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

Example 86 with SymbolTableEntry

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

the class PostProcessingBlock method getEntry.

public SymbolTableEntry getEntry(String id) {
    SymbolTableEntry entry = null;
    entry = ReservedMathSymbolEntries.getEntry(id, true);
    if (entry != null) {
        return entry;
    }
    entry = getMathDescription().getEntry(id);
    if (entry != null) {
        return entry;
    }
    entry = dataGeneratorHashMap.get(id);
    if (entry != null) {
        return entry;
    }
    return null;
}

Example 87 with SymbolTableEntry

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

the class BioModelParametersTableModel method getApplicationEditableSymbolTableEntryList.

private List<EditableSymbolTableEntry> getApplicationEditableSymbolTableEntryList(SimulationContext simulationContext) {
    ArrayList<EditableSymbolTableEntry> parameterList = new ArrayList<EditableSymbolTableEntry>();
    Map<String, SymbolTableEntry> entryMap = new HashMap<String, SymbolTableEntry>();
    simulationContext.getEntries(entryMap);
    for (SymbolTableEntry ste : entryMap.values()) {
        if (ste instanceof EditableSymbolTableEntry && ste.getNameScope() == simulationContext.getNameScope()) {
            parameterList.add((EditableSymbolTableEntry) ste);
        }
    }
    for (StructureMapping mapping : simulationContext.getGeometryContext().getStructureMappings()) {
        parameterList.addAll(mapping.computeApplicableParameterList());
    }
    for (SpeciesContextSpec spec : simulationContext.getReactionContext().getSpeciesContextSpecs()) {
        parameterList.addAll(spec.computeApplicableParameterList());
    }
    for (ElectricalStimulus elect : simulationContext.getElectricalStimuli()) {
        parameterList.addAll(Arrays.asList(elect.getParameters()));
    }
    for (SpatialProcess sp : simulationContext.getSpatialProcesses()) {
        parameterList.addAll(Arrays.asList(sp.getParameters()));
    }
    return parameterList;
}

Example 88 with SymbolTableEntry

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

the class EventPanel method addEventAssignment.

private void addEventAssignment() {
    populateVariableComboBoxModel(getVarNameComboBoxModel(), getSimulationContext());
    JPanel eventAssignmentPanel = getEventAssignmentPanel();
    getEventAssignVarNameComboBox().setModel(getVarNameComboBoxModel());
    getEventAssignExpressionTextField().setText("0.0");
    Set<String> autoCompList = getAutoCompleteList();
    getEventAssignExpressionTextField().setAutoCompletionWords(autoCompList);
    getEventAssignExpressionTextField().setAutoCompleteSymbolFilter(getAutoCompleteFilter());
    // 
    // If the OK option is chosen, get the var name and expression and create a new
    // event assignment, add it to the list of event assignments in bioEvent
    // Else, pop-up an error dialog indicating that event assignment cannot be added.
    // 
    int ok = JOptionPane.showOptionDialog(this, eventAssignmentPanel, "New Action Event", 0, JOptionPane.PLAIN_MESSAGE, null, new String[] { "OK", "Cancel" }, null);
    if (ok == javax.swing.JOptionPane.OK_OPTION) {
        String varName = (String) getEventAssignVarNameComboBox().getSelectedItem();
        EventAssignment newEventAssignment = null;
        try {
            SymbolTableEntry ste = fieldSimContext.getEntry(varName);
            Expression eventAssgnExp = new Expression(getEventAssignExpressionTextField().getText());
            newEventAssignment = fieldBioEvent.new EventAssignment(ste, eventAssgnExp);
            fieldBioEvent.addEventAssignment(newEventAssignment);
        } catch (ExpressionException e) {
            e.printStackTrace(System.out);
        } catch (PropertyVetoException e1) {
            e1.printStackTrace(System.out);
            String targetName = (newEventAssignment != null) ? (newEventAssignment.getTarget().getName()) : ("null");
            DialogUtils.showErrorDialog(this, "Event Assignment '" + targetName + "' cannot be added." + e1.getMessage());
        }
    }
    enableDeleteEventAssgnButton();
}

Example 89 with SymbolTableEntry

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

the class EventPanel method populateVariableComboBoxModel.

public static void populateVariableComboBoxModel(DefaultComboBoxModel<String> defaultComboBoxModel, SimulationContext simContext) /*,boolean bExcludeFuncAndReserved*/
{
    // fill comboboxmodel with possible variables from simContext (symboltable entries) list
    defaultComboBoxModel.removeAllElements();
    Map<String, SymbolTableEntry> entryMap = new HashMap<String, SymbolTableEntry>();
    simContext.getEntries(entryMap);
    ArrayList<String> varNameList = new ArrayList<String>();
    for (String varName : entryMap.keySet()) {
        SymbolTableEntry symbolTableEntry = entryMap.get(varName);
        if (/*bExcludeFuncAndReserved && */
        (symbolTableEntry instanceof SymbolTableFunctionEntry || symbolTableEntry instanceof Model.ReservedSymbol)) {
            continue;
        }
        varNameList.add(varName);
    }
    Collections.sort(varNameList);
    for (String varName : varNameList) {
        defaultComboBoxModel.addElement(varName);
    }
}

Example 90 with SymbolTableEntry

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

the class KymographPanel method configurePlotData.

/**
 * Insert the method's description here.
 * Creation date: (12/16/2004 10:46:05 AM)
 * @param imgX int
 * @param imgY int
 */
private void configurePlotData(int imgX, int imgY) {
    // 
    // TimeScan Data
    // 
    double[][] timeData = new double[2][currentTimes.length];
    timeData[0] = currentTimes;
    timeData[1] = new double[currentTimes.length];
    for (int i = 0; i < currentTimes.length; i += 1) {
        // timeData[1][i] = timeSeriesDataOrig[1+imgX][i];
        timeData[1][i] = rawValues[imgX + (i * RESAMP_SIZE)];
    }
    ;
    localTimeDataMMMH = calcMMM(timeData[1]);
    final int MAX_TITLE_VAL_LENGTH = 9;
    DecimalFormat nf = new DecimalFormat();
    String valS = null;
    valS = currentDistances[imgX] + "";
    if (valS.length() > MAX_TITLE_VAL_LENGTH) {
        nf.applyPattern("#.###E0");
        valS = nf.format(currentDistances[imgX]);
    }
    currentTimeSeriesPlot2D = new SingleXPlot2D(new SymbolTableEntry[] { currentSymbolTablEntry }, multiTimePlotHelper.getDataSymbolMetadataResolver(), "Time", new String[] { currentDataIdentifier.getName() }, timeData, new String[] { "Time Series (d=" + valS + ") Vert", "Time", /*"Time (s)"*/
    "Value" });
    getPlotPaneTimeSeries().setPlot2D(currentTimeSeriesPlot2D);
    // 
    // LineScan Data
    // 
    double[] lineData = new double[timeSeriesDataOrig.length - 1];
    for (int i = 1; i < timeSeriesDataOrig.length; i += 1) {
        lineData[i - 1] = timeSeriesDataOrig[i][imgY];
    }
    double[] lineScanDistances = accumDistancesDataOrig;
    localDistDataMMMH = calcMMM(lineData);
    PlotData plotData = new PlotData(lineScanDistances, lineData);
    valS = currentTimes[imgY] + "";
    if (valS.length() > MAX_TITLE_VAL_LENGTH) {
        valS = nf.format(currentTimes[imgY]);
    }
    currentLineScanPlot2D = new Plot2D(new SymbolTableEntry[] { currentSymbolTablEntry }, multiTimePlotHelper.getDataSymbolMetadataResolver(), new String[] { currentDataIdentifier.getName() }, new PlotData[] { plotData }, new String[] { "Line Scan (t=" + valS + ") Horz", "Distance", /*"Distance (\u00b5m)"*/
    "Value" });
    getPlotPaneLineScan().setPlot2D(currentLineScanPlot2D);
    Range xRangeTime = new Range(currentTimes[0], currentTimes[currentTimes.length - 1]);
    Range xRangeDist = new Range(lineScanDistances[0], lineScanDistances[lineScanDistances.length - 1]);
    Range yRangeTime = (allDataMMMH != null ? allDataMMMH.getRange() : null);
    Range yRangeDist = yRangeTime;
    if (bLocalScaling) {
        yRangeTime = (localTimeDataMMMH != null ? localTimeDataMMMH.getRange() : null);
        yRangeDist = (localDistDataMMMH != null ? localDistDataMMMH.getRange() : null);
    }
    getPlotPaneTimeSeries().forceXYRange(xRangeTime, yRangeTime);
    getPlotPaneLineScan().forceXYRange(xRangeDist, yRangeDist);
    configureMinMax();
    getimagePaneView1().repaint();
}