Examples with Issue org.vcell.util.Issue used on opensource projects

Example 71 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class ReactionRule method checkReactantPatterns.

public void checkReactantPatterns(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.ReactionRule, this);
    int cnt = 0;
    // StringBuilder warning = new StringBuilder();
    for (ReactantPattern rp : reactantPatterns) {
        ++cnt;
        if (rp.getSpeciesPattern().getMolecularTypePatterns().size() == 0) {
            String msg = "Reactant " + 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 {
            rp.getSpeciesPattern().checkSpeciesPattern(issueContext, issueList);
            for (MolecularTypePattern mtpThis : rp.getSpeciesPattern().getMolecularTypePatterns()) {
                checkComponentStateConsistency(issueContext, issueList, mtpThis);
            }
        }
    }
// setReactantWarning(warning.length() == 0 ? null : warning.toString());
}

Example 72 with Issue

use of org.vcell.util.Issue 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 73 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class ReactionRule method checkComponentStateConsistency.

public void checkComponentStateConsistency(IssueContext issueContext, List<Issue> issueList, MolecularTypePattern mtpThis) {
    if (issueList == null) {
        // this may be called during parsing before the model is consistent
        return;
    }
    issueContext = issueContext.newChildContext(ContextType.ReactionRule, this);
    MolecularType mtThat = mtpThis.getMolecularType();
    for (MolecularComponentPattern mcpThis : mtpThis.getComponentPatternList()) {
        if (mcpThis.isImplied()) {
            continue;
        }
        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, mcpThis, issueContext, IssueCategory.Identifiers, msg, 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, msg, 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 = "Component pattern " + mcNameThis + " must be in an explicit State.";
                // issueList.add(new Issue(this, IssueCategory.Identifiers, msg, Issue.SEVERITY_WARNING));
                } else {
                    String csdNameThis = cspThis.getComponentStateDefinition().getName();
                    if (csdNameThis.isEmpty() || (mcThat.getComponentStateDefinition(csdNameThis) == null)) {
                        String msg = "Invalid State " + csdNameThis + " for component pattern " + mcNameThis;
                        issueList.add(new Issue(this, mcpThis, issueContext, IssueCategory.Identifiers, msg, msg, Issue.SEVERITY_WARNING));
                    }
                }
            }
        }
    }
}

Example 74 with Issue

use of org.vcell.util.Issue in project vcell by virtualcell.

the class ReactionStep method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 10:26:42 PM)
 * @param issueList java.util.Vector
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.ReactionStep, this);
    if (fieldKinetics != null) {
        fieldKinetics.gatherIssues(issueContext, issueList);
    }
    if (fieldName != null && fieldName.startsWith("_reverse_")) {
        String msg = "The prefix '_reverse_' is a BioNetGen reserved keyword. Please rename the " + getDisplayType() + ".";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
    }
    if (structure instanceof Membrane) {
        if (fieldKinetics instanceof MassActionKinetics) {
            if ((getNumReactants() > 1) || (getNumProducts() > 1)) {
                if (isForMembraneMembraneMassAction()) {
                    Issue issue = new Issue(this, issueContext, IssueCategory.KineticsExpressionError, "A mass action rate law is not physically correct for bimolecular reactions in membranes (see more).", Severity.WARNING);
                    issue.setHyperlink(MASS_ACTION_ONLINE_DISCUSSION);
                    issueList.add(issue);
                }
            }
        }
        if (getPhysicsOptions() == PHYSICS_ELECTRICAL_ONLY || getPhysicsOptions() == PHYSICS_MOLECULAR_AND_ELECTRICAL) {
            Feature negFeature = getModel().getElectricalTopology().getNegativeFeature((Membrane) structure);
            Feature posFeature = getModel().getElectricalTopology().getPositiveFeature((Membrane) structure);
            if (negFeature == null || posFeature == null) {
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Reaction '" + getName() + "' electrical structure '" + structure.getName() + "' negative and positive compartment must be set", Issue.Severity.ERROR));
            } else {
                for (ReactionParticipant rxParticipant : getReactionParticipants()) {
                    if (rxParticipant.getStructure() != negFeature && rxParticipant.getStructure() != posFeature && rxParticipant.getStructure() != structure) {
                        String msg = "Check STRUCTURE '" + structure.getName() + "' has pos/neg feature settings appropriate for reaction '" + getName() + "' participants";
                        issueList.add(new Issue(structure, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.ERROR));
                    }
                }
            }
        }
    }
    if (fieldKinetics instanceof MassActionKinetics) {
        if (getNumReactants() == 0) {
            String msg = "With Mass Action kinetics this reaction will be interpreted as a degradation of the product.";
            String tool = "Use General Kinetics if you want the product to be generated. As is now this reaction is interpreted as a degradation.";
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, tool, Issue.Severity.WARNING));
        }
    }
}

Example 75 with Issue

use of org.vcell.util.Issue 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));
    }
}