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Added Java AutoDocs

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CelloModeling removed unnecessary code
This commit is contained in:
Pedro Fontanarrosa 2019-04-26 09:52:47 -06:00
parent 412c01c44a
commit 507aa6f3f7
3 changed files with 68 additions and 23 deletions
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29
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/CelloModeling.java
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@ -106,20 +106,20 @@ public class CelloModeling {
removeSensorInteractios(resultMD, sensorMolecules);
HashMap<FunctionalComponent, HashMap<String, String>> celloParameters = new HashMap<FunctionalComponent, HashMap<String, String>>();
boolean CelloModel = false;
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)) {
//retrieve Cello Parameters, if the TU (promoter) has them. If this is true, then we are in the Cello Model Generation
//and both Degradation reactions and Production reactions will be modeled using Hamid's paper for dynamic modeling
//using Cello Parameters.
celloParameters.put(promoter, hasCelloParameters(promoter));
//Check if the TU has Cello Parameters "n", "K", "ymax" and "ymin". If yes, we are in a Cello Model generation case
if (!celloParameters.get(promoter).get("n").isEmpty() && !celloParameters.get(promoter).get("K").isEmpty() && !celloParameters.get(promoter).get("ymax").isEmpty() && !celloParameters.get(promoter).get("ymin").isEmpty()) {
CelloModel = true;
}
}
}
// for (FunctionalComponent promoter : resultMD.getFunctionalComponents()) {
// if (SBOL2SBML.isPromoterComponent(resultMD, promoter, sbolDoc)) {
// //retrieve Cello Parameters, if the TU (promoter) has them. If this is true, then we are in the Cello Model Generation
// //and both Degradation reactions and Production reactions will be modeled using Hamid's paper for dynamic modeling
// //using Cello Parameters.
// celloParameters.put(promoter, hasCelloParameters(promoter));
// //Check if the TU has Cello Parameters "n", "K", "ymax" and "ymin". If yes, we are in a Cello Model generation case
// if (!celloParameters.get(promoter).get("n").isEmpty() && !celloParameters.get(promoter).get("K").isEmpty() && !celloParameters.get(promoter).get("ymax").isEmpty() && !celloParameters.get(promoter).get("ymin").isEmpty()) {
// CelloModel = true;
// }
// }
// }
// Generate SBML Species for each part in the model
@ -670,6 +670,9 @@ public class CelloModeling {
*/
private static HashMap<String, List<String>> productionInteractions(SBOLDocument sbolDoc){
//Since it is not possible to determine in which production reactions each Engineered Region participates in, then we first have to look through all the ER, then through
//all production reactions, and match them
HashMap<String, List<String>> Prot_2_Param = new HashMap <String, List<String>>();
for (ComponentDefinition CD : sbolDoc.getComponentDefinitions()) {
if (CD.containsRole(SequenceOntology.ENGINEERED_REGION)) {

20
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/Converter.java
View file

@ -537,8 +537,8 @@ public class Converter {
SBOLDocument newSbolDoc = sbolDoc.createRecursiveCopy(top);
try {
newSbolDoc = VPRModelGenerator.generateModel(urlVPR, newSbolDoc, vpr_output);
//newSbolDoc = VPRModelGenerator.generateModel(urlVPR, newSbolDoc, "topModule");
//newSbolDoc = VPRModelGenerator.generateModel(urlVPR, newSbolDoc, vpr_output);
newSbolDoc = VPRModelGenerator.generateModel(urlVPR, newSbolDoc, "topModule");
} catch (VPRException e) {
System.err.println("ERROR: VPR generation fails");
e.printStackTrace();
@ -566,8 +566,8 @@ public class Converter {
//TODO PEDRO calling VPR
if (doVPR) {
try {
sbolDoc = VPRModelGenerator.generateModel(urlVPR, sbolDoc, vpr_output);
//sbolDoc = VPRModelGenerator.generateModel(urlVPR, sbolDoc, "topModule");
//sbolDoc = VPRModelGenerator.generateModel(urlVPR, sbolDoc, vpr_output);
sbolDoc = VPRModelGenerator.generateModel(urlVPR, sbolDoc, "topModule");
} catch (VPRException e) {
System.err.println("ERROR: VPR generation fails");
e.printStackTrace();
@ -590,15 +590,15 @@ public class Converter {
CompSBMLDocumentPlugin docPlugin = (CompSBMLDocumentPlugin) topEnvironment.getPlugin("comp");
ExternalModelDefinition exte = docPlugin.getExternalModelDefinition("TopModel");
exte.setId(vpr_output);
exte.setSource(vpr_output + ".xml");
//exte.setId("topModule");
//exte.setSource("topModule.xml");
//exte.setId(vpr_output);
//exte.setSource(vpr_output + ".xml");
exte.setId("topModule");
exte.setSource("topModule.xml");
CompModelPlugin SBMLplugin = (CompModelPlugin) topEnvironment.getModel().getPlugin("comp");
Submodel top = SBMLplugin.getSubmodel("C1");
top.setModelRef(vpr_output);
//top.setModelRef("topModule");
//top.setModelRef(vpr_output);
top.setModelRef("topModule");
SBMLWriter writing = new SBMLWriter();

42
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
View file

@ -2019,6 +2019,21 @@ public class BioModel extends CoreObservable{
return r;
}
/**
* Creates the cello SD production reactions.
*
* @author Pedro Fontanarrosa
* @param mRNA the m RNA
* @param reactionID the reaction ID
* @param TU the tu
* @param kSDdegrad the k S ddegrad
* @param onPort the on port
* @param dimensions the dimensions
* @param targetModel the target model
* @param promoters the promoters
* @param promoterInteractions the promoter interactions
* @return the reaction
*/
//TODO PEDRO createCelloSDProductionReaction
public Reaction createCelloSDProductionReactions(Species mRNA, String reactionID, String TU, String kSDdegrad, boolean onPort, String[] dimensions, BioModel targetModel, Set <String> promoters, HashMap<String, HashMap <String, String>> promoterInteractions) {
@ -2135,6 +2150,23 @@ public class BioModel extends CoreObservable{
return r;
}
/**
* Creates the cello TF production reactions.
*
* @author Pedro Fontanarrosa
* @param mRNA the m RNA
* @param rxnID the rxn ID
* @param products the products
* @param celloParameters the cello parameters
* @param kTFdegrad the k T fdegrad
* @param ko the ko
* @param kb the kb
* @param KoStr the ko str
* @param KaoStr the kao str
* @param onPort the on port
* @param dimensions the dimensions
* @return the reaction
*/
//TODO PEDRO createCelloTFProductionReaction
public Reaction createCelloTFProductionReactions(Species mRNA, String rxnID, List<Participation> products, HashMap<String, List<String>> celloParameters, String kTFdegrad, String ko,
String kb, String KoStr, String KaoStr, boolean onPort, String[] dimensions) {
@ -2264,6 +2296,16 @@ public class BioModel extends CoreObservable{
return reaction;
}
/**
* Creates the cello production kinetic law.
*
* @author Pedro Fontanarrosa
* @param reaction the reaction
* @param celloParameters the cello parameters
* @param promoterInteractions the promoter interactions
* @param promoters the promoters
* @return the string
*/
//TODO PEDRO createCelloProductionKineticLaw
public static String createCelloProductionKineticLaw(Reaction reaction, HashMap<String, List<String>> celloParameters, HashMap<String, HashMap <String, String>> promoterInteractions, Set<String> promoters) {
String kineticLaw = "";