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

Example 51 with Issue

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

the class ReactionSpec method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (11/1/2005 10:06:04 AM)
 * @param issueList java.util.Vector
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueList, ReactionContext rc) {
    ReactionCombo r = new ReactionCombo(this, rc);
    ReactionStep step = getReactionStep();
    if (!isExcluded() && rc.getSimulationContext().isStoch() && (rc.getSimulationContext().getGeometry().getDimension() > 0)) {
        boolean haveParticle = false;
        boolean haveContinuous = false;
        for (ReactionParticipant p : step.getReactionParticipants()) {
            if (p instanceof Product || p instanceof Reactant) {
                SpeciesContextSpec candidate = rc.getSpeciesContextSpec(p.getSpeciesContext());
                if (candidate.isForceContinuous() && !candidate.isConstant()) {
                    haveParticle = true;
                } else if (!candidate.isForceContinuous() && !candidate.isConstant()) {
                    haveContinuous = true;
                }
            }
        }
        if (haveParticle && haveContinuous) {
            String msg = "Reaction " + step.getName() + " has both continuous and particle Participants.";
            String tip = "Mass conservation for reactions of binding between discrete and continuous species is handled approximately. <br>" + "To avoid any algorithmic approximation, which may produce undesired results, the user is advised to indicate <br>" + "the continuous species in those reactions as modifiers (i.e. 'catalysts') in the physiology.";
            issueList.add(new Issue(r, issueContext, IssueCategory.Identifiers, msg, tip, Issue.SEVERITY_WARNING));
        }
    }
}

Example 52 with Issue

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

the class AbstractMathMapping method getIdentifierSubstitutions.

/**
 * Substitutes appropriate variables for speciesContext bindings
 *
 * @return cbit.vcell.parser.Expression
 * @param origExp cbit.vcell.parser.Expression
 * @param structureMapping cbit.vcell.mapping.StructureMapping
 */
protected Expression getIdentifierSubstitutions(Expression origExp, VCUnitDefinition desiredExpUnitDef, GeometryClass geometryClass) throws ExpressionException, MappingException {
    String[] symbols = origExp.getSymbols();
    if (symbols == null) {
        return origExp;
    }
    VCUnitDefinition expUnitDef = null;
    try {
        VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(simContext.getModel().getUnitSystem());
        expUnitDef = unitEvaluator.getUnitDefinition(origExp);
        if (desiredExpUnitDef == null) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            System.out.println("...........exp='" + expStr + "', desiredUnits are null");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[null], observed=[" + expUnitDef.getSymbol() + "]", Issue.SEVERITY_WARNING));
        } else if (expUnitDef == null) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            System.out.println("...........exp='" + expStr + "', evaluated Units are null");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[null]", Issue.SEVERITY_WARNING));
        } else if (desiredExpUnitDef.isTBD()) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            // System.out.println("...........exp='"+expStr+"', desiredUnits are ["+desiredExpUnitDef.getSymbol()+"] and expression units are ["+expUnitDef.getSymbol()+"]");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[" + expUnitDef.getSymbol() + "] for exp = " + expStr, Issue.SEVERITY_WARNING));
        } else if (!desiredExpUnitDef.isEquivalent(expUnitDef) && !expUnitDef.isTBD()) {
            String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
            // System.out.println("...........exp='"+expStr+"', desiredUnits are ["+desiredExpUnitDef.getSymbol()+"] and expression units are ["+expUnitDef.getSymbol()+"]");
            localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + desiredExpUnitDef.getSymbol() + "], observed=[" + expUnitDef.getSymbol() + "] for exp = " + expStr, Issue.SEVERITY_WARNING));
        }
    } catch (VCUnitException e) {
        String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
        System.out.println(".........exp='" + expStr + "' exception='" + e.getMessage() + "'");
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    } catch (ExpressionException e) {
        String expStr = origExp.renameBoundSymbols(getNameScope()).infix();
        System.out.println(".........exp='" + expStr + "' exception='" + e.getMessage() + "'");
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    } catch (Exception e) {
        e.printStackTrace(System.out);
        localIssueList.add(new Issue(origExp, issueContext, IssueCategory.Units, "expected=[" + ((desiredExpUnitDef != null) ? (desiredExpUnitDef.getSymbol()) : ("null")) + "], exception=" + e.getMessage(), Issue.SEVERITY_WARNING));
    }
    Expression newExp = new Expression(origExp);
    // 
    // flatten user-defined functions
    // 
    FunctionInvocation[] functionInvocations = newExp.getFunctionInvocations(new FunctionFilter() {

        @Override
        public boolean accept(String functionName, FunctionType functionType) {
            return functionType == FunctionType.USERDEFINED;
        }
    });
    for (FunctionInvocation functionInvocation : functionInvocations) {
        if (functionInvocation.getSymbolTableFunctionEntry() instanceof Model.ModelFunction) {
            ModelFunction modelFunction = (ModelFunction) functionInvocation.getSymbolTableFunctionEntry();
            newExp.substituteInPlace(functionInvocation.getFunctionExpression(), modelFunction.getFlattenedExpression(functionInvocation));
        }
    }
    // 
    // then substitute Math symbols for Biological symbols.
    // 
    newExp.bindExpression(null);
    for (int i = 0; i < symbols.length; i++) {
        SymbolTableEntry ste = origExp.getSymbolBinding(symbols[i]);
        if (ste == null) {
            throw new ExpressionBindingException("symbol '" + symbols[i] + "' not bound");
        // ste = simContext.getGeometryContext().getModel().getSpeciesContext(symbols[i]);
        }
        if (ste != null) {
            String newName = getMathSymbol(ste, geometryClass);
            if (!newName.equals(symbols[i])) {
                newExp.substituteInPlace(new Expression(symbols[i]), new Expression(newName));
            }
        }
    }
    return newExp;
}

Example 53 with Issue

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

the class IssueManagerContainer method hasErrorIssues.

public boolean hasErrorIssues(Displayable owner, MolecularType mt) {
    if (issueManager == null) {
        return false;
    }
    if (owner == null) {
        return false;
    }
    List<Issue> allIssueList = issueManager.getIssueList();
    for (Issue issue : allIssueList) {
        if (issue.getSeverity() != Issue.Severity.ERROR) {
            continue;
        }
        Object source = issue.getSource();
        Object detailedSource = issue.getDetailedSource();
        if (mt != null & source == owner && detailedSource == mt) {
            return true;
        }
    }
    return false;
}

Example 54 with Issue

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

the class IssueManagerContainer method hasErrorIssues.

public boolean hasErrorIssues(Displayable owner, MolecularComponentPattern mcp, MolecularComponent mc) {
    if (issueManager == null) {
        return false;
    }
    if (owner == null) {
        return false;
    }
    List<Issue> allIssueList = issueManager.getIssueList();
    for (Issue issue : allIssueList) {
        if (issue.getSeverity() != Issue.Severity.ERROR) {
            continue;
        }
        Object source = issue.getSource();
        Object detailedSource = issue.getDetailedSource();
        if (mcp != null && source == owner && detailedSource == mcp) {
            return true;
        } else if (mc != null & source == owner && detailedSource == mc) {
            return true;
        }
    }
    return false;
}

Example 55 with Issue

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

the class IssueManagerContainer method hasErrorIssues.

public boolean hasErrorIssues(Displayable owner, ComponentStatePattern csp, ComponentStateDefinition csd) {
    if (issueManager == null) {
        return false;
    }
    if (owner == null) {
        return false;
    }
    List<Issue> allIssueList = issueManager.getIssueList();
    for (Issue issue : allIssueList) {
        if (issue.getSeverity() != Issue.Severity.ERROR) {
            continue;
        }
        Object source = issue.getSource();
        Object detailedSource = issue.getDetailedSource();
        if (csp != null && source == owner && detailedSource == csp) {
            return true;
        } else if (csd != null & source == owner && detailedSource == csd) {
            return true;
        }
    }
    return false;
}