Examples with CyRootNetwork org.cytoscape.model.subnetwork.CyRootNetwork used on opensource projects

Example 41 with CyRootNetwork

use of org.cytoscape.model.subnetwork.CyRootNetwork in project cytoscape-api by cytoscape.

the class AbstractCyNetworkReader method init.

private void init() {
    name2RootMap = getRootNetworkMap();
    nodeMap = new HashMap<>(10000);
    // initialize the network Collection
    final List<String> rootNames = new ArrayList<>();
    rootNames.addAll(name2RootMap.keySet());
    if (!rootNames.isEmpty()) {
        sort(rootNames);
        rootNames.add(0, CREATE_NEW_COLLECTION_STRING);
    }
    final ListSingleSelection<String> rootNetList = new ListSingleSelection<>(rootNames);
    final CyNetwork net = cyApplicationManager != null ? cyApplicationManager.getCurrentNetwork() : null;
    final CyRootNetwork rootNet = net != null ? cyRootNetworkManager.getRootNetwork(net) : null;
    final String name = rootNet != null ? rootNet.getRow(rootNet).get(CyRootNetwork.NAME, String.class) : CREATE_NEW_COLLECTION_STRING;
    if (rootNames.contains(name))
        rootNetList.setSelectedValue(name);
    else if (rootNames.contains(CREATE_NEW_COLLECTION_STRING))
        rootNetList.setSelectedValue(CREATE_NEW_COLLECTION_STRING);
    setRootNetworkList(rootNetList);
    // initialize renderer list
    final List<NetworkViewRenderer> renderers = new ArrayList<>();
    NetworkViewRenderer defViewRenderer = null;
    if (cyApplicationManager != null) {
        final Set<NetworkViewRenderer> rendererSet = cyApplicationManager.getNetworkViewRendererSet();
        // so the combo-box does not appear to the user, since there is nothing to select anyway.
        if (rendererSet.size() > 1) {
            renderers.addAll(rendererSet);
            Collections.sort(renderers, new Comparator<NetworkViewRenderer>() {

                @Override
                public int compare(NetworkViewRenderer r1, NetworkViewRenderer r2) {
                    return r1.toString().compareToIgnoreCase(r2.toString());
                }
            });
        }
        defViewRenderer = cyApplicationManager.getDefaultNetworkViewRenderer();
    }
    rendererList = new ListSingleSelection<>(renderers);
    if (defViewRenderer != null && renderers.contains(defViewRenderer))
        rendererList.setSelectedValue(defViewRenderer);
}

Example 42 with CyRootNetwork

use of org.cytoscape.model.subnetwork.CyRootNetwork in project clusterMaker2 by RBVI.

the class RankingPanel method createClusterImage.

/**
 * Convert a network to an image.  This is used by the MCODEResultsPanel.
 *
 * @param cluster Input network to convert to an image
 * @param height  Height that the resulting image should be
 * @param width   Width that the resulting image should be
 * @param layouter Reference to the layout algorithm
 * @param layoutNecessary Determinant of cluster size growth or shrinkage, the former requires layout
 * @return The resulting image
 */
public Image createClusterImage(final NodeCluster cluster, final int height, final int width, SpringEmbeddedLayouter layouter, boolean layoutNecessary) {
    // System.out.println("CCI: inside method");
    final CyRootNetwork root = clusterManager.getService(CyRootNetworkManager.class).getRootNetwork(network);
    // need to create a method get the subnetwork for a cluster
    final CyNetwork net = cluster.getSubNetwork(network, root, SavePolicy.DO_NOT_SAVE);
    // System.out.println("CCI: after getting root and network ");
    // Progress reporters.
    // There are three basic tasks, the progress of each is calculated and then combined
    // using the respective weighting to get an overall progress global progress
    // setting up the nodes and edges is deemed as 25% of the whole task
    int weightSetupNodes = 20;
    int weightSetupEdges = 5;
    // layout it is 70%
    double weightLayout = 75.0;
    double goalTotal = weightSetupNodes + weightSetupEdges;
    if (layoutNecessary) {
        goalTotal += weightLayout;
    }
    // keeps track of progress as a percent of the totalGoal
    double progress = 0;
    final VisualStyle vs = getClusterStyle();
    // System.out.println("CCI: after getClusterStyle");
    final CyNetworkView clusterView = createNetworkView(net, vs);
    // System.out.println("CCI: after createNetworkView");
    clusterView.setVisualProperty(NETWORK_WIDTH, new Double(width));
    clusterView.setVisualProperty(NETWORK_HEIGHT, new Double(height));
    for (View<CyNode> nv : clusterView.getNodeViews()) {
        if (interrupted) {
            // problems the next time around
            if (layouter != null)
                layouter.resetDoLayout();
            resetLoading();
            return null;
        }
        // Node position
        final double x;
        final double y;
        // first prevents the program from throwing a null pointer exception in the second condition)
        if (cluster.getView() != null && cluster.getView().getNodeView(nv.getModel()) != null) {
            // If it does, then we take the layout position that was already generated for it
            x = cluster.getView().getNodeView(nv.getModel()).getVisualProperty(NODE_X_LOCATION);
            y = cluster.getView().getNodeView(nv.getModel()).getVisualProperty(NODE_Y_LOCATION);
        } else {
            // Otherwise, randomize node positions before layout so that they don't all layout in a line
            // (so they don't fall into a local minimum for the SpringEmbedder)
            // If the SpringEmbedder implementation changes, this code may need to be removed
            // size is small for many default drawn graphs, thus +100
            x = (clusterView.getVisualProperty(NETWORK_WIDTH) + 100) * Math.random();
            y = (clusterView.getVisualProperty(NETWORK_HEIGHT) + 100) * Math.random();
            if (!layoutNecessary) {
                goalTotal += weightLayout;
                progress /= (goalTotal / (goalTotal - weightLayout));
                layoutNecessary = true;
            }
        }
        nv.setVisualProperty(NODE_X_LOCATION, x);
        nv.setVisualProperty(NODE_Y_LOCATION, y);
    // Might be specific to MCODE
    /*
			// Node shape
			if (cluster.getSeedNode() == nv.getModel().getSUID()) {
				nv.setLockedValue(NODE_SHAPE, NodeShapeVisualProperty.RECTANGLE);
			} else {
				nv.setLockedValue(NODE_SHAPE, NodeShapeVisualProperty.ELLIPSE);
			}
			 */
    /*
			// Update loader
			if (loader != null) {
				progress += 100.0 * (1.0 / (double) clusterView.getNodeViews().size()) *
							((double) weightSetupNodes / (double) goalTotal);
				loader.setProgress((int) progress, "Setup: nodes");
			}

			*/
    }
    if (clusterView.getEdgeViews() != null) {
        for (int i = 0; i < clusterView.getEdgeViews().size(); i++) {
            if (interrupted) {
                // logger.error("Interrupted: Edge Setup");
                if (layouter != null)
                    layouter.resetDoLayout();
                resetLoading();
                return null;
            }
        /*
				if (loader != null) {
					progress += 100.0 * (1.0 / (double) clusterView.getEdgeViews().size()) *
								((double) weightSetupEdges / (double) goalTotal);
					loader.setProgress((int) progress, "Setup: edges");
				}
				*/
        }
    }
    if (layoutNecessary) {
        if (layouter == null) {
            layouter = new SpringEmbeddedLayouter();
        }
        layouter.setGraphView(clusterView);
        // The doLayout method should return true if the process completes without interruption
        if (!layouter.doLayout(weightLayout, goalTotal, progress)) {
            // Otherwise, if layout is not completed, set the interruption to false, and return null, not an image
            resetLoading();
            return null;
        }
    }
    final Image image = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
    final Graphics2D g = (Graphics2D) image.getGraphics();
    SwingUtilities.invokeLater(new Runnable() {

        // @Override
        public void run() {
            try {
                final Dimension size = new Dimension(width, height);
                JPanel panel = new JPanel();
                panel.setPreferredSize(size);
                panel.setSize(size);
                panel.setMinimumSize(size);
                panel.setMaximumSize(size);
                panel.setBackground((Color) vs.getDefaultValue(NETWORK_BACKGROUND_PAINT));
                JWindow window = new JWindow();
                window.getContentPane().add(panel, BorderLayout.CENTER);
                RenderingEngine<CyNetwork> re = renderingEngineFactory.createRenderingEngine(panel, clusterView);
                vs.apply(clusterView);
                clusterView.fitContent();
                clusterView.updateView();
                window.pack();
                window.repaint();
                re.createImage(width, height);
                re.printCanvas(g);
                g.dispose();
                if (clusterView.getNodeViews().size() > 0) {
                    cluster.setView(clusterView);
                }
            } catch (Exception ex) {
                throw new RuntimeException(ex);
            }
        }
    });
    layouter.resetDoLayout();
    resetLoading();
    return image;
}

Example 43 with CyRootNetwork

use of org.cytoscape.model.subnetwork.CyRootNetwork in project clusterMaker2 by RBVI.

the class ResultsPanel method createClusterImage.

/**
 * Convert a network to an image.  This is used by the MCODEResultsPanel.
 *
 * @param cluster Input network to convert to an image
 * @param height  Height that the resulting image should be
 * @param width   Width that the resulting image should be
 * @param layouter Reference to the layout algorithm
 * @param layoutNecessary Determinant of cluster size growth or shrinkage, the former requires layout
 * @return The resulting image
 */
public Image createClusterImage(final NodeCluster cluster, final int height, final int width, SpringEmbeddedLayouter layouter, boolean layoutNecessary) {
    // System.out.println("CCI: inside method");
    final CyRootNetwork root = clusterManager.getService(CyRootNetworkManager.class).getRootNetwork(network);
    // need to create a method get the subnetwork for a cluster
    final CyNetwork net = cluster.getSubNetwork(network, root, SavePolicy.DO_NOT_SAVE);
    // System.out.println("CCI: after getting root and network ");
    // Progress reporters.
    // There are three basic tasks, the progress of each is calculated and then combined
    // using the respective weighting to get an overall progress global progress
    // setting up the nodes and edges is deemed as 25% of the whole task
    int weightSetupNodes = 20;
    int weightSetupEdges = 5;
    // layout it is 70%
    double weightLayout = 75.0;
    double goalTotal = weightSetupNodes + weightSetupEdges;
    if (layoutNecessary) {
        goalTotal += weightLayout;
    }
    // keeps track of progress as a percent of the totalGoal
    double progress = 0;
    final VisualStyle vs = getClusterStyle();
    // System.out.println("CCI: after getClusterStyle");
    final CyNetworkView clusterView = createNetworkView(net, vs);
    // System.out.println("CCI: after createNetworkView");
    clusterView.setVisualProperty(NETWORK_WIDTH, new Double(width));
    clusterView.setVisualProperty(NETWORK_HEIGHT, new Double(height));
    for (View<CyNode> nv : clusterView.getNodeViews()) {
        if (interrupted) {
            // problems the next time around
            if (layouter != null)
                layouter.resetDoLayout();
            resetLoading();
            return null;
        }
        // Node position
        final double x;
        final double y;
        // first prevents the program from throwing a null pointer exception in the second condition)
        if (cluster.getView() != null && cluster.getView().getNodeView(nv.getModel()) != null) {
            // If it does, then we take the layout position that was already generated for it
            x = cluster.getView().getNodeView(nv.getModel()).getVisualProperty(NODE_X_LOCATION);
            y = cluster.getView().getNodeView(nv.getModel()).getVisualProperty(NODE_Y_LOCATION);
        } else {
            // Otherwise, randomize node positions before layout so that they don't all layout in a line
            // (so they don't fall into a local minimum for the SpringEmbedder)
            // If the SpringEmbedder implementation changes, this code may need to be removed
            // size is small for many default drawn graphs, thus +100
            x = (clusterView.getVisualProperty(NETWORK_WIDTH) + 100) * Math.random();
            y = (clusterView.getVisualProperty(NETWORK_HEIGHT) + 100) * Math.random();
            if (!layoutNecessary) {
                goalTotal += weightLayout;
                progress /= (goalTotal / (goalTotal - weightLayout));
                layoutNecessary = true;
            }
        }
        nv.setVisualProperty(NODE_X_LOCATION, x);
        nv.setVisualProperty(NODE_Y_LOCATION, y);
    // Might be specific to MCODE
    /*
			// Node shape
			if (cluster.getSeedNode() == nv.getModel().getSUID()) {
				nv.setLockedValue(NODE_SHAPE, NodeShapeVisualProperty.RECTANGLE);
			} else {
				nv.setLockedValue(NODE_SHAPE, NodeShapeVisualProperty.ELLIPSE);
			}
			 */
    /*
			// Update loader
			if (loader != null) {
				progress += 100.0 * (1.0 / (double) clusterView.getNodeViews().size()) *
							((double) weightSetupNodes / (double) goalTotal);
				loader.setProgress((int) progress, "Setup: nodes");
			}
			
			*/
    }
    if (clusterView.getEdgeViews() != null) {
        for (int i = 0; i < clusterView.getEdgeViews().size(); i++) {
            if (interrupted) {
                // logger.error("Interrupted: Edge Setup");
                if (layouter != null)
                    layouter.resetDoLayout();
                resetLoading();
                return null;
            }
        /*
				if (loader != null) {
					progress += 100.0 * (1.0 / (double) clusterView.getEdgeViews().size()) *
								((double) weightSetupEdges / (double) goalTotal);
					loader.setProgress((int) progress, "Setup: edges");
				}
				*/
        }
    }
    if (layoutNecessary) {
        if (layouter == null) {
            layouter = new SpringEmbeddedLayouter();
        }
        layouter.setGraphView(clusterView);
        // The doLayout method should return true if the process completes without interruption
        if (!layouter.doLayout(weightLayout, goalTotal, progress)) {
            // Otherwise, if layout is not completed, set the interruption to false, and return null, not an image
            resetLoading();
            return null;
        }
    }
    final Image image = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
    final Graphics2D g = (Graphics2D) image.getGraphics();
    SwingUtilities.invokeLater(new Runnable() {

        // @Override
        public void run() {
            try {
                final Dimension size = new Dimension(width, height);
                JPanel panel = new JPanel();
                panel.setPreferredSize(size);
                panel.setSize(size);
                panel.setMinimumSize(size);
                panel.setMaximumSize(size);
                panel.setBackground((Color) vs.getDefaultValue(NETWORK_BACKGROUND_PAINT));
                JWindow window = new JWindow();
                window.getContentPane().add(panel, BorderLayout.CENTER);
                RenderingEngine<CyNetwork> re = renderingEngineFactory.createRenderingEngine(panel, clusterView);
                vs.apply(clusterView);
                clusterView.fitContent();
                clusterView.updateView();
                window.pack();
                window.repaint();
                re.createImage(width, height);
                re.printCanvas(g);
                g.dispose();
                if (clusterView.getNodeViews().size() > 0) {
                    cluster.setView(clusterView);
                }
            } catch (Exception ex) {
                throw new RuntimeException(ex);
            }
        }
    });
    layouter.resetDoLayout();
    resetLoading();
    return image;
}

Example 44 with CyRootNetwork

use of org.cytoscape.model.subnetwork.CyRootNetwork in project cytoscape-impl by cytoscape.

the class GroupUtils method updateMetaEdgeInformation.

public static void updateMetaEdgeInformation(CyNetwork origNet, CyNetwork newNet, CyEdge origEdge, CyEdge newEdge) {
    if (newEdge == null)
        return;
    CyRootNetwork newRoot = ((CySubNetwork) newNet).getRootNetwork();
    CyRootNetwork origRoot = ((CySubNetwork) origNet).getRootNetwork();
    CyTable newTable = newRoot.getTable(CyEdge.class, CyNetwork.HIDDEN_ATTRS);
    if (newTable.getColumn(ISMETA_EDGE_ATTR) == null) {
        newTable.createColumn(ISMETA_EDGE_ATTR, Boolean.class, false);
    }
    CyRow origRow = origRoot.getRow(origEdge, CyNetwork.HIDDEN_ATTRS);
    if (origRow.isSet(ISMETA_EDGE_ATTR)) {
        CyRow newRow = newTable.getRow(newEdge.getSUID());
        Boolean isMeta = origRow.get(ISMETA_EDGE_ATTR, Boolean.class);
        newRow.set(ISMETA_EDGE_ATTR, isMeta);
    }
    return;
}

Example 45 with CyRootNetwork

use of org.cytoscape.model.subnetwork.CyRootNetwork in project cytoscape-impl by cytoscape.

the class CloneNetworkTask method addColumns.

private void addColumns(final CyNetwork origNet, final CyNetwork newNet, final Class<? extends CyIdentifiable> tableType, final String namespace) {
    final CyTable from = origNet.getTable(tableType, namespace);
    final CyTable to = newNet.getTable(tableType, namespace);
    final CyRootNetwork origRoot = rootNetMgr.getRootNetwork(origNet);
    final CyRootNetwork newRoot = rootNetMgr.getRootNetwork(newNet);
    final Map<String, CyTable> origRootTables = netTableMgr.getTables(origRoot, tableType);
    for (final CyColumn col : from.getColumns()) {
        final String name = col.getName();
        if (to.getColumn(name) == null) {
            final VirtualColumnInfo info = col.getVirtualColumnInfo();
            if (info.isVirtual()) {
                if (origRootTables.containsValue(info.getSourceTable())) {
                    // If the virtual column is from a root-network table, do NOT set this virtual column directly to
                    // the new table:
                    // Get the original column (not the virtual one!)
                    final CyColumn origCol = info.getSourceTable().getColumn(info.getSourceColumn());
                    // Copy the original column to the root-network's table first
                    String sourceNamespace = netTableMgr.getTableNamespace(info.getSourceTable());
                    final CyTable newRootTable = newRoot.getTable(tableType, sourceNamespace);
                    if (newRootTable.getColumn(origCol.getName()) == null)
                        copyColumn(origCol, newRootTable);
                    // Now we can add the new "root" column as a virtual one to the new network's table
                    to.addVirtualColumn(name, origCol.getName(), newRootTable, CyIdentifiable.SUID, col.isImmutable());
                } else {
                    // Otherwise (e.g. virtual column from a global table) just add the virtual column directly
                    addVirtualColumn(col, to);
                }
            } else {
                // Not a virtual column, so just copy it to the new network's table
                copyColumn(col, to);
            }
        }
    }
}