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Added stub code

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This commit is contained in:
Chris Myers 2022-03-31 15:31:04 -06:00
parent fce1d9b464
commit 7672cd24b9
2 changed files with 76 additions and 2 deletions
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2
analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/Run.java
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@ -541,6 +541,8 @@ public class Run extends CoreObservable implements ActionListener {
this.notifyObservers(message);
message.setLog("Saving PRISM Property file:\n" + filename.replace(".xml", ".pctl"));
this.notifyObservers(message);
// TODO: LUKAS
// bioModel.convertSBML2PRISM(logFile, filename);
LPN.convertLPN2PRISM(logFile, lhpnFile, filename.replace(".xml", ".prism"), bioModel.getSBMLDocument());
Preferences biosimrc = Preferences.userRoot();
String prismCmd = biosimrc.get("biosim.general.prism", "");

76
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
View file

@ -15,6 +15,7 @@ package edu.utah.ece.async.ibiosim.dataModels.biomodel.parser;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
@ -105,7 +106,6 @@ import edu.utah.ece.async.ibiosim.dataModels.util.observe.BioObservable;
import edu.utah.ece.async.ibiosim.dataModels.util.observe.BioObserver;
import edu.utah.ece.async.ibiosim.dataModels.util.observe.CoreObservable;
/**
* This class describes a GCM file
*
@ -4734,6 +4734,78 @@ public class BioModel extends CoreObservable{
speciesGlyph.getBoundingBox().getDimensions().setHeight(height);
}
}
// TODO: LUKAS
public void convertSBML2PRISM(FileWriter logFile,String filename) {
Model model = sbml.getModel();
// loop over parameters and write constants, if parameter not constant than error
for (int i=0; i < model.getSpeciesCount(); i++) {
Species s = model.getSpecies(i);
if (s.isConstant()) {
// write const
} else {
// write modules
}
}
// write pctl file using the SBML constraints
/*
File file = new File(filename);
try {
FileWriter out = new FileWriter(file);
out.write("ctmc\n");
for (String var : LPN.getVariables()) {
int i=0;
Place place;
String lastValue="";
while ((place = LPN.getPlace(var+i))!=null) {
Transition inTrans = place.getPreset()[0];
ExprTree assign = inTrans.getAssignTree(var);
lastValue = assign.toString();
i++;
}
Variable variable = LPN.getVariable(var);
String initValue = variable.getInitValue();
initValue = Long.toString((Math.round(Double.valueOf(initValue))));
if (lastValue.equals("")) {
out.write("const int "+var+"="+initValue+";\n");
} else {
out.write("module "+var+"_def\n");
out.write(" "+var+" : "+"[0.."+lastValue+"] init "+initValue+";\n");
i=0;
while ((place = LPN.getPlace(var+i))!=null) {
Transition inTrans = place.getPreset()[0];
ExprTree assign = inTrans.getAssignTree(var);
out.write(" [] "+var+"="+assign.toString()+" -> ");
boolean first = true;
for (Transition outTrans : place.getPostset()) {
assign = outTrans.getAssignTree(var);
ExprTree delay = outTrans.getDelayTree();
String rate = delay.toString("prism");
rate = rate.replace("exponential", "");
if (!first) out.write(" + ");
out.write(rate+":("+var+"'="+assign.toString()+")");
first = false;
}
out.write(";\n");
i++;
}
out.write("endmodule\n");
}
}
out.close();
for (int i = 0; i < sbml.getModel().getConstraintCount(); i++) {
file = new File(filename.replace(".prism", ".pctl"));
out = new FileWriter(file);
out.write(SBMLutilities.convertMath2PrismProperty(sbml.getModel().getConstraint(i).getMath()));
out.close();
}
}
catch (IOException e) {
//TODO: Leandro fix Me
//message.setErrorDialog("Error Writing File", "I/O error when writing PRISM file");
}
*/
}
/**
* creates/removes grid species if a file is updated
@ -6471,7 +6543,7 @@ public class BioModel extends CoreObservable{
SBMLDocument result = null;
try {
result = flattenModelWithLibSBML(removeComp);
} catch (Exception e) {
} catch (Exception e) {
}
if (result!=null) {
result.getModel().setName("Created by libsbml flatten routine");