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

Example 66 with Issue

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

the class SimulationWarning method analyzeArea.

private static void analyzeArea(Simulation simulation, double timeStep, Map<MembraneSubDomain, List<DiffusionValue>> diffusionValuesMap, IssueContext issueContext, List<Issue> issueList) {
    double dx = simulation.getMeshSpecification().getDx(true);
    double dy = simulation.getMeshSpecification().getDy(true);
    double dz = simulation.getMeshSpecification().getDz(true);
    int dim = simulation.getMathDescription().getGeometry().getDimension();
    if (dim < 3) {
        throw new RuntimeException("suggested timestep analysis for smoldyn not implemented for " + dim + "D simulations");
    }
    double smallestQuadArea = Math.min(Math.min(dx * dy, dy * dz), dx * dz);
    // 1/2 for quad to triangle, 1/2 for smoother surface
    double averageTriangleSize = smallestQuadArea / 4;
    for (Entry<MembraneSubDomain, List<DiffusionValue>> entry : diffusionValuesMap.entrySet()) {
        MembraneSubDomain msd = entry.getKey();
        for (DiffusionValue dv : entry.getValue()) {
            double ad = averageTriangleSize / dv.value;
            boolean warn = (timeStep >= ad);
            if (lg.isDebugEnabled()) {
                lg.debug("average area " + averageTriangleSize + " diffusion " + dv.value + " time step limit " + ad + "timeStep " + timeStep + " -> warn " + warn);
            }
            if (warn) {
                DecimalFormat f = new DecimalFormat("0.##E0");
                String limit = f.format(ad);
                String m = "Solver time step " + timeStep + " may yield inaccurate results for given mesh size and diffusion coefficient of species " + dv.name + " on membrane " + msd.getName() + "; it is recommended that the time step not exceed " + limit;
                Issue i = new Issue(simulation, issueContext, IssueCategory.SMOLYDN_DIFFUSION, m, m, Severity.WARNING);
                issueList.add(i);
                if (lg.isDebugEnabled()) {
                    lg.debug("Warning " + m);
                }
            }
        }
    }
}

Example 67 with Issue

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

the class NernstKinetics method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 3:26:54 PM)
 * @return cbit.util.Issue[]
 */
@Override
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    super.gatherIssues(issueContext, issueList);
    // 
    // check for correct number of reactants and products
    // 
    int reactantCount = 0;
    int productCount = 0;
    ReactionParticipant[] reactionParticipants = getReactionStep().getReactionParticipants();
    for (int i = 0; i < reactionParticipants.length; i++) {
        if (reactionParticipants[i] instanceof Reactant) {
            reactantCount++;
        }
        if (reactionParticipants[i] instanceof Product) {
            productCount++;
        }
    }
    if (reactantCount != 1) {
        issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.KineticsApplicability, "Nernst Kinetics must have exactly one reactant", Issue.SEVERITY_ERROR));
    }
    if (productCount != 1) {
        issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.KineticsApplicability, "Nernst Kinetics must have exactly one product", Issue.SEVERITY_WARNING));
    }
}

Example 68 with Issue

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

the class RbmKineticLaw method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    if (rateLawType == RbmKineticLaw.RateLawType.MassAction && parameterContext.getLocalParameterFromRole(RbmKineticLaw.RbmKineticLawParameterType.MassActionForwardRate).getExpression() == null) {
        issueList.add(new Issue(this, issueContext, IssueCategory.KineticsExpressionError, "Forward Rate is null", Issue.SEVERITY_ERROR));
    }
    issueContext = issueContext.newChildContext(ContextType.ModelProcessDynamics, this);
    parameterContext.gatherIssues(issueContext, issueList, RbmKineticLawParameterType.UserDefined);
// if((reverseRate == null) && (bReversible == true)) {
// issueList.add(new Issue(this, IssueCategory.KineticsExpressionMissing, "Reverse Rate is null", Issue.SEVERITY_WARNING));
// }
}

Example 69 with Issue

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

the class RbmObservable method gatherIssues.

public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.RbmObservable, this);
    if (name == null) {
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Name of Observable is null", Issue.SEVERITY_ERROR));
    } else if (name.equals("")) {
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Name of Observable is empty", Issue.SEVERITY_WARNING));
    } else {
        if (speciesPatternList == null) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Observable '" + name + "' Species Pattern List is null", Issue.SEVERITY_ERROR));
        } else if (speciesPatternList.isEmpty()) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Observable '" + name + "' Species Pattern List is empty", Issue.SEVERITY_WARNING));
        } else {
            for (SpeciesPattern sp : speciesPatternList) {
                sp.checkSpeciesPattern(issueContext, issueList);
                sp.gatherIssues(issueContext, issueList);
                for (MolecularTypePattern mtpThis : sp.getMolecularTypePatterns()) {
                    checkComponentStateConsistency(issueContext, issueList, mtpThis);
                }
            }
        }
        if (type == null) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "Observable '" + name + "' Type is null", Issue.SEVERITY_ERROR));
        }
    }
    for (SpeciesPattern sp : speciesPatternList) {
        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 an observable.";
                issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            }
        }
    }
    // ---------------------------------------- polymer notation restrictions
    // polymer notation may only contain one species pattern and one type of molecule
    boolean polymerAllowedSingle = true;
    // ---------------,,---------------- molecules in trivial state (question marks for bonds and states)
    boolean polymerAllowedSimple = true;
    if (speciesPatternList.size() > 1) {
        polymerAllowedSingle = false;
    }
    if (speciesPatternList.size() > 0) {
        SpeciesPattern sp = speciesPatternList.get(0);
        if (sp != null && !sp.getMolecularTypePatterns().isEmpty()) {
            if (sp.getMolecularTypePatterns().size() > 1) {
                polymerAllowedSingle = false;
            } else {
                MolecularTypePattern mtp = sp.getMolecularTypePatterns().get(0);
                if (mtp != null) {
                    for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
                        if (mcp.isbVisible()) {
                            polymerAllowedSimple = false;
                            break;
                        }
                    }
                }
            }
        }
    }
    if (!polymerAllowedSingle && sequence != Sequence.Multimolecular) {
        String message = "Polymer may only be specified for Observable containing a single Molecule.";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.ERROR));
    } else if (!polymerAllowedSimple && sequence != Sequence.Multimolecular) {
        String message = "Polymer may only be specified for Observable with all bonds set to 'Possible' and all States set to 'Any'";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.ERROR));
    }
    if (sequence != Sequence.Multimolecular && type == ObservableType.Molecules) {
        String message = "The Polymer Observable must be of type 'Species'.";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.ERROR));
    }
    if (name.equalsIgnoreCase("Rg3")) {
        System.out.println(name);
    }
    for (SpeciesPattern sp : speciesPatternList) {
        // we look for species patterns where the polymer notation would be more suitable
        Set<String> moleculeNames = new HashSet<>();
        boolean isTrivial = true;
        for (MolecularTypePattern mtp : sp.getMolecularTypePatterns()) {
            moleculeNames.add(mtp.getMolecularType().getDisplayName());
            for (MolecularComponentPattern mcp : mtp.getComponentPatternList()) {
                if (mcp.isbVisible()) {
                    isTrivial = false;
                    // we may have more than 1 sp in the observable, check them all
                    continue;
                }
            }
        }
        if (isTrivial && sp.getMolecularTypePatterns().size() > 1 && moleculeNames.size() == 1) {
            String message = "Please use the Polymer notation (i.e. " + moleculeNames.toArray()[0] + "()>" + (sp.getMolecularTypePatterns().size() - 1) + " ) ";
            message += "instead of " + sp.toString();
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, message, Issue.Severity.WARNING));
            // if we find one sp that is suitable for polymer notation we stop here and don't check other sp
            break;
        }
    }
}

Example 70 with Issue

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

the class RbmObservable 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;
    }
    MolecularType mtThat = mtpThis.getMolecularType();
    for (MolecularComponentPattern mcpThis : mtpThis.getComponentPatternList()) {
        if (mcpThis.isImplied()) {
        // continue;
        }
        ComponentStatePattern cspThis = mcpThis.getComponentStatePattern();
        String mcNameThis = mcpThis.getMolecularComponent().getName();
        if (cspThis == null && mcpThis.getMolecularComponent().getComponentStateDefinitions().size() > 0) {
            // String msg = "Component pattern " + mcNameThis + " is in no State while the component has possible States defined.";
            String msg = "One of the possible States must be chosen for " + MolecularComponentPattern.typeName + " " + mcNameThis + ".";
            issueList.add(new Issue(this, mcpThis, issueContext, IssueCategory.Identifiers, msg, null, Issue.SEVERITY_WARNING));
        }
        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, null, 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, issueContext, IssueCategory.Identifiers, 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 + " " + MolecularComponentPattern.typeName + " " + mcNameThis;
                        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_WARNING));
                    }
                }
            }
        }
    }
}