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

Example 96 with SymbolTableEntry

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

the class OutputFunctionsPanel method addOutputFunction.

private void addOutputFunction() {
    if (simulationWorkspace == null) {
        return;
    }
    AsynchClientTask task1 = new AsynchClientTask("refresh math description", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            MathMappingCallback mathMappingCallback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
            if (simulationWorkspace.getSimulationOwner() instanceof SimulationContext) {
                SimulationContext simulationContext = (SimulationContext) simulationWorkspace.getSimulationOwner();
                simulationContext.refreshMathDescription(mathMappingCallback, NetworkGenerationRequirements.AllowTruncatedStandardTimeout);
            }
        // else, for mathModels, nothing to refresh.
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("show dialog", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ArrayList<AnnotatedFunction> outputFunctionList = outputFunctionContext.getOutputFunctionsList();
            String defaultName = null;
            int count = 0;
            while (true) {
                boolean nameUsed = false;
                count++;
                defaultName = "func" + count;
                for (AnnotatedFunction function : outputFunctionList) {
                    if (function.getName().equals(defaultName)) {
                        nameUsed = true;
                    }
                }
                if (!nameUsed) {
                    break;
                }
            }
            final boolean bSpatial = simulationWorkspace.getSimulationOwner().getGeometry().getDimension() > 0;
            // for non-spatial application, set 'Next' to 'Finish'.
            if (!bSpatial) {
                getNextButton().setText("Finish");
            } else {
                getNextButton().setText("Next >>");
            }
            getFunctionNameTextField().setText(defaultName);
            getFunctionExpressionTextField().setText("0.0");
            Set<String> autoCompList = new HashSet<String>();
            Map<String, SymbolTableEntry> entryMap = new HashMap<String, SymbolTableEntry>();
            outputFunctionContext.getEntries(entryMap);
            autoCompList = entryMap.keySet();
            getFunctionExpressionTextField().setAutoCompletionWords(autoCompList);
            getFunctionExpressionTextField().setSymbolTable(outputFunctionContext);
            // 
            // Show the editor with a default name and default expression for the function
            // If the OK option is chosen, get the new name and expression for the function and create a new
            // function, add it to the list of output functions in simulationOwner
            // Else, pop-up an error dialog indicating that function cannot be added.
            // 
            cardLayout.show(getAddFunctionPanel(), funcNameAndExprPanel.getName());
            DialogUtils.showModalJDialogOnTop(getAddFunctionDialog(), OutputFunctionsPanel.this);
        }
    };
    ClientTaskDispatcher.dispatch(OutputFunctionsPanel.this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 97 with SymbolTableEntry

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

the class ParameterEstimationPanel method mapButton_ActionPerformed.

/**
 * Comment
 */
private void mapButton_ActionPerformed() {
    if (getParameterEstimationTask() == null) {
        return;
    }
    SymbolTableEntry[] symbolTableEntries = getParameterEstimationTask().getModelOptimizationSpec().calculateTimeDependentModelObjects(getParameterEstimationTask().getModelOptimizationSpec().getSimulationContext());
    java.util.Comparator<SymbolTableEntry> steComparator = new java.util.Comparator<SymbolTableEntry>() {

        private Class<?>[] classOrder = new Class<?>[] { Model.ReservedSymbol.class, SpeciesContext.class, Model.ModelParameter.class, Kinetics.KineticsParameter.class };

        public int compare(SymbolTableEntry ste1, SymbolTableEntry ste2) {
            int ste1Category = 100;
            int ste2Category = 100;
            for (int i = 0; i < classOrder.length; i++) {
                if (ste1.getClass().equals(classOrder[i])) {
                    ste1Category = i;
                }
                if (ste2.getClass().equals(classOrder[i])) {
                    ste2Category = i;
                }
            }
            if (ste1Category < ste2Category) {
                return 1;
            } else if (ste1Category > ste2Category) {
                return -1;
            } else {
                return ste1.getName().compareTo(ste2.getName());
            }
        }
    };
    java.util.Arrays.sort(symbolTableEntries, steComparator);
    SymbolTableEntry ste = (SymbolTableEntry) DialogUtils.showListDialog(this, symbolTableEntries, "Map Experimental Data", new SymbolTableEntryListCellRenderer());
    if (ste != null && getDataModelMappingTable().getSelectionModel().getMaxSelectionIndex() >= 0) {
        ReferenceDataMappingSpec refDataMappingSpec = getParameterEstimationTask().getModelOptimizationSpec().getReferenceDataMappingSpecs()[getDataModelMappingTable().getSelectionModel().getMaxSelectionIndex()];
        try {
            refDataMappingSpec.setModelObject(ste);
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace(System.out);
            DialogUtils.showErrorDialog(this, e.getMessage());
        }
    }
    return;
}

Example 98 with SymbolTableEntry

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

the class SimulationRepresentation method getParameters.

private static ParameterRepresentation[] getParameters(BioModel bioModel, SimulationRep simulationRep) {
    SimulationContext simContext = null;
    for (SimulationContext sc : bioModel.getSimulationContexts()) {
        if (sc.getMathDescription().getKey().equals(simulationRep.getMathKey())) {
            simContext = sc;
            break;
        }
    }
    if (simContext == null) {
        return null;
    }
    // initialize to old mathDescription in case error generating math
    MathDescription mathDesc = simContext.getMathDescription();
    MathMapping mathMapping = simContext.createNewMathMapping();
    MathSymbolMapping mathSymbolMapping = null;
    try {
        mathDesc = mathMapping.getMathDescription();
        mathSymbolMapping = mathMapping.getMathSymbolMapping();
    } catch (Exception e1) {
        System.err.println(e1.getMessage());
    }
    ArrayList<ParameterRepresentation> parameterReps = new ArrayList<ParameterRepresentation>();
    Enumeration<Constant> enumMath = mathDesc.getConstants();
    while (enumMath.hasMoreElements()) {
        Constant constant = enumMath.nextElement();
        if (constant.getExpression().isNumeric()) {
            SymbolTableEntry biologicalSymbolTableEntry = null;
            if (mathSymbolMapping != null) {
                SymbolTableEntry[] stes = mathSymbolMapping.getBiologicalSymbol(constant);
                if (stes != null && stes.length >= 1) {
                    biologicalSymbolTableEntry = stes[0];
                }
            }
            if (biologicalSymbolTableEntry instanceof ReservedSymbol) {
                continue;
            }
            try {
                parameterReps.add(new ParameterRepresentation(constant.getName(), constant.getExpression().evaluateConstant(), biologicalSymbolTableEntry));
            } catch (ExpressionException e) {
                // can't happen, because constant expression is numeric
                e.printStackTrace();
            }
        }
    }
    return parameterReps.toArray(new ParameterRepresentation[0]);
}

Example 99 with SymbolTableEntry

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

the class TableCellEditorAutoCompletion method stopCellEditing.

@Override
public boolean stopCellEditing() {
    if (thisTable.getCellEditor() == null) {
        return true;
    }
    if (textFieldAutoCompletion.getSelectedIndex() >= 0) {
        return false;
    }
    final int editingRow = thisTable.getEditingRow();
    final int editingColumn = thisTable.getEditingColumn();
    textFieldAutoCompletion.stopEditing();
    boolean bExpressionValid = true;
    if (thisTable.getColumnClass(editingColumn).equals(ScopedExpression.class)) {
        if (textFieldAutoCompletion.getSymbolTable() != null) {
            ScopedExpression scopedExpression = (ScopedExpression) thisTable.getValueAt(editingRow, editingColumn);
            String text = textFieldAutoCompletion.getText();
            if (text.trim().length() > 0) {
                try {
                    Expression exp = new Expression(text);
                    exp.validateUnscopedSymbols();
                    if (scopedExpression == null || scopedExpression.isValidateFunctionBinding()) {
                        FunctionInvocation[] functionInvocations = exp.getFunctionInvocations(null);
                        for (FunctionInvocation functionInvocation : functionInvocations) {
                            String formalDefinition = functionInvocation.getFormalDefinition();
                            if (functionInvocation.getFunctionId() == FunctionType.USERDEFINED) {
                                SymbolTableFunctionEntry stfe = (SymbolTableFunctionEntry) textFieldAutoCompletion.getSymbolTable().getEntry(formalDefinition);
                                if (stfe == null) {
                                    // 
                                    // check for wrong number of arguments
                                    // 
                                    Map<String, SymbolTableEntry> entries = new HashMap<String, SymbolTableEntry>();
                                    textFieldAutoCompletion.getSymbolTable().getEntries(entries);
                                    System.out.println("available symbols");
                                    for (String symbol : entries.keySet()) {
                                        System.out.print(symbol + ",");
                                    }
                                    System.out.println("");
                                    throw new ExpressionBindingException("unknown function " + formalDefinition, formalDefinition);
                                }
                            } else {
                                // built in function, check arguments
                                FunctionType functionType = functionInvocation.getFunctionId();
                                String formalDefinitionBuiltin = ASTFuncNode.getFormalDefinition(functionType.getName(), functionType.getArgTypes());
                                if (!formalDefinition.equals(formalDefinitionBuiltin)) {
                                    throw new ExpressionBindingException("expecting " + formalDefinitionBuiltin, formalDefinition);
                                }
                            }
                        }
                    }
                    if (scopedExpression == null || scopedExpression.isValidateIdentifierBinding()) {
                        exp.bindExpression(textFieldAutoCompletion.getSymbolTable());
                    }
                } catch (ExpressionBindingException ex) {
                    ex.printStackTrace(System.out);
                    DialogUtils.showErrorDialog(thisTable.getParent(), ex.getMessage() + "\n\nUse 'Ctrl-Space' to see a list of available names in your model or 'Esc' to revert to the original expression.");
                    bExpressionValid = false;
                } catch (ExpressionException ex) {
                    ex.printStackTrace(System.out);
                    DialogUtils.showErrorDialog(thisTable.getParent(), ex.getMessage() + "\n\nUse 'Esc' to revert to the original expression.");
                    bExpressionValid = false;
                }
            }
        }
    }
    if (!bExpressionValid) {
        SwingUtilities.invokeLater(new Runnable() {

            public void run() {
                thisTable.requestFocus();
                thisTable.setRowSelectionInterval(editingRow, editingRow);
                ((JComponent) getComponent()).setBorder(new LineBorder(Color.red));
                textFieldAutoCompletion.requestFocus();
            }
        });
        return false;
    }
    return super.stopCellEditing();
}

Example 100 with SymbolTableEntry

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

the class PlotPane method updateLegend.

/**
 * Comment
 */
private void updateLegend() {
    Plot2D plot = getPlot2DPanel1().getPlot2D();
    SymbolTableEntry[] steList = plot.getSymbolTableEntries();
    DataSymbolMetadataResolver metadataResolver = plot.getDataSymbolMetadataResolver();
    String[] plotLabels = plot.getVisiblePlotColumnTitles();
    int[] plotIndices = plot.getVisiblePlotIndices();
    Component[] legends = getJPanelPlotLegends().getComponents();
    // add legends if necessarry
    if (ml == null) {
        ml = new java.awt.event.MouseAdapter() {

            public void mouseClicked(java.awt.event.MouseEvent evt) {
                String name = ((JLabel) evt.getSource()).getText();
                getPlot2DPanel1().setCurrentPlot(name);
            }
        };
    }
    for (int i = 0; i < plotIndices.length - legends.length / 2; i++) {
        JLabel line = new JLabel();
        JLabel text = new JLabel();
        line.setBorder(new EmptyBorder(6, 0, 0, 0));
        text.setBorder(new EmptyBorder(0, 8, 6, 0));
        getJPanelPlotLegends().add(line);
        getJPanelPlotLegends().add(text);
        text.addMouseListener(ml);
    }
    legends = getJPanelPlotLegends().getComponents();
    // update labels and show them,use reverse loop to generate non-repeatable colors
    for (int i = (plotIndices.length - 1); i >= 0; i--) {
        LineIcon icon = new LineIcon(getPlot2DPanel1().getVisiblePlotPaint(i));
        String plotLabel = null;
        if (plot instanceof SingleXPlot2D) {
            plotLabel = plotLabels[i + 1];
        } else {
            plotLabel = plotLabels[2 * i + 1];
        }
        ((JLabel) legends[2 * i]).setIcon(icon);
        final int head = 20;
        final int tail = 0;
        String tooltipString = "";
        String unitSymbol = "";
        if (metadataResolver != null) {
            DataSymbolMetadata metaData = metadataResolver.getDataSymbolMetadata(plotLabel);
            if (metaData != null && metaData.unit != null) {
                VCUnitDefinition ud = metaData.unit;
                if (ud != null) {
                    unitSymbol += ud.getSymbolUnicode();
                }
            }
            if (metaData != null && metaData.tooltipString != null) {
                tooltipString = metaData.tooltipString;
            }
        }
        String shortLabel = plotLabel;
        if (shortLabel.length() > head + 3 + tail) {
            shortLabel = shortLabel.substring(0, head) + "..." + shortLabel.substring(shortLabel.length() - tail, shortLabel.length());
        }
        // shortLabel = "<html>" + shortLabel + "<font color=\"red\">" + " [" + unitSymbol + "] " + "</font></html>";
        shortLabel = "<html>" + shortLabel + "<font color=\"#8B0000\">" + " [" + unitSymbol + "] " + "</font></html>";
        tooltipString = "<html>" + plotLabel + "<font color=\"#0000FF\">" + " " + tooltipString + " " + "</font></html>";
        ((JLabel) legends[2 * i + 1]).setText(shortLabel);
        ((JLabel) legends[2 * i + 1]).setToolTipText(tooltipString);
        legends[2 * i].setVisible(true);
        legends[2 * i + 1].setVisible(true);
    }
    // if extra ones, hide them
    for (int i = 2 * plotIndices.length; i < legends.length; i++) {
        legends[i].setVisible(false);
    }
}