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refactor

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This commit is contained in:
LukasBuecherl 2022-07-25 13:39:02 -06:00
parent 8cffc3062b
commit a93e650de2
1 changed files with 7 additions and 51 deletions
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58
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/Converter.java
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@ -434,72 +434,28 @@ public class Converter {
try
{
/*
org.sbml.libsbml.SBMLReader reader = new org.sbml.libsbml.SBMLReader();
org.sbml.libsbml.SBMLDocument document = reader.readSBML(fullInputFileName);
document.setPackageRequired("comp", true);
org.sbml.libsbml.CompModelPlugin sbmlCompModel = (org.sbml.libsbml.CompModelPlugin) document.getModel().getPlugin("comp");
long numSubModels = sbmlCompModel.getNumSubmodels();
System.err.println(numSubModels);
*/
// Read in the SBML
inputSBMLDoc = SBMLutilities.readSBML(fullInputFileName, null, null);
//SBML2PRISM.convertSBML2PRISM(inputSBMLDoc, fullInputFileName, PrismUnbound);
// Create BioModel to allow flattening
File path = new File(fullInputFileName);
BioModel bioModel = new BioModel(path.getParent());
bioModel.load(fullInputFileName);
bioModel.createCompPlugin();
System.err.println(bioModel.getListOfSubmodels());
// Check if BioModel is hierarchical by checking the number of submodels
bioModel.createCompPlugin();
if(bioModel.getListOfSubmodels().isEmpty())
{
// Not hierarchical
SBML2PRISM.convertSBML2PRISM(inputSBMLDoc, fullInputFileName, PrismUnbound);
}else {
// hierarchical, therefore flatten model
if (bioModel.flattenModel(true) != null) {
SBMLDocument sbml = bioModel.flattenModel(true);
SBML2PRISM.convertSBML2PRISM(sbml, fullInputFileName, PrismUnbound);
}
}
/*
if (bioModel.flattenModel(true) != null) {
SBMLDocument sbml = bioModel.flattenModel(true);
//SBMLDocument sbml = bioModel.getSBMLDocument();
//System.err.println(inputSBMLDoc.equals(inputSBMLDoc));
//System.err.println(sbml.equals(sbml));
//System.err.println(sbml.equals(sbml));
SBML2PRISM.convertSBML2PRISM(sbml, fullInputFileName, PrismUnbound);
}
*/
/*
File path = new File(fullInputFileName);
// BioObservable p = null;
// BioModel bioModel = BioModel.createBioModel(path.getParent(), p);
BioModel bioModel = new BioModel(path.getParent());
bioModel.load(fullInputFileName);
if (bioModel.flattenModel(true) != null) {
//SBMLDocument sbml = bioModel.flattenModel(true);
SBMLDocument sbml = bioModel.getSBMLDocument();
//System.err.println(inputSBMLDoc.equals(inputSBMLDoc));
//System.err.println(sbml.equals(sbml));
//System.err.println(sbml.equals(sbml));
//SBML2PRISM.convertSBML2PRISM(sbml, fullInputFileName, PrismUnbound);
}
*/
}
catch (XMLStreamException e)
{
@ -508,7 +464,7 @@ public class Converter {
}
catch (IOException e)
{
System.err.println("ERROR: Unable to read or write file");
System.err.println("ERROR: Unable to read or write prism file");
e.printStackTrace();
}
catch (BioSimException e) {