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

Example 56 with MolecularComponentPattern

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

the class ReactionRule method deleteStateFromPatterns.

public boolean deleteStateFromPatterns(MolecularType mt, MolecularComponent mc, ComponentStateDefinition csd) {
    for (ProductPattern pp : getProductPatterns()) {
        SpeciesPattern sp = pp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (!(mcp.getMolecularComponent() == mc)) {
                        // not our mc
                        continue;
                    }
                    ComponentStatePattern csp = mcp.getComponentStatePattern();
                    if (csp == null) {
                        continue;
                    }
                    if (csp.isAny()) {
                        if (mc.getComponentStateDefinitions().size() == 1) {
                            // we are about to delete the last possible state, so we set the ComponentStatePattern to null
                            mcp.setComponentStatePattern(null);
                        }
                        continue;
                    }
                    if (csp.getComponentStateDefinition() == csd) {
                        if (mc.getComponentStateDefinitions().size() == 1) {
                            // we are about to delete the last possible state, so we set the ComponentStatePattern to null
                            mcp.setComponentStatePattern(null);
                        } else {
                            // some other state is still available, we set the ComponentStatePattern to Any and let the user deal with it
                            csp = new ComponentStatePattern();
                            mcp.setComponentStatePattern(csp);
                        }
                    }
                }
            }
        }
    }
    for (ReactantPattern rp : getReactantPatterns()) {
        SpeciesPattern sp = rp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (MolecularComponentPattern mcp : componentPatterns) {
                    if (!(mcp.getMolecularComponent() == mc)) {
                        continue;
                    }
                    ComponentStatePattern csp = mcp.getComponentStatePattern();
                    if (csp == null) {
                        continue;
                    }
                    if (csp.isAny()) {
                        if (mc.getComponentStateDefinitions().size() == 1) {
                            mcp.setComponentStatePattern(null);
                        }
                        continue;
                    }
                    if (csp.getComponentStateDefinition() == csd) {
                        if (mc.getComponentStateDefinitions().size() == 1) {
                            mcp.setComponentStatePattern(null);
                        } else {
                            csp = new ComponentStatePattern();
                            mcp.setComponentStatePattern(csp);
                        }
                    }
                }
            }
        }
    }
    return true;
}

Example 57 with MolecularComponentPattern

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

the class ReactionRule method getReactantComponentBondType.

public BondType getReactantComponentBondType(MolecularComponentPattern mcpProduct) {
    MolecularTypePattern mtpProduct = getProductMoleculeOfComponent(mcpProduct);
    MolecularTypePattern mtpReactant = getMatchingReactantMolecule(mtpProduct);
    if (mtpReactant == null) {
        // possible if this product has no matching explicit or implicit reactant
        return null;
    }
    for (MolecularComponentPattern mcpReactant : mtpReactant.getComponentPatternList()) {
        if (mcpReactant.getMolecularComponent() != mcpProduct.getMolecularComponent()) {
            continue;
        }
        return mcpReactant.getBondType();
    }
    return null;
}

Example 58 with MolecularComponentPattern

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

the class SpeciesContext method findComponentUsage.

public void findComponentUsage(MolecularType mt, MolecularComponent mc, Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    if (!hasSpeciesPattern()) {
        return;
    }
    SpeciesPattern sp = getSpeciesPattern();
    for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
        if (mtp.getMolecularType() == mt) {
            List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
            for (MolecularComponentPattern mcp : componentPatterns) {
                if (mcp.getMolecularComponent() == mc) {
                    // here all components are always in use
                    if (mcp.getBond() != null) {
                        // we only care about the components with a bond
                        String key = sp.getDisplayName();
                        key = getDisplayType() + getDisplayName() + key;
                        usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                    }
                }
            }
        }
    }
}

Example 59 with MolecularComponentPattern

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

the class SpeciesContext method checkMolecularTypeConsistency.

// I think this should never fire issues, that's why I keep issue severity to error to force further investigation
// TODO: oct 30, 2015: hasn't fired in 9 months, we replace the issues with exception just to protect ourselves against regressions
private void checkMolecularTypeConsistency(IssueContext issueContext, List<Issue> issueList, MolecularType mtThat, MolecularTypePattern mtpThis) {
    issueContext = issueContext.newChildContext(ContextType.SpeciesContext, this);
    Map<String, MolecularComponent> hashThat = new HashMap<String, MolecularComponent>();
    Map<String, MolecularComponent> hashThis = new HashMap<String, MolecularComponent>();
    for (MolecularComponent mcThat : mtThat.getComponentList()) {
        hashThat.put(mcThat.getName(), mcThat);
    }
    for (MolecularComponentPattern mcpThis : mtpThis.getComponentPatternList()) {
        hashThis.put(mcpThis.getMolecularComponent().getName(), mcpThis.getMolecularComponent());
    }
    Iterator<Entry<String, MolecularComponent>> it = hashThat.entrySet().iterator();
    while (it.hasNext()) {
        String key = ((Map.Entry<String, MolecularComponent>) it.next()).getKey();
        if (hashThis.containsKey(key)) {
            it.remove();
            hashThis.remove(key);
        }
    }
    // any component still present in hashThis it means that it has been deleted in the molecular types definition and is now invalid
    for (String key : hashThat.keySet()) {
        String msg = "All components in the " + mtThat.getDisplayType() + " definition must be present. Missing: " + key + ".";
        throw new RuntimeException(msg);
    // issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_ERROR));
    }
    for (String key : hashThis.keySet()) {
        String msg = "Component " + key + " is no longer defined for the " + mtThat.getDisplayType() + " and must be removed.";
        throw new RuntimeException(msg);
    // issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_ERROR));
    }
}

Example 60 with MolecularComponentPattern

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

the class SpeciesContext method checkBondsSufficiency.

private void checkBondsSufficiency(IssueContext issueContext, List<Issue> issueList, SpeciesPattern sp) {
    if (sp.getMolecularTypePatterns().size() < 2) {
        return;
    }
    int numberOfMolecularTypeCandidates = 0;
    for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
        if (mtp.getComponentPatternList().size() > 0) {
            numberOfMolecularTypeCandidates++;
        }
    }
    if (numberOfMolecularTypeCandidates < 2) {
        // we need at least 2 molecular types with at least 1 component each
        return;
    }
    boolean atLeastOneBad = false;
    for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
        boolean bondSpecifiedExists = false;
        for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
            if (mcp.getBondType() == BondType.Specified) {
                Bond b = mcp.getBond();
                if (b != null) {
                    bondSpecifiedExists = true;
                    break;
                }
            }
        }
        if (!bondSpecifiedExists) {
            atLeastOneBad = true;
        }
    }
    if (atLeastOneBad) {
        String msg = "Each Molecular Pattern of the Species Pattern " + sp.toString() + " needs at least one explicit Bond.\n";
        IssueSource parent = issueContext.getContextObject();
        issueList.add(new Issue(parent, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
    }
}