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[Jsbml-svn] SF.net SVN: jsbml:[2406] trunk/extensions/arrays
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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] |
