Examples with BioModelNode cbit.vcell.desktop.BioModelNode used on opensource projects

Example 46 with BioModelNode

use of cbit.vcell.desktop.BioModelNode in project vcell by virtualcell.

the class MathDescriptionTreeModel method createBaseTree.

/**
 * Insert the method's description here.
 * Creation date: (11/28/00 1:06:51 PM)
 * @return cbit.vcell.desktop.BioModelNode
 * @param docManager cbit.vcell.clientdb.DocumentManager
 */
private BioModelNode createBaseTree() {
    if (getMathDescription() == null) {
        return new BioModelNode(" ", false);
    }
    // 
    // make root node
    // 
    BioModelNode rootNode = new BioModelNode("math description", true);
    // 
    // create subTree of Constants
    // 
    BioModelNode constantRootNode = new BioModelNode("constants", true);
    Enumeration<Constant> enum1 = getMathDescription().getConstants();
    while (enum1.hasMoreElements()) {
        Constant constant = enum1.nextElement();
        BioModelNode constantNode = new BioModelNode(constant, false);
        constantRootNode.add(constantNode);
    }
    if (constantRootNode.getChildCount() > 0) {
        rootNode.add(constantRootNode);
    }
    // 
    // create subTree of Functions
    // 
    BioModelNode functionRootNode = new BioModelNode("functions", true);
    Enumeration<Function> enum2 = getMathDescription().getFunctions();
    while (enum2.hasMoreElements()) {
        Function function = enum2.nextElement();
        BioModelNode functionNode = new BioModelNode(function, false);
        functionRootNode.add(functionNode);
    }
    if (functionRootNode.getChildCount() > 0) {
        rootNode.add(functionRootNode);
    }
    // 
    // create subTree of VolumeSubDomains and MembraneSubDomains
    // 
    BioModelNode volumeRootNode = new BioModelNode("volume domains", true);
    BioModelNode membraneRootNode = new BioModelNode("membrane domains", true);
    Enumeration<SubDomain> enum3 = getMathDescription().getSubDomains();
    while (enum3.hasMoreElements()) {
        SubDomain subDomain = enum3.nextElement();
        if (subDomain instanceof cbit.vcell.math.CompartmentSubDomain) {
            CompartmentSubDomain volumeSubDomain = (CompartmentSubDomain) subDomain;
            BioModelNode volumeSubDomainNode = new BioModelNode(volumeSubDomain, true);
            if (// stochastic subtree
            getMathDescription().isNonSpatialStoch()) {
                // add stoch variable initial conditions
                BioModelNode varIniConditionNode = new BioModelNode("variable_initial_conditions", true);
                for (VarIniCondition varIni : volumeSubDomain.getVarIniConditions()) {
                    BioModelNode varIniNode = new BioModelNode(varIni, false);
                    varIniConditionNode.add(varIniNode);
                }
                volumeSubDomainNode.add(varIniConditionNode);
                // add jump processes
                for (JumpProcess jp : volumeSubDomain.getJumpProcesses()) {
                    BioModelNode jpNode = new BioModelNode(jp, true);
                    // add probability rate.
                    String probRate = "P_" + jp.getName();
                    BioModelNode prNode = new BioModelNode("probability_rate = " + probRate, false);
                    jpNode.add(prNode);
                    // add Actions
                    Enumeration<Action> actions = Collections.enumeration(jp.getActions());
                    while (actions.hasMoreElements()) {
                        Action action = actions.nextElement();
                        BioModelNode actionNode = new BioModelNode(action, false);
                        jpNode.add(actionNode);
                    }
                    volumeSubDomainNode.add(jpNode);
                }
            } else // non-stochastic subtree
            {
                // 
                // add equation children
                // 
                Enumeration<Equation> eqnEnum = volumeSubDomain.getEquations();
                while (eqnEnum.hasMoreElements()) {
                    Equation equation = eqnEnum.nextElement();
                    BioModelNode equationNode = new BioModelNode(equation, false);
                    volumeSubDomainNode.add(equationNode);
                }
                // 
                // add fast system
                // 
                FastSystem fastSystem = volumeSubDomain.getFastSystem();
                if (fastSystem != null) {
                    BioModelNode fsNode = new BioModelNode(fastSystem, true);
                    Enumeration<FastInvariant> enumFI = fastSystem.getFastInvariants();
                    while (enumFI.hasMoreElements()) {
                        FastInvariant fi = enumFI.nextElement();
                        fsNode.add(new BioModelNode(fi, false));
                    }
                    Enumeration<FastRate> enumFR = fastSystem.getFastRates();
                    while (enumFR.hasMoreElements()) {
                        FastRate fr = enumFR.nextElement();
                        fsNode.add(new BioModelNode(fr, false));
                    }
                    volumeSubDomainNode.add(fsNode);
                }
            }
            volumeRootNode.add(volumeSubDomainNode);
        } else if (subDomain instanceof MembraneSubDomain) {
            MembraneSubDomain membraneSubDomain = (MembraneSubDomain) subDomain;
            BioModelNode membraneSubDomainNode = new BioModelNode(membraneSubDomain, true);
            // 
            // add equation children
            // 
            Enumeration<Equation> eqnEnum = membraneSubDomain.getEquations();
            while (eqnEnum.hasMoreElements()) {
                Equation equation = eqnEnum.nextElement();
                BioModelNode equationNode = new BioModelNode(equation, false);
                membraneSubDomainNode.add(equationNode);
            }
            // 
            // add jump condition children
            // 
            Enumeration<JumpCondition> jcEnum = membraneSubDomain.getJumpConditions();
            while (jcEnum.hasMoreElements()) {
                JumpCondition jumpCondition = jcEnum.nextElement();
                BioModelNode jcNode = new BioModelNode(jumpCondition, false);
                membraneSubDomainNode.add(jcNode);
            }
            // 
            // add fast system
            // 
            FastSystem fastSystem = membraneSubDomain.getFastSystem();
            if (fastSystem != null) {
                BioModelNode fsNode = new BioModelNode(fastSystem, true);
                Enumeration<FastInvariant> enumFI = fastSystem.getFastInvariants();
                while (enumFI.hasMoreElements()) {
                    FastInvariant fi = enumFI.nextElement();
                    fsNode.add(new BioModelNode(fi, false));
                }
                Enumeration<FastRate> enumFR = fastSystem.getFastRates();
                while (enumFR.hasMoreElements()) {
                    FastRate fr = enumFR.nextElement();
                    fsNode.add(new BioModelNode(fr, false));
                }
                membraneSubDomainNode.add(fsNode);
            }
            membraneRootNode.add(membraneSubDomainNode);
        }
    }
    if (volumeRootNode.getChildCount() > 0) {
        rootNode.add(volumeRootNode);
    }
    if (membraneRootNode.getChildCount() > 0) {
        rootNode.add(membraneRootNode);
    }
    return rootNode;
}

Example 47 with BioModelNode

use of cbit.vcell.desktop.BioModelNode in project vcell by virtualcell.

the class GuiUtils method selectClickTreePath.

public static void selectClickTreePath(JTree jtree, MouseEvent e) {
    Point mousePoint = e.getPoint();
    TreePath clickPath = jtree.getPathForLocation(mousePoint.x, mousePoint.y);
    if (clickPath == null) {
        return;
    }
    Object rightClickNode = clickPath.getLastPathComponent();
    if (rightClickNode == null || !(rightClickNode instanceof BioModelNode)) {
        return;
    }
    boolean bFound = false;
    TreePath[] selectedPaths = jtree.getSelectionPaths();
    if (selectedPaths != null) {
        for (TreePath tp : selectedPaths) {
            if (tp.equals(clickPath)) {
                bFound = true;
                break;
            }
        }
    }
    if (!bFound) {
        jtree.setSelectionPath(clickPath);
    }
}

Example 48 with BioModelNode

use of cbit.vcell.desktop.BioModelNode in project vcell by virtualcell.

the class BioModelEditorPathwayCommonsPanel method initialize.

private void initialize() {
    searchTextField = new TextFieldAutoCompletion();
    searchTextField.addActionListener(eventHandler);
    searchTextField.putClientProperty("JTextField.variant", "search");
    filterTextField = new TextFieldAutoCompletion();
    filterTextField.addActionListener(eventHandler);
    filterTextField.addKeyListener(eventHandler);
    filterTextField.putClientProperty("JTextField.variant", "filter");
    searchButton = new JButton("Search");
    searchButton.addActionListener(eventHandler);
    sortButton = new JButton("Sort");
    sortButton.addActionListener(eventHandler);
    showPathwayButton = new JButton("Preview");
    showPathwayButton.addActionListener(eventHandler);
    showPathwayButton.setEnabled(false);
    gotoPathwayButton = new JButton("Open Web Link");
    gotoPathwayButton.addActionListener(eventHandler);
    gotoPathwayButton.setEnabled(false);
    responseTree = new JTree();
    responseTreeModel = new ResponseTreeModel();
    responseTree.setModel(responseTreeModel);
    ToolTipManager.sharedInstance().registerComponent(responseTree);
    CollapsiblePanel searchPanel = new CollapsiblePanel("Search", true);
    searchPanel.getContentPanel().setLayout(new GridBagLayout());
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.weightx = 1.0;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.anchor = GridBagConstraints.LINE_START;
    searchPanel.getContentPanel().add(searchTextField, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 0;
    gbc.insets = new Insets(0, 4, 0, 0);
    searchPanel.getContentPanel().add(searchButton, gbc);
    setPreferredSize(new Dimension(475, 300));
    setLayout(new GridBagLayout());
    int gridy = 0;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.weightx = 1.0;
    gbc.gridwidth = GridBagConstraints.REMAINDER;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.insets = new Insets(4, 4, 4, 4);
    add(searchPanel, gbc);
    gridy++;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.weightx = 1.0;
    gbc.weighty = 1.0;
    gbc.gridwidth = GridBagConstraints.REMAINDER;
    gbc.insets = new Insets(4, 4, 4, 4);
    gbc.fill = GridBagConstraints.BOTH;
    add(new JScrollPane(responseTree), gbc);
    gridy++;
    CollapsiblePanel filterPanel = new CollapsiblePanel("Filter", true);
    filterPanel.getContentPanel().setLayout(new GridBagLayout());
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = 0;
    gbc.weightx = 1.0;
    gbc.insets = new Insets(2, 2, 2, 2);
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.anchor = GridBagConstraints.LINE_START;
    filterPanel.getContentPanel().add(filterTextField, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 0;
    gbc.insets = new Insets(0, 4, 0, 0);
    filterPanel.getContentPanel().add(sortButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.weightx = 1.0;
    gbc.gridwidth = GridBagConstraints.REMAINDER;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.insets = new Insets(4, 4, 4, 4);
    filterPanel.expand(true);
    add(filterPanel, gbc);
    // JPanel optionsField = new JPanel(new GridLayout());
    // ButtonGroup buttonGroup = new ButtonGroup();
    // JRadioButton o1, o2, o3;
    // o1 = new JRadioButton(" Entity ");
    // buttonGroup.add(o1);
    // optionsField.add(o1);
    // o2 = new JRadioButton(" Database ");
    // buttonGroup.add(o2);
    // optionsField.add(o2);
    // o3 = new JRadioButton(" Organism ");
    // buttonGroup.add(o3);
    // optionsField.add(o3);
    // o3.setSelected(true);
    // 
    // gridy ++;
    // CollapsiblePanel optionsPanel = new CollapsiblePanel("Group by... ", true);
    // optionsPanel.getContentPanel().setLayout(new GridBagLayout());
    // gbc = new GridBagConstraints();
    // gbc.gridx = 0;
    // gbc.gridy = gridy;
    // gbc.weightx = 1.0;
    // gbc.fill = GridBagConstraints.HORIZONTAL;
    // gbc.anchor = GridBagConstraints.LINE_START;
    // optionsPanel.getContentPanel().add(optionsField, gbc);
    // 
    // gbc = new GridBagConstraints();
    // gbc.gridx = 0;
    // gbc.gridy = gridy;
    // gbc.weightx = 1.0;
    // gbc.gridwidth = GridBagConstraints.REMAINDER;
    // gbc.fill = GridBagConstraints.HORIZONTAL;
    // gbc.insets = new Insets(4,4,4,4);
    // optionsPanel.expand(false);
    // add(optionsPanel, gbc);
    gridy++;
    gbc = new GridBagConstraints();
    gbc.gridx = 0;
    gbc.gridy = gridy;
    gbc.weightx = 1.0;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.insets = new Insets(4, 4, 4, 1);
    add(showPathwayButton, gbc);
    gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = gridy;
    gbc.weightx = 1.0;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    gbc.insets = new Insets(4, 1, 4, 4);
    add(gotoPathwayButton, gbc);
    sortButton.setIcon(bAscending ? VCellIcons.sortDownIcon : VCellIcons.sortUpIcon);
    ResponseTreeCellRenderer renderer = new ResponseTreeCellRenderer();
    // renderer.setLeafIcon(null);
    // renderer.setClosedIcon(null);
    // renderer.setOpenIcon(null);
    renderer.setLeafIcon(VCellIcons.pathwayLeafIcon);
    responseTree.setCellRenderer(renderer);
    responseTree.setRootVisible(false);
    responseTree.getSelectionModel().addTreeSelectionListener(eventHandler);
    responseTree.addMouseListener(new MouseAdapter() {

        public void mouseClicked(MouseEvent e) {
            if (e.getClickCount() <= 1) {
                return;
            }
            showPathway();
        }
    });
    responseTree.getSelectionModel().addTreeSelectionListener(new TreeSelectionListener() {

        public void valueChanged(TreeSelectionEvent e) {
            Object obj = responseTree.getLastSelectedPathComponent();
            if (obj == null || !(obj instanceof BioModelNode)) {
                return;
            }
            BioModelNode selectedNode = (BioModelNode) obj;
            Object userObject = selectedNode.getUserObject();
            setSelectedObjects(new Object[] { userObject });
        }
    });
}

Example 49 with BioModelNode

use of cbit.vcell.desktop.BioModelNode in project vcell by virtualcell.

the class BioModelEditorSabioPanel method computeSelectedKineticLaw.

public SBEntity computeSelectedKineticLaw() {
    Object object = responseTree.getLastSelectedPathComponent();
    if (object == null || !(object instanceof BioModelNode)) {
        return null;
    }
    Object userObject = ((BioModelNode) object).getUserObject();
    if (userObject instanceof SBEntity) {
        return (SBEntity) userObject;
    }
    return null;
}

Example 50 with BioModelNode

use of cbit.vcell.desktop.BioModelNode in project vcell by virtualcell.

the class BioModelEditorTreeCellRenderer method getTreeCellRendererComponent.

public Component getTreeCellRendererComponent(JTree tree, Object value, boolean sel, boolean expanded, boolean leaf, int row, boolean hasFocus) {
    super.getTreeCellRendererComponent(tree, value, sel, expanded, leaf, row, hasFocus);
    if (regularFont == null) {
        regularFont = getFont();
        boldFont = regularFont.deriveFont(Font.BOLD);
    }
    Font font = regularFont;
    Icon icon = null;
    String labelText = null;
    String toolTipPrefix = "";
    String toolTipSuffix = "";
    if (value instanceof LinkNode) {
        LinkNode ln = (LinkNode) value;
        String link = ln.getLink();
        String text = ln.getText();
        String qualifier = ln.getMiriamQualifier().getDescription();
        if (link != null) {
            String colorString = (sel) ? "white" : "blue";
            toolTipPrefix = "double-click to open link " + link;
            labelText = "<html>" + qualifier + "&nbsp;<font color=\"" + colorString + "\"><a href=" + link + ">" + text + "</a></font></html>";
        } else {
            String colorString = (sel) ? "white" : "black";
            labelText = "<html>" + qualifier + "&nbsp;<font color=\"" + colorString + "\">" + text + "</font></html>";
        }
    } else if (value instanceof BioModelNode) {
        BioModelNode node = (BioModelNode) value;
        Object userObj = node.getUserObject();
        if (userObj instanceof BioModel) {
            font = boldFont;
            icon = VCellIcons.documentIcon;
            labelText = ((BioModel) userObj).getName();
            toolTipPrefix = "BioModel: ";
        } else if (userObj instanceof SimulationContext) {
            // --- root: application name
            font = boldFont;
            // icon = VCellIcons.applicationIcon;
            SimulationContext simContext = (SimulationContext) userObj;
            if (simContext.isRuleBased()) {
                if (simContext.getGeometry().getDimension() == 0) {
                    icon = VCellIcons.appRbmNonspIcon;
                    toolTipSuffix = "Rule Based / Non spatial";
                }
            } else if (simContext.isStoch()) {
                if (simContext.getGeometry().getDimension() == 0) {
                    icon = VCellIcons.appStoNonspIcon;
                    toolTipSuffix = "Stochastic / Non spatial";
                } else {
                    icon = VCellIcons.appStoSpatialIcon;
                    toolTipSuffix = "Stochastic / Spatial";
                }
            } else {
                // deterministic
                if (simContext.getGeometry().getDimension() == 0) {
                    icon = VCellIcons.appDetNonspIcon;
                    toolTipSuffix = "Deterministic / Non spatial";
                } else {
                    icon = VCellIcons.appDetSpatialIcon;
                    toolTipSuffix = "Deterministic / Spatial";
                }
            }
            labelText = /*"Application: " + */
            ((SimulationContext) userObj).getName();
            toolTipPrefix = "Application: ";
        } else if (userObj instanceof DocumentEditorTreeFolderNode) {
            // --- 1st level folders
            DocumentEditorTreeFolderNode folder = (DocumentEditorTreeFolderNode) userObj;
            labelText = folder.getName();
            if (folder.isBold()) {
                font = boldFont;
            }
            DocumentEditorTreeFolderClass folderClass = folder.getFolderClass();
            switch(folderClass) {
                // break;
                case REACTIONS_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        int numReactions = bioModel.getModel().getNumReactions();
                        if (bioModel.getModel().getRbmModelContainer() != null) {
                            numReactions += bioModel.getModel().getRbmModelContainer().getReactionRuleList().size();
                        }
                        labelText = folder.getName() + " (" + numReactions + ")";
                    }
                    break;
                case STRUCTURES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getModel().getNumStructures() + ")";
                    }
                    break;
                case SPECIES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getModel().getNumSpeciesContexts() + ")";
                    }
                    break;
                case MOLECULAR_TYPES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                        if (rbmModelContainer == null) {
                            labelText = folder.getName() + "(00000)";
                        } else {
                            labelText = folder.getName() + " (" + rbmModelContainer.getMolecularTypeList().size() + ")";
                        }
                    }
                    break;
                case OBSERVABLES_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        RbmModelContainer rbmModelContainer = bioModel.getModel().getRbmModelContainer();
                        if (rbmModelContainer == null) {
                            labelText = folder.getName() + "(00000)";
                        } else {
                            labelText = folder.getName() + " (" + rbmModelContainer.getObservableList().size() + ")";
                        }
                    }
                    break;
                case APPLICATIONS_NODE:
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getNumSimulationContexts() + ")";
                    }
                    break;
                case REACTION_DIAGRAM_NODE:
                    icon = VCellIcons.diagramIcon;
                    break;
                // break;
                case GEOMETRY_NODE:
                    icon = VCellIcons.geometryIcon;
                    break;
                case SPECIFICATIONS_NODE:
                    icon = VCellIcons.settingsIcon;
                    break;
                case PROTOCOLS_NODE:
                    icon = VCellIcons.protocolsIcon;
                    break;
                case SIMULATIONS_NODE:
                    icon = VCellIcons.simulationIcon;
                    break;
                case PARAMETER_ESTIMATION_NODE:
                    icon = VCellIcons.fittingIcon;
                    break;
                case PATHWAY_DIAGRAM_NODE:
                    icon = VCellIcons.diagramIcon;
                    break;
                case PATHWAY_OBJECTS_NODE:
                    icon = VCellIcons.tableIcon;
                    if (bioModel == null) {
                        labelText = folder.getName() + "(00000)";
                    } else {
                        labelText = folder.getName() + " (" + bioModel.getPathwayModel().getBiopaxObjects().size() + ")";
                    }
                    break;
                case BIOPAX_SUMMARY_NODE:
                    icon = VCellIcons.textNotesIcon;
                    break;
                case BIOPAX_TREE_NODE:
                    icon = VCellIcons.tableIcon;
                    break;
            }
        }
    }
    setIcon(icon);
    setFont(font);
    setText(labelText);
    if (toolTipSuffix.length() == 0) {
        toolTipSuffix = labelText;
    }
    setToolTipText(toolTipPrefix + toolTipSuffix);
    return this;
}