Examples with SymbolTableEntry cbit.vcell.parser.SymbolTableEntry used on opensource projects

Example 21 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class Model method gatherIssues.

/**
 * Insert the method's description here.
 * Creation date: (5/12/2004 10:38:12 PM)
 * @param issueList java.util.Vector
 */
public void gatherIssues(IssueContext issueContext, List<Issue> issueList) {
    issueContext = issueContext.newChildContext(ContextType.Model, this);
    // 
    try {
        for (ModelParameter modelParameter : fieldModelParameters) {
            Expression exp = modelParameter.getExpression();
            String[] symbols = exp.getSymbols();
            if (symbols != null) {
                String issueMsgPrefix = "Global parameter '" + modelParameter.getName() + "' ";
                for (int j = 0; j < symbols.length; j++) {
                    SymbolTableEntry ste = exp.getSymbolBinding(symbols[j]);
                    if (ste == null) {
                        issueList.add(new Issue(modelParameter, issueContext, IssueCategory.ModelParameterExpressionError, issueMsgPrefix + "references undefined symbol '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                    } else if (ste instanceof SpeciesContext) {
                        if (!contains((SpeciesContext) ste)) {
                            issueList.add(new Issue(modelParameter, issueContext, IssueCategory.ModelParameterExpressionError, issueMsgPrefix + "references undefined species '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                        }
                    } else if (ste instanceof ModelParameter) {
                        if (!contains((ModelParameter) ste)) {
                            issueList.add(new Issue(modelParameter, issueContext, IssueCategory.ModelParameterExpressionError, issueMsgPrefix + "references undefined global parameter '" + symbols[j] + "'", Issue.SEVERITY_ERROR));
                        }
                    }
                }
            }
        }
        // 
        for (int i = 0; i < fieldModelParameters.length; i++) {
            try {
                VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(getUnitSystem());
                VCUnitDefinition paramUnitDef = fieldModelParameters[i].getUnitDefinition();
                VCUnitDefinition expUnitDef = unitEvaluator.getUnitDefinition(fieldModelParameters[i].getExpression());
                if (paramUnitDef == null) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "defined unit is null", Issue.SEVERITY_WARNING));
                } else if (expUnitDef == null) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "computed unit is null", Issue.SEVERITY_WARNING));
                } else if (paramUnitDef.isTBD()) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "unit is undefined (" + unitSystem.getInstance_TBD().getSymbol() + ")", Issue.SEVERITY_WARNING));
                } else if (!paramUnitDef.isEquivalent(expUnitDef) && !expUnitDef.isTBD()) {
                    issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "unit mismatch, computed = [" + expUnitDef.getSymbol() + "]", Issue.SEVERITY_WARNING));
                }
            } catch (VCUnitException e) {
                issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "units inconsistent: " + e.getMessage(), Issue.SEVERITY_WARNING));
            } catch (ExpressionException e) {
                issueList.add(new Issue(fieldModelParameters[i], issueContext, IssueCategory.Units, "units inconsistent: " + e.getMessage(), Issue.SEVERITY_WARNING));
            }
        }
    } catch (Throwable e) {
        e.printStackTrace(System.out);
        issueList.add(new Issue(this, issueContext, IssueCategory.Units, "unexpected exception: " + e.getMessage(), Issue.SEVERITY_WARNING));
    }
    // 
    for (Structure struct : fieldStructures) {
        struct.gatherIssues(issueContext, issueList);
    }
    // 
    for (int i = 0; i < fieldReactionSteps.length; i++) {
        fieldReactionSteps[i].gatherIssues(issueContext, issueList);
    }
    // 
    // get issues from species contexts (species patterns)
    // 
    int seedSpeciesCount = 0;
    for (int i = 0; i < fieldSpeciesContexts.length; i++) {
        if (fieldSpeciesContexts[i].hasSpeciesPattern()) {
            seedSpeciesCount++;
        }
        fieldSpeciesContexts[i].gatherIssues(issueContext, issueList);
    }
    if (seedSpeciesCount == 0 && !rbmModelContainer.getReactionRuleList().isEmpty()) {
        String msg = "At least one seed species is required.";
        issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, msg, Issue.Severity.WARNING));
    }
    // 
    // get issues for symbol name clashes (specifically structures with same voltage names or structure names)
    // 
    HashSet<SymbolTableEntry> steHashSet = new HashSet<SymbolTableEntry>();
    gatherLocalEntries(steHashSet);
    Iterator<SymbolTableEntry> iter = steHashSet.iterator();
    Hashtable<String, SymbolTableEntry> symbolHashtable = new Hashtable<String, SymbolTableEntry>();
    while (iter.hasNext()) {
        SymbolTableEntry ste = iter.next();
        SymbolTableEntry existingSTE = symbolHashtable.get(ste.getName());
        if (existingSTE != null) {
            issueList.add(new Issue(this, issueContext, IssueCategory.Identifiers, "model symbol \"" + ste.getName() + "\" is used within \"" + ste.getNameScope().getName() + "\" and \"" + existingSTE.getNameScope().getName() + "\"", Issue.SEVERITY_ERROR));
        } else {
            symbolHashtable.put(ste.getName(), ste);
        }
    }
    // 
    // gather issues for electrical topology (unspecified +ve or -ve features, or +ve feature == -ve feature
    // 
    getElectricalTopology().gatherIssues(issueContext, issueList);
    // 
    if (rbmModelContainer == null) {
        issueList.add(new Issue(this, issueContext, IssueCategory.InternalError, "Rbm Model Container is null", Issue.SEVERITY_WARNING));
    } else {
        rbmModelContainer.gatherIssues(issueContext, issueList);
    }
}

Example 22 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class MathUtilities method substituteModelParameters.

/**
 * This method was created in VisualAge.
 * @return cbit.vcell.parser.Expression
 * @param exp cbit.vcell.parser.Expression
 * @exception java.lang.Exception The exception description.
 */
public static Expression substituteModelParameters(Expression exp, SymbolTable symbolTable) throws ExpressionException {
    Expression exp2 = new Expression(exp);
    // 
    // do until no more functions to substitute
    // 
    int count = 0;
    boolean bSubstituted = true;
    while (bSubstituted) {
        bSubstituted = false;
        if (count++ > 30) {
            throw new ExpressionBindingException("infinite loop in eliminating function nesting");
        }
        String[] symbols = exp2.getSymbols();
        if (symbols != null) {
            for (int i = 0; i < symbols.length; i++) {
                SymbolTableEntry ste = exp2.getSymbolBinding(symbols[i]);
                if (ste != null && !(ste instanceof SymbolTableFunctionEntry)) {
                    Expression steExp = ste.getExpression();
                    if (steExp != null) {
                        exp2.substituteInPlace(new Expression(ste.getName()), steExp);
                        bSubstituted = true;
                    }
                }
            }
        }
    }
    exp2.bindExpression(symbolTable);
    return exp2;
}

Example 23 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class MathUtilities method getRequiredVariablesExplicit.

/**
 * This method was created by a SmartGuide.
 * @return java.util.Enumeration
 * @param exp cbit.vcell.parser.Expression
 */
private static Enumeration<Variable> getRequiredVariablesExplicit(Expression exp, SymbolTable symbolTable) throws ExpressionException {
    Vector<Variable> requiredVarList = new Vector<Variable>();
    if (exp != null) {
        String[] identifiers = exp.getSymbols();
        if (lg.isDebugEnabled()) {
            lg.debug("from expression " + exp + " parsing identifiers " + Arrays.toString(identifiers));
        }
        if (identifiers != null) {
            for (int i = 0; i < identifiers.length; i++) {
                String id = identifiers[i];
                // 
                // look for globally bound variables
                // 
                SymbolTableEntry entry = symbolTable.getEntry(id);
                // 
                if (entry == null) {
                    entry = ReservedMathSymbolEntries.getReservedVariableEntry(id);
                    if (lg.isDebugEnabled()) {
                        lg.debug("id " + id + "not in symbol table looked for reserved symbols,found = " + (entry != null));
                    }
                } else if (lg.isDebugEnabled()) {
                    lg.debug("symbolTable.getEntry( ) returned " + entry + " for " + id);
                }
                // 
                if (entry == null) {
                    SymbolTableEntry ste = exp.getSymbolBinding(id);
                    if (ste instanceof PseudoConstant) {
                        entry = ste;
                    }
                    if (entry == null) {
                        ExpressionBindingException ebe = new ExpressionBindingException("unresolved symbol " + id + " in expression " + exp);
                        lg.debug("found " + ste + "but it's not a PseudoConstant; throwing ", ebe);
                        throw ebe;
                    }
                }
                if (!(entry instanceof Variable)) {
                    throw new RuntimeException("MathUtilities.getRequiredVariablesExplicit() only gets required math variable. Use math side symbol table, e.g. MathDescription, SimulationSymbolTable, etc.");
                }
                requiredVarList.addElement((Variable) entry);
            }
        }
    }
    return requiredVarList.elements();
}

Example 24 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class ReservedMathSymbolEntries method getEntry.

public static SymbolTableEntry getEntry(String symbolName, boolean bIncludePostProcessing) {
    SymbolTableEntry ste = getSymbolTableEntries().get(symbolName);
    if (ste != null) {
        return ste;
    }
    SymbolTableFunctionEntry steFunction = getMathSymbolTableFunctionEntries().get(symbolName);
    if (steFunction != null) {
        return steFunction;
    }
    if (bIncludePostProcessing) {
        steFunction = getPostProcessingSymbolTableFunctionEntries().get(symbolName);
        if (steFunction != null) {
            return steFunction;
        }
    }
    return null;
}

Example 25 with SymbolTableEntry

use of cbit.vcell.parser.SymbolTableEntry in project vcell by virtualcell.

the class PdeTimePlotMultipleVariablesPanel method initialize.

private void initialize() {
    VariableType varType = multiTimePlotHelper.getPdeDatacontext().getDataIdentifier().getVariableType();
    String varName = multiTimePlotHelper.getPdeDatacontext().getVariableName();
    String[] plotNames = new String[pointVector.size()];
    final SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[plotNames.length];
    DefaultListModel<String> pointListModel = new DefaultListModel<String>();
    for (int i = 0; i < pointVector.size(); i++) {
        Coordinate tp = null;
        if (varType.equals(VariableType.VOLUME) || varType.equals(VariableType.VOLUME_REGION) || varType.equals(VariableType.POSTPROCESSING)) {
            SpatialSelectionVolume ssv = (SpatialSelectionVolume) pointVector.get(i);
            tp = ssv.getCurveSelectionInfo().getCurve().getBeginningCoordinate();
        } else if (varType.equals(VariableType.MEMBRANE) || varType.equals(VariableType.MEMBRANE_REGION)) {
            SpatialSelectionMembrane ssm = (SpatialSelectionMembrane) pointVector.get(i);
            double midU = ssm.getCurveSelectionInfo().getCurveUfromSelectionU(.5);
            tp = ((SampledCurve) ssm.getCurveSelectionInfo().getCurve()).coordinateFromNormalizedU(midU);
        }
        plotNames[i] = varName + " at P[" + i + "]";
        String point = "P[" + i + "]  (" + niceCoordinateString(tp) + ")";
        pointListModel.addElement(point);
        if (multiTimePlotHelper.getsimulation() != null) {
            symbolTableEntries[0] = multiTimePlotHelper.getsimulation().getMathDescription().getEntry(varName);
        } else {
            System.out.println("PdeTimePlotMultipleVariablesPanel.initialize() adding artificial symbol table entries for field data");
            SimpleSymbolTable simpleSymbolTable = new SimpleSymbolTable(new String[] { varName });
            symbolTableEntries[0] = simpleSymbolTable.getEntry(varName);
        }
    }
    pointJList.setModel(pointListModel);
    pointJList.setForeground(variableJList.getForeground());
    pointJList.setVisibleRowCount(3);
    pointJList.setBackground(getBackground());
    pointJList.setSelectionBackground(getBackground());
    pointJList.setSelectionForeground(Color.black);
    plotPane = new PlotPane();
    double[][] plotDatas = tsJobResultsNoStats.getTimesAndValuesForVariable(varName);
    Plot2D plot2D = new SingleXPlot2D(symbolTableEntries, multiTimePlotHelper.getDataSymbolMetadataResolver(), ReservedVariable.TIME.getName(), plotNames, plotDatas, new String[] { "Time Plot", ReservedVariable.TIME.getName(), "" });
    plotPane.setPlot2D(plot2D);
    DataIdentifier[] dis = (multiTimePlotHelper.getCopyOfDisplayedDataIdentifiers() != null ? multiTimePlotHelper.getCopyOfDisplayedDataIdentifiers() : DataIdentifier.collectSortedSimilarDataTypes(multiTimePlotHelper.getVariableType(), multiTimePlotHelper.getPdeDatacontext().getDataIdentifiers()));
    Arrays.sort(dis, new Comparator<DataIdentifier>() {

        public int compare(DataIdentifier o1, DataIdentifier o2) {
            int bEqualIgnoreCase = o1.getDisplayName().compareToIgnoreCase(o2.getDisplayName());
            if (bEqualIgnoreCase == 0) {
                return o1.getDisplayName().compareTo(o2.getDisplayName());
            }
            return bEqualIgnoreCase;
        }
    });
    variableJList.setListData(dis);
    initVariableListSelected(variableJList, multiTimePlotHelper.getPdeDatacontext().getDataIdentifier());
    variableJList.setCellRenderer(multiTimePlotHelper.getListCellRenderer());
    setLayout(new GridBagLayout());
    JLabel label = new JLabel("Selected Points");
    label.setFont(label.getFont().deriveFont(Font.BOLD));
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.insets = new java.awt.Insets(15, 10, 4, 4);
    add(label, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 0;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.gridheight = 4;
    gbc.weightx = 1;
    gbc.weighty = 1;
    gbc.fill = GridBagConstraints.BOTH;
    gbc.insets = new java.awt.Insets(0, 4, 0, 0);
    add(plotPane, gbc);
    JScrollPane sp = new JScrollPane(pointJList);
    sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
    sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 1;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.weighty = 0.5;
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    gbc.insets = new java.awt.Insets(4, 10, 4, 4);
    add(sp, gbc);
    label = new JLabel("Y Axis");
    label.setFont(label.getFont().deriveFont(Font.BOLD));
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 2;
    gbc.anchor = GridBagConstraints.WEST;
    gbc.insets = new java.awt.Insets(4, 10, 4, 4);
    add(label, gbc);
    sp = new JScrollPane(variableJList);
    sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
    sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 3;
    gbc.weightx = 0.2;
    gbc.weighty = 1;
    gbc.insets = new java.awt.Insets(4, 10, 50, 4);
    gbc.fill = java.awt.GridBagConstraints.BOTH;
    add(sp, gbc);
    variableJList.addListSelectionListener(eventHandler);
    multiTimePlotHelper.addPropertyChangeListener(eventHandler);
}