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[Jsbml-svn] SF.net SVN: jsbml:[2378] trunk
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From: <nik...@us...> - 2015-10-09 16:03:27
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Revision: 2378
http://sourceforge.net/p/jsbml/code/2378
Author: niko-rodrigue
Date: 2015-10-09 16:03:25 +0000 (Fri, 09 Oct 2015)
Log Message:
-----------
modified the build files so that two jar are generated for the two versions of ASTNode + reverted some changes made by Victor on VectorCompiler + started to update the NEW file
Modified Paths:
--------------
trunk/NEWS.txt
trunk/build.xml
trunk/core/build.xml
trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java
Modified: trunk/NEWS.txt
===================================================================
--- trunk/NEWS.txt 2015-10-09 12:21:58 UTC (rev 2377)
+++ trunk/NEWS.txt 2015-10-09 16:03:25 UTC (rev 2378)
@@ -1,12 +1,21 @@
JSBML NEWS -- History of user-visible changes
===========================================================================
-Version 1.1 (xx-xx-2015)
+Version 1.1-b1 (xx-10-2015)
===========================================================================
* New Features:
+ - implemented FBC version 2
+ - implemented distrib version 1 draft
+
+ - merged with the ASTNode2 branch
+
+* Layout
+
+ - added a createCurve method to ReactionGlyph
+
* Bug Fixes:
- Methods that accepted Double/Integer/Boolean values or returned those
@@ -18,6 +27,7 @@
not implemented so we have to compare the content of the StringBuilder
or use other utility method to compare properly the StringBuilders.
+
===========================================================================
Version 1.0 (09-12-2014)
===========================================================================
Modified: trunk/build.xml
===================================================================
--- trunk/build.xml 2015-10-09 12:21:58 UTC (rev 2377)
+++ trunk/build.xml 2015-10-09 16:03:25 UTC (rev 2378)
@@ -46,7 +46,7 @@
<property name="Name" value="JSBML" />
<property name="name" value="jsbml" />
- <property name="version" value="1.1-dev" />
+ <property name="version" value="1.1-b1" />
<property name="api.version" value="1.0" />
<property name="year" value="${YEAR}" />
@@ -190,14 +190,13 @@
<property name="prepare.src.target.done" value="true"/>
- <echo message="Value of the use-old-astnode property = '${use.old.astnodes}'"/>
-
<ant dir="${core.base.dir}" inheritAll="false" inheritRefs="false">
- <property name="use.old.astnodes" value="${use.old.astnodes}"/>
+ <property name="use.old.astnodes" value="true"/>
<target name="clean" />
<target name="jar" />
</ant>
+
<copy todir="${build.src}">
<fileset dir="${core.base.dir}/build/src" includes="**/*"/>
</copy>
@@ -473,6 +472,7 @@
<!-- Cleaning before starting -->
<antcall target="clean" inheritrefs="true" inheritall="true"/>
+ <!-- generate the jars using the old ASTNode class -->
<!-- Creates the standard jar files -->
<antcall target="jar" inheritrefs="true" inheritall="true"/>
@@ -493,23 +493,41 @@
<fileset dir="${build.javadocs}/" includes="**/*"/>
</copy>
- <!-- generate the jars using the old ASTNode class -->
- <property name="use.old.astnodes" value="true"/>
- <!-- backup the jars using the new ASTNode class -->
- <copy tofile="${dist.dir}/${name}-${version}-newASTNode-with-dependencies.jar" file="${dist.dir}/${name}-${version}-with-dependencies.jar" />
- <copy tofile="${dist.dir}/${name}-${version}-newASTNode.jar" file="${dist.dir}/${name}-${version}.jar" />
- <antcall target="jar" inheritrefs="true" inheritall="true"/>
- <antcall target="bigjar" inheritrefs="true" inheritall="true"/>
- <!-- rename and copy all jars, restore the jars using the new ASTNode class as the default -->
- <copy tofile="${dist.root}/${name}-${version}-oldASTNode-with-dependencies.jar" file="${dist.dir}/${name}-${version}-with-dependencies.jar" />
- <copy tofile="${dist.root}/${name}-${version}-oldASTNode.jar" file="${dist.dir}/${name}-${version}.jar" />
+ <!-- backup the jars using the old ASTNode class -->
<copy tofile="${dist.dir}/${name}-${version}-oldASTNode-with-dependencies.jar" file="${dist.dir}/${name}-${version}-with-dependencies.jar" />
<copy tofile="${dist.dir}/${name}-${version}-oldASTNode.jar" file="${dist.dir}/${name}-${version}.jar" />
- <copy file="${dist.dir}/${name}-${version}-newASTNode-with-dependencies.jar" tofile="${dist.dir}/${name}-${version}-with-dependencies.jar" overwrite="true"/>
- <copy file="${dist.dir}/${name}-${version}-newASTNode.jar" tofile="${dist.dir}/${name}-${version}.jar" overwrite="true"/>
- <delete file="${dist.dir}/${name}-${version}-newASTNode.jar" verbose="true"/>
- <delete file="${dist.dir}/${name}-${version}-newASTNode-with-dependencies.jar" verbose="true"/>
+
+ <!-- re-generating the jsbml-core jar file -->
+ <!-- copying by hand the ASTNode2 facade -->
+ <copy file="${core.base.dir}/src/org/sbml/jsbml/ASTNode.java.newASTNode" tofile="${core.base.dir}/src/org/sbml/jsbml/ASTNode.java" overwrite="yes"/>
+ <copy file="${core.base.dir}/src/org/sbml/jsbml/ASTNode.java.newASTNode" tofile="${core.base.dir}/build/src/org/sbml/jsbml/ASTNode.java" overwrite="yes"/>
+ <delete file="${build.dest}/org/sbml/jsbml/test/ASTNodeVersionTest.class" />
+
+ <ant dir="${core.base.dir}" inheritAll="false" inheritRefs="false">
+ <target name="clean" />
+ <target name="jar" />
+ </ant>
+ <copy file="${core.base.dir}/src/org/sbml/jsbml/ASTNode.java.newASTNode" tofile="${build.dir}/org/sbml/jsbml/ASTNode.java" overwrite="yes"/>
+
+ <!-- re-generating the global jsbml jar files -->
+ <antcall target="jar" inheritrefs="true" inheritall="true"/>
+ <antcall target="bigjar" inheritrefs="true" inheritall="true"/>
+
+ <!-- restoring the ASTNode class -->
+ <copy file="${core.base.dir}/src/org/sbml/jsbml/ASTNode.java.oldASTNode" tofile="${core.base.dir}/src/org/sbml/jsbml/ASTNode.java" overwrite="yes"/>
+ <copy file="${core.base.dir}/src/org/sbml/jsbml/ASTNode.java.oldASTNode" tofile="${core.base.dir}/build/src/org/sbml/jsbml/ASTNode.java" overwrite="yes"/>
+
+ <!-- rename and copy all jars, restore the jars using the old ASTNode class as the default -->
+ <copy tofile="${dist.root}/${name}-${version}-newASTNode-with-dependencies.jar" file="${dist.dir}/${name}-${version}-with-dependencies.jar" />
+ <copy tofile="${dist.root}/${name}-${version}-newASTNode.jar" file="${dist.dir}/${name}-${version}.jar" />
+ <copy tofile="${dist.dir}/${name}-${version}-newASTNode-with-dependencies.jar" file="${dist.dir}/${name}-${version}-with-dependencies.jar" />
+ <copy tofile="${dist.dir}/${name}-${version}-newASTNode.jar" file="${dist.dir}/${name}-${version}.jar" />
+ <copy file="${dist.dir}/${name}-${version}-oldASTNode-with-dependencies.jar" tofile="${dist.dir}/${name}-${version}-with-dependencies.jar" overwrite="true"/>
+ <copy file="${dist.dir}/${name}-${version}-oldASTNode.jar" tofile="${dist.dir}/${name}-${version}.jar" overwrite="true"/>
+ <delete file="${dist.dir}/${name}-${version}-oldASTNode.jar" verbose="true"/>
+ <delete file="${dist.dir}/${name}-${version}-oldASTNode-with-dependencies.jar" verbose="true"/>
+
<!-- Copy the source files -->
<copy todir="${dist.dir}/src">
<fileset dir="${build.src}/" includes="**/*"/>
@@ -692,6 +710,7 @@
</delete>
</target>
+
</project>
<!-- End of file -->
Modified: trunk/core/build.xml
===================================================================
--- trunk/core/build.xml 2015-10-09 12:21:58 UTC (rev 2377)
+++ trunk/core/build.xml 2015-10-09 16:03:25 UTC (rev 2378)
@@ -167,7 +167,7 @@
<copy todir="${build.src}" overwrite="yes">
<fileset
dir="${src.dir}"
- excludes="**/.svn*, **/*.class, **/*~, **/*.tgz, **/*.zip">
+ excludes="**/.svn*, **/*.class, **/*~, **/*.tgz, **/*.zip **/*.java.*">
</fileset>
</copy>
@@ -188,24 +188,23 @@
</copy>
<echo message="Value of the use-old-astnode property in core = '${use.old.astnodes}'"/>
- <antcall target="prepare-old-astnode" inheritrefs="true" inheritall="true"/>
+ <antcall target="prepare-new-astnode" inheritrefs="true" inheritall="true"/>
</target>
<!-- =================================================================== -->
- <!-- Prepares the source code to use the old ASTNode class -->
+ <!-- Prepares the source code to use the new ASTNode class -->
<!-- =================================================================== -->
<target
- name="prepare-old-astnode"
- description="Prepares the source code to use the old ASTNode class"
- if="${use.old.astnodes}"
+ name="prepare-new-astnode"
+ description="Prepares the source code to use the new ASTNode class"
+ unless="${use.old.astnodes}"
>
- <echo message="Building JSBML core using the old ASTNode class!"/>
- <copy file="${src.dir}/org/sbml/jsbml/ASTNode.java" tofile="${build.src}/org/sbml/jsbml/ASTNode.java.newASTNode" overwrite="yes"/>
- <copy file="${src.dir}/org/sbml/jsbml/ASTNode.java.oldASTNode" tofile="${build.src}/org/sbml/jsbml/ASTNode.java" overwrite="yes"/>
+ <echo message="Building JSBML core using the new ASTNode class!"/>
+ <copy file="${src.dir}/org/sbml/jsbml/ASTNode.java" tofile="${build.src}/org/sbml/jsbml/ASTNode.java.oldASTNode" overwrite="yes"/>
+ <copy file="${src.dir}/org/sbml/jsbml/ASTNode.java.newASTNode" tofile="${build.src}/org/sbml/jsbml/ASTNode.java" overwrite="yes"/>
+ <copy file="${src.dir}/org/sbml/jsbml/ASTNode.java.newASTNode" tofile="${build.src}/org/sbml/jsbml/ASTNode.java.newASTNode" overwrite="yes"/>
- <property name="version" value="${version}-oldASTNode"/>
-
</target>
<!-- =================================================================== -->
@@ -303,7 +302,7 @@
<jar jarfile="${build.dir}/${name}-${version}.jar" basedir="${build.dest}" manifest="${build.dest}/META-INF/MANIFEST.MF"/>
<echo message="Value of the use-old-astnode property in core = '${use.old.astnodes}'"/>
- <antcall target="revert-old-astnode" inheritrefs="true" inheritall="true"/>
+ <antcall target="revert-new-astnode" inheritrefs="true" inheritall="true"/>
</target>
<!-- =================================================================== -->
@@ -377,15 +376,13 @@
<!-- Revert the source code to use the new ASTNode class -->
<!-- =================================================================== -->
<target
- name="revert-old-astnode"
- description="Prepares the source code to use the new ASTNode class"
- if="${use.old.astnodes}"
+ name="revert-new-astnode"
+ description="Prepares the source code to use the old ASTNode class"
+ unless="${use.old.astnodes}"
>
- <echo message="Reverting JSBML core using the new ASTNode class!"/>
- <copy file="${src.dir}/org/sbml/jsbml/ASTNode.java" tofile="${build.src}/org/sbml/jsbml/ASTNode.java" overwrite="yes"/>
+ <echo message="Reverting JSBML core using the old ASTNode class!"/>
+ <copy file="${build.src}/org/sbml/jsbml/ASTNode.java.oldASTNode" tofile="${build.src}/org/sbml/jsbml/ASTNode.java" overwrite="yes"/>
- <property name="version" value="${version}-oldASTNode"/>
-
</target>
<!-- =================================================================== -->
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 2015-10-09 12:21:58 UTC (rev 2377)
+++ trunk/extensions/arrays/src/org/sbml/jsbml/ext/arrays/compiler/VectorCompiler.java 2015-10-09 16:03:25 UTC (rev 2378)
@@ -3686,11 +3686,13 @@
private void plusRecursive(List<ASTNode> values, ASTNode node) throws IndexOutOfBoundsException, SBMLException{
if (!node.isVector()) {
double result = 0;
- // TODO: Set type was causing a new ASTNode2 object to be created
- // and this was preventing the children of the original node
- // object from being updated.
- //node.getChildren().clear();
- //node.setType(ASTNode.Type.PLUS);
+
+ 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);
@@ -3702,9 +3704,7 @@
throw new SBMLException();
}
}
- // TODO: Find a better fix
- //node.addChild(new ASTNode(result));
- node.setValue(result);
+ node.addChild(new ASTNode(result));
return;
}
}
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