Examples with LocalParameter cbit.vcell.mapping.ParameterContext.LocalParameter used on opensource projects

Example 36 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class TriggerTemplatePanel method init.

public void init(SimulationContext simulationContext, AutoCompleteSymbolFilter autoCompleteSymbolFilter, BioEvent existingBioEvent) {
    if (simulationContext != null) {
        // mathOpComboBox.removeAllItems();
        // mathOpComboBox.addItem(BioEvent.TriggerComparison.greaterThan);
        // mathOpComboBox.addItem(BioEvent.TriggerComparison.lessThan);
        // mathOpComboBox.addItem(BioEvent.TriggerComparison.greaterThanOrEqual);
        // mathOpComboBox.addItem(BioEvent.TriggerComparison.lessThanOrEqual);
        varAboveComboBox.removeAllItems();
        varBelowComboBox.removeAllItems();
        SymbolTableEntry[] triggerExprSymbols = ModelOptimizationSpec.calculateTimeDependentModelObjects(simulationContext);
        Arrays.sort(triggerExprSymbols, new Comparator<SymbolTableEntry>() {

            @Override
            public int compare(SymbolTableEntry o1, SymbolTableEntry o2) {
                return o1.getName().compareToIgnoreCase(o2.getName());
            }
        });
        for (SymbolTableEntry ste : triggerExprSymbols) {
            if (!(ste instanceof ReservedSymbol)) {
                varAboveComboBox.addItem(ste);
                varBelowComboBox.addItem(ste);
            }
        }
        // setVerifier(simulationContext);
        Map<String, SymbolTableEntry> entryMap = new HashMap<String, SymbolTableEntry>();
        simulationContext.getEntries(entryMap);
        textFieldAboveVarVal.setAutoCompleteSymbolFilter(autoCompleteSymbolFilter);
        textFieldAboveVarVal.setAutoCompletionWords(entryMap.keySet());
        textFieldBelowVarVal.setAutoCompleteSymbolFilter(autoCompleteSymbolFilter);
        textFieldBelowVarVal.setAutoCompletionWords(entryMap.keySet());
        textFieldSingleTime.setAutoCompleteSymbolFilter(autoCompleteSymbolFilter);
        textFieldSingleTime.setAutoCompletionWords(entryMap.keySet());
        textFieldGeneral.setAutoCompleteSymbolFilter(autoCompleteSymbolFilter);
        textFieldGeneral.setAutoCompletionWords(entryMap.keySet());
        if (existingBioEvent != null) {
            // Edit Trigger mode
            switch(existingBioEvent.getTriggerType()) {
                case GeneralTrigger:
                    {
                        textFieldGeneral.setText(existingBioEvent.getParameter(BioEventParameterType.GeneralTriggerFunction).getExpression().infix());
                        rdbtnGeneral.setSelected(true);
                        break;
                    }
                case LogRangeTimes:
                    {
                        LocalParameter rangeMinParam = existingBioEvent.getParameter(BioEventParameterType.RangeMinTime);
                        if (rangeMinParam != null && rangeMinParam.getExpression() != null) {
                            textFieldLogMin.setText(rangeMinParam.getExpression().infix());
                        } else {
                            textFieldLogMin.setText("");
                        }
                        LocalParameter rangeMaxParam = existingBioEvent.getParameter(BioEventParameterType.RangeMaxTime);
                        if (rangeMaxParam != null && rangeMaxParam.getExpression() != null) {
                            textFieldLogMax.setText(rangeMaxParam.getExpression().infix());
                        } else {
                            textFieldLogMax.setText("");
                        }
                        LocalParameter rangeNumParam = existingBioEvent.getParameter(BioEventParameterType.RangeNumTimes);
                        if (rangeNumParam != null && rangeNumParam.getExpression() != null) {
                            textFieldLogNum.setText(rangeNumParam.getExpression().infix());
                        } else {
                            textFieldLogNum.setText("");
                        }
                        rdbtnLogTimeRange.setSelected(true);
                        break;
                    }
                case LinearRangeTimes:
                    {
                        LocalParameter rangeMinParam = existingBioEvent.getParameter(BioEventParameterType.RangeMinTime);
                        if (rangeMinParam != null && rangeMinParam.getExpression() != null) {
                            textFieldLinearMin.setText(rangeMinParam.getExpression().infix());
                        } else {
                            textFieldLinearMin.setText("");
                        }
                        LocalParameter rangeMaxParam = existingBioEvent.getParameter(BioEventParameterType.RangeMaxTime);
                        if (rangeMaxParam != null && rangeMaxParam.getExpression() != null) {
                            textFieldLinearMax.setText(rangeMaxParam.getExpression().infix());
                        } else {
                            textFieldLinearMax.setText("");
                        }
                        LocalParameter rangeNumParam = existingBioEvent.getParameter(BioEventParameterType.RangeNumTimes);
                        if (rangeNumParam != null && rangeNumParam.getExpression() != null) {
                            textFieldLinearNum.setText(rangeNumParam.getExpression().infix());
                        } else {
                            textFieldLinearNum.setText("");
                        }
                        rdbtnLinearTimeRange.setSelected(true);
                        break;
                    }
                case ListOfTimes:
                    {
                        StringBuffer sb = new StringBuffer();
                        for (LocalParameter p : existingBioEvent.getEventParameters()) {
                            if (p.getRole() == BioEventParameterType.TimeListItem) {
                                if (sb.length() > 0) {
                                    sb.append(",");
                                }
                                sb.append(p.getExpression().infix());
                            }
                        }
                        textFieldListTimes.setText(sb.toString());
                        rdbtnListTimes.setSelected(true);
                        break;
                    }
                case ObservableAboveThreshold:
                    {
                        LocalParameter observableParameter = existingBioEvent.getParameter(BioEventParameterType.Observable);
                        SymbolTableEntry ste = null;
                        if (observableParameter != null && observableParameter.getExpression() != null && observableParameter.getExpression().isIdentifier()) {
                            ste = observableParameter.getExpression().getSymbolBinding(observableParameter.getExpression().getSymbols()[0]);
                            varAboveComboBox.setSelectedItem(ste);
                        }
                        textFieldAboveVarVal.setText(existingBioEvent.getParameter(BioEventParameterType.Threshold).getExpression().infix());
                        rdbtnVarAboveThreshold.setSelected(true);
                        break;
                    }
                case ObservableBelowThreshold:
                    {
                        LocalParameter observableParameter = existingBioEvent.getParameter(BioEventParameterType.Observable);
                        SymbolTableEntry ste = null;
                        if (observableParameter != null && observableParameter.getExpression() != null && observableParameter.getExpression().isIdentifier()) {
                            ste = observableParameter.getExpression().getSymbolBinding(observableParameter.getExpression().getSymbols()[0]);
                            varBelowComboBox.setSelectedItem(ste);
                        }
                        textFieldBelowVarVal.setText(existingBioEvent.getParameter(BioEventParameterType.Threshold).getExpression().infix());
                        rdbtnVarBelowThreshold.setSelected(true);
                        break;
                    }
                case SingleTriggerTime:
                    {
                        LocalParameter parameter = existingBioEvent.getParameter(BioEventParameterType.SingleTriggerTime);
                        textFieldSingleTime.setText(parameter.getExpression().infix());
                        rdbtnSingleTime.setSelected(true);
                        break;
                    }
            }
        }
    }
}

Example 37 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class TriggerTemplatePanel method setTrigger.

// private void setVerifier(final SimulationContext simulationContext){
// textFieldGeneral.setInputVerifier(new InputVerifier() {
// @Override
// public boolean verify(JComponent input) {
// boolean bValid = true;
// if (textFieldGeneral.isEnabled()) {
// String text = textFieldGeneral.getText();
// String errorText = null;
// if (text == null || text.trim().length() == 0) {
// bValid = false;
// errorText = "Trigger expression cannot be empty";
// }else{
// Expression expr = null;
// try{
// expr = EventPanel.bindTriggerExpression(textFieldGeneral.getText(),simulationContext);
// }catch(Exception e){
// bValid = false;
// errorText = e.getMessage();
// }
// }
// if (bValid) {
// textFieldGeneral.setBorder(UIManager.getBorder("TextField.border"));
// //						getBtnPlotTrigger().setEnabled(true);
// textFieldGeneral.setToolTipText(null);
// } else {
// textFieldGeneral.setBorder(GuiConstants.ProblematicTextFieldBorder);
// //						getBtnPlotTrigger().setEnabled(false);
// textFieldGeneral.setToolTipText(errorText);
// //						SwingUtilities.invokeLater(new Runnable() {
// //						    public void run() {
// //						    	getTriggerTextField().requestFocus();
// //						    }
// //						});
// }
// }
// return bValid;
// }
// });
// 
// }
public void setTrigger(BioEvent bioEvent) throws Exception {
    LocalParameter delayParam = bioEvent.getParameter(BioEventParameterType.TriggerDelay);
    if (rdbtnGeneral.isSelected()) {
        bioEvent.setTriggerType(TriggerType.GeneralTrigger);
        bioEvent.setParameterValue(BioEventParameterType.GeneralTriggerFunction, new Expression(textFieldGeneral.getText()));
    } else if (rdbtnListTimes.isSelected()) {
        bioEvent.setTriggerType(TriggerType.ListOfTimes);
        Expression[] listExps = new Expression("myFunc(" + textFieldListTimes.getText() + ")").getFunctionInvocations(null)[0].getArguments();
        bioEvent.setTimeList(listExps);
    } else if (rdbtnLinearTimeRange.isSelected()) {
        bioEvent.setTriggerType(TriggerType.LinearRangeTimes);
        bioEvent.setParameterValue(BioEventParameterType.RangeMinTime, new Expression(textFieldLinearMin.getText()));
        bioEvent.setParameterValue(BioEventParameterType.RangeMaxTime, new Expression(textFieldLinearMax.getText()));
        bioEvent.setParameterValue(BioEventParameterType.RangeNumTimes, new Expression(textFieldLinearNum.getText()));
    } else if (rdbtnLogTimeRange.isSelected()) {
        bioEvent.setTriggerType(TriggerType.LogRangeTimes);
        bioEvent.setParameterValue(BioEventParameterType.RangeMinTime, new Expression(textFieldLogMin.getText()));
        bioEvent.setParameterValue(BioEventParameterType.RangeMaxTime, new Expression(textFieldLogMax.getText()));
        bioEvent.setParameterValue(BioEventParameterType.RangeNumTimes, new Expression(textFieldLogNum.getText()));
    } else if (rdbtnSingleTime.isSelected()) {
        bioEvent.setTriggerType(TriggerType.SingleTriggerTime);
        bioEvent.setParameterValue(BioEventParameterType.SingleTriggerTime, new Expression(textFieldSingleTime.getText()));
    } else if (rdbtnVarAboveThreshold.isSelected()) {
        bioEvent.setTriggerType(TriggerType.ObservableAboveThreshold);
        bioEvent.setParameterValue(BioEventParameterType.Observable, new Expression(((SymbolTableEntry) varAboveComboBox.getSelectedItem()).getName()));
        bioEvent.setParameterValue(BioEventParameterType.Threshold, new Expression(textFieldAboveVarVal.getText()));
    } else if (rdbtnVarBelowThreshold.isSelected()) {
        bioEvent.setTriggerType(TriggerType.ObservableBelowThreshold);
        bioEvent.setParameterValue(BioEventParameterType.Observable, new Expression(((SymbolTableEntry) varBelowComboBox.getSelectedItem()).getName()));
        bioEvent.setParameterValue(BioEventParameterType.Threshold, new Expression(textFieldBelowVarVal.getText()));
    }
    if (delayParam.getExpression() != null) {
        bioEvent.setParameterValue(BioEventParameterType.TriggerDelay, delayParam.getExpression());
    }
}

Example 38 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class ReactionRuleKineticsPropertiesPanel method setReversible.

private void setReversible(boolean bReversible) {
    reactionRule.setReversible(bReversible);
    if (!bReversible && reactionRule != null) {
        // we know for sure it must be MassAction
        LocalParameter lp = reactionRule.getKineticLaw().getLocalParameter(RbmKineticLawParameterType.MassActionReverseRate);
        try {
            lp.setExpression(new Expression(0.0d));
        } catch (ExpressionBindingException e) {
            e.printStackTrace();
        }
    }
    getReactionRulePropertiesTableModel().refreshData();
}

Example 39 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class ReactionRulePropertiesTableModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    if (evt.getSource() == this && evt.getPropertyName().equals("reactionRule")) {
        ReactionRule oldValue = (ReactionRule) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            oldValue.getKineticLaw().removePropertyChangeListener(this);
            for (int i = 0; i < oldValue.getKineticLaw().getLocalParameters().length; i++) {
                oldValue.getKineticLaw().getLocalParameters()[i].removePropertyChangeListener(this);
            }
            for (int i = 0; i < oldValue.getKineticLaw().getProxyParameters().length; i++) {
                oldValue.getKineticLaw().getProxyParameters()[i].removePropertyChangeListener(this);
            }
        }
        ReactionRule newValue = (ReactionRule) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            newValue.getKineticLaw().addPropertyChangeListener(this);
            for (int i = 0; i < newValue.getKineticLaw().getLocalParameters().length; i++) {
                newValue.getKineticLaw().getLocalParameters()[i].addPropertyChangeListener(this);
            }
            for (int i = 0; i < newValue.getKineticLaw().getProxyParameters().length; i++) {
                newValue.getKineticLaw().getProxyParameters()[i].addPropertyChangeListener(this);
            }
            autoCompleteSymbolFilter = reactionRule.getAutoCompleteSymbolFilter();
        }
        refreshData();
    }
    if (evt.getSource() == reactionRule && evt.getPropertyName().equals(ReactionRule.PROPERTY_NAME_KINETICLAW)) {
        RbmKineticLaw oldValue = (RbmKineticLaw) evt.getOldValue();
        if (oldValue != null) {
            oldValue.removePropertyChangeListener(this);
            for (int i = 0; i < oldValue.getLocalParameters().length; i++) {
                oldValue.getLocalParameters()[i].removePropertyChangeListener(this);
            }
            for (int i = 0; i < oldValue.getProxyParameters().length; i++) {
                oldValue.getProxyParameters()[i].removePropertyChangeListener(this);
            }
        }
        RbmKineticLaw newValue = (RbmKineticLaw) evt.getNewValue();
        if (newValue != null) {
            newValue.addPropertyChangeListener(this);
            for (int i = 0; i < newValue.getLocalParameters().length; i++) {
                newValue.getLocalParameters()[i].addPropertyChangeListener(this);
            }
            for (int i = 0; i < newValue.getProxyParameters().length; i++) {
                newValue.getProxyParameters()[i].addPropertyChangeListener(this);
            }
        }
        refreshData();
    }
    if (evt.getSource() instanceof RbmKineticLaw && (evt.getPropertyName().equals("localParameters") || evt.getPropertyName().equals("proxyParameters"))) {
        Parameter[] oldParams = (Parameter[]) evt.getOldValue();
        Parameter[] newParams = (Parameter[]) evt.getNewValue();
        for (int i = 0; oldParams != null && i < oldParams.length; i++) {
            oldParams[i].removePropertyChangeListener(this);
        }
        for (int i = 0; newParams != null && i < newParams.length; i++) {
            newParams[i].addPropertyChangeListener(this);
        }
        refreshData();
    }
    if (evt.getSource() instanceof LocalParameter || evt.getSource() instanceof LocalProxyParameter) {
        refreshData();
    }
    if (evt.getSource() instanceof Parameter) {
        fireTableRowsUpdated(0, getRowCount() - 1);
    }
}

Example 40 with LocalParameter

use of cbit.vcell.mapping.ParameterContext.LocalParameter in project vcell by virtualcell.

the class EventPanel method updateEventPanel.

private void updateEventPanel() {
    if (getBioEvent() == null) {
        setEnabled(false);
    } else {
        if (getSimulationContext().getGeometry() != null && getSimulationContext().getGeometry().getDimension() > 0 || getSimulationContext().isStoch()) {
            getAddEventAssgnButton().setEnabled(false);
        }
        getDeleteEventAssgnButton().setEnabled(false);
        setEnabled(true);
        // we are initializing EventsPanel, hence no focuslistener should not be active on the text fields
        // getTriggerTextField().removeFocusListener(ivjEventHandler);
        // getDelayTextField().removeFocusListener(ivjEventHandler);
        // set
        // getTriggerTextField().setText(fieldBioEvent.getTriggerExpression().infix());
        // try{
        // String expr = fieldBioEvent.getTrigger().getGeneratedExpression().infix();
        // getLabelTriggerType().setText(
        // getBioEvent().getTrigger().getClass().getSimpleName()+
        // " '"+
        // BeanUtils.forceStringSize(expr, 15, " ", false)+
        // (expr.length()>10?"...":"")+"'");
        // }catch(ExpressionException e){
        // e.printStackTrace();
        // getLabelTriggerType().setText(getBioEvent().getTrigger().getClass().getSimpleName());
        // }
        getLabelTriggerType().setText(getBioEvent().getTriggerType().name());
        LocalParameter delayParam = getBioEvent().getParameter(BioEventParameterType.TriggerDelay);
        if (delayParam != null) {
            if (delayParam.getExpression() != null) {
                getDelayTextField().setText(delayParam.getExpression().infix());
            }
            enableTriggerRadioButtons(true);
            if (getBioEvent().getUseValuesFromTriggerTime()) {
                getRdbtnTrigTime().setSelected(true);
            } else {
                getRdbtnDelayTime().setSelected(true);
            }
        // getUseValuesAtTriggerTimeCheckBox().setSelected(delay.useValuesFromTriggerTime());
        } else {
            getDelayTextField().setText("");
            enableTriggerRadioButtons(false);
        }
        getEventAssignmentsTableModel().setSimulationContext(fieldSimContext);
        getEventAssignmentsTableModel().setBioEvent(fieldBioEvent);
    // for some reason, when events are selected in the table, the delayTextField gains focus (this fires table update whenever
    // another selection is made. To avoid this, adding a request focus for the events table.
    // requestFocusInWindow();
    // addFocusListener(new FocusListener() {
    // public void focusLost(FocusEvent e) {
    // }
    // public void focusGained(FocusEvent e) {
    // removeFocusListener(this);
    // getTriggerTextField().addFocusListener(ivjEventHandler);
    // getDelayTextField().addFocusListener(ivjEventHandler);
    // }
    // });
    }
}