Thread: [Jsbml-svn] SF.net SVN: jsbml:[2189] branches/astnode2-merging-alternate

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Revision: 2189
          http://sourceforge.net/p/jsbml/code/2189
Author:   niko-rodrigue
Date:     2015-04-21 11:48:11 +0000 (Tue, 21 Apr 2015)
Log Message:
-----------
cleaned a bit by removing the bin folder + added some cast to be able to compile the code + moved one test file from core to the base dir as it was using the arrays package

Modified Paths:
--------------
    branches/astnode2-merging-alternate/core/build.xml
    branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java
    branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java

Added Paths:
-----------
    branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/
    branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/test/
    branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/test/RecursionTest.java

Removed Paths:
-------------
    branches/astnode2-merging-alternate/bin/
    branches/astnode2-merging-alternate/core/dist/jsbml-1.1-a1/
    branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/RecursionTest.java

Modified: branches/astnode2-merging-alternate/core/build.xml
===================================================================

--- branches/astnode2-merging-alternate/core/build.xml	2015-04-20 14:08:25 UTC (rev 2188)
+++ branches/astnode2-merging-alternate/core/build.xml	2015-04-21 11:48:11 UTC (rev 2189)
@@ -167,8 +167,7 @@
 		<copy todir="${build.src}" overwrite="yes">
 			<fileset 
             dir="${src.dir}"
-            excludes="**/.svn*, **/*.class, **/*~, **/*.tgz, **/*.zip org/sbml/jsbml/math/**">
-				<!-- TODO remove org/sbml/jsbml/math from the filters when the package is ready -->
+            excludes="**/.svn*, **/*.class, **/*~, **/*.tgz, **/*.zip">
 			</fileset>
 		</copy>
 

Modified: branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java
===================================================================
--- branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java	2015-04-20 14:08:25 UTC (rev 2188)
+++ branches/astnode2-merging-alternate/core/src/org/sbml/jsbml/math/compiler/UnitsCompiler.java	2015-04-21 11:48:11 UTC (rev 2189)
@@ -122,7 +122,7 @@
    */
   @Override
   public <T> ASTNode2Value<Boolean> and(List<ASTNode2> values) throws SBMLException {
-    ASTNode2Value<Boolean> value = dimensionless();
+    ASTNode2Value<Boolean> value = (ASTNode2Value<Boolean>) dimensionless();
     boolean val = true;
     for (ASTNode2 v : values) {
       val &= v.compile(this).toBoolean();
@@ -647,7 +647,7 @@
    */
   @Override
   public <T> ASTNode2Value<Double> getConstantE() {
-    ASTNode2Value<Double> v = dimensionless();
+    ASTNode2Value<Double> v = (ASTNode2Value<Double>) dimensionless();
     v.setValue(Math.E);
     return v;
   }
@@ -657,7 +657,7 @@
    */
   @Override
   public <T> ASTNode2Value<Boolean> getConstantFalse() {
-    ASTNode2Value<Boolean> v = dimensionless();
+    ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
     v.setValue(false);
     return v;
   }
@@ -667,7 +667,7 @@
    */
   @Override
   public <T> ASTNode2Value<Double> getConstantPi() {
-    ASTNode2Value<Double> v = dimensionless();
+    ASTNode2Value<Double> v = (ASTNode2Value<Double>) dimensionless();
     v.setValue(Math.PI);
     return v;
   }
@@ -677,7 +677,7 @@
    */
   @Override
   public <T> ASTNode2Value<Boolean> getConstantTrue() {
-    ASTNode2Value<Boolean> v = dimensionless();
+    ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
     v.setValue(true);
     return v;
   }
@@ -796,7 +796,7 @@
   @Override
   // TODO: Specify generic type T i.e. ASTNode2Value<?>
   public <T> ASTNode2Value<?> lt(ASTNode2 left, ASTNode2 right) throws SBMLException {
-    ASTNode2Value<?> v = dimensionless(), leftvalue, rightvalue;
+    ASTNode2Value<?> v = (ASTNode2Value<?>) dimensionless(), leftvalue, rightvalue;
     leftvalue = left.compile(this);
     rightvalue = right.compile(this);
     unifyUnits(leftvalue, rightvalue);
@@ -851,7 +851,7 @@
   @Override
   // TODO: Specify type T i.e. ASTNode2Value<Boolean>
   public ASTNode2Value<?> neq(ASTNode2 left, ASTNode2 right) throws SBMLException {
-    ASTNode2Value<?> v = dimensionless(), leftvalue, rightvalue;
+    ASTNode2Value<?> v = (ASTNode2Value<?>) dimensionless(), leftvalue, rightvalue;
     leftvalue = left.compile(this);
     rightvalue = right.compile(this);
     unifyUnits(leftvalue, rightvalue);
@@ -864,7 +864,7 @@
    */
   @Override
   public <T> ASTNode2Value<Boolean> not(ASTNode2 value) throws SBMLException {
-    ASTNode2Value<Boolean> v = dimensionless();
+    ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
     v.setValue(!value.compile(this).toBoolean());
     return v;
   }
@@ -874,7 +874,7 @@
    */
   @Override
   public <T> ASTNode2Value<Boolean> or(List<ASTNode2> values) throws SBMLException {
-    ASTNode2Value<Boolean> v = dimensionless();
+    ASTNode2Value<Boolean> v = (ASTNode2Value<Boolean>) dimensionless();
     v.setValue(false);
     for (ASTNode2 value : values) {
       if (value.compile(this).toBoolean()) {
@@ -1326,7 +1326,7 @@
    */
   @Override
   public <T> ASTNode2Value<Boolean> xor(List<ASTNode2> values) throws SBMLException {
-    ASTNode2Value<Boolean> value = dimensionless();
+    ASTNode2Value<Boolean> value = (ASTNode2Value<Boolean>) dimensionless();
     boolean v = false;
     for (int i = 0; i < values.size(); i++) {
       if (values.get(i).compile(this).toBoolean()) {

Deleted: branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/RecursionTest.java
===================================================================
--- branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/RecursionTest.java	2015-04-20 14:08:25 UTC (rev 2188)
+++ branches/astnode2-merging-alternate/core/test/org/sbml/jsbml/math/test/RecursionTest.java	2015-04-21 11:48:11 UTC (rev 2189)
@@ -1,119 +0,0 @@
-/*
- * $Id: RecursionTest.java 2088 2014-11-16 06:56:46Z kofiav $
- * $URL: svn://svn.code.sf.net/p/jsbml/code/trunk/core/test/org/sbml/jsbml/math/test/RecursionTest.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) 2009-2014 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.math.test;
-
-import javax.swing.JOptionPane;
-import javax.swing.JScrollPane;
-import javax.swing.JTree;
-
-import org.sbml.jsbml.ASTNode;
-import org.sbml.jsbml.AssignmentRule;
-import org.sbml.jsbml.Model;
-import org.sbml.jsbml.Parameter;
-import org.sbml.jsbml.SBMLDocument;
-import org.sbml.jsbml.ext.arrays.ArraysConstants;
-import org.sbml.jsbml.ext.arrays.ArraysSBasePlugin;
-import org.sbml.jsbml.ext.arrays.Dimension;
-import org.sbml.jsbml.ext.arrays.Index;
-import org.sbml.jsbml.text.parser.ParseException;
-
-/**
- * 
- * @author Andreas Dr&auml;ger
- * @version $Rev: 2088 $
- * @since 1.0
- * @date 16.10.2014
- */
-public class RecursionTest {
-
-  /**
-   * @param args
-   * @throws ParseException
-   */
-  public static void main(String[] args) throws ParseException {
-//    ASTNode ast = ASTNode.parseFormula("3 * 1/1");
-//    System.out.println(ast.getType());
-//    JOptionPane.showMessageDialog(null, new JScrollPane(new JTree(ast)));
-//    System.out.println(ast.toFormula());
-    
-    SBMLDocument doc = new SBMLDocument(3,1);
-    Model model = doc.createModel();
-  
-    Parameter n = new Parameter("n");
-    n.setValue(10);
-    model.addParameter(n);
-
-    Parameter X = new Parameter("X");
-
-    model.addParameter(X);
-    ArraysSBasePlugin arraysSBasePluginX = new ArraysSBasePlugin(X);
-
-    X.addExtension(ArraysConstants.shortLabel, arraysSBasePluginX);
-
-    Dimension dimX = new Dimension("i");
-    dimX.setSize(n.getId());
-    dimX.setArrayDimension(0);
-
-    arraysSBasePluginX.addDimension(dimX);
-
-    Parameter Y = new Parameter("Y");
-
-    model.addParameter(Y);
-    ArraysSBasePlugin arraysSBasePluginY = new ArraysSBasePlugin(Y);
-
-    Y.addExtension(ArraysConstants.shortLabel, arraysSBasePluginY);
-    Dimension dimY = new Dimension("i");
-    dimY.setSize(n.getId());
-    dimY.setArrayDimension(0);
-
-    arraysSBasePluginY.addDimension(dimY);
-
-    AssignmentRule rule = new AssignmentRule();
-    model.addRule(rule);
-    rule.setMetaId("rule");
-    
-    ArraysSBasePlugin arraysSBasePluginRule = new ArraysSBasePlugin(rule);
-    rule.addExtension(ArraysConstants.shortLabel, arraysSBasePluginRule);
-    
-    Dimension dimRule = new Dimension("i");
-    dimRule.setSize(n.getId());
-    dimRule.setArrayDimension(0);
-    arraysSBasePluginRule.addDimension(dimRule);
-    
-    Index indexRule = new Index();
-    indexRule.setArrayDimension(0);
-    indexRule.setReferencedAttribute("variable");
-    ASTNode indexMath = new ASTNode();
-    
-    indexMath = ASTNode.diff(new ASTNode(9), new ASTNode("i"));
-    indexRule.setMath(indexMath);
-    arraysSBasePluginRule.addIndex(indexRule);
-    
-    rule.setVariable("Y");
-    ASTNode ruleMath = ASTNode.parseFormula("selector(X, i)");
-    
-    rule.setMath(ruleMath);
-    
-    JOptionPane.showMessageDialog(null, new JScrollPane(new JTree(indexMath)));
-
-  }
-
-}

Modified: branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java
===================================================================
--- branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java	2015-04-20 14:08:25 UTC (rev 2188)
+++ branches/astnode2-merging-alternate/extensions/spatial/src/org/sbml/jsbml/ext/spatial/AdjacentDomains.java	2015-04-21 11:48:11 UTC (rev 2189)
@@ -25,6 +25,7 @@
 import java.util.Map;
 import java.util.ResourceBundle;
 
+import org.sbml.jsbml.ListOf;
 import org.sbml.jsbml.PropertyUndefinedError;
 import org.sbml.jsbml.util.ResourceManager;
 
@@ -303,5 +304,5 @@
     builder.append("]");
     return builder.toString();
   }
-
+
 }

Added: branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/test/RecursionTest.java
===================================================================
--- branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/test/RecursionTest.java	                        (rev 0)
+++ branches/astnode2-merging-alternate/test/org/sbml/jsbml/math/test/RecursionTest.java	2015-04-21 11:48:11 UTC (rev 2189)
@@ -0,0 +1,119 @@
+/*
+ * $Id: RecursionTest.java 2088 2014-11-16 06:56:46Z kofiav $
+ * $URL: svn://svn.code.sf.net/p/jsbml/code/trunk/core/test/org/sbml/jsbml/math/test/RecursionTest.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) 2009-2014 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.math.test;
+
+import javax.swing.JOptionPane;
+import javax.swing.JScrollPane;
+import javax.swing.JTree;
+
+import org.sbml.jsbml.ASTNode;
+import org.sbml.jsbml.AssignmentRule;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.Parameter;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.ext.arrays.ArraysConstants;
+import org.sbml.jsbml.ext.arrays.ArraysSBasePlugin;
+import org.sbml.jsbml.ext.arrays.Dimension;
+import org.sbml.jsbml.ext.arrays.Index;
+import org.sbml.jsbml.text.parser.ParseException;
+
+/**
+ * 
+ * @author Andreas Dr&auml;ger
+ * @version $Rev: 2088 $
+ * @since 1.0
+ * @date 16.10.2014
+ */
+public class RecursionTest {
+
+  /**
+   * @param args
+   * @throws ParseException
+   */
+  public static void main(String[] args) throws ParseException {
+//    ASTNode ast = ASTNode.parseFormula("3 * 1/1");
+//    System.out.println(ast.getType());
+//    JOptionPane.showMessageDialog(null, new JScrollPane(new JTree(ast)));
+//    System.out.println(ast.toFormula());
+    
+    SBMLDocument doc = new SBMLDocument(3,1);
+    Model model = doc.createModel();
+  
+    Parameter n = new Parameter("n");
+    n.setValue(10);
+    model.addParameter(n);
+
+    Parameter X = new Parameter("X");
+
+    model.addParameter(X);
+    ArraysSBasePlugin arraysSBasePluginX = new ArraysSBasePlugin(X);
+
+    X.addExtension(ArraysConstants.shortLabel, arraysSBasePluginX);
+
+    Dimension dimX = new Dimension("i");
+    dimX.setSize(n.getId());
+    dimX.setArrayDimension(0);
+
+    arraysSBasePluginX.addDimension(dimX);
+
+    Parameter Y = new Parameter("Y");
+
+    model.addParameter(Y);
+    ArraysSBasePlugin arraysSBasePluginY = new ArraysSBasePlugin(Y);
+
+    Y.addExtension(ArraysConstants.shortLabel, arraysSBasePluginY);
+    Dimension dimY = new Dimension("i");
+    dimY.setSize(n.getId());
+    dimY.setArrayDimension(0);
+
+    arraysSBasePluginY.addDimension(dimY);
+
+    AssignmentRule rule = new AssignmentRule();
+    model.addRule(rule);
+    rule.setMetaId("rule");
+    
+    ArraysSBasePlugin arraysSBasePluginRule = new ArraysSBasePlugin(rule);
+    rule.addExtension(ArraysConstants.shortLabel, arraysSBasePluginRule);
+    
+    Dimension dimRule = new Dimension("i");
+    dimRule.setSize(n.getId());
+    dimRule.setArrayDimension(0);
+    arraysSBasePluginRule.addDimension(dimRule);
+    
+    Index indexRule = new Index();
+    indexRule.setArrayDimension(0);
+    indexRule.setReferencedAttribute("variable");
+    ASTNode indexMath = new ASTNode();
+    
+    indexMath = ASTNode.diff(new ASTNode(9), new ASTNode("i"));
+    indexRule.setMath(indexMath);
+    arraysSBasePluginRule.addIndex(indexRule);
+    
+    rule.setVariable("Y");
+    ASTNode ruleMath = ASTNode.parseFormula("selector(X, i)");
+    
+    rule.setMath(ruleMath);
+    
+    JOptionPane.showMessageDialog(null, new JScrollPane(new JTree(indexMath)));
+
+  }
+
+}

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Thread: [Jsbml-svn] SF.net SVN: jsbml:[2189] branches/astnode2-merging-alternate

The Java library for working with the SBML format.

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