use of cbit.vcell.model.Kinetics.UnresolvedParameter in project vcell by virtualcell.
the class SBMLImporter method addReactions.
/**
* addReactions:
*/
protected void addReactions(VCMetaData metaData) {
if (sbmlModel == null) {
throw new SBMLImportException("SBML model is NULL");
}
ListOf<Reaction> reactions = sbmlModel.getListOfReactions();
final int numReactions = reactions.size();
if (numReactions == 0) {
lg.info("No Reactions");
return;
}
// all reactions
ArrayList<ReactionStep> vcReactionList = new ArrayList<>();
// just the fast ones
ArrayList<ReactionStep> fastReactionList = new ArrayList<>();
Model vcModel = vcBioModel.getSimulationContext(0).getModel();
ModelUnitSystem vcModelUnitSystem = vcModel.getUnitSystem();
SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
try {
for (Reaction sbmlRxn : reactions) {
ReactionStep vcReaction = null;
String rxnName = sbmlRxn.getId();
boolean bReversible = true;
if (sbmlRxn.isSetReversible()) {
bReversible = sbmlRxn.getReversible();
}
// Check of reaction annotation is present; if so, does it have
// an embedded element (flux or simpleRxn).
// Create a fluxReaction or simpleReaction accordingly.
Element sbmlImportRelatedElement = sbmlAnnotationUtil.readVCellSpecificAnnotation(sbmlRxn);
Structure reactionStructure = getReactionStructure(sbmlRxn, vcSpeciesContexts, sbmlImportRelatedElement);
if (sbmlImportRelatedElement != null) {
Element embeddedRxnElement = getEmbeddedElementInAnnotation(sbmlImportRelatedElement, REACTION);
if (embeddedRxnElement != null) {
if (embeddedRxnElement.getName().equals(XMLTags.FluxStepTag)) {
// If embedded element is a flux reaction, set flux
// reaction's strucure, flux carrier, physicsOption
// from the element attributes.
String structName = embeddedRxnElement.getAttributeValue(XMLTags.StructureAttrTag);
CastInfo<Membrane> ci = SBMLHelper.getTypedStructure(Membrane.class, vcModel, structName);
if (!ci.isGood()) {
throw new SBMLImportException("Appears that the flux reaction is occuring on " + ci.actualName() + ", not a membrane.");
}
vcReaction = new FluxReaction(vcModel, ci.get(), null, rxnName, bReversible);
vcReaction.setModel(vcModel);
// Set the fluxOption on the flux reaction based on
// whether it is molecular, molecular & electrical,
// electrical.
String fluxOptionStr = embeddedRxnElement.getAttributeValue(XMLTags.FluxOptionAttrTag);
if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularOnly)) {
((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_ONLY);
} else if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularAndElectrical)) {
((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_AND_ELECTRICAL);
} else if (fluxOptionStr.equals(XMLTags.FluxOptionElectricalOnly)) {
((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_ELECTRICAL_ONLY);
} else {
localIssueList.add(new Issue(vcReaction, issueContext, IssueCategory.SBMLImport_Reaction, "Unknown FluxOption : " + fluxOptionStr + " for SBML reaction : " + rxnName, Issue.SEVERITY_WARNING));
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.ErrorType.ReactionError,
// "Unknown FluxOption : " + fluxOptionStr +
// " for SBML reaction : " + rxnName);
}
} else if (embeddedRxnElement.getName().equals(XMLTags.SimpleReactionTag)) {
// if embedded element is a simple reaction, set
// simple reaction's structure from element
// attributes
vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
}
} else {
vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
}
} else {
vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnName, bReversible);
}
// set annotations and notes on vcReactions[i]
sbmlAnnotationUtil.readAnnotation(vcReaction, sbmlRxn);
sbmlAnnotationUtil.readNotes(vcReaction, sbmlRxn);
// the limit on the reactionName length.
if (rxnName.length() > 64) {
String freeTextAnnotation = metaData.getFreeTextAnnotation(vcReaction);
if (freeTextAnnotation == null) {
freeTextAnnotation = "";
}
StringBuffer oldRxnAnnotation = new StringBuffer(freeTextAnnotation);
oldRxnAnnotation.append("\n\n" + rxnName);
metaData.setFreeTextAnnotation(vcReaction, oldRxnAnnotation.toString());
}
// Now add the reactants, products, modifiers as specified by
// the sbmlRxn
addReactionParticipants(sbmlRxn, vcReaction);
KineticLaw kLaw = sbmlRxn.getKineticLaw();
Kinetics kinetics = null;
if (kLaw != null) {
// Convert the formula from kineticLaw into MathML and then
// to an expression (infix) to be used in VCell kinetics
ASTNode sbmlRateMath = kLaw.getMath();
Expression kLawRateExpr = getExpressionFromFormula(sbmlRateMath);
Expression vcRateExpression = new Expression(kLawRateExpr);
// modifier (catalyst) to the reaction.
for (int k = 0; k < vcSpeciesContexts.length; k++) {
if (vcRateExpression.hasSymbol(vcSpeciesContexts[k].getName())) {
if ((vcReaction.getReactant(vcSpeciesContexts[k].getName()) == null) && (vcReaction.getProduct(vcSpeciesContexts[k].getName()) == null) && (vcReaction.getCatalyst(vcSpeciesContexts[k].getName()) == null)) {
// This means that the speciesContext is not a
// reactant, product or modifier : it has to be
// added to the VC Rxn as a catalyst
vcReaction.addCatalyst(vcSpeciesContexts[k]);
}
}
}
// set kinetics on VCell reaction
if (bSpatial) {
// if spatial SBML ('isSpatial' attribute set), create
// DistributedKinetics)
SpatialReactionPlugin ssrplugin = (SpatialReactionPlugin) sbmlRxn.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
// 'spatial'
if (ssrplugin != null && ssrplugin.getIsLocal()) {
kinetics = new GeneralKinetics(vcReaction);
} else {
kinetics = new GeneralLumpedKinetics(vcReaction);
}
} else {
kinetics = new GeneralLumpedKinetics(vcReaction);
}
// set kinetics on vcReaction
vcReaction.setKinetics(kinetics);
// If the name of the rate parameter has been changed by
// user, or matches with global/local param,
// it has to be changed.
resolveRxnParameterNameConflicts(sbmlRxn, kinetics, sbmlImportRelatedElement);
/**
* Now, based on the kinetic law expression, see if the rate
* is expressed in concentration/time or substance/time : If
* the compartment_id of the compartment corresponding to
* the structure in which the reaction takes place occurs in
* the rate law expression, it is in concentration/time;
* divide it by the compartment size and bring in the rate
* law as 'Distributed' kinetics. If not, the rate law is in
* substance/time; bring it in (as is) as 'Lumped' kinetics.
*/
ListOf<LocalParameter> localParameters = kLaw.getListOfLocalParameters();
for (LocalParameter p : localParameters) {
String paramName = p.getId();
KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
if (kineticsParameter == null) {
// add unresolved for now to prevent errors in kinetics.setParameterValue(kp,vcRateExpression) below
kinetics.addUnresolvedParameter(paramName);
}
}
KineticsParameter kp = kinetics.getAuthoritativeParameter();
if (lg.isDebugEnabled()) {
lg.debug("Setting " + kp.getName() + ": " + vcRateExpression.infix());
}
kinetics.setParameterValue(kp, vcRateExpression);
// If there are any global parameters used in the kinetics,
// and if they have species,
// check if the species are already reactionParticipants in
// the reaction. If not, add them as catalysts.
KineticsProxyParameter[] kpps = kinetics.getProxyParameters();
for (int j = 0; j < kpps.length; j++) {
if (kpps[j].getTarget() instanceof ModelParameter) {
ModelParameter mp = (ModelParameter) kpps[j].getTarget();
HashSet<String> refSpeciesNameHash = new HashSet<String>();
getReferencedSpeciesInExpr(mp.getExpression(), refSpeciesNameHash);
java.util.Iterator<String> refSpIterator = refSpeciesNameHash.iterator();
while (refSpIterator.hasNext()) {
String spName = refSpIterator.next();
org.sbml.jsbml.Species sp = sbmlModel.getSpecies(spName);
ArrayList<ReactionParticipant> rpArray = getVCReactionParticipantsFromSymbol(vcReaction, sp.getId());
if (rpArray == null || rpArray.size() == 0) {
// This means that the speciesContext is not
// a reactant, product or modifier : it has
// to be added as a catalyst
vcReaction.addCatalyst(vcModel.getSpeciesContext(sp.getId()));
}
}
}
}
// model - local params cannot be defined by rules.
for (LocalParameter param : localParameters) {
String paramName = param.getId();
Expression exp = new Expression(param.getValue());
String unitString = param.getUnits();
VCUnitDefinition paramUnit = sbmlUnitIdentifierHash.get(unitString);
if (paramUnit == null) {
paramUnit = vcModelUnitSystem.getInstance_TBD();
}
// check if sbml local param is in kinetic params list;
// if so, add its value.
boolean lpSet = false;
KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
if (kineticsParameter != null) {
if (lg.isDebugEnabled()) {
lg.debug("Setting local " + kineticsParameter.getName() + ": " + exp.infix());
}
kineticsParameter.setExpression(exp);
kineticsParameter.setUnitDefinition(paramUnit);
lpSet = true;
} else {
UnresolvedParameter ur = kinetics.getUnresolvedParameter(paramName);
if (ur != null) {
kinetics.addUserDefinedKineticsParameter(paramName, exp, paramUnit);
lpSet = true;
}
}
if (!lpSet) {
// check if it is a proxy parameter (specifically,
// speciesContext or model parameter (structureSize
// too)).
KineticsProxyParameter kpp = kinetics.getProxyParameter(paramName);
// and units to local param values
if (kpp != null && kpp.getTarget() instanceof ModelParameter) {
kinetics.convertParameterType(kpp, false);
kineticsParameter = kinetics.getKineticsParameter(paramName);
kinetics.setParameterValue(kineticsParameter, exp);
kineticsParameter.setUnitDefinition(paramUnit);
}
}
}
} else {
// sbmlKLaw was null, so creating a GeneralKinetics with 0.0
// as rate.
kinetics = new GeneralKinetics(vcReaction);
}
// end - if-else KLaw != null
// set the reaction kinetics, and add reaction to the vcell
// model.
kinetics.resolveUndefinedUnits();
// System.out.println("ADDED SBML REACTION : \"" + rxnName +
// "\" to VCModel");
vcReactionList.add(vcReaction);
if (sbmlRxn.isSetFast() && sbmlRxn.getFast()) {
fastReactionList.add(vcReaction);
}
}
// end - for vcReactions
ReactionStep[] array = vcReactionList.toArray(new ReactionStep[vcReactionList.size()]);
vcModel.setReactionSteps(array);
final ReactionContext rc = vcBioModel.getSimulationContext(0).getReactionContext();
for (ReactionStep frs : fastReactionList) {
final ReactionSpec rs = rc.getReactionSpec(frs);
rs.setReactionMapping(ReactionSpec.FAST);
}
} catch (ModelPropertyVetoException mpve) {
throw new SBMLImportException(mpve.getMessage(), mpve);
} catch (Exception e1) {
e1.printStackTrace(System.out);
throw new SBMLImportException(e1.getMessage(), e1);
}
}
use of cbit.vcell.model.Kinetics.UnresolvedParameter in project vcell by virtualcell.
the class BioModelParametersTableModel method propertyChange.
@Override
public void propertyChange(java.beans.PropertyChangeEvent evt) {
super.propertyChange(evt);
if (evt.getSource() instanceof EditableSymbolTableEntry) {
int changeRow = getRowIndex((EditableSymbolTableEntry) evt.getSource());
if (changeRow >= 0) {
fireTableRowsUpdated(changeRow, changeRow);
}
} else {
String propertyName = evt.getPropertyName();
if (evt.getSource() == bioModel.getModel()) {
if (propertyName.equals(Model.PROPERTY_NAME_MODEL_PARAMETERS)) {
ModelParameter[] oldValue = (ModelParameter[]) evt.getOldValue();
if (oldValue != null) {
for (EditableSymbolTableEntry parameter : oldValue) {
parameter.removePropertyChangeListener(this);
}
}
ModelParameter[] newValue = (ModelParameter[]) evt.getNewValue();
if (newValue != null) {
for (EditableSymbolTableEntry parameter : newValue) {
parameter.addPropertyChangeListener(this);
}
}
refreshData();
} else if (propertyName.equals(Model.PROPERTY_NAME_SPECIES_CONTEXTS)) {
SpeciesContext[] oldValue = (SpeciesContext[]) evt.getOldValue();
if (oldValue != null) {
for (SpeciesContext sc : oldValue) {
sc.removePropertyChangeListener(this);
}
}
SpeciesContext[] newValue = (SpeciesContext[]) evt.getNewValue();
if (newValue != null) {
for (SpeciesContext sc : newValue) {
sc.addPropertyChangeListener(this);
}
}
refreshData();
} else if (propertyName.equals(Model.PROPERTY_NAME_REACTION_STEPS)) {
ReactionStep[] oldValue = (ReactionStep[]) evt.getOldValue();
if (oldValue != null) {
for (ReactionStep reactionStep : oldValue) {
reactionStep.removePropertyChangeListener(this);
reactionStep.getKinetics().removePropertyChangeListener(this);
for (KineticsParameter kineticsEditableSymbolTableEntry : reactionStep.getKinetics().getKineticsParameters()) {
kineticsEditableSymbolTableEntry.removePropertyChangeListener(this);
}
for (ProxyParameter proxyEditableSymbolTableEntry : reactionStep.getKinetics().getProxyParameters()) {
proxyEditableSymbolTableEntry.removePropertyChangeListener(this);
}
for (UnresolvedParameter unresolvedEditableSymbolTableEntry : reactionStep.getKinetics().getUnresolvedParameters()) {
unresolvedEditableSymbolTableEntry.removePropertyChangeListener(this);
}
}
}
ReactionStep[] newValue = (ReactionStep[]) evt.getNewValue();
if (newValue != null) {
for (ReactionStep reactionStep : newValue) {
reactionStep.addPropertyChangeListener(this);
reactionStep.getKinetics().addPropertyChangeListener(this);
for (KineticsParameter kineticsEditableSymbolTableEntry : reactionStep.getKinetics().getKineticsParameters()) {
kineticsEditableSymbolTableEntry.addPropertyChangeListener(this);
}
for (ProxyParameter proxyEditableSymbolTableEntry : reactionStep.getKinetics().getProxyParameters()) {
proxyEditableSymbolTableEntry.addPropertyChangeListener(this);
}
for (UnresolvedParameter unresolvedEditableSymbolTableEntry : reactionStep.getKinetics().getUnresolvedParameters()) {
unresolvedEditableSymbolTableEntry.addPropertyChangeListener(this);
}
}
}
refreshData();
} else if (evt.getPropertyName().equals(RbmModelContainer.PROPERTY_NAME_REACTION_RULE_LIST)) {
List<ReactionRule> oldValue = (List<ReactionRule>) evt.getOldValue();
if (oldValue != null) {
for (ReactionRule rs : oldValue) {
rs.removePropertyChangeListener(this);
}
}
List<ReactionRule> newValue = (List<ReactionRule>) evt.getNewValue();
if (newValue != null) {
for (ReactionRule rs : newValue) {
rs.addPropertyChangeListener(this);
}
}
refreshData();
}
} else if (evt.getSource() == bioModel) {
if (propertyName.equals(BioModel.PROPERTY_NAME_SIMULATION_CONTEXTS)) {
SimulationContext[] oldValue = (SimulationContext[]) evt.getOldValue();
for (SimulationContext simulationContext : oldValue) {
simulationContext.removePropertyChangeListener(this);
simulationContext.getGeometryContext().removePropertyChangeListener(this);
for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
mapping.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
simulationContext.getReactionContext().removePropertyChangeListener(this);
for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
spec.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : spec.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
elect.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : elect.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
spatialObject.removePropertyChangeListener(this);
}
for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
spatialProcess.removePropertyChangeListener(this);
for (LocalParameter p : spatialProcess.getParameters()) {
p.removePropertyChangeListener(this);
}
}
for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
p.removePropertyChangeListener(this);
}
}
SimulationContext[] newValue = (SimulationContext[]) evt.getNewValue();
for (SimulationContext simulationContext : newValue) {
simulationContext.addPropertyChangeListener(this);
simulationContext.getGeometryContext().addPropertyChangeListener(this);
for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
mapping.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
simulationContext.getReactionContext().addPropertyChangeListener(this);
for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
spec.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : spec.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
elect.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : elect.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
spatialObject.addPropertyChangeListener(this);
}
for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
spatialProcess.addPropertyChangeListener(this);
for (LocalParameter p : spatialProcess.getParameters()) {
p.addPropertyChangeListener(this);
}
}
for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
p.addPropertyChangeListener(this);
}
}
refreshData();
}
} else if (evt.getSource() instanceof GeometryContext && evt.getPropertyName().equals(GeometryContext.PROPERTY_STRUCTURE_MAPPINGS)) {
StructureMapping[] oldValue = (StructureMapping[]) evt.getOldValue();
if (oldValue != null) {
for (StructureMapping mapping : oldValue) {
mapping.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
}
StructureMapping[] newValue = (StructureMapping[]) evt.getNewValue();
if (newValue != null) {
for (StructureMapping mapping : newValue) {
mapping.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
}
refreshData();
} else if (evt.getSource() instanceof ReactionStep && (evt.getPropertyName().equals(ReactionStep.PROPERTY_NAME_KINETICS))) {
Kinetics oldValue = (Kinetics) evt.getOldValue();
if (oldValue != null) {
oldValue.removePropertyChangeListener(this);
for (KineticsParameter kineticsEditableSymbolTableEntry : oldValue.getKineticsParameters()) {
kineticsEditableSymbolTableEntry.removePropertyChangeListener(this);
}
for (ProxyParameter proxyEditableSymbolTableEntry : oldValue.getProxyParameters()) {
proxyEditableSymbolTableEntry.removePropertyChangeListener(this);
}
for (UnresolvedParameter unresolvedEditableSymbolTableEntry : oldValue.getUnresolvedParameters()) {
unresolvedEditableSymbolTableEntry.removePropertyChangeListener(this);
}
}
Kinetics newValue = (Kinetics) evt.getNewValue();
if (newValue != null) {
newValue.addPropertyChangeListener(this);
for (KineticsParameter kineticsEditableSymbolTableEntry : newValue.getKineticsParameters()) {
kineticsEditableSymbolTableEntry.addPropertyChangeListener(this);
}
for (ProxyParameter proxyEditableSymbolTableEntry : newValue.getProxyParameters()) {
proxyEditableSymbolTableEntry.addPropertyChangeListener(this);
}
for (UnresolvedParameter unresolvedEditableSymbolTableEntry : newValue.getUnresolvedParameters()) {
unresolvedEditableSymbolTableEntry.addPropertyChangeListener(this);
}
}
refreshData();
} else if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_SPATIALPROCESSES)) {
SpatialProcess[] oldValue = (SpatialProcess[]) evt.getOldValue();
if (oldValue != null) {
for (SpatialProcess process : oldValue) {
process.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : process.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
}
SpatialProcess[] newValue = (SpatialProcess[]) evt.getNewValue();
if (newValue != null) {
for (SpatialProcess process : newValue) {
process.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : process.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
}
refreshData();
} else if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_SPATIALOBJECTS)) {
SpatialObject[] oldValue = (SpatialObject[]) evt.getOldValue();
if (oldValue != null) {
for (SpatialObject spatialObject : oldValue) {
spatialObject.removePropertyChangeListener(this);
}
}
SpatialObject[] newValue = (SpatialObject[]) evt.getNewValue();
if (newValue != null) {
for (SpatialObject spatialObject : newValue) {
spatialObject.addPropertyChangeListener(this);
}
}
refreshData();
} else if (evt.getSource() instanceof SpatialObject && evt.getPropertyName().equals(SpatialObject.PROPERTY_NAME_QUANTITYCATEGORIESENABLED)) {
refreshData();
} else if (evt.getSource() instanceof SimulationContext && evt.getPropertyName().equals(SimulationContext.PROPERTY_NAME_SIMULATIONCONTEXTPARAMETERS)) {
SimulationContextParameter[] oldValue = (SimulationContextParameter[]) evt.getOldValue();
if (oldValue != null) {
for (SimulationContextParameter param : oldValue) {
param.removePropertyChangeListener(this);
}
}
SimulationContextParameter[] newValue = (SimulationContextParameter[]) evt.getNewValue();
if (newValue != null) {
for (SimulationContextParameter param : newValue) {
param.addPropertyChangeListener(this);
}
}
refreshData();
} else if (evt.getSource() instanceof Kinetics && (evt.getPropertyName().equals(Kinetics.PROPERTY_NAME_KINETICS_PARAMETERS))) {
EditableSymbolTableEntry[] oldValue = (EditableSymbolTableEntry[]) evt.getOldValue();
if (oldValue != null) {
for (int i = 0; i < oldValue.length; i++) {
oldValue[i].removePropertyChangeListener(this);
}
}
EditableSymbolTableEntry[] newValue = (EditableSymbolTableEntry[]) evt.getNewValue();
if (newValue != null) {
for (int i = 0; i < newValue.length; i++) {
newValue[i].addPropertyChangeListener(this);
}
}
refreshData();
// } else if(evt.getSource() instanceof ReactionRuleEmbedded) {
// ReactionRuleEmbedded reactionRule = (ReactionRuleEmbedded) evt.getSource();
// int changeRow = getRowIndex(reactionRule);
// if (changeRow >= 0) {
// fireTableRowsUpdated(changeRow, changeRow);
// }
}
}
}
use of cbit.vcell.model.Kinetics.UnresolvedParameter in project vcell by virtualcell.
the class ParameterTableModel method isCellEditable.
/**
* Insert the method's description here.
* Creation date: (2/24/01 12:27:46 AM)
* @return boolean
* @param rowIndex int
* @param columnIndex int
*/
public boolean isCellEditable(int rowIndex, int columnIndex) {
if (!bEditable) {
return false;
}
Parameter parameter = getValueAt(rowIndex);
if (reactionStep != null && parameter instanceof KineticsParameter) {
KineticsParameter kp = (KineticsParameter) parameter;
if (kp.getRole() == Kinetics.ROLE_KReverse) {
if (!reactionStep.isReversible()) {
// disable Kr if rule is not reversible
return false;
}
}
}
switch(columnIndex) {
case COLUMN_NAME:
return parameter.isNameEditable();
case COLUMN_DESCRIPTION:
return false;
case COLUMN_IS_GLOBAL:
// if the parameter is reaction rate param or a ReservedSymbol in the model, it should not be editable
if ((parameter instanceof KineticsParameter) && (((KineticsParameter) parameter).getRole() != Kinetics.ROLE_UserDefined)) {
return false;
}
if (parameter instanceof UnresolvedParameter) {
return false;
}
if (parameter instanceof KineticsProxyParameter) {
KineticsProxyParameter kpp = (KineticsProxyParameter) parameter;
SymbolTableEntry ste = kpp.getTarget();
if ((ste instanceof Model.ReservedSymbol) || (ste instanceof SpeciesContext) || (ste instanceof ModelQuantity)) {
return false;
}
}
return true;
case COLUMN_VALUE:
return parameter.isExpressionEditable();
case COLUMN_UNITS:
return parameter.isUnitEditable();
}
return false;
}
use of cbit.vcell.model.Kinetics.UnresolvedParameter in project vcell by virtualcell.
the class SBMLImporter method addReactions.
/**
* addReactions:
*/
protected void addReactions(VCMetaData metaData, Map<String, String> vcToSbmlNameMap, Map<String, String> sbmlToVcNameMap) {
if (sbmlModel == null) {
throw new SBMLImportException("SBML model is NULL");
}
ListOf<Reaction> reactions = sbmlModel.getListOfReactions();
final int numReactions = reactions.size();
if (numReactions == 0) {
lg.info("No Reactions");
return;
}
// all reactions
ArrayList<ReactionStep> vcReactionList = new ArrayList<>();
// just the fast ones
ArrayList<ReactionStep> fastReactionList = new ArrayList<>();
Model vcModel = vcBioModel.getSimulationContext(0).getModel();
ModelUnitSystem vcModelUnitSystem = vcModel.getUnitSystem();
SpeciesContext[] vcSpeciesContexts = vcModel.getSpeciesContexts();
try {
for (Reaction sbmlRxn : reactions) {
ReactionStep vcReaction = null;
String rxnSbmlId = sbmlRxn.getId();
String rxnSbmlName = sbmlRxn.getName();
if (isRestrictedXYZT(rxnSbmlId)) {
// simply rename any x,y,z reaction if non-spatial model
rxnSbmlId = "r_" + rxnSbmlId;
vcToSbmlNameMap.put(rxnSbmlId, sbmlRxn.getId());
sbmlToVcNameMap.put(sbmlRxn.getId(), rxnSbmlId);
}
boolean bReversible = true;
if (sbmlRxn.isSetReversible()) {
bReversible = sbmlRxn.getReversible();
}
// Check of reaction annotation is present; if so, does it have
// an embedded element (flux or simpleRxn).
// Create a fluxReaction or simpleReaction accordingly.
Element sbmlImportRelatedElement = sbmlAnnotationUtil.readVCellSpecificAnnotation(sbmlRxn);
Structure reactionStructure = getReactionStructure(sbmlRxn, vcSpeciesContexts, sbmlImportRelatedElement);
if (sbmlImportRelatedElement != null) {
Element embeddedRxnElement = getEmbeddedElementInAnnotation(sbmlImportRelatedElement, REACTION);
if (embeddedRxnElement != null) {
if (embeddedRxnElement.getName().equals(XMLTags.FluxStepTag)) {
// If embedded element is a flux reaction, set flux
// reaction's strucure, flux carrier, physicsOption
// from the element attributes.
String structName = embeddedRxnElement.getAttributeValue(XMLTags.StructureAttrTag);
CastInfo<Membrane> ci = SBMLHelper.getTypedStructure(Membrane.class, vcModel, structName);
if (!ci.isGood()) {
throw new SBMLImportException("Appears that the flux reaction is occuring on " + ci.actualName() + ", not a membrane.");
}
vcReaction = new FluxReaction(vcModel, ci.get(), null, rxnSbmlId, bReversible);
vcReaction.setModel(vcModel);
// Set the fluxOption on the flux reaction based on
// whether it is molecular, molecular & electrical,
// electrical.
String fluxOptionStr = embeddedRxnElement.getAttributeValue(XMLTags.FluxOptionAttrTag);
if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularOnly)) {
((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_ONLY);
} else if (fluxOptionStr.equals(XMLTags.FluxOptionMolecularAndElectrical)) {
((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_MOLECULAR_AND_ELECTRICAL);
} else if (fluxOptionStr.equals(XMLTags.FluxOptionElectricalOnly)) {
((FluxReaction) vcReaction).setPhysicsOptions(ReactionStep.PHYSICS_ELECTRICAL_ONLY);
} else {
localIssueList.add(new Issue(vcReaction, issueContext, IssueCategory.SBMLImport_Reaction, "Unknown FluxOption : " + fluxOptionStr + " for SBML reaction : " + rxnSbmlId, Issue.SEVERITY_WARNING));
// logger.sendMessage(VCLogger.Priority.MediumPriority,
// VCLogger.ErrorType.ReactionError,
// "Unknown FluxOption : " + fluxOptionStr +
// " for SBML reaction : " + rxnName);
}
} else if (embeddedRxnElement.getName().equals(XMLTags.SimpleReactionTag)) {
// if embedded element is a simple reaction, set
// simple reaction's structure from element attributes
vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnSbmlId, bReversible);
}
} else {
vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnSbmlId, bReversible);
}
} else {
vcReaction = new SimpleReaction(vcModel, reactionStructure, rxnSbmlId, bReversible);
}
if (rxnSbmlName != null && !rxnSbmlName.isEmpty()) {
vcReaction.setSbmlName(rxnSbmlName);
}
// set annotations and notes on vcReactions[i]
sbmlAnnotationUtil.readAnnotation(vcReaction, sbmlRxn);
sbmlAnnotationUtil.readNotes(vcReaction, sbmlRxn);
// the limit on the reactionName length.
if (rxnSbmlId.length() > 64) {
String freeTextAnnotation = metaData.getFreeTextAnnotation(vcReaction);
if (freeTextAnnotation == null) {
freeTextAnnotation = "";
}
StringBuffer oldRxnAnnotation = new StringBuffer(freeTextAnnotation);
oldRxnAnnotation.append("\n\n" + rxnSbmlId);
metaData.setFreeTextAnnotation(vcReaction, oldRxnAnnotation.toString());
}
// Now add the reactants, products, modifiers as specified by
// the sbmlRxn
addReactionParticipants(sbmlRxn, vcReaction, sbmlToVcNameMap);
KineticLaw kLaw = sbmlRxn.getKineticLaw();
Kinetics kinetics = null;
if (kLaw != null) {
// Convert the formula from kineticLaw into MathML and then
// to an expression (infix) to be used in VCell kinetics
ASTNode sbmlRateMath = kLaw.getMath();
Expression kLawRateExpr = getExpressionFromFormula(sbmlRateMath);
// we don't need to make sure it's not spatial here, we checked before renaming the variables
for (Map.Entry<String, String> entry : sbmlToVcNameMap.entrySet()) {
String sbmlName = entry.getKey();
String vcName = entry.getValue();
kLawRateExpr.substituteInPlace(new Expression(sbmlName), new Expression(vcName));
}
Expression vcRateExpression = new Expression(kLawRateExpr);
// modifier (catalyst) to the reaction.
for (int k = 0; k < vcSpeciesContexts.length; k++) {
SpeciesContext sc = vcSpeciesContexts[k];
if (vcRateExpression.hasSymbol(sc.getName())) {
ReactionParticipant r = vcReaction.getReactant(sc.getName());
ReactionParticipant p = vcReaction.getProduct(sc.getName());
ReactionParticipant c = vcReaction.getCatalyst(sc.getName());
if ((r == null) && (p == null) && (c == null)) {
// This means that the speciesContext is not a
// reactant, product or modifier : it has to be
// added to the VC Rxn as a catalyst
vcReaction.addCatalyst(sc);
}
}
}
// set kinetics on VCell reaction
if (bSpatial) {
// if spatial SBML ('isSpatial' attribute set), create
// DistributedKinetics)
SpatialReactionPlugin ssrplugin = (SpatialReactionPlugin) sbmlRxn.getPlugin(SBMLUtils.SBML_SPATIAL_NS_PREFIX);
// (a) the requiredElements attributes should be 'spatial'
if (ssrplugin != null && ssrplugin.getIsLocal()) {
kinetics = new GeneralKinetics(vcReaction);
} else {
kinetics = new GeneralLumpedKinetics(vcReaction);
}
} else {
kinetics = new GeneralLumpedKinetics(vcReaction);
}
// set kinetics on vcReaction
vcReaction.setKinetics(kinetics);
// If the name of the rate parameter has been changed by
// user, or matches with global/local param, it has to be changed.
resolveRxnParameterNameConflicts(sbmlRxn, kinetics, sbmlImportRelatedElement);
/**
* Now, based on the kinetic law expression, see if the rate
* is expressed in concentration/time or substance/time : If
* the compartment_id of the compartment corresponding to
* the structure in which the reaction takes place occurs in
* the rate law expression, it is in concentration/time;
* divide it by the compartment size and bring in the rate
* law as 'Distributed' kinetics. If not, the rate law is in
* substance/time; bring it in (as is) as 'Lumped' kinetics.
*/
ListOf<LocalParameter> localParameters = kLaw.getListOfLocalParameters();
for (LocalParameter p : localParameters) {
String paramName = p.getId();
KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
if (kineticsParameter == null) {
// add unresolved for now to prevent errors in kinetics.setParameterValue(kp,vcRateExpression) below
kinetics.addUnresolvedParameter(paramName);
}
}
KineticsParameter kp = kinetics.getAuthoritativeParameter();
if (lg.isDebugEnabled()) {
lg.debug("Setting " + kp.getName() + ": " + vcRateExpression.infix());
}
kinetics.setParameterValue(kp, vcRateExpression);
// If there are any global parameters used in the kinetics,
// and if they have species,
// check if the species are already reactionParticipants in
// the reaction. If not, add them as catalysts.
KineticsProxyParameter[] kpps = kinetics.getProxyParameters();
for (int j = 0; j < kpps.length; j++) {
if (kpps[j].getTarget() instanceof ModelParameter) {
ModelParameter mp = (ModelParameter) kpps[j].getTarget();
HashSet<String> refSpeciesNameHash = new HashSet<String>();
getReferencedSpeciesInExpr(mp.getExpression(), refSpeciesNameHash);
java.util.Iterator<String> refSpIterator = refSpeciesNameHash.iterator();
while (refSpIterator.hasNext()) {
String spName = refSpIterator.next();
org.sbml.jsbml.Species sp = sbmlModel.getSpecies(spName);
String spId = sp.getId();
String vcSpeciesName = spId;
if (sbmlToVcNameMap.get(spId) != null) {
vcSpeciesName = sbmlToVcNameMap.get(spId);
}
ArrayList<ReactionParticipant> rpArray = getVCReactionParticipantsFromSymbol(vcReaction, vcSpeciesName);
if (rpArray == null || rpArray.size() == 0) {
// This means that the speciesContext is not a reactant,
// product or modifier : it has to be added as a catalyst
vcReaction.addCatalyst(vcModel.getSpeciesContext(vcSpeciesName));
}
}
}
}
// model - local params cannot be defined by rules.
for (LocalParameter param : localParameters) {
String paramName = param.getId();
Expression exp = new Expression(param.getValue());
String unitString = param.getUnits();
VCUnitDefinition paramUnit = sbmlUnitIdentifierHash.get(unitString);
if (paramUnit == null) {
paramUnit = vcModelUnitSystem.getInstance_TBD();
}
// check if sbml local param is in kinetic params list;
// if so, add its value.
boolean lpSet = false;
KineticsParameter kineticsParameter = kinetics.getKineticsParameter(paramName);
if (kineticsParameter != null) {
if (lg.isDebugEnabled()) {
lg.debug("Setting local " + kineticsParameter.getName() + ": " + exp.infix());
}
kineticsParameter.setExpression(exp);
kineticsParameter.setUnitDefinition(paramUnit);
lpSet = true;
} else {
UnresolvedParameter ur = kinetics.getUnresolvedParameter(paramName);
if (ur != null) {
kinetics.addUserDefinedKineticsParameter(paramName, exp, paramUnit);
lpSet = true;
}
}
if (!lpSet) {
// check if it is a proxy parameter (specifically,
// speciesContext or model parameter (structureSize
// too)).
KineticsProxyParameter kpp = kinetics.getProxyParameter(paramName);
// and units to local param values
if (kpp != null && kpp.getTarget() instanceof ModelParameter) {
kinetics.convertParameterType(kpp, false);
kineticsParameter = kinetics.getKineticsParameter(paramName);
kinetics.setParameterValue(kineticsParameter, exp);
kineticsParameter.setUnitDefinition(paramUnit);
}
}
}
} else {
// sbmlKLaw was null, so creating a GeneralKinetics with 0.0
// as rate.
kinetics = new GeneralKinetics(vcReaction);
}
// end - if-else KLaw != null
// set the reaction kinetics, and add reaction to the vcell
// model.
kinetics.resolveUndefinedUnits();
// System.out.println("ADDED SBML REACTION : \"" + rxnName +
// "\" to VCModel");
vcReactionList.add(vcReaction);
if (sbmlRxn.isSetFast() && sbmlRxn.getFast()) {
fastReactionList.add(vcReaction);
}
}
// end - for vcReactions
ReactionStep[] array = vcReactionList.toArray(new ReactionStep[vcReactionList.size()]);
vcModel.setReactionSteps(array);
final ReactionContext rc = vcBioModel.getSimulationContext(0).getReactionContext();
for (ReactionStep frs : fastReactionList) {
final ReactionSpec rs = rc.getReactionSpec(frs);
rs.setReactionMapping(ReactionSpec.FAST);
}
} catch (ModelPropertyVetoException mpve) {
throw new SBMLImportException(mpve.getMessage(), mpve);
} catch (Exception e1) {
e1.printStackTrace(System.out);
throw new SBMLImportException(e1.getMessage(), e1);
}
}
use of cbit.vcell.model.Kinetics.UnresolvedParameter in project vcell by virtualcell.
the class BioModelParametersTableModel method bioModelChange.
@Override
protected void bioModelChange(PropertyChangeEvent evt) {
super.bioModelChange(evt);
BioModel oldValue = (BioModel) evt.getOldValue();
if (oldValue != null) {
for (EditableSymbolTableEntry parameter : oldValue.getModel().getModelParameters()) {
parameter.removePropertyChangeListener(this);
}
for (SpeciesContext sc : oldValue.getModel().getSpeciesContexts()) {
sc.removePropertyChangeListener(this);
}
for (ReactionStep reactionStep : oldValue.getModel().getReactionSteps()) {
reactionStep.removePropertyChangeListener(this);
Kinetics kinetics = reactionStep.getKinetics();
kinetics.removePropertyChangeListener(this);
for (KineticsParameter kineticsEditableSymbolTableEntry : kinetics.getKineticsParameters()) {
kineticsEditableSymbolTableEntry.removePropertyChangeListener(this);
}
for (ProxyParameter proxyEditableSymbolTableEntry : kinetics.getProxyParameters()) {
proxyEditableSymbolTableEntry.removePropertyChangeListener(this);
}
for (UnresolvedParameter unresolvedEditableSymbolTableEntry : kinetics.getUnresolvedParameters()) {
unresolvedEditableSymbolTableEntry.removePropertyChangeListener(this);
}
}
for (SimulationContext simulationContext : oldValue.getSimulationContexts()) {
simulationContext.removePropertyChangeListener(this);
simulationContext.getGeometryContext().removePropertyChangeListener(this);
for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
mapping.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
simulationContext.getReactionContext().removePropertyChangeListener(this);
for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
spec.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : spec.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
elect.removePropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : elect.getParameters()) {
parameter.removePropertyChangeListener(this);
}
}
for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
spatialObject.removePropertyChangeListener(this);
}
for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
spatialProcess.removePropertyChangeListener(this);
for (LocalParameter p : spatialProcess.getParameters()) {
p.removePropertyChangeListener(this);
}
}
for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
p.removePropertyChangeListener(this);
}
}
}
BioModel newValue = (BioModel) evt.getNewValue();
if (newValue != null) {
for (ModelParameter modelEditableSymbolTableEntry : newValue.getModel().getModelParameters()) {
modelEditableSymbolTableEntry.addPropertyChangeListener(this);
}
for (SpeciesContext sc : newValue.getModel().getSpeciesContexts()) {
sc.addPropertyChangeListener(this);
}
for (ReactionStep reactionStep : newValue.getModel().getReactionSteps()) {
reactionStep.addPropertyChangeListener(this);
Kinetics kinetics = reactionStep.getKinetics();
kinetics.addPropertyChangeListener(this);
for (KineticsParameter kineticsEditableSymbolTableEntry : kinetics.getKineticsParameters()) {
kineticsEditableSymbolTableEntry.addPropertyChangeListener(this);
}
for (ProxyParameter proxyEditableSymbolTableEntry : kinetics.getProxyParameters()) {
proxyEditableSymbolTableEntry.addPropertyChangeListener(this);
}
for (UnresolvedParameter unresolvedEditableSymbolTableEntry : kinetics.getUnresolvedParameters()) {
unresolvedEditableSymbolTableEntry.addPropertyChangeListener(this);
}
}
for (SimulationContext simulationContext : newValue.getSimulationContexts()) {
simulationContext.addPropertyChangeListener(this);
simulationContext.getGeometryContext().addPropertyChangeListener(this);
for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
mapping.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : mapping.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
simulationContext.getReactionContext().addPropertyChangeListener(this);
for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
spec.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : spec.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
elect.addPropertyChangeListener(this);
for (EditableSymbolTableEntry parameter : elect.getParameters()) {
parameter.addPropertyChangeListener(this);
}
}
for (SpatialObject spatialObject : simulationContext.getSpatialObjects()) {
spatialObject.addPropertyChangeListener(this);
}
for (SpatialProcess spatialProcess : simulationContext.getSpatialProcesses()) {
spatialProcess.addPropertyChangeListener(this);
for (LocalParameter p : spatialProcess.getParameters()) {
p.addPropertyChangeListener(this);
}
}
for (SimulationContextParameter p : simulationContext.getSimulationContextParameters()) {
p.addPropertyChangeListener(this);
}
}
}
}
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