use of org.vcell.model.rbm.RuleAnalysis.MolecularComponentEntry in project vcell by virtualcell.
the class ModelRuleFactory method createRuleEntry.
public ModelRuleEntry createRuleEntry(ReactionRule reactionRule, int reactionRuleIndex, ReactionRuleDirection direction) {
ModelRuleEntry rule = new ModelRuleEntry(reactionRule, reactionRuleIndex);
//
// for each molecular type in reactant, find all possible matches in products (without regard for consistency).
//
int participantIndex = 0;
for (ReactantPattern rp : reactionRule.getReactantPatterns()) {
ModelParticipantEntry reactantEntry = new ModelParticipantEntry(rule, participantIndex, rp);
rule.reactantEntries.add(reactantEntry);
int moleculeIndex = 0;
for (MolecularTypePattern mtp : rp.getSpeciesPattern().getMolecularTypePatterns()) {
ModelMolecularTypeEntry molecularTypeEntry = new ModelMolecularTypeEntry(reactantEntry, moleculeIndex, mtp);
rule.reactantMolecularTypeEntries.add(molecularTypeEntry);
int componentIndex = 0;
for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
// TODO: divergence point vs. MathRuleFactory
// we need to look at all components when we compare reactants to products looking for changes
// if(mcp.getBondType() == BondType.Possible && (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny())) {
// continue;
// }
ModelMolecularComponentEntry mce = new ModelMolecularComponentEntry(molecularTypeEntry, componentIndex, mcp);
rule.reactantMolecularComponentEntries.add(mce);
//
// if this reactant component has a bond, find partner already in list (will always find second binding site where first one is in the list already).
//
Bond bond = mcp.getBond();
if (bond != null) {
ReactantBondEntry bondEntry = null;
for (MolecularComponentEntry otherMCE : rule.reactantMolecularComponentEntries) {
if (((ModelMolecularComponentEntry) otherMCE).molecularComponentPattern == bond.molecularComponentPattern) {
bondEntry = new ReactantBondEntry(otherMCE, mce);
break;
}
}
if (bondEntry != null) {
rule.reactantBondEntries.add(bondEntry);
}
}
componentIndex++;
}
moleculeIndex++;
}
participantIndex++;
}
participantIndex = 0;
for (ProductPattern pp : reactionRule.getProductPatterns()) {
ModelParticipantEntry productEntry = new ModelParticipantEntry(rule, participantIndex, pp);
rule.productEntries.add(productEntry);
int moleculeIndex = 0;
for (MolecularTypePattern mtp : pp.getSpeciesPattern().getMolecularTypePatterns()) {
ModelMolecularTypeEntry molecularTypeEntry = new ModelMolecularTypeEntry(productEntry, moleculeIndex, mtp);
rule.productMolecularTypeEntries.add(molecularTypeEntry);
int componentIndex = 0;
for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
// TODO: divergence point vs. MathRuleFactory
// we need to look at all components when we compare reactants to products looking for changes
// if(mcp.getBondType() == BondType.Possible && (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny())) {
// continue;
// }
ModelMolecularComponentEntry mce = new ModelMolecularComponentEntry(molecularTypeEntry, componentIndex, mcp);
rule.productMolecularComponentEntries.add(mce);
//
// if this product component has a bond, find partner already in list (will always find second binding site where first one is in the list already).
//
Bond bond = mcp.getBond();
if (bond != null) {
ProductBondEntry bondEntry = null;
for (MolecularComponentEntry otherMCE : rule.productMolecularComponentEntries) {
if (((ModelMolecularComponentEntry) otherMCE).molecularComponentPattern == bond.molecularComponentPattern) {
bondEntry = new ProductBondEntry(otherMCE, mce);
break;
}
}
if (bondEntry != null) {
rule.productBondEntries.add(bondEntry);
}
}
componentIndex++;
}
moleculeIndex++;
}
participantIndex++;
}
return rule;
}
use of org.vcell.model.rbm.RuleAnalysis.MolecularComponentEntry in project vcell by virtualcell.
the class MathRuleFactory method createRuleEntry.
public MathRuleEntry createRuleEntry(ParticleJumpProcess particleJumpProcess, int particleJumpProcessIndex) {
MathRuleEntry rule = new MathRuleEntry(particleJumpProcess, particleJumpProcessIndex);
ArrayList<ParticleSpeciesPattern> selectedPatterns = new ArrayList<ParticleSpeciesPattern>();
for (ParticleVariable particleVariable : particleJumpProcess.getParticleVariables()) {
if (!(particleVariable instanceof ParticleSpeciesPattern)) {
throw new RuntimeException("expecting only " + ParticleSpeciesPattern.class.getSimpleName() + "s for " + ParticleJumpProcess.class.getSimpleName() + " " + particleJumpProcess.getName());
}
selectedPatterns.add((ParticleSpeciesPattern) particleVariable);
}
ArrayList<ParticleSpeciesPattern> createdPatterns = new ArrayList<ParticleSpeciesPattern>();
HashSet<ParticleSpeciesPattern> destroyedPatterns = new HashSet<ParticleSpeciesPattern>();
for (Action action : particleJumpProcess.getActions()) {
if (!(action.getVar() instanceof ParticleSpeciesPattern)) {
throw new RuntimeException("expecting only " + ParticleSpeciesPattern.class.getSimpleName() + "s for " + ParticleJumpProcess.class.getSimpleName() + " " + particleJumpProcess.getName());
}
if (action.getOperation().equals(Action.ACTION_CREATE)) {
createdPatterns.add((VolumeParticleSpeciesPattern) action.getVar());
} else if (action.getOperation().equals(Action.ACTION_DESTROY)) {
destroyedPatterns.add((VolumeParticleSpeciesPattern) action.getVar());
} else {
throw new RuntimeException("unexpected action operation " + action.getOperation() + " for jump process " + particleJumpProcess.getName());
}
}
ArrayList<ParticleSpeciesPattern> productSpeciesPatterns = new ArrayList<ParticleSpeciesPattern>(selectedPatterns);
productSpeciesPatterns.removeAll(destroyedPatterns);
productSpeciesPatterns.addAll(createdPatterns);
//
// for each molecular type in reactant, find all possible matches in products (without regard for consistency).
//
int participantIndex = 0;
for (ParticleSpeciesPattern particleSpeciesPattern : selectedPatterns) {
MathParticipantEntry reactantEntry = new MathParticipantEntry(rule, participantIndex, particleSpeciesPattern, ParticipantType.Reactant);
rule.reactantEntries.add(reactantEntry);
int moleculeIndex = 0;
for (ParticleMolecularTypePattern mtp : particleSpeciesPattern.getParticleMolecularTypePatterns()) {
MathMolecularTypeEntry molecularTypeEntry = new MathMolecularTypeEntry(reactantEntry, moleculeIndex, mtp);
rule.reactantMolecularTypeEntries.add(molecularTypeEntry);
int componentIndex = 0;
for (ParticleMolecularComponentPattern mcp : mtp.getMolecularComponentPatternList()) {
// here we skip the trivial components
if (mcp.getBondType() == ParticleBondType.Possible && (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny())) {
continue;
}
MathMolecularComponentEntry mce = new MathMolecularComponentEntry(molecularTypeEntry, componentIndex, mcp);
rule.reactantMolecularComponentEntries.add(mce);
//
if (mcp.getBondType() == ParticleBondType.Specified) {
ReactantBondEntry bondEntry = null;
for (MolecularComponentEntry otherMCE : rule.reactantMolecularComponentEntries) {
if (mce.isBoundTo(otherMCE)) {
bondEntry = new ReactantBondEntry(otherMCE, mce);
break;
}
}
if (bondEntry != null) {
rule.reactantBondEntries.add(bondEntry);
}
}
componentIndex++;
}
moleculeIndex++;
}
participantIndex++;
}
participantIndex = 0;
for (ParticleSpeciesPattern particleSpeciesPattern : productSpeciesPatterns) {
MathParticipantEntry productEntry = new MathParticipantEntry(rule, participantIndex, particleSpeciesPattern, ParticipantType.Product);
rule.productEntries.add(productEntry);
int moleculeIndex = 0;
for (ParticleMolecularTypePattern mtp : particleSpeciesPattern.getParticleMolecularTypePatterns()) {
MathMolecularTypeEntry molecularTypeEntry = new MathMolecularTypeEntry(productEntry, moleculeIndex, mtp);
rule.productMolecularTypeEntries.add(molecularTypeEntry);
int componentIndex = 0;
for (ParticleMolecularComponentPattern mcp : mtp.getMolecularComponentPatternList()) {
// here we skip the trivial components
if (mcp.getBondType() == ParticleBondType.Possible && (mcp.getComponentStatePattern() == null || mcp.getComponentStatePattern().isAny())) {
continue;
}
MathMolecularComponentEntry mce = new MathMolecularComponentEntry(molecularTypeEntry, componentIndex, mcp);
rule.productMolecularComponentEntries.add(mce);
//
if (mcp.getBondType() == ParticleBondType.Specified) {
ProductBondEntry bondEntry = null;
for (MolecularComponentEntry otherMCE : rule.productMolecularComponentEntries) {
if (mce.isBoundTo(otherMCE)) {
bondEntry = new ProductBondEntry(otherMCE, mce);
break;
}
}
if (bondEntry != null) {
rule.productBondEntries.add(bondEntry);
}
}
componentIndex++;
}
moleculeIndex++;
}
participantIndex++;
}
return rule;
}
use of org.vcell.model.rbm.RuleAnalysis.MolecularComponentEntry in project vcell by virtualcell.
the class ParticipantSignatureShapePanel method hasBondChanged.
public RuleAnalysisChanged hasBondChanged(String key, MolecularComponentPattern molecularComponentPattern) {
ReactionRule reactionRule = reactionRuleMap.get(key);
if (reactionRule == null) {
return RuleAnalysisChanged.ANALYSISFAILED;
}
ModelRuleEntry modelRuleEntry = modelRuleEntryMap.get(key);
RuleAnalysisReport report = reportMap.get(key);
if (modelRuleEntry == null || report == null) {
System.out.println("modelRuleEntry == null || report == null, NOT GOOD!");
// refreshRuleAnalysis();
}
if (!bRuleAnalysisFailed && report != null) {
MolecularComponentEntry molecularComponentEntry = modelRuleEntry.findMolecularComponentEntry(molecularComponentPattern);
if (report.hasBondChanged(molecularComponentEntry)) {
return RuleAnalysisChanged.CHANGED;
} else {
return RuleAnalysisChanged.UNCHANGED;
}
} else {
return RuleAnalysisChanged.ANALYSISFAILED;
}
}
use of org.vcell.model.rbm.RuleAnalysis.MolecularComponentEntry in project vcell by virtualcell.
the class ParticipantSignatureShapePanel method hasStateChanged.
public RuleAnalysisChanged hasStateChanged(String key, MolecularComponentPattern molecularComponentPattern) {
ReactionRule reactionRule = reactionRuleMap.get(key);
if (reactionRule == null) {
return RuleAnalysisChanged.ANALYSISFAILED;
}
ModelRuleEntry modelRuleEntry = modelRuleEntryMap.get(key);
RuleAnalysisReport report = reportMap.get(key);
if (modelRuleEntry == null || report == null) {
System.out.println("modelRuleEntry == null || report == null, NOT GOOD!");
// refreshRuleAnalysis();
}
if (!bRuleAnalysisFailed && report != null) {
MolecularComponentEntry molecularComponentEntry = modelRuleEntry.findMolecularComponentEntry(molecularComponentPattern);
if (report.hasStateChanged(molecularComponentEntry)) {
return RuleAnalysisChanged.CHANGED;
} else {
return RuleAnalysisChanged.UNCHANGED;
}
} else {
return RuleAnalysisChanged.ANALYSISFAILED;
}
}
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