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[Jsbml-svn] SF.net SVN: jsbml:[2499] trunk
|
From: <nik...@us...> - 2016-05-04 12:44:44
|
Revision: 2499
http://sourceforge.net/p/jsbml/code/2499
Author: niko-rodrigue
Date: 2016-05-04 12:44:42 +0000 (Wed, 04 May 2016)
Log Message:
-----------
changes to be able to support biojava-ontology >= 4 and log4j2. Upgraded the source and target jdk version to 1.7 for now and made it easy to update by having to change only one properties file and that will change it on all ant build files.
Modified Paths:
--------------
trunk/build.xml
trunk/core/build.xml
trunk/core/pom.xml
trunk/core/src/org/sbml/jsbml/SBO.java
trunk/core/src/org/sbml/jsbml/ontology/Term.java
trunk/core/src/org/sbml/jsbml/ontology/Triple.java
trunk/extensions/arrays/build.xml
trunk/extensions/comp/build.xml
trunk/extensions/distrib/build.xml
trunk/extensions/dyn/build.xml
trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/CBO.java
trunk/extensions/fbc/build.xml
trunk/extensions/groups/build.xml
trunk/extensions/layout/build.xml
trunk/extensions/multi/build.xml
trunk/extensions/qual/build.xml
trunk/extensions/render/build.xml
trunk/extensions/req/build.xml
trunk/extensions/spatial/build.xml
trunk/jsbml-build.properties
trunk/modules/tidy/build.xml
Added Paths:
-----------
trunk/core/lib/biojava-ontology-4.0.0.jar
trunk/core/lib/log4j-1.2-api-2.3.jar
trunk/core/lib/log4j-api-2.3.jar
trunk/core/lib/log4j-core-2.3.jar
trunk/core/lib/log4j-slf4j-impl-2.3.jar
trunk/core/lib/slf4j-api-1.7.21.jar
trunk/core/resources/log4j2.xml
Removed Paths:
-------------
trunk/core/lib/biojava3-ontology-3.1.0.jar
trunk/core/lib/log4j-1.2.17.jar
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -44,7 +44,9 @@
</classpath>
</taskdef>
- <property name="Name" value="JSBML" />
+ <property file="${basedir}/jsbml-build.properties"/>
+
+ <property name="Name" value="${jsbml.Name}" />
<property name="name" value="jsbml" />
<property name="version" value="1.2-SNAPSHOT" />
<property name="api.version" value="1.2" />
@@ -218,8 +220,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
</target>
Modified: trunk/core/build.xml
===================================================================
--- trunk/core/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/core/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -41,6 +41,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../jsbml-build.properties"/>
+
<property name="Name" value="JSBML"/>
<property name="name" value="jsbml"/>
<property name="version" value="1.2-SNAPSHOT"/>
@@ -253,8 +255,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
<!-- <compilerarg value="-Xlint:deprecation"/>
<compilerarg value="-Xlint:unchecked"/> -->
Added: trunk/core/lib/biojava-ontology-4.0.0.jar
===================================================================
(Binary files differ)
Index: trunk/core/lib/biojava-ontology-4.0.0.jar
===================================================================
--- trunk/core/lib/biojava-ontology-4.0.0.jar 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/core/lib/biojava-ontology-4.0.0.jar 2016-05-04 12:44:42 UTC (rev 2499)
Property changes on: trunk/core/lib/biojava-ontology-4.0.0.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Deleted: trunk/core/lib/biojava3-ontology-3.1.0.jar
===================================================================
(Binary files differ)
Added: trunk/core/lib/log4j-1.2-api-2.3.jar
===================================================================
(Binary files differ)
Index: trunk/core/lib/log4j-1.2-api-2.3.jar
===================================================================
--- trunk/core/lib/log4j-1.2-api-2.3.jar 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/core/lib/log4j-1.2-api-2.3.jar 2016-05-04 12:44:42 UTC (rev 2499)
Property changes on: trunk/core/lib/log4j-1.2-api-2.3.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Deleted: trunk/core/lib/log4j-1.2.17.jar
===================================================================
(Binary files differ)
Added: trunk/core/lib/log4j-api-2.3.jar
===================================================================
(Binary files differ)
Index: trunk/core/lib/log4j-api-2.3.jar
===================================================================
--- trunk/core/lib/log4j-api-2.3.jar 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/core/lib/log4j-api-2.3.jar 2016-05-04 12:44:42 UTC (rev 2499)
Property changes on: trunk/core/lib/log4j-api-2.3.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/core/lib/log4j-core-2.3.jar
===================================================================
(Binary files differ)
Index: trunk/core/lib/log4j-core-2.3.jar
===================================================================
--- trunk/core/lib/log4j-core-2.3.jar 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/core/lib/log4j-core-2.3.jar 2016-05-04 12:44:42 UTC (rev 2499)
Property changes on: trunk/core/lib/log4j-core-2.3.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/core/lib/log4j-slf4j-impl-2.3.jar
===================================================================
(Binary files differ)
Index: trunk/core/lib/log4j-slf4j-impl-2.3.jar
===================================================================
--- trunk/core/lib/log4j-slf4j-impl-2.3.jar 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/core/lib/log4j-slf4j-impl-2.3.jar 2016-05-04 12:44:42 UTC (rev 2499)
Property changes on: trunk/core/lib/log4j-slf4j-impl-2.3.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Added: trunk/core/lib/slf4j-api-1.7.21.jar
===================================================================
(Binary files differ)
Index: trunk/core/lib/slf4j-api-1.7.21.jar
===================================================================
--- trunk/core/lib/slf4j-api-1.7.21.jar 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/core/lib/slf4j-api-1.7.21.jar 2016-05-04 12:44:42 UTC (rev 2499)
Property changes on: trunk/core/lib/slf4j-api-1.7.21.jar
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Modified: trunk/core/pom.xml
===================================================================
--- trunk/core/pom.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/core/pom.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -107,11 +107,16 @@
<dependencies>
<dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- <version>1.2.8</version>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-core</artifactId>
+ <version>2.3</version>
</dependency>
<dependency>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-1.2-api</artifactId>
+ <version>2.3</version>
+ </dependency>
+ <dependency>
<groupId>com.fasterxml.woodstox</groupId>
<artifactId>woodstox-core</artifactId>
<version>5.0.1</version>
@@ -123,17 +128,10 @@
</dependency>
<dependency>
<groupId>org.biojava</groupId>
- <artifactId>biojava3-ontology</artifactId>
- <version>3.1.0</version>
+ <artifactId>biojava-ontology</artifactId>
+ <version>4.0.0</version>
</dependency>
- <!--
<dependency>
- <groupId>org.biojava</groupId>
- <artifactId>biojava3-core</artifactId>
- <version>3.0.1</version>
- </dependency>
- -->
- <dependency>
<groupId>com.thoughtworks.xstream</groupId>
<artifactId>xstream</artifactId>
<version>1.3.1</version>
@@ -153,19 +151,7 @@
<scope>test</scope>
</dependency>
-<!-- Should be included by staxmate and woodstox
<dependency>
- <groupId>javax.xml.stream</groupId>
- <artifactId>stax-api</artifactId>
- <version>1.0.2</version>
- </dependency>
- <dependency>
- <groupId>org.codehaus.woodstox</groupId>
- <artifactId>stax2-api</artifactId>
- <version>3.1.4</version>
- </dependency>
- -->
- <dependency>
<groupId>org.mangosdk.spi</groupId>
<artifactId>spi</artifactId>
<version>0.2.4</version>
Added: trunk/core/resources/log4j2.xml
===================================================================
--- trunk/core/resources/log4j2.xml (rev 0)
+++ trunk/core/resources/log4j2.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -0,0 +1,59 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Configuration status="WARN" name="XMLConfigTest" packages="org.sbml.*">
+ <Properties>
+ <Property name="filename">jsbml.log</Property>
+ </Properties>
+ <ThresholdFilter level="trace"/>
+
+ <Appenders>
+ <Console name="console">
+ <PatternLayout pattern="%5p (%F:%L) - %m%n"/>
+ </Console>
+ <File name="file" fileName="${filename}">
+ <PatternLayout>
+ <pattern>%d %p %C{1.} [%t] %m%n</pattern>
+ </PatternLayout>
+ </File>
+ </Appenders>
+
+ <Loggers>
+ <Logger name="org.sbml" level="info" additivity="false">
+ <AppenderRef ref="console"/>
+ <AppenderRef ref="file"/>
+ </Logger>
+<!--
+ <Logger name="org.sbml.jsbml.xml.stax.SBMLWriter" level="info" additivity="false">
+ <AppenderRef ref="console"/>
+ <AppenderRef ref="file"/>
+ </Logger>
+-->
+<!--
+# org.sbml.jsbml.test.SimpleSBaseChangeListener - DEBUG : it will display all add, remove or change event (lot of output when reading an SBML file)
+# org.sbml.jsbml.xml.parsers.SBMLCoreParser - ERROR to DEBUG : anything related to problems when parsing the SBML core elements.
+# org.sbml.jsbml.xml.parsers.StringParser - ERROR to DEBUG : (lot of output) display all the event when reading XHTML
+# org.sbml.jsbml.xml.parsers.AnnotationParser - DEBUG : output when reading non RDF annotations.
+# org.sbml.jsbml.xml.parsers.XMLNodeWriter - DEBUG : output events when writing XMLNode, so HTML block
+# org.sbml.jsbml.xml.stax.SBMLReader - ERROR to DEBUG : (lot of output) display all the event when reading an SBML file
+# org.sbml.jsbml.xml.stax.SBMLWriter - ERROR to DEBUG : (lot of output) display all the event when writing an SBML file
+# org.sbml.jsbml.util.StringTools - WARN : warning when there is a problem with the conversion of a String into a number or boolean.
+# org.sbml.jsbml.util.compilers.MathMLXMLStreamCompiler - WARN to DEBUG : (lot of output) display all the event when writing mathML
+# org.sbml.jsbml.xml.parsers.MathMLStaxParser - ERROR to DEBUG : (lot of output) display all the event when reading a MathML block
+# org.sbml.jsbml.SBMLDocument - ERROR to DEBUG : will display problems related to the checkConsistency call
+# org.sbml.jsbml.validator.SBMLValidator - DEBUG : will print the xml result file from http://sbml.org/validator/ with few others checks when the parsing is done
+# org.sbml.jsbml.util.SubModel - DEBUG : will print the details of the submodel building
+# org.sbml.jsbml.ASTNode - ERROR to DEBUG
+# org.sbml.jsbml.xml.parsers.AbstractReaderWriter - DEBUG : events when reading or writing L3 packages block (if the parser extends this abstract class)
+# org.sbml.jsbml.xml.parsers.QualParser - DEBUG : events when reading/writing the qual package/extension.
+# org.sbml.jsbml.ext.comp.CompModelPlugin - DEBUG: register and unregister debug output for the comp package id namespace
+# org.sbml.jsbml.ext.comp.ArraysSBasePlugin - DEBUG: register and unregister debug output for the arrays package id namespace
+# org.sbml.jsbml.Model - DEBUG: register and unregister debug output for the core package id namespace
+# org.sbml.jsbml.xml.parsers.SBMLRDFAnnotationParser - DEBUG: debug output when reading and writing RDF annotations
+
+
+-->
+ <Root level="info">
+ <AppenderRef ref="file"/>
+ </Root>
+ </Loggers>
+
+</Configuration>
Modified: trunk/core/src/org/sbml/jsbml/SBO.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SBO.java 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/core/src/org/sbml/jsbml/SBO.java 2016-05-04 12:44:42 UTC (rev 2499)
@@ -30,8 +30,8 @@
import java.util.Set;
import org.apache.log4j.Logger;
-import org.biojava3.ontology.Ontology;
-import org.biojava3.ontology.io.OboParser;
+import org.biojava.nbio.ontology.Ontology;
+import org.biojava.nbio.ontology.io.OboParser;
import org.sbml.jsbml.ontology.Term;
import org.sbml.jsbml.ontology.Triple;
import org.sbml.jsbml.resources.Resource;
@@ -1000,19 +1000,19 @@
* Return the set of terms of the SBO Ontology.
*
* <p> This methods return only Term object and no Triple object that represent the
- * relationship between terms. If you want to access the full set of {@link org.biojava3.ontology.Term}
- * containing also the {@link org.biojava3.ontology.Triple}, use {@link SBO#getOntology()}
+ * relationship between terms. If you want to access the full set of {@link org.biojava.nbio.ontology.Term}
+ * containing also the {@link org.biojava.nbio.ontology.Triple}, use {@link SBO#getOntology()}
* to get the underlying biojava object.
*
* @return the set of terms of the SBO Ontology.
*/
public static Set<Term> getTerms() {
if (terms.size() < sbo.getTerms().size()) {
- for (org.biojava3.ontology.Term term : sbo.getTerms()) {
+ for (org.biojava.nbio.ontology.Term term : sbo.getTerms()) {
- if (term instanceof org.biojava3.ontology.Triple) {
+ if (term instanceof org.biojava.nbio.ontology.Triple) {
// does nothing
- } else if (term instanceof org.biojava3.ontology.Term) {
+ } else if (term instanceof org.biojava.nbio.ontology.Term) {
terms.add(new Term(term));
}
}
@@ -1124,12 +1124,12 @@
* @param object the object to search for, or {@code null}.
* @return a set of Triple which match the supplied subject, predicate and object.
*
- * @see org.biojava3.ontology.Ontology#getTriples(org.biojava3.ontology.Term,
- * org.biojava3.ontology.Term, org.biojava3.ontology.Term)
+ * @see org.biojava.nbio.ontology.Ontology#getTriples(org.biojava.nbio.ontology.Term,
+ * org.biojava.nbio.ontology.Term, org.biojava.nbio.ontology.Term)
*/
public static Set<Triple> getTriples(Term subject, Term predicate, Term object) {
Set<Triple> triples = new HashSet<Triple>();
- for (org.biojava3.ontology.Triple triple : sbo.getTriples(
+ for (org.biojava.nbio.ontology.Triple triple : sbo.getTriples(
subject != null ? subject.getTerm() : null,
object != null ? object.getTerm() : null,
predicate != null ? predicate.getTerm() : null)) {
@@ -1264,9 +1264,9 @@
if (subject.equals(object)) {
return true;
}
- Set<org.biojava3.ontology.Triple> relations = sbo.getTriples(
+ Set<org.biojava.nbio.ontology.Triple> relations = sbo.getTriples(
subject != null ? subject.getTerm() : null, null, null);
- for (org.biojava3.ontology.Triple triple : relations) {
+ for (org.biojava.nbio.ontology.Triple triple : relations) {
if (triple.getObject().equals(object.getTerm())) {
return true;
}
@@ -1989,7 +1989,7 @@
}
}
System.out.println("\nThere is " + i + " terms in the SBO ontology.");
-
-
+
+ System.out.println("\nGet term by id = " + Term.printTerm(getTerm("SBO:0000620")));
}
}
Modified: trunk/core/src/org/sbml/jsbml/ontology/Term.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ontology/Term.java 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/core/src/org/sbml/jsbml/ontology/Term.java 2016-05-04 12:44:42 UTC (rev 2499)
@@ -26,18 +26,18 @@
import java.util.HashSet;
import java.util.Set;
-import org.biojava3.ontology.Synonym;
-import org.biojava3.ontology.utils.Annotation;
+import org.biojava.nbio.ontology.Synonym;
+import org.biojava.nbio.ontology.utils.Annotation;
import org.sbml.jsbml.SBO;
import org.sbml.jsbml.util.StringTools;
/**
* This is a convenient wrapper class for the corresponding implementation
- * of {@link org.biojava3.ontology.Term} in BioJava as it provides
+ * of {@link org.biojava.nbio.ontology.Term} in BioJava as it provides
* specialized methods to obtain the information from the SBO OBO file
* directly and under the same name as the keys are given in that file.
*
- * @see org.biojava3.ontology.Term
+ * @see org.biojava.nbio.ontology.Term
*/
public class Term implements Cloneable, Comparable<Term>, Serializable {
@@ -54,8 +54,8 @@
*/
public static String printTerm(Term term) {
StringBuilder sb = new StringBuilder();
- StringTools.append(sb, "[Term]\nid: ", term.getId(), "\nname: ",
- term.getName(), "\ndef: ", term.getDefinition());
+ StringTools.append(sb, "[Term]\nid: ", term.getId(), "\nname: '",
+ term.getName(), "'\ndef: ", term.getDefinition());
if (term.isObsolete()) {
sb.append("\nis_obsolete: true");
}
@@ -93,16 +93,16 @@
private String def;
/**
- * The underlying BioJava {@link org.biojava3.ontology.Term}.
+ * The underlying BioJava {@link Term}.
*/
- private org.biojava3.ontology.Term term;
+ private org.biojava.nbio.ontology.Term term;
/**
* Creates a new Term instance.
*
- * @param term a {@link org.biojava3.ontology.Term} object
+ * @param term a {@link org.biojava.nbio.ontology.Term} object
*/
- public Term(org.biojava3.ontology.Term term) {
+ public Term(org.biojava.nbio.ontology.Term term) {
if (term == null) {
throw new NullPointerException("Term must not be null.");
}
@@ -217,7 +217,7 @@
Set<Term> parents = new HashSet<Term>();
- for (org.biojava3.ontology.Triple triple : term.getOntology().getTriples(term, null, term.getOntology().getTerm("is_a")))
+ for (org.biojava.nbio.ontology.Triple triple : term.getOntology().getTriples(term, null, term.getOntology().getTerm("is_a")))
{
parents.add(new Term(triple.getObject()));
}
@@ -251,7 +251,7 @@
* @return the underlying BioJava
* {@link org.biojava3.ontology.Term}.
*/
- public org.biojava3.ontology.Term getTerm() {
+ public org.biojava.nbio.ontology.Term getTerm() {
return term;
}
Modified: trunk/core/src/org/sbml/jsbml/ontology/Triple.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/ontology/Triple.java 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/core/src/org/sbml/jsbml/ontology/Triple.java 2016-05-04 12:44:42 UTC (rev 2499)
@@ -27,10 +27,10 @@
/**
* This is a wrapper class for the corresponding BioJava class
- * {@link org.biojava3.ontology.Triple}, to allow for simplified access to
+ * {@link org.biojava.nbio.ontology.Triple}, to allow for simplified access to
* the properties of a subject-predicate-object triple in this ontology.
*
- * @see org.biojava3.ontology.Triple
+ * @see org.biojava.nbio.ontology.Triple
*/
public class Triple implements Cloneable, Comparable<Triple>, Serializable {
@@ -40,9 +40,9 @@
private static final long serialVersionUID = 7289048361260650338L;
/**
- * The BioJava {@link org.biojava3.ontology.Triple}.
+ * The BioJava {@link org.biojava.nbio.ontology.Triple}.
*/
- private org.biojava3.ontology.Triple triple;
+ private org.biojava.nbio.ontology.Triple triple;
/**
* Creates a new {@link Triple} from a given corresponding object from
@@ -50,7 +50,7 @@
*
* @param triple
*/
- public Triple(org.biojava3.ontology.Triple triple) {
+ public Triple(org.biojava.nbio.ontology.Triple triple) {
if (triple == null) {
throw new NullPointerException("Triple must not be null.");
}
@@ -132,12 +132,12 @@
/**
* Grants access to the original BioJava
- * {@link org.biojava3.ontology.Triple}.
+ * {@link org.biojava.nbio.ontology.Triple}.
*
* @return the original BioJava
- * {@link org.biojava3.ontology.Triple}.
+ * {@link org.biojava.nbio.ontology.Triple}.
*/
- public org.biojava3.ontology.Triple getTriple() {
+ public org.biojava.nbio.ontology.Triple getTriple() {
return triple;
}
Modified: trunk/extensions/arrays/build.xml
===================================================================
--- trunk/extensions/arrays/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/arrays/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -33,6 +33,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Arrays L3 package"/>
<property name="name" value="jsbml-arrays"/>
<property name="version" value="0.9-b1"/>
@@ -196,8 +198,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/extensions/comp/build.xml
===================================================================
--- trunk/extensions/comp/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/comp/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -33,6 +33,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Hierarchical Model Composition L3 package"/>
<property name="name" value="jsbml-comp"/>
<property name="version" value="1.0-b1"/>
@@ -195,8 +197,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/extensions/distrib/build.xml
===================================================================
--- trunk/extensions/distrib/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/distrib/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -32,6 +32,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Distributions L3 package"/>
<property name="name" value="jsbml-distrib"/>
<property name="version" value="0.5"/>
@@ -194,8 +196,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/extensions/dyn/build.xml
===================================================================
--- trunk/extensions/dyn/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/dyn/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -31,6 +31,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Dynamic L3 package"/>
<property name="name" value="jsbml-dyn"/>
@@ -198,8 +200,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/CBO.java
===================================================================
--- trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/CBO.java 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/dyn/src/org/sbml/jsbml/ext/dyn/CBO.java 2016-05-04 12:44:42 UTC (rev 2499)
@@ -29,8 +29,8 @@
import java.util.NoSuchElementException;
import java.util.Set;
-import org.biojava3.ontology.Ontology;
-import org.biojava3.ontology.io.OboParser;
+import org.biojava.nbio.ontology.Ontology;
+import org.biojava.nbio.ontology.io.OboParser;
import org.sbml.jsbml.ontology.Term;
import org.sbml.jsbml.ontology.Triple;
import org.sbml.jsbml.resources.Resource;
@@ -145,16 +145,16 @@
* <p>
* This methods return only Term object and no Triple object that represent
* the relationship between terms. If you want to access the full set of
- * {@link org.biojava3.ontology.Term} containing also the
- * {@link org.biojava3.ontology.Triple}, use {@link CBO#getOntology()} to get
+ * {@link org.biojava.nbio.ontology.Term} containing also the
+ * {@link org.biojava.nbio.ontology.Triple}, use {@link CBO#getOntology()} to get
* the underlying biojava object.
*
* @return the set of terms of the CBO.
*/
public static Set<Term> getTerms() {
if (terms.size() < cbo.getTerms().size()) {
- for (org.biojava3.ontology.Term term : cbo.getTerms()) {
- if (term instanceof org.biojava3.ontology.Term) {
+ for (org.biojava.nbio.ontology.Term term : cbo.getTerms()) {
+ if (term instanceof org.biojava.nbio.ontology.Term) {
terms.add(new Term(term));
}
}
@@ -179,13 +179,13 @@
* @return a set of Triple which match the supplied subject, predicate and
* object.
*
- * @see org.biojava3.ontology.Ontology#getTriples(org.biojava3.ontology.Term,
- * org.biojava3.ontology.Term, org.biojava3.ontology.Term)
+ * @see org.biojava.nbio.ontology.Ontology#getTriples(org.biojava.nbio.ontology.Term,
+ * org.biojava.nbio.ontology.Term, org.biojava.nbio.ontology.Term)
*/
public static Set<Triple> getTriples(Term subject, Term predicate,
Term object) {
Set<Triple> triples = new HashSet<Triple>();
- for (org.biojava3.ontology.Triple triple : cbo.getTriples(
+ for (org.biojava.nbio.ontology.Triple triple : cbo.getTriples(
subject != null ? subject.getTerm() : null,
object != null ? object.getTerm() : null,
predicate != null ? predicate.getTerm() : null)) {
Modified: trunk/extensions/fbc/build.xml
===================================================================
--- trunk/extensions/fbc/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/fbc/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -32,6 +32,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Flux Balance Constraints L3 package"/>
<property name="name" value="jsbml-fbc"/>
<property name="version" value="1.0-b1"/>
@@ -194,8 +196,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/extensions/groups/build.xml
===================================================================
--- trunk/extensions/groups/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/groups/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -31,6 +31,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Groups L3 package"/>
<property name="name" value="jsbml-groups"/>
<property name="version" value="0.4-b1"/> <!-- follow the specs 0.4 from 31/05/2013 -->
@@ -193,8 +195,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/extensions/layout/build.xml
===================================================================
--- trunk/extensions/layout/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/layout/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -32,6 +32,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Layout L3 package"/>
<property name="name" value="jsbml-layout"/>
<property name="version" value="1.0-b1"/>
@@ -194,8 +196,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/extensions/multi/build.xml
===================================================================
--- trunk/extensions/multi/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/multi/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -31,6 +31,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Multistate multicomponent species L3 package"/>
<property name="name" value="jsbml-multi"/>
<property name="version" value="0.1-a1"/>
@@ -193,8 +195,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/extensions/qual/build.xml
===================================================================
--- trunk/extensions/qual/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/qual/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -31,6 +31,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Qualitative L3 package"/>
<property name="name" value="jsbml-qual"/>
@@ -198,8 +200,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/extensions/render/build.xml
===================================================================
--- trunk/extensions/render/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/render/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -32,6 +32,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Render L3 package"/>
<property name="name" value="jsbml-render"/>
<property name="version" value="0.8-a1"/>
@@ -195,8 +197,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/extensions/req/build.xml
===================================================================
--- trunk/extensions/req/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/req/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -31,6 +31,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Required Elements L3 package"/>
<property name="name" value="jsbml-req"/>
<property name="version" value="0.2-b1"/>
@@ -193,8 +195,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/extensions/spatial/build.xml
===================================================================
--- trunk/extensions/spatial/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/extensions/spatial/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -31,6 +31,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property name="Name" value="JSBML Spatial Processes L3 package"/>
<property name="name" value="jsbml-spatial"/>
<property name="version" value="0.8-b1"/>
@@ -193,8 +195,8 @@
debug="${debug}"
optimize="${optimize}"
verbose="${verbose}"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
<manifest file="${build.dest}/META-INF/MANIFEST.MF">
Modified: trunk/jsbml-build.properties
===================================================================
--- trunk/jsbml-build.properties 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/jsbml-build.properties 2016-05-04 12:44:42 UTC (rev 2499)
@@ -5,3 +5,5 @@
jsbml.api.version=1.2
jsbml.groupId=org.sbml.jsbml
jsbml.artifactId=jsbml-parent
+jsbml.build.javac.source=1.7
+jsbml.build.javac.target=1.7
Modified: trunk/modules/tidy/build.xml
===================================================================
--- trunk/modules/tidy/build.xml 2016-04-21 13:41:07 UTC (rev 2498)
+++ trunk/modules/tidy/build.xml 2016-05-04 12:44:42 UTC (rev 2499)
@@ -37,6 +37,8 @@
<format property="YEAR" pattern="yyyy"/>
</tstamp>
+ <property file="${basedir}/../../jsbml-build.properties"/>
+
<property file="${basedir}/tidy-build.properties"/>
<property name="Name" value="${tidy.Name}"/>
@@ -194,8 +196,8 @@
memoryMaximumSize="512M"
compiler="modern"
nowarn="no"
- source="1.6"
- target="1.6"
+ source="${jsbml.build.javac.source}"
+ target="${jsbml.build.javac.target}"
classpathref="classpath">
</javac>
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