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Some cleanup and starting test file.

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This commit is contained in:
leandrohw 2018-03-25 21:50:32 -07:00
parent 8553a3dcef
commit e493cfc7bb
20 changed files with 402 additions and 223 deletions
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34
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/AbstractSimulator.java
View file

@ -13,7 +13,12 @@
*******************************************************************************/
package edu.utah.ece.async.ibiosim.analysis.simulation;
import java.io.IOException;
import javax.xml.stream.XMLStreamException;
import edu.utah.ece.async.ibiosim.dataModels.util.Message;
import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.BioSimException;
import edu.utah.ece.async.ibiosim.dataModels.util.observe.CoreObservable;
/**
@ -24,11 +29,30 @@ import edu.utah.ece.async.ibiosim.dataModels.util.observe.CoreObservable;
* @version $Rev$
* @version %I%
*/
public abstract class AbstractSimulator extends CoreObservable implements ParentSimulator
public abstract class AbstractSimulator extends CoreObservable
{
protected final Message message = new Message();
/**
*
*/
public abstract void simulate() throws IOException, XMLStreamException, BioSimException;
/**
*
*/
public abstract void cancel();
/**
*
* @param newRun
*/
public abstract void setupForNewRun(int newRun) throws IOException;
/**
*
*/
public abstract void printStatisticsTSD();
protected final Message message = new Message();
}

66
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/ParentSimulator.java
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@ -1,66 +0,0 @@
/*******************************************************************************
*
* This file is part of iBioSim. Please visit <http://www.async.ece.utah.edu/ibiosim>
* for the latest version of iBioSim.
*
* Copyright (C) 2017 University of Utah
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the Apache License. A copy of the license agreement is provided
* in the file named "LICENSE.txt" included with this software distribution
* and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
*
*******************************************************************************/
package edu.utah.ece.async.ibiosim.analysis.simulation;
import java.io.IOException;
import javax.xml.stream.XMLStreamException;
import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.BioSimException;
/**
*
*
* @author Leandro Watanabe
* @author Chris Myers
* @author <a href="http://www.async.ece.utah.edu/ibiosim#Credits"> iBioSim Contributors </a>
* @version %I%
*/
public interface ParentSimulator
{
/**
*
*/
public abstract void simulate() throws IOException, XMLStreamException, BioSimException;
/**
*
*/
public abstract void cancel();
/**
*
*/
public abstract void clear();
/**
*
* @param newRun
*/
public abstract void setupForNewRun(int newRun) throws IOException;
/**
*
*/
public abstract void printStatisticsTSD();
/**
*
* @param randomSeed
* @param runNumber
* @throws IOException
* @throws XMLStreamException
*/
public abstract void initialize(long randomSeed, int runNumber) throws IOException, XMLStreamException, BioSimException;
}

1
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/flattened/Simulator.java
View file

@ -525,7 +525,6 @@ public abstract class Simulator extends AbstractSimulator
/**
* clears data structures for new run
*/
@Override
public abstract void clear();
/**

1
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/flattened/SimulatorODERK.java
View file

@ -67,7 +67,6 @@ public class SimulatorODERK extends Simulator
initialize(randomSeed, 1);
}
@Override
public void initialize(long randomSeed, int runNumber) throws IOException
{

1
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/flattened/SimulatorSSACR.java
View file

@ -452,7 +452,6 @@ public class SimulatorSSACR extends Simulator
* @throws IOException
* @throws XMLStreamException
*/
@Override
public void initialize(long randomSeed, int runNumber) throws IOException
{

1
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/flattened/SimulatorSSADirect.java
View file

@ -225,7 +225,6 @@ public class SimulatorSSADirect extends Simulator
* @throws IOException
* @throws XMLStreamException
*/
@Override
public void initialize(long randomSeed, int runNumber) throws IOException
{

91
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/HierarchicalSimulation.java
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@ -17,18 +17,12 @@ import java.io.File;
import java.io.IOException;
import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.PriorityQueue;
import java.util.Random;
import java.util.Set;
import javax.xml.stream.XMLStreamException;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBMLErrorLog;
import org.sbml.jsbml.SBMLReader;
import edu.utah.ece.async.ibiosim.analysis.properties.AnalysisProperties;
import edu.utah.ece.async.ibiosim.analysis.properties.SimulationProperties;
import edu.utah.ece.async.ibiosim.analysis.simulation.AbstractSimulator;
@ -69,15 +63,11 @@ public abstract class HierarchicalSimulation extends AbstractSimulator
private boolean cancelFlag;
private int currentRun;
private boolean printConcentrations;
private boolean sbmlHasErrorsFlag;
private String abstraction;
protected PriorityQueue<TriggeredEventNode> triggeredEventList;
protected boolean isInitialized;
protected boolean hasEvents;
private boolean isGrid;
private Random randomNumberGenerator;
private HierarchicalModel topmodel;
@ -126,9 +116,7 @@ public abstract class HierarchicalSimulation extends AbstractSimulator
{
this.properties = copy.properties;
this.printTime = copy.printTime;
this.abstraction = copy.abstraction;
this.type = copy.type;
this.isGrid = copy.isGrid;
this.topmodel = copy.topmodel;
this.currentTime = copy.currentTime;
this.randomNumberGenerator = copy.randomNumberGenerator;
@ -177,7 +165,7 @@ public abstract class HierarchicalSimulation extends AbstractSimulator
/**
* @return the cancelFlag
*/
public boolean isCancelFlag()
protected boolean isCancelFlag()
{
return cancelFlag;
}
@ -199,23 +187,6 @@ public abstract class HierarchicalSimulation extends AbstractSimulator
}
/**
* @return the printConcentrations
*/
public boolean isPrintConcentrations()
{
return printConcentrations;
}
/**
* @return the sbmlHasErrorsFlag
*/
public boolean isSbmlHasErrorsFlag()
{
return sbmlHasErrorsFlag;
}
/**
* @param cancelFlag
* the cancelFlag to set
@ -244,52 +215,12 @@ public abstract class HierarchicalSimulation extends AbstractSimulator
}
/**
* @param printConcentrations
* the printConcentrations to set
*/
public void setPrintConcentrations(boolean printConcentrations)
{
this.printConcentrations = printConcentrations;
}
/**
* @param sbmlHasErrorsFlag
* the sbmlHasErrorsFlag to set
*/
public void setSbmlHasErrorsFlag(boolean sbmlHasErrorsFlag)
{
this.sbmlHasErrorsFlag = sbmlHasErrorsFlag;
}
/**
*
* @return
*/
public String getAbstraction()
{
return abstraction;
}
/**
*
* @param abstraction
*/
public void setAbstraction(String abstraction)
{
this.abstraction = abstraction;
}
/**
* @return the randomNumberGenerator
*/
public Random getRandomNumberGenerator()
protected double getRandom()
{
return randomNumberGenerator;
return randomNumberGenerator.nextDouble();
}
@ -302,22 +233,6 @@ public abstract class HierarchicalSimulation extends AbstractSimulator
return topmodel;
}
/**
* @return the isGrid
*/
public boolean isGrid()
{
return isGrid;
}
/**
* @param isGrid
* the isGrid to set
*/
public void setGrid(boolean isGrid)
{
this.isGrid = isGrid;
}
/**
* @param topmodel
* the topmodel to set

13
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/methods/HierarchicalFBASimulator.java
View file

@ -86,13 +86,6 @@ class HierarchicalFBASimulator extends HierarchicalSimulation
}
@Override
public void clear()
{
// TODO Auto-generated method stub
}
@Override
public void setupForNewRun(int newRun)
{
@ -107,12 +100,6 @@ class HierarchicalFBASimulator extends HierarchicalSimulation
}
@Override
public void initialize(long randomSeed, int runNumber) throws IOException, XMLStreamException
{
}
public void getState()
{

6
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/methods/HierarchicalMixedSimulator.java
View file

@ -55,7 +55,6 @@ public final class HierarchicalMixedSimulator extends HierarchicalSimulation
}
@Override
public void initialize(long randomSeed, int runNumber) throws IOException, XMLStreamException, BioSimException
{
if (!isInitialized)
@ -136,11 +135,6 @@ public final class HierarchicalMixedSimulator extends HierarchicalSimulation
{
}
@Override
public void clear()
{
}
@Override
public void setupForNewRun(int newRun)
{

9
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/methods/HierarchicalODERKSimulator.java
View file

@ -81,14 +81,7 @@ public final class HierarchicalODERKSimulator extends HierarchicalSimulation {
public void cancel() {
setCancelFlag(true);
}
@Override
public void clear() {
}
@Override
public void initialize(long randomSeed, int runNumber)
throws IOException, XMLStreamException, BioSimException {
if (!isInitialized) {

19
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/methods/HierarchicalSSADirectSimulator.java
View file

@ -62,8 +62,6 @@ public class HierarchicalSSADirectSimulator extends HierarchicalSimulation
}
@Override
public void initialize(long randomSeed, int runNumber) throws IOException, XMLStreamException, BioSimException
{
if (!isInitialized)
@ -102,15 +100,6 @@ public class HierarchicalSSADirectSimulator extends HierarchicalSimulation
setCancelFlag(true);
}
/**
* clears data structures for new run
*/
@Override
public void clear()
{
}
@Override
public void setupForNewRun(int newRun) throws IOException
{
@ -129,10 +118,6 @@ public class HierarchicalSSADirectSimulator extends HierarchicalSimulation
double r1 = 0, r2 = 0, totalPropensity = 0, delta_t = 0, nextReactionTime = 0, previousTime = 0, nextEventTime = 0, nextMaxTime = 0;
double timeLimit = simProperties.getTimeLimit();
double maxTimeStep = simProperties.getMaxTimeStep();
if (isSbmlHasErrorsFlag())
{
return;
}
if (!isInitialized)
{
@ -149,8 +134,8 @@ public class HierarchicalSSADirectSimulator extends HierarchicalSimulation
// return;
// }
double currentTime = this.currentTime.getState().getStateValue();
r1 = getRandomNumberGenerator().nextDouble();
r2 = getRandomNumberGenerator().nextDouble();
r1 = getRandom();
r2 = getRandom();
computePropensities();
totalPropensity = getTotalPropensity();
delta_t = Math.log(1 / r1) / totalPropensity;

33
analysis/src/test/java/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/HierarchyTest.java
View file

@ -2,19 +2,46 @@ package edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical;
import static org.junit.Assert.*;
import java.io.IOException;
import javax.xml.stream.XMLStreamException;
import org.junit.Before;
import org.junit.Test;
import edu.utah.ece.async.ibiosim.analysis.properties.AnalysisProperties;
import edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.methods.HierarchicalSSADirectSimulator;
import edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.model.HierarchicalModel;
import edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.model.HierarchicalModel.ModelType;
import edu.utah.ece.async.ibiosim.analysis.simulation.hierarchical.util.setup.ModelSetup;
import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.BioSimException;
public class HierarchyTest {
private AnalysisProperties properties;
@Before
public void setUp() throws Exception {
String root = HierarchyTest.class.getResource(".").getPath();
properties = new AnalysisProperties("", "", root, false);
}
@Test
public void test() {
fail("Not yet implemented");
public void test_basic_setup() {
try {
properties.setModelFile("00001-sbml-l3v2.xml");
HierarchicalSimulation simulator = new HierarchicalSSADirectSimulator(properties);
ModelSetup.setupModels(simulator, ModelType.NONE);
assertEquals(simulator.getListOfHierarchicalModels().size(), 1);
HierarchicalModel model = simulator.getListOfHierarchicalModels().get(0);
assertEquals(model.getReactions().size(), 1);
assertEquals(model.getNode("S1").getState().getState(0).getStateValue(), 0.00015, 1e-9);
assertEquals(model.getNode("S2").getState().getState(0).getStateValue(), 0, 0);
assertEquals(model.getNode("compartment").getState().getState(0).getStateValue(), 1, 0);
assertEquals(model.getNode("k1").getState().getState(0).getStateValue(), 1, 0);
} catch (IOException | XMLStreamException | BioSimException e) {
fail("Could not initialize");
}
}
}

52
analysis/src/test/resources/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/00001-sbml-l3v2.xml Normal file
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@ -0,0 +1,52 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="_case00001" id="case00001" name="case00001" timeUnits="time">
<listOfUnitDefinitions>
<unitDefinition id="volume">
<listOfUnits>
<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="substance">
<listOfUnits>
<unit kind="mole" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="time">
<listOfUnits>
<unit kind="second" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1" name="S1" compartment="compartment" initialAmount="0.00015" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="1" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="reaction1" name="reaction1" reversible="false">
<listOfReactants>
<speciesReference species="S1" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S2" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> compartment </ci>
<ci> k1 </ci>
<ci> S1 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

35
analysis/src/test/resources/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/00029-sbml-l3v2.xml Normal file
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@ -0,0 +1,35 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="_case00029" id="case00029" name="case00029" timeUnits="time">
<listOfUnitDefinitions>
<unitDefinition id="volume">
<listOfUnits>
<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="substance">
<listOfUnits>
<unit kind="mole" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="time">
<listOfUnits>
<unit kind="second" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1" name="S1" compartment="compartment" initialAmount="7" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfRules>
<assignmentRule metaid="rule1" variable="S1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<cn type="integer"> 7 </cn>
</math>
</assignmentRule>
</listOfRules>
</model>
</sbml>

79
analysis/src/test/resources/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/00119-sbml-l3v2.xml Normal file
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@ -0,0 +1,79 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="_case00119" id="case00119" name="case00119" timeUnits="time">
<listOfFunctionDefinitions>
<functionDefinition id="multiply" name="multiply">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> x </ci>
</bvar>
<bvar>
<ci> y </ci>
</bvar>
<apply>
<times/>
<ci> x </ci>
<ci> y </ci>
</apply>
</lambda>
</math>
</functionDefinition>
</listOfFunctionDefinitions>
<listOfUnitDefinitions>
<unitDefinition id="volume">
<listOfUnits>
<unit kind="litre" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="substance">
<listOfUnits>
<unit kind="mole" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="time">
<listOfUnits>
<unit kind="second" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="compartment" name="compartment" spatialDimensions="3" size="1" units="volume" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="S1" name="S1" compartment="compartment" initialAmount="1.5" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S2" name="S2" compartment="compartment" initialAmount="0" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="S3" name="S3" compartment="compartment" initialAmount="2" substanceUnits="substance" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="true"/>
</listOfSpecies>
<listOfParameters>
<parameter id="k1" name="k1" value="1.5" constant="true"/>
</listOfParameters>
<listOfReactions>
<reaction id="reaction1" name="reaction1" reversible="false">
<listOfReactants>
<speciesReference species="S1" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="S2" stoichiometry="1" constant="true"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="S3"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> compartment </ci>
<ci> k1 </ci>
<apply>
<ci> multiply </ci>
<ci> S1 </ci>
<ci> S3 </ci>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>

56
analysis/src/test/resources/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/00163-sbml-l3v2.xml Normal file
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@ -0,0 +1,56 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="_case00163" id="case00163" name="case00163" timeUnits="time">
<listOfUnitDefinitions>
<unitDefinition id="time">
<listOfUnits>
<unit kind="second" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfParameters>
<parameter id="S1" name="S1" value="0.015" constant="false"/>
<parameter id="S2" name="S2" value="0" constant="false"/>
<parameter id="k1" name="k1" value="0.5" constant="true"/>
<parameter id="k2" name="k2" value="0.5" constant="true"/>
</listOfParameters>
<listOfRules>
<rateRule metaid="rule1" variable="S1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<times/>
<ci> k2 </ci>
<ci> S2 </ci>
</apply>
<apply>
<times/>
<cn type="integer"> -1 </cn>
<ci> k1 </ci>
<ci> S1 </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule metaid="rule2" variable="S2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<times/>
<ci> k1 </ci>
<ci> S1 </ci>
</apply>
<apply>
<times/>
<cn type="integer"> -1 </cn>
<ci> k2 </ci>
<ci> S2 </ci>
</apply>
</apply>
</math>
</rateRule>
</listOfRules>
</model>
</sbml>

60
analysis/src/test/resources/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/00171-sbml-l3v2.xml Normal file
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@ -0,0 +1,60 @@
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model metaid="_case00171" id="case00171" name="case00171" timeUnits="time">
<listOfFunctionDefinitions>
<functionDefinition id="multiply" name="multiply">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<bvar>
<ci> x </ci>
</bvar>
<bvar>
<ci> y </ci>
</bvar>
<apply>
<times/>
<ci> x </ci>
<ci> y </ci>
</apply>
</lambda>
</math>
</functionDefinition>
</listOfFunctionDefinitions>
<listOfUnitDefinitions>
<unitDefinition id="time">
<listOfUnits>
<unit kind="second" exponent="1" scale="0" multiplier="1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfParameters>
<parameter id="S1" name="S1" value="0.015" constant="false"/>
<parameter id="S2" name="S2" value="0.015" constant="false"/>
<parameter id="k1" name="k1" value="1" constant="true"/>
</listOfParameters>
<listOfRules>
<rateRule metaid="rule1" variable="S1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<cn type="integer"> -1 </cn>
<apply>
<ci> multiply </ci>
<ci> k1 </ci>
<ci> S1 </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule metaid="rule2" variable="S2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<ci> multiply </ci>
<ci> k1 </ci>
<ci> S1 </ci>
</apply>
</math>
</rateRule>
</listOfRules>
</model>
</sbml>

45
analysis/src/test/resources/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/01311-sbml-l3v2.xml Normal file
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@ -0,0 +1,45 @@
<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.9.0 with libSBML version 5.14.1. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model id="case01311" name="case01311">
<listOfFunctionDefinitions>
<functionDefinition id="three">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<cn type="integer"> 3 </cn>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="getthree">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<apply>
<ci> three </ci>
</apply>
</lambda>
</math>
</functionDefinition>
<functionDefinition id="getgetthree">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<lambda>
<apply>
<ci> getthree </ci>
</apply>
</lambda>
</math>
</functionDefinition>
</listOfFunctionDefinitions>
<listOfParameters>
<parameter id="p1" constant="true"/>
</listOfParameters>
<listOfInitialAssignments>
<initialAssignment symbol="p1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<ci> getgetthree </ci>
</apply>
</math>
</initialAssignment>
</listOfInitialAssignments>
</model>
</sbml>

10
analysis/src/test/resources/edu/utah/ece/async/ibiosim/analysis/simulation/hierarchical/README.md Normal file
View file

@ -0,0 +1,10 @@
# Test cases for the hierarchical simulator
## From the SBML Test Suite
- 00001-sbml-l3v2.xml
- 00029-sbml-l3v2.xml
- 00119-sbml-l3v2.xml
- 00163-sbml-l3v2.xml
- 00171-sbml-l3v2.xml
- 01311-sbml-l3v2.xml

13
learn/src/main/java/edu/utah/ece/async/ibiosim/learn/parameterestimator/ParameterEstimator.java
View file

@ -44,18 +44,6 @@ import edu.utah.ece.async.ibiosim.learn.parameterestimator.methods.sres.SRES;
*/
public class ParameterEstimator
{
static double relativeError = 1e-6;
static double absoluteError = 1e-9;
static int numSteps;
static double maxTimeStep = Double.POSITIVE_INFINITY;
static double minTimeStep = 0.0;
static long randomSeed = 0;
static int runs = 1;
static double stoichAmpValue = 1.0;
static boolean genStats = false;
static String selectedSimulator = "";
static ArrayList<String> interestingSpecies = new ArrayList<String>();
static String quantityType = "amount";
/**
* This function is used to execute parameter estimation from a given SBML file. The input model serves
@ -83,7 +71,6 @@ public class ParameterEstimator
double[] lowerbounds = new double[numberofparameters];
double[] upperbounds = new double[numberofparameters];
HierarchicalSimulation sim = new HierarchicalODERKSimulator(properties, false);
sim.initialize(randomSeed, 0);
for (int i = 0; i < numberofparameters; i++)
{