Examples with ComponentStatePattern org.vcell.model.rbm.ComponentStatePattern used on opensource projects

Example 6 with ComponentStatePattern

use of org.vcell.model.rbm.ComponentStatePattern in project vcell by virtualcell.

the class RulebasedMathMapping method addSpeciesPatterns.

private HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> addSpeciesPatterns(Domain domain, List<ReactionRule> rrList) throws MathException {
    // Particle Molecular Types
    // 
    Model model = getSimulationContext().getModel();
    List<RbmObservable> observableList = model.getRbmModelContainer().getObservableList();
    List<MolecularType> molecularTypeList = model.getRbmModelContainer().getMolecularTypeList();
    for (MolecularType molecularType : molecularTypeList) {
        ParticleMolecularType particleMolecularType = new ParticleMolecularType(molecularType.getName());
        for (MolecularComponent molecularComponent : molecularType.getComponentList()) {
            String pmcName = molecularComponent.getName();
            String pmcId = particleMolecularType.getName() + "_" + molecularComponent.getName();
            ParticleMolecularComponent particleMolecularComponent = new ParticleMolecularComponent(pmcId, pmcName);
            for (ComponentStateDefinition componentState : molecularComponent.getComponentStateDefinitions()) {
                ParticleComponentStateDefinition pcsd = particleMolecularComponent.getComponentStateDefinition(componentState.getName());
                if (pcsd == null) {
                    particleMolecularComponent.addComponentStateDefinition(new ParticleComponentStateDefinition(componentState.getName()));
                }
            }
            particleMolecularType.addMolecularComponent(particleMolecularComponent);
        }
        if (!molecularType.isAnchorAll()) {
            List<String> anchorList = new ArrayList<>();
            for (Structure struct : molecularType.getAnchors()) {
                anchorList.add(struct.getName());
            }
            particleMolecularType.setAnchorList(anchorList);
        }
        mathDesc.addParticleMolecularType(particleMolecularType);
    }
    // 
    // Assemble list of all Species Patterns (from observables, reaction rules, and seed species).
    // 
    // linked hash set maintains insertion order
    LinkedHashMap<SpeciesPattern, Structure> speciesPatternStructureMap = new LinkedHashMap<SpeciesPattern, Structure>();
    for (RbmObservable observable : observableList) {
        for (SpeciesPattern speciesPattern : observable.getSpeciesPatternList()) {
            speciesPatternStructureMap.put(speciesPattern, observable.getStructure());
        }
    }
    for (ReactionRule reactionRule : rrList) {
        for (ReactantPattern rp : reactionRule.getReactantPatterns()) {
            speciesPatternStructureMap.put(rp.getSpeciesPattern(), rp.getStructure());
        }
        for (ProductPattern pp : reactionRule.getProductPatterns()) {
            speciesPatternStructureMap.put(pp.getSpeciesPattern(), pp.getStructure());
        }
    }
    for (SpeciesContext sc : model.getSpeciesContexts()) {
        if (!sc.hasSpeciesPattern()) {
            continue;
        }
        speciesPatternStructureMap.put(sc.getSpeciesPattern(), sc.getStructure());
    }
    // 
    // add list of unique speciesPatterns
    // 
    HashMap<String, VolumeParticleSpeciesPattern> speciesPatternVCMLMap = new HashMap<String, VolumeParticleSpeciesPattern>();
    HashMap<SpeciesPattern, VolumeParticleSpeciesPattern> speciesPatternMap = new HashMap<SpeciesPattern, VolumeParticleSpeciesPattern>();
    String speciesPatternName = "speciesPattern0";
    for (SpeciesPattern speciesPattern : speciesPatternStructureMap.keySet()) {
        VolumeParticleSpeciesPattern volumeParticleSpeciesPattern = new VolumeParticleSpeciesPattern(speciesPatternName, domain, speciesPatternStructureMap.get(speciesPattern).getName());
        for (MolecularTypePattern molecularTypePattern : speciesPattern.getMolecularTypePatterns()) {
            ParticleMolecularType particleMolecularType = mathDesc.getParticleMolecularType(molecularTypePattern.getMolecularType().getName());
            ParticleMolecularTypePattern particleMolecularTypePattern = new ParticleMolecularTypePattern(particleMolecularType);
            String participantMatchLabel = molecularTypePattern.getParticipantMatchLabel();
            if (molecularTypePattern.getParticipantMatchLabel() != null) {
                particleMolecularTypePattern.setMatchLabel(participantMatchLabel);
            }
            for (MolecularComponentPattern molecularComponentPattern : molecularTypePattern.getComponentPatternList()) {
                MolecularComponent molecularComponent = molecularComponentPattern.getMolecularComponent();
                ParticleMolecularComponent particleMolecularComponent = particleMolecularType.getMolecularComponent(molecularComponent.getName());
                ParticleMolecularComponentPattern particleMolecularComponentPattern = new ParticleMolecularComponentPattern(particleMolecularComponent);
                ComponentStatePattern componentState = molecularComponentPattern.getComponentStatePattern();
                if (componentState != null) {
                    if (componentState.isAny()) {
                        ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern();
                        particleMolecularComponentPattern.setComponentStatePattern(pcsp);
                    } else {
                        String name = componentState.getComponentStateDefinition().getName();
                        ParticleComponentStateDefinition pcsd = particleMolecularComponent.getComponentStateDefinition(name);
                        // ParticleComponentStateDefinition pcsd = new ParticleComponentStateDefinition(componentState.getComponentStateDefinition().getName());
                        // particleMolecularComponent.addComponentStateDefinition(pcsd);
                        ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern(pcsd);
                        particleMolecularComponentPattern.setComponentStatePattern(pcsp);
                    }
                } else {
                    ParticleComponentStatePattern pcsp = new ParticleComponentStatePattern();
                    particleMolecularComponentPattern.setComponentStatePattern(pcsp);
                }
                switch(molecularComponentPattern.getBondType()) {
                    case Specified:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.Specified);
                            particleMolecularComponentPattern.setBondId(molecularComponentPattern.getBondId());
                            break;
                        }
                    case Exists:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.Exists);
                            particleMolecularComponentPattern.setBondId(-1);
                            break;
                        }
                    case None:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.None);
                            particleMolecularComponentPattern.setBondId(-1);
                            break;
                        }
                    case Possible:
                        {
                            particleMolecularComponentPattern.setBondType(ParticleBondType.Possible);
                            particleMolecularComponentPattern.setBondId(-1);
                            break;
                        }
                }
                particleMolecularTypePattern.addMolecularComponentPattern(particleMolecularComponentPattern);
            }
            volumeParticleSpeciesPattern.addMolecularTypePattern(particleMolecularTypePattern);
        }
        String speciesPatternVCML = volumeParticleSpeciesPattern.getVCML("tempName");
        VolumeParticleSpeciesPattern uniqueVolumeParticleSpeciesPattern = speciesPatternVCMLMap.get(speciesPatternVCML);
        if (uniqueVolumeParticleSpeciesPattern == null) {
            speciesPatternVCMLMap.put(speciesPatternVCML, volumeParticleSpeciesPattern);
            speciesPatternName = TokenMangler.getNextEnumeratedToken(speciesPatternName);
            speciesPatternMap.put(speciesPattern, volumeParticleSpeciesPattern);
        } else {
            speciesPatternMap.put(speciesPattern, uniqueVolumeParticleSpeciesPattern);
        }
    }
    return speciesPatternMap;
}

Example 7 with ComponentStatePattern

use of org.vcell.model.rbm.ComponentStatePattern in project vcell by virtualcell.

the class RbmObservable method resolveStates.

// TODO: this will have to go once we get rid of ComponentStatePattern
// use as a stopgap measure to eliminate a bug where the ComponentStatePattern is null
// instead of being Any (which happens when the MolecularComponent has states defined)
private void resolveStates() {
    for (SpeciesPattern sp : speciesPatternList) {
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
                if (mcp.getComponentStatePattern() == null && mcp.getMolecularComponent().getComponentStateDefinitions().size() > 0) {
                    ComponentStatePattern csp = new ComponentStatePattern();
                    mcp.setComponentStatePattern(csp);
                }
            }
        }
    }
}

Example 8 with ComponentStatePattern

use of org.vcell.model.rbm.ComponentStatePattern in project vcell by virtualcell.

the class RbmObservable method findStateUsage.

public void findStateUsage(MolecularType mt, MolecularComponent mc, ComponentStateDefinition csd, Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    for (SpeciesPattern sp : getSpeciesPatternList()) {
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (mcp.isImplied()) {
                        // we don't care about these
                        continue;
                    }
                    if (mcp.getMolecularComponent() == mc) {
                        // found mc in use
                        // now let's look at component state definition
                        ComponentStatePattern csp = mcp.getComponentStatePattern();
                        if (csp == null) {
                            continue;
                        }
                        if (csp.getComponentStateDefinition() == csd) {
                            String key = sp.getDisplayName();
                            key = getDisplayType() + getDisplayName() + key;
                            usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                        }
                    }
                }
            }
        }
    }
}

Example 9 with ComponentStatePattern

use of org.vcell.model.rbm.ComponentStatePattern in project vcell by virtualcell.

the class ReactionRule method gatherIssues.

// -----------------------------------------------------------------------------------------------------
// 
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.ReactionRule, this);
    if (name == null || name.isEmpty()) {
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Label is missing", Issue.Severity.ERROR));
    }
    if (name != null && name.startsWith("_reverse_")) {
        String msg = "The prefix '_reverse_' is a BioNetGen reserved keyword. Please rename the " + typeName + ".";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
    }
    for (MolecularType mt : model.getRbmModelContainer().getMolecularTypeList()) {
        if (mt.getName().equals(name)) {
            String msg = "Name '" + name + "' name already used for " + mt.getDisplayType() + " '" + mt.getName() + "'.";
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.WARNING));
            // no need to look further, we won't find another match since Molecule names are unique
            break;
        }
    }
    if (reactantPatterns == null) {
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Reactant Pattern is null", Issue.Severity.ERROR));
    } else if (reactantPatterns.isEmpty()) {
        String msg = typeName + " " + name + " does not have any Reactants.\n";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
    } else {
        checkReactantPatterns(issueContext, issueList);
        for (ReactantPattern rp : reactantPatterns) {
            issueContext = issueContext.newChildContext(ContextType.ReactionRule, this);
            rp.getSpeciesPattern().gatherIssues(issueContext, issueList);
        }
    }
    if (productPatterns == null) {
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Product Pattern is null", Issue.Severity.ERROR));
    } else if (productPatterns.isEmpty()) {
        String msg = typeName + " " + name + " does not have any Products.\n";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
    } else {
        checkProductPatterns(issueContext, issueList);
        for (ProductPattern pp : productPatterns) {
            issueContext = issueContext.newChildContext(ContextType.ReactionRule, this);
            pp.getSpeciesPattern().gatherIssues(issueContext, issueList);
        }
    }
    kineticLaw.gatherIssues(issueContext, issueList);
    if (molecularTypeMappings == null) {
        issueList.add(new Issue(this, issueContext, IssueCategory.KineticsExpressionMissing, MolecularType.typeName + " Mapping is null", Issue.Severity.WARNING));
    }
    // the structure must be in the list of anchors, if anchors are being used -------------------------------
    for (ReactantPattern rp : reactantPatterns) {
        SpeciesPattern sp = rp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            MolecularType mt = mtp.getMolecularType();
            if (mt.isAnchorAll()) {
                // no restrictions for this molecular type
                continue;
            }
            if (!mt.getAnchors().contains(rp.getStructure())) {
                String message = "The Structure " + structure.getName() + " is not allowed for the Molecule " + mt.getDisplayName();
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.ERROR));
            }
        }
    }
    for (ProductPattern pp : productPatterns) {
        SpeciesPattern sp = pp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            MolecularType mt = mtp.getMolecularType();
            if (mt.isAnchorAll()) {
                // no restrictions for this molecular type
                continue;
            }
            if (!mt.getAnchors().contains(pp.getStructure())) {
                String message = "The Structure " + structure.getName() + " is not allowed for the Molecule " + mt.getDisplayName();
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.ERROR));
            }
        }
    }
    for (ReactantPattern rp : reactantPatterns) {
        SpeciesPattern sp = rp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            String name = mtp.getMolecularType().getDisplayName().toLowerCase();
            if (name.equals("trash")) {
                String message = "'Trash' is a reserved NFSim keyword and it cannot be used as a reactant.";
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            }
        }
    }
    if (bReversible) {
        for (ProductPattern pp : productPatterns) {
            SpeciesPattern sp = pp.getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                String name = mtp.getMolecularType().getDisplayName().toLowerCase();
                if (name.equals("trash")) {
                    String message = "'Trash' is a reserved NFSim keyword and it cannot be used as a reactant.";
                    issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
                }
            }
        }
    }
    // match management
    issueContext = issueContext.newChildContext(ContextType.ReactionRule, this);
    Map<String, Integer> matchedReactants = new LinkedHashMap<String, Integer>();
    Map<String, Integer> unmatchedReactants = new LinkedHashMap<String, Integer>();
    Map<String, MolecularTypePattern> rMatches = new LinkedHashMap<String, MolecularTypePattern>();
    for (ReactantPattern rp : reactantPatterns) {
        SpeciesPattern sp = rp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            String thisName = mtp.getMolecularType().getDisplayName();
            if (!mtp.hasExplicitParticipantMatch()) {
                if (unmatchedReactants.containsKey(thisName)) {
                    int newCounter = unmatchedReactants.get(thisName) + 1;
                    unmatchedReactants.put(thisName, newCounter);
                } else {
                    unmatchedReactants.put(thisName, 1);
                }
                continue;
            }
            // the value doesn't matter, it's important to be there
            matchedReactants.put(thisName, 99);
            String key = mtp.getParticipantMatchLabel();
            if (rMatches.containsKey(key)) {
                // no duplicates in reactants allowed
                String message = "Multiple Reactants with the same match id " + key + " are not allowed.";
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            } else {
                rMatches.put(key, mtp);
            }
        }
    }
    Map<String, Integer> matchedProducts = new LinkedHashMap<String, Integer>();
    Map<String, Integer> unmatchedProducts = new LinkedHashMap<String, Integer>();
    Map<String, MolecularTypePattern> pMatches = new LinkedHashMap<String, MolecularTypePattern>();
    for (ProductPattern pp : productPatterns) {
        SpeciesPattern sp = pp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            String thisName = mtp.getMolecularType().getDisplayName();
            if (!mtp.hasExplicitParticipantMatch()) {
                if (unmatchedProducts.containsKey(thisName)) {
                    int newCounter = unmatchedProducts.get(thisName) + 1;
                    unmatchedProducts.put(thisName, newCounter);
                } else {
                    unmatchedProducts.put(thisName, 1);
                }
                continue;
            }
            matchedProducts.put(thisName, 100);
            String key = mtp.getParticipantMatchLabel();
            if (pMatches.containsKey(key)) {
                // no duplicates in products allowed
                String message = "Multiple Products with the same match id " + key + " are not allowed.";
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            } else {
                pMatches.put(key, mtp);
            }
        }
    }
    // 2+ unmatched reactants and 1+ unmatched products of same molecule mean error (or vice-versa: 1+ && 2+)
    for (String key : unmatchedReactants.keySet()) {
        if (unmatchedProducts.containsKey(key)) {
            // both maps have the same unmatched molecule, anything larger than 1 and 1 means matching error
            int rCounter = unmatchedReactants.get(key);
            int pCounter = unmatchedProducts.get(key);
            if ((rCounter > 1 && pCounter > 1) || (rCounter > 0 && pCounter > 1)) {
                String message = "Matching missing for Molecule " + key;
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.ERROR));
            }
        }
    }
    // must look also for combination with matches and unmatches for the same molecule like pA rA matched AND also pA and rA unmatched - one of each unmatched
    for (String key : unmatchedReactants.keySet()) {
        if (unmatchedProducts.containsKey(key) && matchedProducts.containsKey(key) && matchedReactants.containsKey(key)) {
            int rCounter = matchedReactants.get(key);
            int pCounter = matchedProducts.get(key);
            if (rCounter == 1 && pCounter == 1) {
                // the cases when either is >1 was addressed above, don't need duplicates
                String message = "Matching missing for Molecule " + key;
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.ERROR));
            }
        }
    }
    // unmatched products must be unambiguous (bond can't be 'possible' and state can't be 'any')
    for (ProductPattern pp : productPatterns) {
        SpeciesPattern sp = pp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            MolecularTypePattern match = getMatchingReactantMolecule(mtp);
            if (match == null) {
                // this product has no reactant to match
                for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
                    if (mcp.isAmbiguousBond()) {
                        String message = "Ambiguous bond '" + mcp.getBondType().name() + "' in site '" + mcp.getMolecularComponent().getDisplayName() + "' in unmatched product molecule '" + mtp.getMolecularType().getDisplayName() + "'";
                        issueList.add(new Issue(this, mcp, issueContext, IssueCategory.Identifiers, message, message, Issue.Severity.ERROR));
                    }
                    if (mcp.isAmbiguousState()) {
                        String message = "Ambiguous state 'any' in site '" + mcp.getMolecularComponent().getDisplayName() + "' in unmatched product molecule '" + mtp.getMolecularType().getDisplayName() + "'";
                        issueList.add(new Issue(this, mcp, issueContext, IssueCategory.Identifiers, message, message, Issue.Severity.ERROR));
                    }
                }
            }
        }
    }
    if (bReversible) {
        // same as above for reactants if the rule is reversible
        for (ReactantPattern rp : reactantPatterns) {
            SpeciesPattern sp = rp.getSpeciesPattern();
            for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
                MolecularTypePattern match = getMatchingProductMolecule(mtp);
                if (match == null) {
                    for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
                        if (mcp.isAmbiguousBond()) {
                            String message = "Ambiguous bond '" + mcp.getBondType().name() + "' in site '" + mcp.getMolecularComponent().getDisplayName() + "' in unmatched reactant molecule '" + mtp.getMolecularType().getDisplayName() + "'";
                            issueList.add(new Issue(this, mcp, issueContext, IssueCategory.Identifiers, message, message, Issue.Severity.ERROR));
                        }
                        if (mcp.isAmbiguousState()) {
                            String message = "Ambiguous state 'any' in site '" + mcp.getMolecularComponent().getDisplayName() + "' in unmatched reactant molecule '" + mtp.getMolecularType().getDisplayName() + "'";
                            issueList.add(new Issue(this, mcp, issueContext, IssueCategory.Identifiers, message, message, Issue.Severity.ERROR));
                        }
                    }
                }
            }
        }
    }
    // invalid combinations of bonds / states for corresponding reactant/product component pairs
    for (ReactantPattern rp : reactantPatterns) {
        SpeciesPattern sp = rp.getSpeciesPattern();
        for (MolecularTypePattern mtpReactant : sp.getMolecularTypePatterns()) {
            MolecularTypePattern mtpProduct = getMatchingProductMolecule(mtpReactant);
            // mtpProduct may be null (perhaps we don't have yet any explicit or implicit match for this reactant)
            if (mtpProduct == null) {
                continue;
            }
            for (MolecularComponentPattern mcpReactant : mtpReactant.getComponentPatternList()) {
                // search for a match of the component in this product molecule
                MolecularComponentPattern mcpProduct = ReactionRule.getMatchingComponent(mtpProduct, mcpReactant);
                if (mcpProduct == null) {
                    throw new RuntimeException("Reactant Site " + mcpReactant.getDisplayName() + " is missing its matching Product Site.");
                }
                boolean incompatibleBonds = false;
                switch(mcpReactant.getBondType()) {
                    case Exists:
                        switch(mcpProduct.getBondType()) {
                            case Exists:
                                break;
                            case None:
                                incompatibleBonds = true;
                                break;
                            case Possible:
                                incompatibleBonds = true;
                                break;
                            case Specified:
                                incompatibleBonds = true;
                                break;
                        }
                        break;
                    case None:
                        switch(mcpProduct.getBondType()) {
                            case Exists:
                                incompatibleBonds = true;
                                break;
                            case None:
                                break;
                            case Possible:
                                incompatibleBonds = true;
                                break;
                            case Specified:
                                break;
                        }
                        break;
                    case Possible:
                        switch(mcpProduct.getBondType()) {
                            case Exists:
                                incompatibleBonds = true;
                                break;
                            case None:
                                incompatibleBonds = true;
                                break;
                            case Possible:
                                break;
                            case Specified:
                                incompatibleBonds = true;
                                break;
                        }
                        break;
                    case Specified:
                        switch(mcpProduct.getBondType()) {
                            case Exists:
                                incompatibleBonds = true;
                                break;
                            case None:
                                break;
                            case Possible:
                                incompatibleBonds = true;
                                break;
                            case Specified:
                                break;
                        }
                        break;
                }
                // ----- end of bonds switch
                if (incompatibleBonds) {
                    String message = "Reactant " + MolecularComponentPattern.typeName + " " + mcpReactant.getDisplayName();
                    message += " and its matching Product " + MolecularComponentPattern.typeName + " " + mcpProduct.getDisplayName() + " have incompatible Bond Types.";
                    issueList.add(new Issue(this, mcpProduct, issueContext, IssueCategory.Identifiers, message, message, Issue.Severity.ERROR));
                }
                boolean incompatibleStates = true;
                if (mcpReactant.getMolecularComponent().getComponentStateDefinitions().isEmpty()) {
                // nothing to do if there are no States defined
                } else {
                    ComponentStatePattern cspReactant = mcpReactant.getComponentStatePattern();
                    ComponentStatePattern cspProduct = mcpProduct.getComponentStatePattern();
                    if (cspReactant == null) {
                        String message = "Required " + ComponentStatePattern.typeName + " missing for " + MolecularComponentPattern.typeName + " " + mcpReactant.getDisplayName();
                        issueList.add(new Issue(this, mcpReactant, issueContext, IssueCategory.Identifiers, message, message, Issue.Severity.ERROR));
                    }
                    if (cspProduct == null) {
                        String message = "Required " + ComponentStatePattern.typeName + " missing for " + MolecularComponentPattern.typeName + " " + mcpProduct.getDisplayName();
                        issueList.add(new Issue(this, mcpProduct, issueContext, IssueCategory.Identifiers, message, message, Issue.Severity.ERROR));
                    }
                    if (cspReactant.isAny() && cspProduct.isAny()) {
                        incompatibleStates = false;
                    } else if (!cspReactant.isAny() && !cspProduct.isAny()) {
                        incompatibleStates = false;
                    }
                    if (incompatibleStates) {
                        String message = "Reactant " + MolecularComponentPattern.typeName + " " + mcpReactant.getDisplayName();
                        message += " and its matching Product " + MolecularComponentPattern.typeName + " " + mcpProduct.getDisplayName() + " have incompatible States";
                        issueList.add(new Issue(this, mcpProduct, issueContext, IssueCategory.Identifiers, message, message, Issue.Severity.ERROR));
                    }
                }
            }
        }
    }
}

Example 10 with ComponentStatePattern

use of org.vcell.model.rbm.ComponentStatePattern in project vcell by virtualcell.

the class SpeciesContext method checkComponentStateConsistency.

public void checkComponentStateConsistency(IssueContext issueContext, List<Issue> issueList, MolecularTypePattern mtpThis) {
    issueContext = issueContext.newChildContext(ContextType.SpeciesContext, this);
    MolecularType mtThat = mtpThis.getMolecularType();
    for (MolecularComponentPattern mcpThis : mtpThis.getComponentPatternList()) {
        ComponentStatePattern cspThis = mcpThis.getComponentStatePattern();
        String mcNameThis = mcpThis.getMolecularComponent().getName();
        MolecularComponent[] mcThatList = mtThat.getMolecularComponents(mcNameThis);
        if (mcThatList.length == 0) {
            System.out.println("we already fired an issue about component missing");
            // nothing to do here, we already fired an issue about component missing
            continue;
        } else if (mcThatList.length > 1) {
            String msg = "Multiple " + MolecularComponent.typeName + "s with the same name are not yet supported.";
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_ERROR));
        } else {
            // found exactly 1 component
            MolecularComponent mcThat = mcThatList[0];
            List<ComponentStateDefinition> csdListThat = mcThat.getComponentStateDefinitions();
            if (csdListThat.size() == 0) {
                // component has no states, we check if mcpThis has any states... it shouldn't
                if (cspThis == null) {
                    // all is well
                    continue;
                }
                if (!cspThis.isAny() || (cspThis.getComponentStateDefinition() != null)) {
                    String msg = MolecularComponentPattern.typeName + " " + mcNameThis + " is in an invalid State.";
                    issueList.add(new Issue(this, mcpThis, issueContext, IssueCategory.Identifiers, msg, null, Issue.SEVERITY_WARNING));
                }
            } else {
                // we check if mcpThis has any of these states... it should!
                if ((cspThis == null) || cspThis.isAny() || (cspThis.getComponentStateDefinition() == null)) {
                    String msg = MolecularComponentPattern.typeName + " " + mcNameThis + " must be in an explicit State.";
                    issueList.add(new Issue(this, mcpThis, issueContext, IssueCategory.Identifiers, msg, null, Issue.Severity.ERROR));
                } else {
                    String csdNameThis = cspThis.getComponentStateDefinition().getName();
                    if (csdNameThis.isEmpty() || (mcThat.getComponentStateDefinition(csdNameThis) == null)) {
                        String msg = "Invalid State " + csdNameThis + " for " + MolecularComponentPattern.typeName + " " + mcNameThis;
                        issueList.add(new Issue(this, mcpThis, issueContext, IssueCategory.Identifiers, msg, null, Issue.SEVERITY_WARNING));
                    }
                }
            }
        }
    }
}