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This commit is contained in:
Pedro Fontanarrosa 2019-04-29 09:26:28 -07:00
parent 507aa6f3f7
commit 878d0ff031
2 changed files with 36 additions and 35 deletions
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63
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/CelloModeling.java
View file

@ -20,7 +20,6 @@ import org.sbml.jsbml.Model;
import org.sbml.jsbml.Reaction;
import org.sbml.jsbml.Species;
import org.sbml.jsbml.ext.comp.CompSBasePlugin;
import org.sbml.jsbml.ext.comp.Port;
import org.sbml.jsbml.ext.comp.Submodel;
import org.sbolstandard.core2.Annotation;
import org.sbolstandard.core2.Component;
@ -106,7 +105,7 @@ public class CelloModeling {
removeSensorInteractios(resultMD, sensorMolecules);
HashMap<FunctionalComponent, HashMap<String, String>> celloParameters = new HashMap<FunctionalComponent, HashMap<String, String>>();
boolean CelloModel = true;
//boolean CelloModel = true;
// TODO there has to be a better way to determine if we are in a Cello model generation or not
// for (FunctionalComponent promoter : resultMD.getFunctionalComponents()) {
// if (SBOL2SBML.isPromoterComponent(resultMD, promoter, sbolDoc)) {
@ -136,14 +135,15 @@ public class CelloModeling {
SBOL2SBML.generateOutputPort(comp, targetModel);
}
} else if (SBOL2SBML.isPromoterComponent(resultMD, comp, sbolDoc)) {
generateTUSpecies(comp, sbolDoc, targetModel);
// If CelloModel, generate only one species for each TU
if (CelloModel) {
generateTUSpecies(comp, sbolDoc, targetModel);
}
// else, we are in normal model generation, which creates one species for each promoter in the TU
else {
SBOL2SBML.generatePromoterSpecies(comp, sbolDoc, targetModel);
}
// if (CelloModel) {
// generateTUSpecies(comp, sbolDoc, targetModel);
// }
// // else, we are in normal model generation, which creates one species for each promoter in the TU
// else {
// SBOL2SBML.generatePromoterSpecies(comp, sbolDoc, targetModel);
// }
if (SBOL2SBML.isInputComponent(comp)) {
SBOL2SBML.generateInputPort(comp, targetModel);
} else if (SBOL2SBML.isOutputComponent(comp)){
@ -272,26 +272,31 @@ public class CelloModeling {
if (!promoterToPartici.containsKey(promoter))
promoterToPartici.put(promoter, new LinkedList<Participation>());
//Check if the TU has Cello Parameters "n", "K", "ymax" and "ymin". If yes, Call new model generating method
if (CelloModel) {
//go to the new generateProductionRxn method
System.out.println("you are in new method call");
//Generate the Cello production reactions for mRNAs and Products for this TU (promoter)
generateCelloProductionRxns(promoter, promoterToPartici.get(promoter), promoterToProductions.get(promoter),
promoterToActivations.get(promoter), promoterToRepressions.get(promoter), promoterToProducts.get(promoter),
promoterToTranscribed.get(promoter), promoterToActivators.get(promoter),
promoterToRepressors.get(promoter), resultMD, sbolDoc, targetModel, Prot_2_Param, promoterInteractions);
//TODO PEDRO calling cello methods
//generateCelloDegradationRxn for all species produced, and for all mRNAs produced for each TU
}
//else call the normal model generating method
else {
SBOL2SBML.generateProductionRxn(promoter, promoterToPartici.get(promoter), promoterToProductions.get(promoter),
promoterToActivations.get(promoter), promoterToRepressions.get(promoter), promoterToProducts.get(promoter),
promoterToTranscribed.get(promoter), promoterToActivators.get(promoter),
promoterToRepressors.get(promoter), resultMD, sbolDoc, targetModel);
}
generateCelloProductionRxns(promoter, promoterToPartici.get(promoter), promoterToProductions.get(promoter),
promoterToActivations.get(promoter), promoterToRepressions.get(promoter), promoterToProducts.get(promoter),
promoterToTranscribed.get(promoter), promoterToActivators.get(promoter),
promoterToRepressors.get(promoter), resultMD, sbolDoc, targetModel, Prot_2_Param, promoterInteractions);
// //Check if the TU has Cello Parameters "n", "K", "ymax" and "ymin". If yes, Call new model generating method
// if (CelloModel) {
// //go to the new generateProductionRxn method
// System.out.println("you are in new method call");
//
// //Generate the Cello production reactions for mRNAs and Products for this TU (promoter)
// generateCelloProductionRxns(promoter, promoterToPartici.get(promoter), promoterToProductions.get(promoter),
// promoterToActivations.get(promoter), promoterToRepressions.get(promoter), promoterToProducts.get(promoter),
// promoterToTranscribed.get(promoter), promoterToActivators.get(promoter),
// promoterToRepressors.get(promoter), resultMD, sbolDoc, targetModel, Prot_2_Param, promoterInteractions);
// //TODO PEDRO calling cello methods
// //generateCelloDegradationRxn for all species produced, and for all mRNAs produced for each TU
// }
// //else call the normal model generating method
// else {
// SBOL2SBML.generateProductionRxn(promoter, promoterToPartici.get(promoter), promoterToProductions.get(promoter),
// promoterToActivations.get(promoter), promoterToRepressions.get(promoter), promoterToProducts.get(promoter),
// promoterToTranscribed.get(promoter), promoterToActivators.get(promoter),
// promoterToRepressors.get(promoter), resultMD, sbolDoc, targetModel);
// }
}
}

8
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
View file

@ -2419,13 +2419,10 @@ public class BioModel extends CoreObservable{
ymax_p.setId(ymax);
LocalParameter ymin_p = reaction.getKineticLaw().createLocalParameter();
ymin_p.setId(ymin);
//numerator = "piecewise(piece(" + ymin_p + " ," + sensor + " == 0.0), otherwise(" + ymax_p + "))";
numerator = "piecewise(" + ymin + ", (" + sensor + " == 0), " + ymax + ")";
System.out.println(numerator);
if (celloParameters.get(sensor) != null) {
double ymax_value = Double.parseDouble(celloParameters.get(sensor).get(0));
ymax_p.setValue(ymax_value);
@ -2440,7 +2437,6 @@ public class BioModel extends CoreObservable{
}
kineticLaw += " + " + "kdegrad" + "*" + in_parentesis;
}
System.out.println(kineticLaw);
return kineticLaw;
}