Examples with Feature cbit.vcell.model.Feature used on opensource projects

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Example 31 with Feature

use of cbit.vcell.model.Feature in project vcell by virtualcell.

the class StructurePropertiesPanel method initialize.

/**
 * Initialize the class.
 */
private void initialize() {
    try {
        setName(this.getClass().getName());
        setLayout(new GridBagLayout());
        nameTextField = new JTextField();
        nameTextField.setEditable(false);
        nameTextField.addActionListener(eventHandler);
        sizeTextField = new JTextField();
        sizeTextField.setEditable(false);
        voltageLabel = new JLabel("Voltage Variable Name");
        voltageTextField = new JTextField();
        voltageTextField.setEditable(false);
        electrophysiologyLabel = new JLabel("<html><u>Electrophysiology</u></html>");
        electrophysiologyExplanationLabel = new JLabel();
        positiveFeatureLabel = new JLabel("Positive (inside feature)");
        positiveFeatureComboBox = new JComboBox<String>();
        negativeFeatureLabel = new JLabel("Negative (outside feature)");
        negativeFeatureComboBox = new JComboBox<String>();
        annotationTextArea = new javax.swing.JTextArea("", 1, 30);
        annotationTextArea.setLineWrap(true);
        annotationTextArea.setWrapStyleWord(true);
        annotationTextArea.setFont(new Font("monospaced", Font.PLAIN, 11));
        annotationTextArea.setEditable(false);
        int gridy = 0;
        GridBagConstraints gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.gridwidth = 2;
        gbc.insets = new java.awt.Insets(0, 4, 0, 4);
        gbc.fill = GridBagConstraints.HORIZONTAL;
        JLabel label = new JLabel("<html><u>Select only one structure to edit properties</u></html>");
        label.setHorizontalAlignment(SwingConstants.CENTER);
        label.setFont(label.getFont().deriveFont(Font.BOLD));
        add(label, gbc);
        // name
        gridy++;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.anchor = GridBagConstraints.LINE_END;
        label = new JLabel("Structure Name");
        add(label, gbc);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.anchor = GridBagConstraints.LINE_START;
        add(nameTextField, gbc);
        // size
        gridy++;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.anchor = GridBagConstraints.LINE_END;
        label = new JLabel("Size Variable Name");
        add(label, gbc);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.anchor = GridBagConstraints.LINE_START;
        add(sizeTextField, gbc);
        // electrophysiology
        gbc = new java.awt.GridBagConstraints();
        gridy++;
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.gridwidth = 2;
        gbc.insets = new java.awt.Insets(0, 4, 0, 4);
        gbc.fill = GridBagConstraints.HORIZONTAL;
        electrophysiologyLabel.setHorizontalAlignment(SwingConstants.CENTER);
        electrophysiologyLabel.setFont(label.getFont().deriveFont(Font.BOLD));
        add(electrophysiologyLabel, gbc);
        // voltage
        gridy++;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.anchor = GridBagConstraints.LINE_END;
        add(voltageLabel, gbc);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.anchor = GridBagConstraints.LINE_START;
        voltageTextField.setForeground(Color.blue);
        add(voltageTextField, gbc);
        // positive (feature) voltage
        gridy++;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.anchor = GridBagConstraints.LINE_END;
        add(positiveFeatureLabel, gbc);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.anchor = GridBagConstraints.LINE_START;
        positiveFeatureComboBox.setForeground(Color.blue);
        add(positiveFeatureComboBox, gbc);
        // negative (feature) voltage
        gbc = new java.awt.GridBagConstraints();
        gridy++;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.anchor = GridBagConstraints.LINE_END;
        add(negativeFeatureLabel, gbc);
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.weightx = 1.0;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(0, 4, 4, 4);
        gbc.anchor = GridBagConstraints.LINE_START;
        negativeFeatureComboBox.setForeground(Color.blue);
        add(negativeFeatureComboBox, gbc);
        // electrophysiology
        gbc = new java.awt.GridBagConstraints();
        gridy++;
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.gridwidth = 2;
        gbc.insets = new java.awt.Insets(0, 4, 0, 4);
        gbc.fill = GridBagConstraints.HORIZONTAL;
        electrophysiologyExplanationLabel.setHorizontalAlignment(SwingConstants.CENTER);
        // electrophysiologyExplanationLabel.setFont(label.getFont().deriveFont(Font.BOLD));
        add(electrophysiologyExplanationLabel, gbc);
        // annotation
        gridy++;
        gbc = new java.awt.GridBagConstraints();
        gbc.gridx = 0;
        gbc.gridy = gridy;
        gbc.insets = new Insets(9, 8, 4, 6);
        gbc.anchor = GridBagConstraints.FIRST_LINE_END;
        add(new JLabel("Annotation "), gbc);
        javax.swing.JScrollPane jsp = new javax.swing.JScrollPane(annotationTextArea);
        gbc = new java.awt.GridBagConstraints();
        gbc.weightx = 1.0;
        gbc.weighty = 1;
        gbc.gridx = 1;
        gbc.gridy = gridy;
        gbc.anchor = GridBagConstraints.LINE_START;
        gbc.fill = java.awt.GridBagConstraints.BOTH;
        gbc.insets = new Insets(4, 4, 4, 4);
        add(jsp, gbc);
        DefaultListCellRenderer comboBoxListCellRenderer = new DefaultListCellRenderer() {

            @Override
            public Component getListCellRendererComponent(JList<?> list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
                super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
                if (value instanceof Feature) {
                    setText(((Structure) value).getName());
                }
                return this;
            }
        };
        positiveFeatureComboBox.setRenderer(comboBoxListCellRenderer);
        negativeFeatureComboBox.setRenderer(comboBoxListCellRenderer);
        setBackground(Color.white);
        initConnections();
    } catch (java.lang.Throwable ivjExc) {
        handleException(ivjExc);
    }
}
Also used : GridBagConstraints(java.awt.GridBagConstraints) Insets(java.awt.Insets) Insets(java.awt.Insets) GridBagLayout(java.awt.GridBagLayout) JLabel(javax.swing.JLabel) JTextField(javax.swing.JTextField) GridBagConstraints(java.awt.GridBagConstraints) Feature(cbit.vcell.model.Feature) Font(java.awt.Font) DefaultListCellRenderer(javax.swing.DefaultListCellRenderer) JTextArea(javax.swing.JTextArea) JList(javax.swing.JList)

Example 32 with Feature

use of cbit.vcell.model.Feature in project vcell by virtualcell.

the class StructurePropertiesPanel method setModel.

public void setModel(Model model) {
    fieldModel = model;
    DefaultComboBoxModel<String> dataModelPos = new DefaultComboBoxModel<String>();
    DefaultComboBoxModel<String> dataModelNeg = new DefaultComboBoxModel<String>();
    dataModelPos.addElement("");
    dataModelNeg.addElement("");
    for (Structure s : model.getStructures()) {
        if (s instanceof Feature) {
            dataModelPos.addElement(s.getName());
            dataModelNeg.addElement(s.getName());
        }
    }
    // fill the comboBoxes with feature names from the model.
    positiveFeatureComboBox.setModel(dataModelPos);
    // if selected structure is a membrane, if it has +ve/-ve feature set, set the comboBox with that selection.
    if (structure instanceof Membrane) {
        Membrane membrane = (Membrane) structure;
        if (fieldModel.getElectricalTopology().getPositiveFeature(membrane) != null) {
            positiveFeatureComboBox.setSelectedItem(fieldModel.getElectricalTopology().getPositiveFeature(membrane).getName());
        }
    }
    negativeFeatureComboBox.setModel(dataModelNeg);
    if (structure instanceof Membrane) {
        Membrane membrane = (Membrane) structure;
        if (fieldModel.getElectricalTopology().getNegativeFeature(membrane) != null) {
            negativeFeatureComboBox.setSelectedItem(fieldModel.getElectricalTopology().getNegativeFeature(membrane).getName());
        }
    }
}
Also used : Membrane(cbit.vcell.model.Membrane) DefaultComboBoxModel(javax.swing.DefaultComboBoxModel) Structure(cbit.vcell.model.Structure) Feature(cbit.vcell.model.Feature)

Example 33 with Feature

use of cbit.vcell.model.Feature in project vcell by virtualcell.

the class StructurePropertiesPanel method updateInterface.

/**
 * Comment
 */
private void updateInterface() {
    boolean bNonNullStructure = structure != null && fieldModel != null;
    nameTextField.setEditable(bNonNullStructure);
    annotationTextArea.setEditable(bNonNullStructure);
    boolean bMembrane = bNonNullStructure && structure instanceof Membrane;
    voltageLabel.setVisible(bMembrane);
    voltageTextField.setVisible(bMembrane);
    electrophysiologyLabel.setVisible(bMembrane);
    positiveFeatureLabel.setVisible(bMembrane);
    positiveFeatureComboBox.setVisible(bMembrane);
    negativeFeatureLabel.setVisible(bMembrane);
    negativeFeatureComboBox.setVisible(bMembrane);
    electrophysiologyExplanationLabel.setVisible(bMembrane);
    if (bNonNullStructure) {
        nameTextField.setText(structure.getName());
        annotationTextArea.setText(fieldModel.getVcMetaData().getFreeTextAnnotation(structure));
        StructureSize structureSize = structure.getStructureSize();
        sizeTextField.setText(structureSize.getName() + " [" + structureSize.getUnitDefinition().getSymbolUnicode() + "]");
        if (bMembrane) {
            Membrane membrane = (Membrane) structure;
            MembraneVoltage memVoltage = membrane.getMembraneVoltage();
            voltageTextField.setText(memVoltage.getName() + " [" + memVoltage.getUnitDefinition().getSymbolUnicode() + "]");
            // if membrane has +ve/-ve feature set, set the comboBox with that selection.
            ElectricalTopology electricalTopology = fieldModel.getElectricalTopology();
            Feature positiveFeature = electricalTopology.getPositiveFeature(membrane);
            if (positiveFeature != null) {
                positiveFeatureComboBox.setSelectedItem(positiveFeature.getName());
            }
            Feature negativeFeature = electricalTopology.getNegativeFeature(membrane);
            if (negativeFeature != null) {
                negativeFeatureComboBox.setSelectedItem(negativeFeature.getName());
            }
            this.electrophysiologyExplanationLabel.setText(getExplanationText());
        }
    } else {
        annotationTextArea.setText(null);
        nameTextField.setText(null);
        sizeTextField.setText(null);
        voltageTextField.setText(null);
    }
}
Also used : MembraneVoltage(cbit.vcell.model.Membrane.MembraneVoltage) ElectricalTopology(cbit.vcell.model.Model.ElectricalTopology) Membrane(cbit.vcell.model.Membrane) StructureSize(cbit.vcell.model.Structure.StructureSize) Feature(cbit.vcell.model.Feature)

Example 34 with Feature

use of cbit.vcell.model.Feature in project vcell by virtualcell.

the class ReactionCartoonTool method lineAction.

private void lineAction(ReactionStep reactionStart, Structure endStructure) throws Exception {
    Structure startStructure = reactionStart.getStructure();
    if (StructureUtil.reactionHereCanHaveParticipantThere(startStructure, endStructure)) {
        // if reactionStart is a SimpleRxn OR FluxRxn without a product, add speciesContext as pdt
        if ((reactionStart instanceof SimpleReaction) || ((reactionStart instanceof FluxReaction) && !reactionStart.hasProduct())) {
            SpeciesContext speciesContext = getModel().createSpeciesContext(endStructure);
            reactionStart.addProduct(speciesContext, 1);
            positionShapeForObject(endStructure, speciesContext, edgeShape.getEnd());
        }
        if (((startStructure instanceof Feature && endStructure instanceof Feature) || (startStructure instanceof Membrane && endStructure instanceof Membrane)) && startStructure != endStructure) {
        // ============ change kinetics to lumped or warn user ?????????
        // reactionStart.setKinetics(new GeneralLumpedKinetics(reactionStart));
        }
        getReactionCartoon().notifyChangeEvent();
    }
}
Also used : SimpleReaction(cbit.vcell.model.SimpleReaction) Membrane(cbit.vcell.model.Membrane) FluxReaction(cbit.vcell.model.FluxReaction) SpeciesContext(cbit.vcell.model.SpeciesContext) Structure(cbit.vcell.model.Structure) Feature(cbit.vcell.model.Feature)

Example 35 with Feature

use of cbit.vcell.model.Feature in project vcell by virtualcell.

the class BioCartoonTool method askUserResolveMembraneConnections.

private static HashMap<ReactionParticipant, Structure> askUserResolveMembraneConnections(Component requester, Structure[] allStructures, Structure currentStruct, Structure fromRxnStruct, Structure toRxnStruct, ReactionParticipant[] copyFromRxParticipantArr, StructureTopology toStructureTopology, StructureTopology structTopology) {
    HashMap<ReactionParticipant, Structure> userMap = new HashMap<>();
    boolean bMembrane = toRxnStruct instanceof Membrane;
    if (!bMembrane) {
        for (int i = 0; i < copyFromRxParticipantArr.length; i += 1) {
            userMap.put(copyFromRxParticipantArr[i], null);
            for (Structure struct : allStructures) {
                if (fromRxnStruct.getName().equals(copyFromRxParticipantArr[i].getStructure().getName())) {
                    userMap.put(copyFromRxParticipantArr[i], toRxnStruct);
                }
            }
        }
    // return userMap;
    } else {
        for (int i = 0; i < copyFromRxParticipantArr.length; i += 1) {
            Structure pasteToStruct = currentStruct;
            Membrane oldMembr = (Membrane) fromRxnStruct;
            pasteToStruct = matchMembraneAdjacentStructure(allStructures, currentStruct, copyFromRxParticipantArr[i].getStructure(), structTopology, toStructureTopology, oldMembr, pasteToStruct);
            userMap.put(copyFromRxParticipantArr[i], pasteToStruct);
        }
    }
    JScrollPane jScrollPane = null;
    JPanel rxMapperPanel = null;
    Hashtable<JLabel, ReactionParticipant> mapLabelToPart = null;
    boolean bUnselected;
    do {
        bUnselected = false;
        if (jScrollPane == null) {
            rxMapperPanel = new JPanel();
            rxMapperPanel.setLayout(new BoxLayout(rxMapperPanel, BoxLayout.Y_AXIS));
            // ((BoxLayout)rxMapperPanel.getLayout())
            int height = 0;
            final int[] widthlabels = new int[] { 0 };
            int widthcombo = 0;
            mapLabelToPart = new Hashtable<>();
            for (ReactionParticipant rxPart : userMap.keySet()) {
                if (!bMembrane || (rxPart.getStructure() instanceof Feature)) {
                    JPanel row = new JPanel();
                    JLabel rxpartLabel = new JLabel(rxPart.getName());
                    row.add(rxpartLabel);
                    mapLabelToPart.put(rxpartLabel, rxPart);
                    JComboBox<Structure> structJC = new JComboBox<>();
                    structJC.setRenderer(new ListCellRenderer<Structure>() {

                        @Override
                        public Component getListCellRendererComponent(JList<? extends Structure> list, Structure value, int index, boolean isSelected, boolean cellHasFocus) {
                            // TODO Auto-generated method stub
                            JLabel label = new JLabel(value.getName());
                            widthlabels[0] = Math.max(widthlabels[0], label.getPreferredSize().width);
                            return label;
                        }
                    });
                    height += structJC.getPreferredSize().getHeight();
                    widthcombo = Math.max(widthcombo, structJC.getPreferredSize().width);
                    try {
                        Feature dummyFeature = new Feature(DUMMY_CHOOSE);
                        structJC.addItem(dummyFeature);
                    } catch (Exception e) {
                        e.printStackTrace();
                    }
                    for (Structure struct : allStructures) {
                        if (!bMembrane || (struct instanceof Feature)) {
                            structJC.addItem(struct);
                        }
                    }
                    structJC.setSelectedItem((userMap.get(rxPart) == null ? 0 : userMap.get(rxPart)));
                    row.add(structJC);
                    rxMapperPanel.add(row);
                }
            }
            height += 25;
            rxMapperPanel.setSize(widthcombo + widthlabels[0], height);
            rxMapperPanel.setPreferredSize(new Dimension(widthcombo + widthlabels[0], height));
            jScrollPane = new JScrollPane(rxMapperPanel);
            jScrollPane.setPreferredSize(new Dimension(150, 100));
        }
        if (rxMapperPanel.getComponentCount() != 0) {
            int result = DialogUtils.showComponentOKCancelDialog(requester, jScrollPane, "Assign Compartments for RX '" + copyFromRxParticipantArr[0].getReactionStep().getName() + "' Participants");
            if (result != JOptionPane.OK_OPTION) {
                throw UserCancelException.CANCEL_GENERIC;
            }
            for (int i = 0; i < rxMapperPanel.getComponentCount(); i++) {
                JLabel label0 = (JLabel) (((Container) rxMapperPanel.getComponent(i)).getComponent(0));
                JComboBox<Structure> struct0 = (JComboBox<Structure>) (((Container) rxMapperPanel.getComponent(i)).getComponent(1));
                if (((Structure) struct0.getSelectedItem()).getName().equals(DUMMY_CHOOSE)) {
                    bUnselected = true;
                    DialogUtils.showWarningDialog(requester, "Choose a valid compartment for each ReactionParticipant");
                    break;
                }
                userMap.put(mapLabelToPart.get(label0), (Structure) struct0.getSelectedItem());
            }
        }
    } while (bUnselected);
    return userMap;
}
Also used : JScrollPane(javax.swing.JScrollPane) JPanel(javax.swing.JPanel) JComboBox(javax.swing.JComboBox) IdentityHashMap(java.util.IdentityHashMap) HashMap(java.util.HashMap) LinkedHashMap(java.util.LinkedHashMap) BoxLayout(javax.swing.BoxLayout) JLabel(javax.swing.JLabel) Dimension(java.awt.Dimension) Feature(cbit.vcell.model.Feature) PropertyVetoException(java.beans.PropertyVetoException) ExpressionBindingException(cbit.vcell.parser.ExpressionBindingException) ModelException(cbit.vcell.model.ModelException) UserCancelException(org.vcell.util.UserCancelException) RbmModelContainer(cbit.vcell.model.Model.RbmModelContainer) Container(java.awt.Container) Membrane(cbit.vcell.model.Membrane) Structure(cbit.vcell.model.Structure) Component(java.awt.Component) ReactionParticipant(cbit.vcell.model.ReactionParticipant)

Aggregations

Feature (cbit.vcell.model.Feature)71 Membrane (cbit.vcell.model.Membrane)50 Structure (cbit.vcell.model.Structure)36 Expression (cbit.vcell.parser.Expression)29 SpeciesContext (cbit.vcell.model.SpeciesContext)25 PropertyVetoException (java.beans.PropertyVetoException)18 Model (cbit.vcell.model.Model)16 StructureTopology (cbit.vcell.model.Model.StructureTopology)16 SimpleReaction (cbit.vcell.model.SimpleReaction)15 SubVolume (cbit.vcell.geometry.SubVolume)14 MembraneMapping (cbit.vcell.mapping.MembraneMapping)14 SurfaceClass (cbit.vcell.geometry.SurfaceClass)13 FeatureMapping (cbit.vcell.mapping.FeatureMapping)13 ExpressionException (cbit.vcell.parser.ExpressionException)13 FluxReaction (cbit.vcell.model.FluxReaction)12 ReactionStep (cbit.vcell.model.ReactionStep)12 KeyValue (org.vcell.util.document.KeyValue)12 BioModel (cbit.vcell.biomodel.BioModel)11 StructureMapping (cbit.vcell.mapping.StructureMapping)11 ModelUnitSystem (cbit.vcell.model.ModelUnitSystem)11
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