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Added correct species information for small molecules

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Added correct species information for small molecules
(boundarycondition, substanceunits, etc) in sub-models
This commit is contained in:
Pedro Fontanarrosa 2019-03-07 12:40:52 -07:00
parent 418e45e39e
commit ba1826dd55
1 changed files with 5 additions and 2 deletions
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7
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
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@ -2062,9 +2062,12 @@ public class BioModel extends CoreObservable{
Species smallMolecule = targetModel.getSBMLDocument().getModel().createSpecies();
smallMolecule.setId(promoterInteractions.get(promoter).get(modifi));
smallMolecule.setSBOTerm(GlobalConstants.SBO_SIMPLE_CHEMICAL);
smallMolecule.setCompartment(r.getCompartment());
smallMolecule.setHasOnlySubstanceUnits(true);
smallMolecule.setBoundaryCondition(true);
smallMolecule.setConstant(false);
//smallMolecule.setBoundaryCondition(true);
smallMolecule.setInitialAmount(0.0);
SBMLutilities.copyDimensionsToEdgeIndex(r, sbml.getModel().getSpecies(promoterInteractions.get(promoter).get(modifi)), input, "species");
createDirPort(smallMolecule.getId(), GlobalConstants.INPUT);