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

Example 61 with MolecularTypePattern

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

the class ReactionRule method resolveMatches.

private void resolveMatches() {
    // for each molecular type, make a lists of all corresponding molecular type patterns, one for reactants, one for products
    Map<MolecularType, List<MolecularTypePattern>> reactantMap = new LinkedHashMap<MolecularType, List<MolecularTypePattern>>();
    Map<MolecularType, List<MolecularTypePattern>> productMap = new LinkedHashMap<MolecularType, List<MolecularTypePattern>>();
    for (MolecularType mt : model.getRbmModelContainer().getMolecularTypeList()) {
        List<MolecularTypePattern> mtpReactantList = populateMaps(mt, ReactionRuleParticipantType.Reactant);
        reactantMap.put(mt, mtpReactantList);
        List<MolecularTypePattern> mtpProductList = populateMaps(mt, ReactionRuleParticipantType.Product);
        productMap.put(mt, mtpProductList);
    }
    // we'll build a list with all tha mapped pairs so that we won't have to worry about them
    Map<String, MolecularTypePattern> pairAlreadyMapped = new LinkedHashMap<String, MolecularTypePattern>();
    // if, for a certain MolecularType, we have 0 or 1 MoleculartypePatterns both in reactant and product we ignore because it's trivial
    for (MolecularType mt : model.getRbmModelContainer().getMolecularTypeList()) {
        if (reactantMap.get(mt).size() < 2 && productMap.get(mt).size() < 2) {
            // we make sure that the match flag is "*" (indifferent) for these
            if (reactantMap.get(mt).size() == 1) {
                reactantMap.get(mt).get(0).setParticipantMatchLabel("*");
            }
            if (productMap.get(mt).size() == 1) {
                productMap.get(mt).get(0).setParticipantMatchLabel("*");
            }
            continue;
        }
        // those patterns with a valid match we take out from this lists and we put them in separate lists
        // if we find orphans either in the reactant or product list we set them to indifferent / any
        List<MolecularTypePattern> mtpReactantList = reactantMap.get(mt);
        List<MolecularTypePattern> mtpProductList = productMap.get(mt);
        List<MolecularTypePattern> mtpReactantsToRemove = new ArrayList<MolecularTypePattern>();
        for (MolecularTypePattern mtpr : mtpReactantList) {
            if (mtpr.hasExplicitParticipantMatch()) {
                String matchKey = mtpr.getParticipantMatchLabel();
                // we look for a match in the products
                MolecularTypePattern mtpp = findMatch(matchKey, mtpProductList);
                if (mtpp == null) {
                    // no product has the matching key, so this reactant must be orphan
                    // we set it to any
                    mtpr.setParticipantMatchLabel("*");
                } else {
                    // we add this pair to the map of already mapped pairs and take it out from here
                    if (pairAlreadyMapped.containsKey(matchKey)) {
                        // key already in use, we generate a new one
                        matchKey = generateNewMatchKey(pairAlreadyMapped);
                        mtpr.setParticipantMatchLabel(matchKey);
                        mtpp.setParticipantMatchLabel(matchKey);
                    }
                    // we'll remove the reactants after finishing the iterations
                    mtpReactantsToRemove.add(mtpr);
                    mtpProductList.remove(mtpp);
                    pairAlreadyMapped.put(matchKey, mtpr);
                }
            }
        }
        for (MolecularTypePattern mtpr : mtpReactantsToRemove) {
            // now we can remove the reactants without generating concurrent exceptions
            mtpReactantList.remove(mtpr);
        }
        // mtpProductList may still contain orphans with match flag set to something not "any", we need to fix them
        for (MolecularTypePattern mtpp : mtpProductList) {
            if (mtpp.hasExplicitParticipantMatch()) {
                String matchKey = mtpp.getParticipantMatchLabel();
                // we look for a match in the reactants
                MolecularTypePattern mtpr = findMatch(matchKey, mtpReactantList);
                if (mtpr == null) {
                    // no reactant has the matching key, so this product must be orphan
                    // we set it to any
                    mtpp.setParticipantMatchLabel("*");
                } else {
                    throw new RuntimeException("Found a reactant match for an orphan product, this should not be possible.");
                }
            }
        }
        // we try to match orphaned reactant mtp and product mtp of the same kind, as long neither list is empty
        for (MolecularTypePattern mtpr : mtpReactantList) {
            if (mtpProductList.isEmpty()) {
                // nothing left to match
                break;
            }
            MolecularTypePattern mtpp = mtpProductList.get(0);
            if (mtpp != null) {
                // these 2 are orphans and can be matched to each other
                String matchKey = generateNewMatchKey(pairAlreadyMapped);
                mtpr.setParticipantMatchLabel(matchKey);
                mtpp.setParticipantMatchLabel(matchKey);
                // mtpReactantList.remove(mtpr);		// we can't remove them because of concurrent exception and actually we don't need to
                mtpProductList.remove(mtpp);
                pairAlreadyMapped.put(matchKey, mtpr);
            }
        }
    }
}

Example 62 with MolecularTypePattern

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

the class ReactionRule method deleteComponentFromPatterns.

public boolean deleteComponentFromPatterns(MolecularType mt, MolecularComponent mc) {
    for (ProductPattern pp : getProductPatterns()) {
        SpeciesPattern sp = pp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (Iterator<MolecularComponentPattern> iterator = componentPatterns.iterator(); iterator.hasNext(); ) {
                    MolecularComponentPattern mcp = iterator.next();
                    if (mcp.getMolecularComponent() == mc) {
                        iterator.remove();
                    }
                }
            }
        }
        sp.resolveBonds();
    }
    for (ReactantPattern rp : getReactantPatterns()) {
        SpeciesPattern sp = rp.getSpeciesPattern();
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            if (mtp.getMolecularType() == mt) {
                List<MolecularComponentPattern> componentPatterns = mtp.getComponentPatternList();
                for (Iterator<MolecularComponentPattern> iterator = componentPatterns.iterator(); iterator.hasNext(); ) {
                    MolecularComponentPattern mcp = iterator.next();
                    if (mcp.getMolecularComponent() == mc) {
                        iterator.remove();
                    }
                }
            }
        }
        sp.resolveBonds();
    }
    return true;
}

Example 63 with MolecularTypePattern

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

the class ReactionRule method checkProductPatterns.

public void checkProductPatterns(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.ReactionRule, this);
    int reactantCnt = 0;
    for (ReactantPattern rp : reactantPatterns) {
        reactantCnt += rp.getSpeciesPattern().getMolecularTypePatterns().size();
    }
    int productCnt = 0;
    int cnt = 0;
    // StringBuilder warning = new StringBuilder();
    for (ProductPattern pp : productPatterns) {
        productCnt += pp.getSpeciesPattern().getMolecularTypePatterns().size();
        ++cnt;
        if (pp.getSpeciesPattern().getMolecularTypePatterns().size() == 0) {
            String msg = "Product " + cnt + " does not have any molecules.\n";
            // warning.append(msg);
            if (issueList != null) {
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
            }
        } else {
            pp.getSpeciesPattern().checkSpeciesPattern(issueContext, issueList);
            for (MolecularTypePattern mtpThis : pp.getSpeciesPattern().getMolecularTypePatterns()) {
                checkComponentStateConsistency(issueContext, issueList, mtpThis);
            }
        }
    }
    if (productCnt != reactantCnt) {
        String msg = "The number of molecules in products does not match the number of molecules in reactants.";
        // warning.append(msg);
        if (issueList != null) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_INFO));
        }
    }
// setProductWarning(warning.length() == 0 ? null : warning.toString());
}

Example 64 with MolecularTypePattern

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

the class ReactionRule method findStateUsage.

public void findStateUsage(MolecularType mt, MolecularComponent mc, ComponentStateDefinition csd, Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    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.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 = getDisplayType() + getDisplayName() + sp.getDisplayName();
                            usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                        }
                    }
                }
            }
        }
    }
    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.isImplied()) {
                        continue;
                    }
                    if (mcp.getMolecularComponent() == mc) {
                        ComponentStatePattern csp = mcp.getComponentStatePattern();
                        if (csp == null) {
                            continue;
                        }
                        if (csp.getComponentStateDefinition() == csd) {
                            String key = getDisplayType() + getDisplayName() + sp.getDisplayName();
                            usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                        }
                    }
                }
            }
        }
    }
}

Example 65 with MolecularTypePattern

use of org.vcell.model.rbm.MolecularTypePattern 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;
}