj_la1[10] = jj_gen;
- break label_6;
+ jj_la1[12] = jj_gen;
+ break label_8;
}
jj_consume_token(SPLITTER);
- furtherChild = termLevel2();
- arguments.add(furtherChild);
+ node = termLevel2();
+ vector.addChild(node);
}
- jj_consume_token(CLOSE_PAR);
- s = t.image;
- Type type = null;
- if (ignoreCase)
- {
- s = s.toLowerCase();
- }
- if (stringToType.containsKey(s))
- {
- type = ASTNode.Type.valueOf(stringToType.getProperty(s.toLowerCase()).toUpperCase());
- }
- if (s.equals("pow") || s.equals("power"))
- {
- checkSize(arguments, 1);
- node.addChild(child);
- }
- else if (s.equals("sqr"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- node.addChild(new ASTNode(2));
- }
- else if (s.equals("sqrt"))
- {
- checkSize(arguments, 0);
- node.addChild(new ASTNode(2));
- node.addChild(child);
- }
- else if (s.equals("not"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- type = Type.LOGICAL_NOT;
- }
- else if (s.equals("ln"))
- {
- checkSize(arguments, 0);
- node.addChild(child);
- type = Type.FUNCTION_LN;
- }
- else if (s.equals("lambda"))
- {
- node.addChild(child);
- type = Type.LAMBDA;
- }
- else if (s.equals("piecewise"))
- {
- type = ASTNode.Type.FUNCTION_PIECEWISE;
- node.addChild(child);
- type = Type.FUNCTION_PIECEWISE;
- }
- else if (s.equals("modulo") || s.equals("mod"))
- {
- checkSize(arguments, 1);
- ASTNode rightChild = arguments.get(0);
- arguments.clear();
- node = createModulo(child, rightChild);
- {if (true) {
- return node;
- }}
- }
- else
- {
- node.addChild(child);
- }
- if (type != null)
- {
- node.setType(type);
- // TODO - should we set the name of the ASTNode for FUNCTION, ...
- }
- else
- {
- node.setName(s);
- }
- for (ASTNode argument : arguments)
- {
- node.addChild(argument);
- }
- {if (true) {
- return node;
- }}
- } else {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case OPEN_PAR:
- jj_consume_token(OPEN_PAR);
- node = termLevel2();
- jj_consume_token(CLOSE_PAR);
- {if (true) {
- return node;
- }}
- break;
- default:
- jj_la1[15] = jj_gen;
- if (jj_2_2(4)) {
- t = jj_consume_token(STRING);
- ASTNode selector = new ASTNode();
- selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
- selector.addChild(new ASTNode(t.image));
- label_7:
- while (true) {
- jj_consume_token(LEFT_BRACKET);
- node = termLevel2();
- selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[11] = jj_gen;
- break label_7;
- }
- }
- {if (true) {
- return selector;
- }}
- } else if (jj_2_3(2)) {
- jj_consume_token(LEFT_BRACES);
- node = termLevel2();
- ASTNode selector = new ASTNode();
- vector = new ASTNode();
- boolean isSelector = false;
- selector.setType(ASTNode.Type.FUNCTION_SELECTOR);
- vector.setType(ASTNode.Type.VECTOR);
- vector.addChild(node);
- label_8:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case SPLITTER:
- ;
- break;
- default:
- jj_la1[12] = jj_gen;
- break label_8;
- }
- jj_consume_token(SPLITTER);
- node = termLevel2();
- vector.addChild(node);
- }
- jj_consume_token(RIGHT_BRACES);
- selector.addChild(vector);
- label_9:
- while (true) {
- switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACKET:
- ;
- break;
- default:
- jj_la1[13] = jj_gen;
- break label_9;
- }
- jj_consume_token(LEFT_BRACKET);
- node = termLevel2();
- isSelector = true;
- selector.addChild(node);
- jj_consume_token(RIGHT_BRACKET);
- }
- {if (true) {
- return isSelector ? selector : vector;
- }}
- } else {
+ jj_consume_token(RIGHT_BRACES);
+ selector.addChild(vector);
+ label_9:
+ while (true) {
switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
- case LEFT_BRACES:
- jj_consume_token(LEFT_BRACES);
- vector = new ASTNode();
- vector.setType(ASTNode.Type.VECTOR);
- jj_consume_token(RIGHT_BRACES);
- {if (true) {
- return vector;
- }}
+ case LEFT_BRACKET:
+ ;
break;
- case STRING:
- t = jj_consume_token(STRING);
- s = t.image;
- if (ignoreCase)
- {
- s = s.toLowerCase();
- }
- // TODO - should we set the name of the ASTNode
- if (s.equalsIgnoreCase("true")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Type.CONSTANT_TRUE);
- }
- else if (s.equalsIgnoreCase("false")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Type.CONSTANT_FALSE);
- }
- else if (s.equals("pi"))
- {
- node = new ASTNode(Type.CONSTANT_PI);
- }
- else if (s.equals("avogadro"))
- {
- node = new ASTNode(Type.NAME_AVOGADRO);
- }
- else if (s.equals("time")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Type.NAME_TIME);
- }
- else if (s.equals("exponentiale"))
- {
- node = new ASTNode(Type.CONSTANT_E);
- }
- else if (s.equals("-infinity") || s.equals("-INF"))
- {
- node = new ASTNode(Double.NEGATIVE_INFINITY);
- }
- else if (s.equals("infinity") || s.equals("INF"))
- {
- node = new ASTNode(Double.POSITIVE_INFINITY);
- }
- else if (s.equals("NotANumber") || s.equals("NaN")) // TODO - do we want to ignore the case for those ?
- {
- node = new ASTNode(Double.NaN);
- }
- else
- {
- node = new ASTNode(s);
- }
- {if (true) {
- return node;
- }}
- break;
default:
- jj_la1[16] = jj_gen;
- jj_consume_token(-1);
- throw new ParseException();
+ jj_la1[13] = jj_gen;
+ break label_9;
}
+ jj_consume_token(LEFT_BRACKET);
+ node = termLevel2();
+ isSelector = true;
+ selector.addChild(node);
+ jj_consume_token(RIGHT_BRACKET);
}
+ {if (true) return isSelector ? selector : vector;}
+ } else {
+ switch ((jj_ntk==-1)?jj_ntk():jj_ntk) {
+ case LEFT_BRACES:
+ jj_consume_token(LEFT_BRACES);
+ vector = new ASTNode();
+ vector.setType(ASTNode.Type.VECTOR);
+ jj_consume_token(RIGHT_BRACES);
+ {if (true) return vector;}
+ break;
+ case STRING:
+ t = jj_consume_token(STRING);
+ s = t.image;
+ if (ignoreCase)
+ {
+ s = s.toLowerCase();
+ }
+ // TODO - should we set the name of the ASTNode
+ if (s.equalsIgnoreCase("true")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Type.CONSTANT_TRUE);
+ }
+ else if (s.equalsIgnoreCase("false")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Type.CONSTANT_FALSE);
+ }
+ else if (s.equals("pi"))
+ {
+ node = new ASTNode(Type.CONSTANT_PI);
+ }
+ else if (s.equals("avogadro"))
+ {
+ node = new ASTNode(Type.NAME_AVOGADRO);
+ }
+ else if (s.equals("time")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Type.NAME_TIME);
+ }
+ else if (s.equals("exponentiale"))
+ {
+ node = new ASTNode(Type.CONSTANT_E);
+ }
+ else if (s.equals("-infinity") || s.equals("-INF"))
+ {
+ node = new ASTNode(Double.NEGATIVE_INFINITY);
+ }
+ else if (s.equals("infinity") || s.equals("INF"))
+ {
+ node = new ASTNode(Double.POSITIVE_INFINITY);
+ }
+ else if (s.equals("NotANumber") || s.equals("NaN")) // TODO - do we want to ignore the case for those ?
+ {
+ node = new ASTNode(Double.NaN);
+ }
+ else
+ {
+ node = new ASTNode(s);
+ }
+ {if (true) return node;}
+ break;
+ default:
+ jj_la1[15] = jj_gen;
+ jj_consume_token(-1);
+ throw new ParseException();
+ }
}
}
}
@@ -1203,121 +1126,39 @@
finally { jj_save(2, xla); }
}
- private boolean jj_3R_19() {
- Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_23()) {
- jj_scanpos = xsp;
- if (jj_3R_24()) {
- jj_scanpos = xsp;
- if (jj_3R_25()) {
- return true;
- }
- }
- }
+ private boolean jj_3R_28() {
+ if (jj_scan_token(MODULO)) return true;
return false;
}
- private boolean jj_3R_23() {
- if (jj_scan_token(MINUS)) {
- return true;
- }
- if (jj_3R_29()) {
- return true;
- }
+ private boolean jj_3R_22() {
+ if (jj_scan_token(MINUS)) return true;
return false;
}
- private boolean jj_3R_11() {
- if (jj_scan_token(LEFT_BRACKET)) {
- return true;
- }
- if (jj_3R_12()) {
- return true;
- }
- if (jj_scan_token(RIGHT_BRACKET)) {
- return true;
- }
+ private boolean jj_3R_31() {
+ if (jj_scan_token(POWER)) return true;
return false;
}
- private boolean jj_3R_36() {
- if (jj_scan_token(LEFT_BRACES)) {
- return true;
- }
- if (jj_scan_token(RIGHT_BRACES)) {
- return true;
- }
+ private boolean jj_3R_14() {
+ if (jj_scan_token(BOOLEAN_LOGIC)) return true;
return false;
}
- private boolean jj_3_1() {
- if (jj_3R_10()) {
- return true;
- }
- if (jj_scan_token(OPEN_PAR)) {
- return true;
- }
+ private boolean jj_3_3() {
+ if (jj_scan_token(LEFT_BRACES)) return true;
+ if (jj_3R_12()) return true;
return false;
}
- private boolean jj_3_2() {
- if (jj_scan_token(STRING)) {
- return true;
- }
- Token xsp;
- if (jj_3R_11()) {
- return true;
- }
- while (true) {
- xsp = jj_scanpos;
- if (jj_3R_11()) { jj_scanpos = xsp; break; }
- }
+ private boolean jj_3R_34() {
+ if (jj_scan_token(STRING)) return true;
return false;
}
- private boolean jj_3R_28() {
- if (jj_scan_token(MODULO)) {
- return true;
- }
- return false;
- }
-
- private boolean jj_3R_22() {
- if (jj_scan_token(MINUS)) {
- return true;
- }
- return false;
- }
-
- private boolean jj_3R_35() {
- if (jj_scan_token(OPEN_PAR)) {
- return true;
- }
- if (jj_3R_12()) {
- return true;
- }
- return false;
- }
-
- private boolean jj_3R_31() {
- if (jj_scan_token(POWER)) {
- return true;
- }
- return false;
- }
-
- private boolean jj_3R_14() {
- if (jj_scan_token(BOOLEAN_LOGIC)) {
- return true;
- }
- return false;
- }
-
private boolean jj_3R_29() {
- if (jj_3R_30()) {
- return true;
- }
+ if (jj_3R_30()) return true;
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1327,9 +1168,7 @@
}
private boolean jj_3R_12() {
- if (jj_3R_13()) {
- return true;
- }
+ if (jj_3R_13()) return true;
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1342,32 +1181,24 @@
Token xsp;
xsp = jj_scanpos;
if (jj_3R_21()) {
- jj_scanpos = xsp;
- if (jj_3R_22()) {
- return true;
- }
+ jj_scanpos = xsp;
+ if (jj_3R_22()) return true;
}
return false;
}
private boolean jj_3R_21() {
- if (jj_scan_token(PLUS)) {
- return true;
- }
+ if (jj_scan_token(PLUS)) return true;
return false;
}
private boolean jj_3R_16() {
- if (jj_scan_token(COMPARISON)) {
- return true;
- }
+ if (jj_scan_token(COMPARISON)) return true;
return false;
}
private boolean jj_3R_15() {
- if (jj_3R_17()) {
- return true;
- }
+ if (jj_3R_17()) return true;
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1376,17 +1207,8 @@
return false;
}
- private boolean jj_3R_34() {
- if (jj_scan_token(EXPNUMBER)) {
- return true;
- }
- return false;
- }
-
private boolean jj_3R_13() {
- if (jj_3R_15()) {
- return true;
- }
+ if (jj_3R_15()) return true;
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1395,103 +1217,86 @@
return false;
}
+ private boolean jj_3R_11() {
+ if (jj_scan_token(LEFT_BRACKET)) return true;
+ if (jj_3R_12()) return true;
+ if (jj_scan_token(RIGHT_BRACKET)) return true;
+ return false;
+ }
+
private boolean jj_3R_33() {
- if (jj_scan_token(NUMBER)) {
- return true;
- }
+ if (jj_scan_token(LEFT_BRACES)) return true;
+ if (jj_scan_token(RIGHT_BRACES)) return true;
return false;
}
private boolean jj_3R_27() {
- if (jj_scan_token(DIVIDE)) {
- return true;
- }
+ if (jj_scan_token(DIVIDE)) return true;
return false;
}
private boolean jj_3R_25() {
- if (jj_3R_29()) {
- return true;
- }
+ if (jj_3R_29()) return true;
return false;
}
private boolean jj_3R_10() {
Token xsp;
xsp = jj_scanpos;
- if (jj_scan_token(26)) {
- jj_scanpos = xsp;
- if (jj_scan_token(27)) {
- return true;
- }
+ if (jj_scan_token(23)) {
+ jj_scanpos = xsp;
+ if (jj_scan_token(24)) return true;
}
return false;
}
- private boolean jj_3_3() {
- if (jj_scan_token(LEFT_BRACES)) {
- return true;
+ private boolean jj_3R_30() {
+ Token xsp;
+ xsp = jj_scanpos;
+ if (jj_3_1()) {
+ jj_scanpos = xsp;
+ if (jj_3R_32()) {
+ jj_scanpos = xsp;
+ if (jj_3_2()) {
+ jj_scanpos = xsp;
+ if (jj_3_3()) {
+ jj_scanpos = xsp;
+ if (jj_3R_33()) {
+ jj_scanpos = xsp;
+ if (jj_3R_34()) return true;
}
- if (jj_3R_12()) {
- return true;
}
+ }
+ }
+ }
return false;
}
- private boolean jj_3R_32() {
- if (jj_scan_token(INTEGER)) {
- return true;
- }
+ private boolean jj_3_1() {
+ if (jj_3R_10()) return true;
+ if (jj_scan_token(OPEN_PAR)) return true;
return false;
}
- private boolean jj_3R_30() {
+ private boolean jj_3_2() {
+ if (jj_scan_token(STRING)) return true;
Token xsp;
- xsp = jj_scanpos;
- if (jj_3R_32()) {
- jj_scanpos = xsp;
- if (jj_3R_33()) {
- jj_scanpos = xsp;
- if (jj_3R_34()) {
- jj_scanpos = xsp;
- if (jj_3_1()) {
- jj_scanpos = xsp;
- if (jj_3R_35()) {
- jj_scanpos = xsp;
- if (jj_3_2()) {
- jj_scanpos = xsp;
- if (jj_3_3()) {
- jj_scanpos = xsp;
- if (jj_3R_36()) {
- jj_scanpos = xsp;
- if (jj_3R_37()) {
- return true;
- }
- }
- }
- }
- }
- }
- }
- }
+ if (jj_3R_11()) return true;
+ while (true) {
+ xsp = jj_scanpos;
+ if (jj_3R_11()) { jj_scanpos = xsp; break; }
}
return false;
}
private boolean jj_3R_26() {
- if (jj_scan_token(TIMES)) {
- return true;
- }
+ if (jj_scan_token(TIMES)) return true;
return false;
}
private boolean jj_3R_24() {
- if (jj_scan_token(NOT)) {
- return true;
- }
- if (jj_3R_29()) {
- return true;
- }
+ if (jj_scan_token(NOT)) return true;
+ if (jj_3R_29()) return true;
return false;
}
@@ -1499,28 +1304,23 @@
Token xsp;
xsp = jj_scanpos;
if (jj_3R_26()) {
- jj_scanpos = xsp;
- if (jj_3R_27()) {
- jj_scanpos = xsp;
- if (jj_3R_28()) {
- return true;
- }
- }
+ jj_scanpos = xsp;
+ if (jj_3R_27()) {
+ jj_scanpos = xsp;
+ if (jj_3R_28()) return true;
}
+ }
return false;
}
- private boolean jj_3R_37() {
- if (jj_scan_token(STRING)) {
- return true;
- }
+ private boolean jj_3R_32() {
+ if (jj_scan_token(OPEN_PAR)) return true;
+ if (jj_3R_12()) return true;
return false;
}
private boolean jj_3R_17() {
- if (jj_3R_19()) {
- return true;
- }
+ if (jj_3R_19()) return true;
Token xsp;
while (true) {
xsp = jj_scanpos;
@@ -1529,6 +1329,25 @@
return false;
}
+ private boolean jj_3R_19() {
+ Token xsp;
+ xsp = jj_scanpos;
+ if (jj_3R_23()) {
+ jj_scanpos = xsp;
+ if (jj_3R_24()) {
+ jj_scanpos = xsp;
+ if (jj_3R_25()) return true;
+ }
+ }
+ return false;
+ }
+
+ private boolean jj_3R_23() {
+ if (jj_scan_token(MINUS)) return true;
+ if (jj_3R_29()) return true;
+ return false;
+ }
+
/** Generated Token Manager. */
public CobraFormulaParserTokenManager token_source;
SimpleCharStream jj_input_stream;
@@ -1540,21 +1359,21 @@
private Token jj_scanpos, jj_lastpos;
private int jj_la;
private int jj_gen;
- final private int[] jj_la1 = new int[17];
+ final private int[] jj_la1 = new int[16];
static private int[] jj_la1_0;
static {
- jj_la1_init_0();
- }
- private static void jj_la1_init_0() {
- jj_la1_0 = new int[] {0xc000000,0x40000001,0x200000,0x100000,0x500,0x500,0x3800,0x3800,0xe014468,0x200,0x80,0x40000,0x80,0x40000,0x68,0x4000,0x8010000,};
- }
+ jj_la1_init_0();
+ }
+ private static void jj_la1_init_0() {
+ jj_la1_0 = new int[] {0x1800000,0x8000001,0x40000,0x20000,0xa0,0xa0,0x700,0x700,0x1c02880,0x40,0x10,0x8000,0x10,0x8000,0x800,0x1002000,};
+ }
final private JJCalls[] jj_2_rtns = new JJCalls[3];
private boolean jj_rescan = false;
private int jj_gc = 0;
/** Constructor with InputStream. */
public CobraFormulaParser(java.io.InputStream stream) {
- this(stream, null);
+ this(stream, null);
}
/** Constructor with InputStream and supplied encoding */
public CobraFormulaParser(java.io.InputStream stream, String encoding) {
@@ -1563,33 +1382,23 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) {
- jj_la1[i] = -1;
- }
- for (int i = 0; i < jj_2_rtns.length; i++) {
- jj_2_rtns[i] = new JJCalls();
- }
+ for (int i = 0; i < 16; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
/** Reinitialise. */
- @Override
public void ReInit(java.io.InputStream stream) {
- ReInit(stream, null);
+ ReInit(stream, null);
}
/** Reinitialise. */
- @Override
public void ReInit(java.io.InputStream stream, String encoding) {
try { jj_input_stream.ReInit(stream, encoding, 1, 1); } catch(java.io.UnsupportedEncodingException e) { throw new RuntimeException(e); }
token_source.ReInit(jj_input_stream);
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) {
- jj_la1[i] = -1;
- }
- for (int i = 0; i < jj_2_rtns.length; i++) {
- jj_2_rtns[i] = new JJCalls();
- }
+ for (int i = 0; i < 16; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
/** Constructor. */
@@ -1599,28 +1408,19 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) {
- jj_la1[i] = -1;
- }
- for (int i = 0; i < jj_2_rtns.length; i++) {
- jj_2_rtns[i] = new JJCalls();
- }
+ for (int i = 0; i < 16; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
/** Reinitialise. */
- @Override
public void ReInit(java.io.Reader stream) {
jj_input_stream.ReInit(stream, 1, 1);
token_source.ReInit(jj_input_stream);
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) {
- jj_la1[i] = -1;
- }
- for (int i = 0; i < jj_2_rtns.length; i++) {
- jj_2_rtns[i] = new JJCalls();
- }
+ for (int i = 0; i < 16; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
/** Constructor with generated Token Manager. */
@@ -1629,12 +1429,8 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) {
- jj_la1[i] = -1;
- }
- for (int i = 0; i < jj_2_rtns.length; i++) {
- jj_2_rtns[i] = new JJCalls();
- }
+ for (int i = 0; i < 16; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
/** Reinitialise. */
@@ -1643,21 +1439,14 @@
token = new Token();
jj_ntk = -1;
jj_gen = 0;
- for (int i = 0; i < 17; i++) {
- jj_la1[i] = -1;
- }
- for (int i = 0; i < jj_2_rtns.length; i++) {
- jj_2_rtns[i] = new JJCalls();
- }
+ for (int i = 0; i < 16; i++) jj_la1[i] = -1;
+ for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = new JJCalls();
}
private Token jj_consume_token(int kind) throws ParseException {
Token oldToken;
- if ((oldToken = token).next != null) {
- token = token.next;
- } else {
- token = token.next = token_source.getNextToken();
- }
+ if ((oldToken = token).next != null) token = token.next;
+ else token = token.next = token_source.getNextToken();
jj_ntk = -1;
if (token.kind == kind) {
jj_gen++;
@@ -1666,9 +1455,7 @@
for (int i = 0; i < jj_2_rtns.length; i++) {
JJCalls c = jj_2_rtns[i];
while (c != null) {
- if (c.gen < jj_gen) {
- c.first = null;
- }
+ if (c.gen < jj_gen) c.first = null;
c = c.next;
}
}
@@ -1696,51 +1483,38 @@
if (jj_rescan) {
int i = 0; Token tok = token;
while (tok != null && tok != jj_scanpos) { i++; tok = tok.next; }
- if (tok != null) {
- jj_add_error_token(kind, i);
- }
+ if (tok != null) jj_add_error_token(kind, i);
}
- if (jj_scanpos.kind != kind) {
- return true;
- }
- if (jj_la == 0 && jj_scanpos == jj_lastpos) {
- throw jj_ls;
- }
+ if (jj_scanpos.kind != kind) return true;
+ if (jj_la == 0 && jj_scanpos == jj_lastpos) throw jj_ls;
return false;
}
- /** Get the next Token. */
+/** Get the next Token. */
final public Token getNextToken() {
- if (token.next != null) {
- token = token.next;
- } else {
- token = token.next = token_source.getNextToken();
- }
+ if (token.next != null) token = token.next;
+ else token = token.next = token_source.getNextToken();
jj_ntk = -1;
jj_gen++;
return token;
}
- /** Get the specific Token. */
+/** Get the specific Token. */
final public Token getToken(int index) {
Token t = token;
for (int i = 0; i < index; i++) {
- if (t.next != null) {
- t = t.next;
- } else {
- t = t.next = token_source.getNextToken();
- }
+ if (t.next != null) t = t.next;
+ else t = t.next = token_source.getNextToken();
}
return t;
}
private int jj_ntk() {
- if ((jj_nt=token.next) == null) {
+ if ((jj_nt=token.next) == null)
return (jj_ntk = (token.next=token_source.getNextToken()).kind);
- } else {
+ else
return (jj_ntk = jj_nt.kind);
- }
}
private java.util.List<int[]> jj_expentries = new java.util.ArrayList<int[]>();
@@ -1750,9 +1524,7 @@
private int jj_endpos;
private void jj_add_error_token(int kind, int pos) {
- if (pos >= 100) {
- return;
- }
+ if (pos >= 100) return;
if (pos == jj_endpos + 1) {
jj_lasttokens[jj_endpos++] = kind;
} else if (jj_endpos != 0) {
@@ -1772,21 +1544,19 @@
break jj_entries_loop;
}
}
- if (pos != 0) {
- jj_lasttokens[(jj_endpos = pos) - 1] = kind;
- }
+ if (pos != 0) jj_lasttokens[(jj_endpos = pos) - 1] = kind;
}
}
/** Generate ParseException. */
public ParseException generateParseException() {
jj_expentries.clear();
- boolean[] la1tokens = new boolean[31];
+ boolean[] la1tokens = new boolean[28];
if (jj_kind >= 0) {
la1tokens[jj_kind] = true;
jj_kind = -1;
}
- for (int i = 0; i < 17; i++) {
+ for (int i = 0; i < 16; i++) {
if (jj_la1[i] == jj_gen) {
for (int j = 0; j < 32; j++) {
if ((jj_la1_0[i] & (1<<j)) != 0) {
@@ -1795,7 +1565,7 @@
}
}
}
- for (int i = 0; i < 31; i++) {
+ for (int i = 0; i < 28; i++) {
if (la1tokens[i]) {
jj_expentry = new int[1];
jj_expentry[0] = i;
@@ -1823,19 +1593,19 @@
private void jj_rescan_token() {
jj_rescan = true;
for (int i = 0; i < 3; i++) {
- try {
- JJCalls p = jj_2_rtns[i];
- do {
- if (p.gen > jj_gen) {
- jj_la = p.arg; jj_lastpos = jj_scanpos = p.first;
- switch (i) {
+ try {
+ JJCalls p = jj_2_rtns[i];
+ do {
+ if (p.gen > jj_gen) {
+ jj_la = p.arg; jj_lastpos = jj_scanpos = p.first;
+ switch (i) {
case 0: jj_3_1(); break;
case 1: jj_3_2(); break;
case 2: jj_3_3(); break;
- }
}
- p = p.next;
- } while (p != null);
+ }
+ p = p.next;
+ } while (p != null);
} catch(LookaheadSuccess ls) { }
}
jj_rescan = false;
Modified: trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.jj
===================================================================
--- trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.jj 2015-10-20 15:57:25 UTC (rev 2388)
+++ trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParser.jj 2015-10-28 10:35:08 UTC (rev 2389)
@@ -576,33 +576,33 @@
+//TOKEN :
+//{
+// < INTEGER : (< DIGIT >)+ >
+//}
TOKEN :
{
- < INTEGER : (< DIGIT >)+ >
-}
-TOKEN :
-{
< DIGIT : [ "0"-"9" ] >
}
-TOKEN :
-{
- < NUMBER :
- (< DIGIT >)+
- (
- "." (< DIGIT >)+
- )?
- | "." (< DIGIT >)+ >
-}
+//TOKEN :
+//{
+// < NUMBER :
+// (< DIGIT >)+
+// (
+// "." (< DIGIT >)+
+// )?
+// | "." (< DIGIT >)+ >
+//}
+//
+//TOKEN :
+//{
+// < EXPNUMBER : ([ "-" ])? < NUMBER > [ "E", "e" ] ([ "+", "-" ])? < INTEGER > >
+//}
TOKEN :
{
- < EXPNUMBER : ([ "-" ])? < NUMBER > [ "E", "e" ] ([ "+", "-" ])? < INTEGER > >
-}
-
-TOKEN :
-{
< SPLITTER : [ "," ] >
}
@@ -698,9 +698,10 @@
< AND :
"And"
| "AND"
+ | "and"
| "&&" >
}
-/* "and"
+/*
| "or"
"not"
| "xor"
@@ -712,6 +713,7 @@
< OR :
"OR"
| "Or"
+ | "or"
| "||" >
}
@@ -742,7 +744,7 @@
TOKEN :
{
- < IDCHAR : < LETTER > | < DIGIT > | "_" >
+ < IDCHAR : < LETTER > | < DIGIT > | "_" | "." >
}
TOKEN :
@@ -1034,35 +1036,8 @@
ArrayList < ASTNode > arguments = new ArrayList < ASTNode > ();
}
{
- t = < INTEGER >
- {
- i = Integer.parseInt(t.image); // Could use StringTools.parseXXX methods here but not doing so allow to support different locale ??
- node.setValue(i);
- return node;
- }
-| t = < NUMBER >
- {
- d = Double.parseDouble(t.image);
- node.setValue(d);
- return node;
- }
-| t = < EXPNUMBER >
- {
- s = t.image;
- vals = s.toLowerCase().split("e");
- if (vals [ 1 ].startsWith("+"))
- {
- i = Integer.parseInt(vals [ 1 ].substring(1));
- }
- else
- {
- i = Integer.parseInt(vals [ 1 ]);
- }
- node.setValue(Double.parseDouble(vals [ 0 ]), i);
- return node;
- }
// Function call: f(...)
-| LOOKAHEAD(2)
+ LOOKAHEAD(2)
t = string() < OPEN_PAR > child = termLevel2()
(
< SPLITTER > furtherChild = termLevel2()
Modified: trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParserConstants.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParserConstants.java 2015-10-20 15:57:25 UTC (rev 2388)
+++ trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParserConstants.java 2015-10-28 10:35:08 UTC (rev 2389)
@@ -32,61 +32,55 @@
/** End of File. */
int EOF = 0;
/** RegularExpression Id. */
- int INTEGER = 3;
+ int DIGIT = 3;
/** RegularExpression Id. */
- int DIGIT = 4;
+ int SPLITTER = 4;
/** RegularExpression Id. */
- int NUMBER = 5;
+ int PLUS = 5;
/** RegularExpression Id. */
- int EXPNUMBER = 6;
+ int POWER = 6;
/** RegularExpression Id. */
- int SPLITTER = 7;
+ int MINUS = 7;
/** RegularExpression Id. */
- int PLUS = 8;
+ int TIMES = 8;
/** RegularExpression Id. */
- int POWER = 9;
+ int DIVIDE = 9;
/** RegularExpression Id. */
- int MINUS = 10;
+ int MODULO = 10;
/** RegularExpression Id. */
- int TIMES = 11;
+ int OPEN_PAR = 11;
/** RegularExpression Id. */
- int DIVIDE = 12;
+ int CLOSE_PAR = 12;
/** RegularExpression Id. */
- int MODULO = 13;
+ int LEFT_BRACES = 13;
/** RegularExpression Id. */
- int OPEN_PAR = 14;
+ int RIGHT_BRACES = 14;
/** RegularExpression Id. */
- int CLOSE_PAR = 15;
+ int LEFT_BRACKET = 15;
/** RegularExpression Id. */
- int LEFT_BRACES = 16;
+ int RIGHT_BRACKET = 16;
/** RegularExpression Id. */
- int RIGHT_BRACES = 17;
+ int COMPARISON = 17;
/** RegularExpression Id. */
- int LEFT_BRACKET = 18;
+ int BOOLEAN_LOGIC = 18;
/** RegularExpression Id. */
- int RIGHT_BRACKET = 19;
+ int AND = 19;
/** RegularExpression Id. */
- int COMPARISON = 20;
+ int OR = 20;
/** RegularExpression Id. */
- int BOOLEAN_LOGIC = 21;
+ int XOR = 21;
/** RegularExpression Id. */
- int AND = 22;
+ int NOT = 22;
/** RegularExpression Id. */
- int OR = 23;
+ int LOG = 23;
/** RegularExpression Id. */
- int XOR = 24;
+ int STRING = 24;
/** RegularExpression Id. */
- int NOT = 25;
+ int IDCHAR = 25;
/** RegularExpression Id. */
- int LOG = 26;
+ int LETTER = 26;
/** RegularExpression Id. */
- int STRING = 27;
- /** RegularExpression Id. */
- int IDCHAR = 28;
- /** RegularExpression Id. */
- int LETTER = 29;
- /** RegularExpression Id. */
- int EOL = 30;
+ int EOL = 27;
/** Lexical state. */
int DEFAULT = 0;
@@ -96,10 +90,7 @@
"<EOF>",
"\" \"",
"\"\\t\"",
- "<INTEGER>",
"<DIGIT>",
- "<NUMBER>",
- "<EXPNUMBER>",
"<SPLITTER>",
"\"+\"",
"\"^\"",
Modified: trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParserTokenManager.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParserTokenManager.java 2015-10-20 15:57:25 UTC (rev 2388)
+++ trunk/core/src/org/sbml/jsbml/text/parser/CobraFormulaParserTokenManager.java 2015-10-28 10:35:08 UTC (rev 2389)
@@ -43,20 +43,18 @@
switch (pos)
{
case 0:
- if ((active0 & 0x4000000L) != 0L)
+ if ((active0 & 0x800000L) != 0L)
{
- jjmatchedKind = 27;
- return 38;
+ jjmatchedKind = 24;
+ return 31;
}
- if ((active0 & 0x400L) != 0L)
- return 7;
return -1;
case 1:
- if ((active0 & 0x4000000L) != 0L)
+ if ((active0 & 0x800000L) != 0L)
{
- jjmatchedKind = 27;
+ jjmatchedKind = 24;
jjmatchedPos = 1;
- return 61;
+ return 50;
}
return -1;
default :
@@ -78,31 +76,31 @@
switch(curChar)
{
case 37:
- return jjStopAtPos(0, 13);
+ return jjStopAtPos(0, 10);
case 40:
- return jjStopAtPos(0, 14);
+ return jjStopAtPos(0, 11);
case 41:
- return jjStopAtPos(0, 15);
+ return jjStopAtPos(0, 12);
case 42:
- return jjStopAtPos(0, 11);
+ return jjStopAtPos(0, 8);
case 43:
- retu...
[truncated message content] |
![http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">](http://sbml.org/images/7/79/xJsbml-logo-54px.png.pagespeed.ic.am7oEUtfpP.png">){kind=link}