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[Jsbml-svn] SF.net SVN: jsbml:[2332] trunk
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From: <and...@us...> - 2015-06-14 23:35:51
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Revision: 2332
http://sourceforge.net/p/jsbml/code/2332
Author: andreas-draeger
Date: 2015-06-14 23:35:49 +0000 (Sun, 14 Jun 2015)
Log Message:
-----------
* Updated SBO
* Enums inside of CVTerm are now easier to extend because each entry contains now information about itself that had been stored in complex switch statements before.
* TidySBMLWriter is now able to interpret the user's choice of the indentation count and character (tabs vs. spaces) and its settings were alphabetically ordered.
Modified Paths:
--------------
trunk/core/resources/org/sbml/jsbml/resources/cfg/SBO_OBO.obo
trunk/core/src/org/sbml/jsbml/AbstractSBase.java
trunk/core/src/org/sbml/jsbml/CVTerm.java
trunk/core/src/org/sbml/jsbml/SBase.java
trunk/core/src/org/sbml/jsbml/util/compilers/FormulaCompiler.java
trunk/modules/tidy/src/org/sbml/jsbml/TidySBMLWriter.java
Modified: trunk/core/resources/org/sbml/jsbml/resources/cfg/SBO_OBO.obo
===================================================================
--- trunk/core/resources/org/sbml/jsbml/resources/cfg/SBO_OBO.obo 2015-06-14 16:46:08 UTC (rev 2331)
+++ trunk/core/resources/org/sbml/jsbml/resources/cfg/SBO_OBO.obo 2015-06-14 23:35:49 UTC (rev 2332)
@@ -1,5 +1,5 @@
format-version: 1.2
-date: 14:05:2015 07:00
+date: 14:06:2015 07:00
data-version: 13:05:2015 13:49
saved-by: SBO community
auto-generated-by: SBO Browser (http://www.ebi.ac.uk/sbo/)
@@ -1066,19 +1066,6 @@
is_a: SBO:0000041 ! mass action rate law for irreversible reactions
[Term]
-id: SBO:0000231
-name: occurring entity representation
-def: "Representation of an entity that manifests, unfolds or develops through time, such as a discrete event, or a mutual or reciprocal action or influence that happens between participating physical entities, and/or other occurring entities. " [src_code:NR]
-comment: modified as part of ontology 'refactoring' process \[SF bug #3172586\]\nName changed to \"interaction\" on November 18 2008 by Nicolas Le Novere.\nDefinition changed to mention interaction with other interactions, in order to cover \"process\" and \"relationship\".
-is_a: SBO:0000000 ! systems biology representation
-
-[Term]
-id: SBO:0000232
-name: obsolete event
-def: "A phenomenon that takes place and which may be observable, or may be determined to have occurred as the result of an action or process." [src_code:NR]
-is_obsolete: true
-
-[Term]
id: SBO:0000167
name: biochemical or transport reaction
def: "An event involving one or more physical entities that modifies the structure, location or free energy of at least one of the participants." [src_code:NR]
@@ -1517,6 +1504,19 @@
is_a: SBO:0000227 ! mass density of an entity
[Term]
+id: SBO:0000231
+name: occurring entity representation
+def: "Representation of an entity that manifests, unfolds or develops through time, such as a discrete event, or a mutual or reciprocal action or influence that happens between participating physical entities, and/or other occurring entities. " [src_code:NR]
+comment: modified as part of ontology 'refactoring' process \[SF bug #3172586\]\nName changed to \"interaction\" on November 18 2008 by Nicolas Le Novere.\nDefinition changed to mention interaction with other interactions, in order to cover \"process\" and \"relationship\".
+is_a: SBO:0000000 ! systems biology representation
+
+[Term]
+id: SBO:0000232
+name: obsolete event
+def: "A phenomenon that takes place and which may be observable, or may be determined to have occurred as the result of an action or process." [src_code:NR]
+is_obsolete: true
+
+[Term]
id: SBO:0000233
name: hydroxylation
def: "Addition of an hydroxyl group (-OH) to a chemical entity. " [src_code:NR]
Modified: trunk/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-06-14 16:46:08 UTC (rev 2331)
+++ trunk/core/src/org/sbml/jsbml/AbstractSBase.java 2015-06-14 23:35:49 UTC (rev 2332)
@@ -1905,7 +1905,7 @@
* @see org.sbml.jsbml.SBase#setMetaId(java.lang.String)
*/
@Override
- public void setMetaId(String metaId) {
+ public void setMetaId(String metaId) throws IllegalArgumentException {
if (metaId != null) {
if (isSetMetaId() && getMetaId().equals(metaId)) {
/* Do nothing if the identical metaId has already been assigned to this
Modified: trunk/core/src/org/sbml/jsbml/CVTerm.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/CVTerm.java 2015-06-14 16:46:08 UTC (rev 2331)
+++ trunk/core/src/org/sbml/jsbml/CVTerm.java 2015-06-14 23:35:49 UTC (rev 2332)
@@ -209,36 +209,7 @@
* @return
*/
public static Qualifier getBiologicalQualifierFor(String elementNameEquivalent) {
-
- if (elementNameEquivalent.equals(BQB_ENCODES.nameEquivalent)) {
- return BQB_ENCODES;
- } else if (elementNameEquivalent.equals(BQB_HAS_PART.nameEquivalent)) {
- return BQB_HAS_PART;
- } else if (elementNameEquivalent.equals(BQB_HAS_VERSION.nameEquivalent)) {
- return BQB_HAS_VERSION;
- } else if (elementNameEquivalent.equals(BQB_HAS_PROPERTY.nameEquivalent)) {
- return BQB_HAS_PROPERTY;
- } else if (elementNameEquivalent.equals(BQB_HAS_TAXON.nameEquivalent)) {
- return BQB_HAS_TAXON;
- } else if (elementNameEquivalent.equals(BQB_IS_PROPERTY_OF.nameEquivalent)) {
- return BQB_IS_PROPERTY_OF;
- } else if (elementNameEquivalent.equals(BQB_IS.nameEquivalent)) {
- return BQB_IS;
- } else if (elementNameEquivalent.equals(BQB_IS_DESCRIBED_BY.nameEquivalent)) {
- return BQB_IS_DESCRIBED_BY;
- } else if (elementNameEquivalent.equals(BQB_IS_ENCODED_BY.nameEquivalent)) {
- return BQB_IS_ENCODED_BY;
- } else if (elementNameEquivalent.equals(BQB_IS_HOMOLOG_TO.nameEquivalent)) {
- return BQB_IS_HOMOLOG_TO;
- } else if (elementNameEquivalent.equals(BQB_IS_PART_OF.nameEquivalent)) {
- return BQB_IS_PART_OF;
- } else if (elementNameEquivalent.equals(BQB_IS_VERSION_OF.nameEquivalent)) {
- return BQB_IS_VERSION_OF;
- } else if (elementNameEquivalent.equals(BQB_OCCURS_IN.nameEquivalent)) {
- return BQB_OCCURS_IN;
- }
-
- return BQB_UNKNOWN;
+ return getQualifierFor(elementNameEquivalent, "BQB_", BQB_UNKNOWN);
}
/**
@@ -247,20 +218,23 @@
* @return
*/
public static Qualifier getModelQualifierFor(String elementNameEquivalent) {
+ return getQualifierFor(elementNameEquivalent, "BQM_", BQM_UNKNOWN);
+ }
- if (elementNameEquivalent.equals(BQM_IS.nameEquivalent)) {
- return BQM_IS;
- } else if (elementNameEquivalent.equals(BQM_IS_DESCRIBED_BY.nameEquivalent)) {
- return BQM_IS_DESCRIBED_BY;
- } else if (elementNameEquivalent.equals(BQM_IS_DERIVED_FROM.nameEquivalent)) {
- return BQM_IS_DERIVED_FROM;
- } else if (elementNameEquivalent.equals(BQM_IS_INSTANCE_OF.nameEquivalent)) {
- return BQM_IS_INSTANCE_OF;
- } else if (elementNameEquivalent.equals(BQM_HAS_INSTANCE.nameEquivalent)) {
- return BQM_HAS_INSTANCE;
+ /**
+ * @param elementNameEquivalent
+ * @param prefix
+ * @param unknownQualifier
+ * @return
+ */
+ private static Qualifier getQualifierFor(String elementNameEquivalent,
+ String prefix, Qualifier unknownQualifier) {
+ for (Qualifier q : values()) {
+ if (q.name().startsWith(prefix) && q.getElementNameEquivalent().equals(elementNameEquivalent)) {
+ return q;
+ }
}
-
- return BQM_UNKNOWN;
+ return unknownQualifier;
}
@@ -305,7 +279,9 @@
public boolean isModelQualifier() {
return toString().startsWith("BQM_");
}
+
}
+
/**
* This enum list all the possible MIRIAM qualifiers type.
*
Modified: trunk/core/src/org/sbml/jsbml/SBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SBase.java 2015-06-14 16:46:08 UTC (rev 2331)
+++ trunk/core/src/org/sbml/jsbml/SBase.java 2015-06-14 23:35:49 UTC (rev 2332)
@@ -940,11 +940,14 @@
*
* @param metaid
* the meatId to be set.
+ * @throws IllegalArgumentException
+ * if the given metaid does not follow the pattern for valid metaids
+ * ore if it is already used in the {@link SBMLDocument}
* @throws PropertyNotAvailableException
* in SBML level 1, as this attribute was introduced only from SBML
* level 2.
*/
- public void setMetaId(String metaid);
+ public void setMetaId(String metaid) throws IllegalArgumentException;
/**
* Sets the notes with 'notes'.
Modified: trunk/core/src/org/sbml/jsbml/util/compilers/FormulaCompiler.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/util/compilers/FormulaCompiler.java 2015-06-14 16:46:08 UTC (rev 2331)
+++ trunk/core/src/org/sbml/jsbml/util/compilers/FormulaCompiler.java 2015-06-14 23:35:49 UTC (rev 2332)
@@ -67,8 +67,11 @@
public class FormulaCompiler extends StringTools implements ASTNodeCompiler {
+ /**
+ *
+ */
public static final String FORMULA_ARGUMENT_SEPARATOR = "";
-
+
/**
* Basic method which links several elements with a mathematical operator.
* All empty StringBuffer object are excluded.
@@ -480,7 +483,7 @@
/**
* Creates brackets if needed.
*
- * @param nodes
+ * @param node
* @return
* @throws SBMLException
*/
@@ -492,7 +495,7 @@
|| node.isFunction()) {
return term;
}
-
+
return term = brackets(term).toString();
}
Modified: trunk/modules/tidy/src/org/sbml/jsbml/TidySBMLWriter.java
===================================================================
--- trunk/modules/tidy/src/org/sbml/jsbml/TidySBMLWriter.java 2015-06-14 16:46:08 UTC (rev 2331)
+++ trunk/modules/tidy/src/org/sbml/jsbml/TidySBMLWriter.java 2015-06-14 23:35:49 UTC (rev 2332)
@@ -59,25 +59,24 @@
/**
*
*/
- private static Tidy tidy = new Tidy(); // obtain a new Tidy instance
+ private static final transient Tidy tidy = new Tidy(); // obtain a new Tidy instance
static {
-
// set desired configuration options using tidy setters
- tidy.setXmlTags(true);
+ tidy.setDropEmptyParas(false);
+ tidy.setHideComments(false);
tidy.setIndentContent(true);
- tidy.setXmlOut(true);
tidy.setInputEncoding("UTF-8");
tidy.setOutputEncoding("UTF-8");
-
- tidy.setDropEmptyParas(false);
-
+ tidy.setQuiet(true);
tidy.setSmartIndent(true);
+ tidy.setTrimEmptyElements(true);
+ tidy.setWraplen(200);
+ tidy.setWrapAttVals(false);
tidy.setWrapScriptlets(true);
- tidy.setWraplen(200);
- tidy.setSpaces(2);
+ tidy.setXmlOut(true);
tidy.setXmlSpace(true);
- tidy.setQuiet(true);
+ tidy.setXmlTags(true);
}
/**
@@ -111,10 +110,23 @@
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument);
+ setIndentation(indentChar, indentCount);
tidy.parse(new StringReader(sbmlDocString), new FileWriter(file)); // run tidy, providing an input and output stream
}
/**
+ * @param indentChar
+ * @param indentCount
+ */
+ public static void setIndentation(char indentChar, short indentCount) {
+ if (indentChar == ' ') {
+ tidy.setSpaces(indentCount);
+ } else {
+ tidy.setTabsize(indentCount);
+ }
+ }
+
+ /**
* Writes the given SBML document to a {@link File}.
* <p>
*
@@ -146,6 +158,7 @@
SBMLWriter sbmlWriter = new SBMLWriter();
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument, programName, programVersion);
+ setIndentation(' ', (short) 2);
tidy.parse(new StringReader(sbmlDocString), new FileWriter(file)); // run tidy, providing an input and output stream
}
@@ -189,6 +202,7 @@
sbmlWriter.setIndentationCount(indentCount);
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument, programName, programVersion);
+ setIndentation(indentChar, indentCount);
tidy.parse(new StringReader(sbmlDocString), new FileWriter(file)); // run tidy, providing an input and output stream
}
@@ -213,6 +227,7 @@
sbmlWriter.setIndentationCount(indentCount);
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument);
+ setIndentation(indentChar, indentCount);
tidy.parse(new StringReader(sbmlDocString), stream); // run tidy, providing an input and output stream
}
@@ -244,6 +259,7 @@
SBMLWriter sbmlWriter = new SBMLWriter();
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument, programName, programVersion);
+ setIndentation(' ', (short) 2);
tidy.parse(new StringReader(sbmlDocString), stream); // run tidy, providing an input and output stream
}
@@ -283,6 +299,7 @@
sbmlWriter.setIndentationCount(indentCount);
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument, programName, programVersion);
+ setIndentation(indentChar, indentCount);
tidy.parse(new StringReader(sbmlDocString), stream); // run tidy, providing an input and output stream
}
@@ -318,6 +335,7 @@
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument);
try {
+ setIndentation(indentChar, indentCount);
tidy.parse(new StringReader(sbmlDocString), new FileWriter(fileName)); // run tidy, providing an input and output stream
} catch (IOException e) {
throw new SBMLException(e);
@@ -357,6 +375,7 @@
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument, programName, programVersion);
try {
+ setIndentation(' ', (short) 2);
tidy.parse(new StringReader(sbmlDocString), new FileWriter(fileName)); // run tidy, providing an input and output stream
} catch (IOException e) {
throw new SBMLException(e);
@@ -405,6 +424,7 @@
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument, programName, programVersion);
try {
+ setIndentation(indentChar, indentCount);
tidy.parse(new StringReader(sbmlDocString), new FileWriter(fileName)); // run tidy, providing an input and output stream
} catch (IOException e) {
throw new SBMLException(e);
@@ -518,6 +538,7 @@
{
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument);
+ setIndentation(' ', (short) 2);
tidy.parse(new StringReader(sbmlDocString), new FileWriter(file)); // run tidy, providing an input and output stream
}
@@ -546,6 +567,7 @@
{
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument, getProgramName(), getProgramVersion());
+ setIndentation(' ', (short) 2);
tidy.parse(new StringReader(sbmlDocString), stream); // run tidy, providing an input and output stream
}
@@ -579,6 +601,7 @@
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument, getProgramName(), getProgramVersion());
try {
+ setIndentation(' ', (short) 2);
tidy.parse(new StringReader(sbmlDocString), new FileWriter(fileName)); // run tidy, providing an input and output stream
} catch (IOException e) {
throw new SBMLException(e);
@@ -613,6 +636,7 @@
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument, getProgramName(), getProgramVersion());
try {
+ setIndentation(' ', (short) 2);
tidy.parse(new StringReader(sbmlDocString), new FileWriter(file)); // run tidy, providing an input and output stream
} catch (IOException e) {
throw new SBMLException(e);
@@ -672,6 +696,7 @@
String sbmlDocString = sbmlWriter.writeSBMLToString(sbmlDocument, getProgramName(), getProgramVersion());
StringWriter stringWriter = new StringWriter();
+ setIndentation(' ', (short) 2);
tidy.parse(new StringReader(sbmlDocString), stringWriter); // run tidy, providing an input and output stream
return stringWriter.toString();
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