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

Example 11 with Displayable

use of org.vcell.util.Displayable 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 12 with Displayable

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

the class SpeciesContext method findStateUsage.

public void findStateUsage(MolecularType mt, MolecularComponent mc, ComponentStateDefinition csd, 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 some state is always in use if available
                    ComponentStatePattern csp = mcp.getComponentStatePattern();
                    if (csp == null) {
                        System.out.println("This component " + mc.getName() + " should have had some State specified.");
                        continue;
                    }
                    if ((csp.getComponentStateDefinition() == csd) && (mcp.getBond() != null)) {
                        // we only care if there's a bond
                        String key = sp.getDisplayName();
                        key = getDisplayType() + getDisplayName() + key;
                        usedHere.put(key, new Pair<Displayable, SpeciesPattern>(this, sp));
                    }
                }
            }
        }
    }
}

Example 13 with Displayable

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

the class Kinetics method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 2:53:13 PM)
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.ModelProcessDynamics, this);
    // 
    for (int i = 0; fieldUnresolvedParameters != null && i < fieldUnresolvedParameters.length; i++) {
        issueList.add(new Issue(fieldUnresolvedParameters[i], issueContext, IssueCategory.UnresolvedParameter, "Unresolved parameter '" + fieldUnresolvedParameters[i].getName() + "' in reaction '" + reactionStep.getName() + "'", Issue.SEVERITY_ERROR));
    }
    // 
    for (int i = 0; fieldKineticsParameters != null && i < fieldKineticsParameters.length; i++) {
        if (fieldKineticsParameters[i].getRole() == ROLE_UserDefined) {
            try {
                if (!isReferenced(fieldKineticsParameters[i], 0)) {
                    issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.KineticsUnreferencedParameter, "Unreferenced Kinetic Parameter '" + fieldKineticsParameters[i].getName() + "' in reaction '" + reactionStep.getName() + "'", Issue.SEVERITY_WARNING));
                }
            } catch (ExpressionException e) {
                issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.KineticsExpressionError, "error resolving expression " + e.getMessage(), Issue.SEVERITY_WARNING));
            } catch (ModelException e) {
                issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.CyclicDependency, "cyclic dependency in the parameter definitions", Issue.SEVERITY_ERROR));
            }
        }
    }
    // 
    if (fieldKineticsParameters != null) {
        for (KineticsParameter kineticsParameter : fieldKineticsParameters) {
            if (kineticsParameter.getExpression() == null) {
                issueList.add(new Issue(kineticsParameter, issueContext, IssueCategory.KineticsExpressionMissing, "expression is missing", Issue.SEVERITY_INFO));
            } else {
                Expression exp = kineticsParameter.getExpression();
                String[] symbols = exp.getSymbols();
                String issueMessagePrefix = "Kinetic parameter '" + kineticsParameter.getName() + "' in reaction '" + getReactionStep().getName() + "' ";
                if (symbols != null) {
                    for (int j = 0; j < symbols.length; j++) {
                        SymbolTableEntry ste = exp.getSymbolBinding(symbols[j]);
                        if (ste instanceof KineticsProxyParameter) {
                            ste = ((KineticsProxyParameter) ste).getTarget();
                        }
                        if (ste == null) {
                            issueList.add(new Issue(kineticsParameter, issueContext, IssueCategory.KineticsExpressionUndefinedSymbol, issueMessagePrefix + "references undefined symbol '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                        } else if (ste instanceof SpeciesContext) {
                            if (!getReactionStep().getModel().contains((SpeciesContext) ste)) {
                                issueList.add(new Issue(kineticsParameter, issueContext, IssueCategory.KineticsExpressionUndefinedSymbol, issueMessagePrefix + "references undefined species '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                            }
                            if (reactionStep.countNumReactionParticipants((SpeciesContext) ste) == 0) {
                                issueList.add(new Issue(kineticsParameter, issueContext, IssueCategory.KineticsExpressionNonParticipantSymbol, issueMessagePrefix + "references species context '" + symbols[j] + "', but it is not a reactant/product/catalyst of this reaction", Issue.SEVERITY_WARNING));
                            }
                        } else if (ste instanceof ModelParameter) {
                            if (!getReactionStep().getModel().contains((ModelParameter) ste)) {
                                issueList.add(new Issue(kineticsParameter, issueContext, IssueCategory.KineticsExpressionUndefinedSymbol, issueMessagePrefix + "references undefined global parameter '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                            }
                        }
                    }
                }
            }
        }
        // looking for local param which masks a global and issueing a warning
        for (KineticsParameter kineticsParameter : fieldKineticsParameters) {
            String name = kineticsParameter.getName();
            SymbolTableEntry ste = getReactionStep().getNameScope().getExternalEntry(name, getReactionStep());
            String steName;
            if (ste != null) {
                if (ste instanceof Displayable) {
                    steName = ((Displayable) ste).getDisplayType() + " " + ste.getName();
                } else {
                    steName = ste.getClass().getSimpleName() + " " + ste.getName();
                }
                String msg = steName + " is overriden by a local parameter " + name + " in reaction " + getReactionStep().getName();
                issueList.add(new Issue(kineticsParameter, issueContext, IssueCategory.Identifiers, msg, Issue.SEVERITY_WARNING));
            }
        }
    }
    try {
        // 
        // determine unit consistency for each expression
        // 
        ModelUnitSystem modelUnitSystem = getReactionStep().getModel().getUnitSystem();
        VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(modelUnitSystem);
        for (int i = 0; i < fieldKineticsParameters.length; i++) {
            try {
                VCUnitDefinition paramUnitDef = fieldKineticsParameters[i].getUnitDefinition();
                VCUnitDefinition expUnitDef = unitEvaluator.getUnitDefinition(fieldKineticsParameters[i].getExpression());
                if (paramUnitDef == null) {
                    issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, "defined unit is null", Issue.SEVERITY_WARNING));
                } else if (paramUnitDef.isTBD()) {
                    issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, "undefined unit " + modelUnitSystem.getInstance_TBD().getSymbol(), Issue.SEVERITY_WARNING));
                } else if (expUnitDef == null) {
                    issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, "computed unit is null", Issue.SEVERITY_WARNING));
                } else if (paramUnitDef.isTBD() || (!paramUnitDef.isEquivalent(expUnitDef) && !expUnitDef.isTBD())) {
                    issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, "inconsistent units, defined=[" + fieldKineticsParameters[i].getUnitDefinition().getSymbol() + "], computed=[" + expUnitDef.getSymbol() + "]", Issue.SEVERITY_WARNING));
                }
            } catch (VCUnitException e) {
                issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, e.getMessage(), Issue.SEVERITY_WARNING));
            } catch (ExpressionException e) {
                issueList.add(new Issue(fieldKineticsParameters[i], issueContext, IssueCategory.Units, e.getMessage(), Issue.SEVERITY_WARNING));
            }
        }
    } catch (Throwable e) {
        issueList.add(new Issue(getReactionStep(), issueContext, IssueCategory.Units, "unexpected exception: " + e.getMessage(), Issue.SEVERITY_INFO));
    }
    // 
    for (int i = 0; i < fieldKineticsParameters.length; i++) {
        RealInterval simpleBounds = bounds[fieldKineticsParameters[i].getRole()];
        if (simpleBounds != null) {
            String parmName = reactionStep.getNameScope().getName() + "." + fieldKineticsParameters[i].getName();
            issueList.add(new SimpleBoundsIssue(fieldKineticsParameters[i], issueContext, simpleBounds, "parameter " + parmName + ": must be within " + simpleBounds.toString()));
        }
    }
}

Example 14 with Displayable

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

the class ComponentStateDefinition method dependenciesToHtml.

public String dependenciesToHtml(Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    String errMsg = "State '<b>" + getDisplayName() + "'</b> is already being used by:<br>";
    final int MaxListSize = 7;
    int count = 0;
    for (String key : usedHere.keySet()) {
        System.out.println(key);
        if (count >= MaxListSize) {
            errMsg += "<br> ... and more.";
            break;
        }
        Pair<Displayable, SpeciesPattern> o = usedHere.get(key);
        Displayable e = o.one;
        SpeciesPattern sp = o.two;
        errMsg += "<br> - " + e.getDisplayType().toLowerCase() + " <b>" + e.getDisplayName() + "</b>";
        errMsg += ", " + sp.getDisplayType().toLowerCase() + " " + " <b>" + sp.getDisplayName() + "</b>";
        count++;
    }
    return errMsg;
}

Example 15 with Displayable

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

the class MolecularComponent method dependenciesToHtml.

public String dependenciesToHtml(Map<String, Pair<Displayable, SpeciesPattern>> usedHere) {
    String errMsg = typeName + " '<b>" + getDisplayName() + "'</b> is already being used by:<br>";
    final int MaxListSize = 7;
    int count = 0;
    for (String key : usedHere.keySet()) {
        System.out.println(key);
        if (count >= MaxListSize) {
            errMsg += "<br> ... and more.";
            break;
        }
        Pair<Displayable, SpeciesPattern> o = usedHere.get(key);
        Displayable e = o.one;
        SpeciesPattern sp = o.two;
        errMsg += "<br> - " + e.getDisplayType().toLowerCase() + " <b>" + e.getDisplayName() + "</b>";
        errMsg += ", " + sp.getDisplayType().toLowerCase() + " " + " <b>" + sp.getDisplayName() + "</b>";
        count++;
    }
    return errMsg;
}