Examples with TreeViewModel edu.ucsf.rbvi.clusterMaker2.internal.treeview.model.TreeViewModel used on opensource projects

Example 1 with TreeViewModel

use of edu.ucsf.rbvi.clusterMaker2.internal.treeview.model.TreeViewModel in project clusterMaker2 by RBVI.

the class HeatMapView method startup.

protected void startup() {
    CyProperty cyProperty = manager.getService(CyProperty.class, "(cyPropertyName=cytoscape3.props)");
    List<String> nodeAttributeList = context.attributeList.getNodeAttributeList();
    String edgeAttribute = context.attributeList.getEdgeAttribute();
    if (nodeAttributeList == null && edgeAttribute == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must select either one edge column or two or more node columns");
        return;
    }
    if (nodeAttributeList != null && nodeAttributeList.size() > 0 && edgeAttribute != null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't have both node and edge columns selected");
        return;
    }
    if (nodeAttributeList != null && nodeAttributeList.size() < 2) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must have at least two node columns for cluster weighting");
        return;
    }
    String[] nodeArray;
    // Handle selected only
    if (!context.selectedOnly) {
        nodeArray = new String[myNetwork.getNodeCount()];
        int index = 0;
        for (CyNode node : myNetwork.getNodeList()) {
            nodeArray[index++] = ModelUtils.getName(myNetwork, node);
        }
    } else {
        if (edgeAttribute != null && edgeAttribute.length() > 0) {
            List<CyEdge> selectedEdges = CyTableUtil.getEdgesInState(myNetwork, CyNetwork.SELECTED, true);
            Set<CyNode> nodesSeen = new HashSet<CyNode>();
            for (CyEdge edge : selectedEdges) {
                nodesSeen.add(edge.getSource());
                nodesSeen.add(edge.getTarget());
            }
            int index = 0;
            nodeArray = new String[nodesSeen.size()];
            for (CyNode node : nodesSeen) nodeArray[index++] = ModelUtils.getName(myNetwork, node);
        } else {
            List<CyNode> selectedNodes = CyTableUtil.getNodesInState(myNetwork, CyNetwork.SELECTED, true);
            nodeArray = new String[selectedNodes.size()];
            int index = 0;
            for (CyNode node : selectedNodes) {
                nodeArray[index++] = ModelUtils.getName(myNetwork, node);
            }
        }
    }
    Arrays.sort(nodeArray);
    ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.NODE_ORDER_ATTRIBUTE, Arrays.asList(nodeArray), List.class, String.class);
    // Edge attribute?
    if (edgeAttribute != null && edgeAttribute.length() > 0) {
        ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.ARRAY_ORDER_ATTRIBUTE, Arrays.asList(nodeArray), List.class, String.class);
        ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.CLUSTER_EDGE_ATTRIBUTE, "edge." + edgeAttribute, String.class, null);
    } else {
        int index = 0;
        Collections.sort(nodeAttributeList);
        ModelUtils.createAndSetLocal(myNetwork, myNetwork, ClusterManager.ARRAY_ORDER_ATTRIBUTE, nodeAttributeList, List.class, String.class);
    }
    // Get our data model
    dataModel = new TreeViewModel(monitor, myNetwork, myView, manager);
    // Set up the global config
    setConfigDefaults(new PropertyConfig(cyProperty, globalConfigName(), "ProgramConfig"));
    // Set up our configuration
    PropertyConfig documentConfig = new PropertyConfig(cyProperty, getShortName(), "DocumentConfig");
    dataModel.setDocumentConfig(documentConfig);
    // Create our view frame
    TreeViewFrame frame = new TreeViewFrame(this, appName);
    // Set the data model
    frame.setDataModel(dataModel);
    frame.setLoaded(true);
    frame.addWindowListener(this);
    frame.setVisible(true);
    geneSelection = frame.getGeneSelection();
    geneSelection.addObserver(this);
    arraySelection = frame.getArraySelection();
    arraySelection.addObserver(this);
    manager.registerService(this, RowsSetListener.class, new Properties());
}

Example 2 with TreeViewModel

use of edu.ucsf.rbvi.clusterMaker2.internal.treeview.model.TreeViewModel in project clusterMaker2 by RBVI.

the class DendroView method getButtonBox.

private JPanel getButtonBox() {
    // Get our border
    JPanel buttonBox = new JPanel();
    buttonBox.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
    // Now add our buttons
    // The Settings button will bring up the Pixel Settings dialog
    {
        JButton settingsButton = createButton("Settings...");
        settingsButton.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent actionEvent) {
                ColorExtractor ce = null;
                try {
                    ce = ((DoubleArrayDrawer) arrayDrawer).getColorExtractor();
                } catch (Exception e) {
                }
                PixelSettingsSelector pssSelector = new PixelSettingsSelector(globalXmap, globalYmap, getZoomXmap(), getZoomYmap(), ce, colorPresets);
                JDialog popup = new ModelessSettingsDialog(viewFrame, "Pixel Settings", pssSelector);
                popup.addWindowListener(PropertyConfig.getStoreOnWindowClose(getDataModel().getDocumentConfig()));
                popup.pack();
                popup.setVisible(true);
            }
        });
        buttonBox.add(settingsButton);
    }
    // The Save Data button brings up a file dialog and saves the .CDT, .GTR, and .ATR files
    {
        JButton saveButton = createButton("Save Data...");
        saveButton.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent actionEvent) {
                JFileChooser chooser = new JFileChooser();
                int returnVal = chooser.showSaveDialog(viewFrame);
                if (returnVal == JFileChooser.APPROVE_OPTION) {
                    // Save the data
                    // Get the name of the file
                    String filePath = chooser.getSelectedFile().getAbsolutePath();
                    if (filePath.length() == 0)
                        return;
                    DataModelWriter writer = new DataModelWriter(dataModel);
                    if (dataModel.aidFound())
                        writer.writeAtr(filePath + ".atr");
                    if (dataModel.gidFound())
                        writer.writeGtr(filePath + ".gtr");
                    writer.writeCdt(filePath + ".cdt");
                }
            }
        });
        buttonBox.add(saveButton);
    }
    // The Export Graphics button brings up a new dialog that allows the user
    // to produce images for publication
    {
        JButton exportButton = createButton("Export Graphics...");
        exportButton.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent actionevent) {
                GraphicsExportPanel graphicsExport = new GraphicsExportPanel(myView);
                graphicsExport.setGeneFont(textview.getFont());
                graphicsExport.setArrayFont(arraynameview.getFont());
                JDialog popup = new CancelableSettingsDialog(viewFrame, "Export Graphics", graphicsExport);
                popup.addWindowListener(PropertyConfig.getStoreOnWindowClose(getDataModel().getDocumentConfig()));
                popup.pack();
                popup.setVisible(true);
            }
        });
        buttonBox.add(exportButton);
    }
    if (dataModel.aidFound()) {
        JButton flipButton = createButton("Flip Tree Nodes");
        flipButton.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent actionEvent) {
                flipSelectedATRNode();
            }
        });
        buttonBox.add(flipButton);
    }
    // Map the visual properties onto the network
    if (dataModel instanceof TreeViewModel) {
        final ClusterManager clusterManager = ((TreeViewModel) dataModel).getClusterManager();
        JButton vizMapButton = createButton("Map Colors Onto Network...");
        vizMapButton.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent evt) {
                // Get the colors from the view
                ColorExtractor ce = null;
                try {
                    ce = ((DoubleArrayDrawer) arrayDrawer).getColorExtractor();
                } catch (Exception e) {
                    // this shouldn't happen at this point!
                    ce = new ColorExtractor();
                    ce.setDefaultColorSet(colorPresets.getDefaultColorSet());
                }
                List<String> attributes = new ArrayList();
                if (dataModel.isSymmetrical()) {
                } else {
                    // Get the node attributes
                    int[] selections = arraySelection.getSelectedIndexes();
                    HeaderInfo arrayInfo = dataModel.getArrayHeaderInfo();
                    if (selections.length >= 1) {
                        for (int i = 0; i < selections.length; i++) {
                            attributes.add(arrayInfo.getHeader(selections[i])[0]);
                        }
                    } else {
                        // Nothing selected, add them all
                        int count = arrayInfo.getNumHeaders();
                        for (int i = 0; i < count; i++) {
                            attributes.add(arrayInfo.getHeader(i)[0]);
                        }
                    }
                }
                // Bring up the dialog
                NetworkColorDialog ncd = new NetworkColorDialog(null, ce, attributes, viewFrame, clusterManager, dataModel.getDataMatrix().getMinValue(), dataModel.getDataMatrix().getMaxValue(), dataModel.isSymmetrical());
            }
        });
        buttonBox.add(vizMapButton);
    }
    // The Close button exits clusterViz
    {
        JButton closeButton = createButton("Close");
        closeButton.addActionListener(new ActionListener() {

            // called when close button hit
            public void actionPerformed(ActionEvent evt) {
                viewFrame.closeWindow();
            }
        });
        // 
        buttonBox.add(closeButton);
    }
    return buttonBox;
}

Example 3 with TreeViewModel

use of edu.ucsf.rbvi.clusterMaker2.internal.treeview.model.TreeViewModel in project clusterMaker2 by RBVI.

the class TreeView method startup.

protected void startup() {
    CyProperty cyProperty = manager.getService(CyProperty.class, "(cyPropertyName=cytoscape3.props)");
    // Get our data model
    dataModel = new TreeViewModel(monitor, myNetwork, myView, manager);
    // Set up the global config
    setConfigDefaults(new PropertyConfig(cyProperty, globalConfigName(), "ProgramConfig"));
    // Set up our configuration
    PropertyConfig documentConfig = new PropertyConfig(cyProperty, getShortName(), "DocumentConfig");
    dataModel.setDocumentConfig(documentConfig);
    // Create our view frame
    TreeViewFrame frame = new TreeViewFrame(this, appName);
    // Set the data model
    frame.setDataModel(dataModel);
    frame.setLoaded(true);
    frame.addWindowListener(this);
    frame.setVisible(true);
    geneSelection = frame.getGeneSelection();
    geneSelection.addObserver(this);
    arraySelection = frame.getArraySelection();
    arraySelection.addObserver(this);
    manager.registerService(this, RowsSetListener.class, new Properties());
}