Examples with Node org.cytoscape.io.internal.util.session.model.Node used on opensource projects

Example 1 with Node

use of org.cytoscape.io.internal.util.session.model.Node in project cytoscape-impl by cytoscape.

the class Cy2SessionReaderImpl method extractSessionState.

private void extractSessionState(InputStream is, String entryName) throws Exception {
    CyPropertyReader reader = propertyReaderMgr.getReader(is, entryName);
    reader.run(taskMonitor);
    cysession = (Cysession) reader.getProperty();
    if (cysession != null) {
        // Network attributes and visual styles
        if (cysession.getNetworkTree() != null) {
            for (final Network net : cysession.getNetworkTree().getNetwork()) {
                // so let's ignore a network with that name.
                if (net.getId().equals(NETWORK_ROOT))
                    continue;
                final String netName = net.getId();
                List<Node> selNodes = null;
                List<Edge> selEdges = null;
                if (net.getSelectedNodes() != null)
                    selNodes = net.getSelectedNodes().getNode();
                if (net.getSelectedEdges() != null)
                    selEdges = net.getSelectedEdges().getEdge();
                nodeSelectionLookup.put(netName, selNodes);
                edgeSelectionLookup.put(netName, selEdges);
            }
        }
        // Convert the old cysession to core the required 3.0 core plugin files:
        // Actually we just need to extract the "networkFrames" and "cytopanels" data from the Cysession object
        // and write an XML file that will be parsed by swing-application.
        StringBuilder sb = new StringBuilder("<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>\n");
        sb.append("<sessionState documentVersion=\"1.0\">\n");
        sb.append("    <networkFrames>\n");
        if (cysession.getSessionState() != null && cysession.getSessionState().getDesktop() != null) {
            NetworkFrames netFrames = cysession.getSessionState().getDesktop().getNetworkFrames();
            if (netFrames != null) {
                for (NetworkFrame nf : netFrames.getNetworkFrame()) {
                    String id = nf.getFrameID();
                    String x = nf.getX() != null ? nf.getX().toString() : "0";
                    String y = nf.getY() != null ? nf.getY().toString() : "0";
                    sb.append("        <networkFrame networkViewID=\"" + id + "\" x=\"" + x + "\" y=\"" + y + "\"/>\n");
                }
            }
        }
        sb.append("    </networkFrames>\n");
        sb.append("    <cytopanels>\n");
        SessionState sessionState = cysession.getSessionState();
        if (sessionState != null) {
            Cytopanels cytopanels = sessionState.getCytopanels();
            if (cytopanels != null) {
                List<Cytopanel> cytopanelsList = cytopanels.getCytopanel();
                for (Cytopanel cytopanel : cytopanelsList) {
                    String id = cytopanel.getId();
                    String state = cytopanel.getPanelState();
                    String selection = cytopanel.getSelectedPanel();
                    sb.append("        <cytopanel id=\"" + id + "\">\n");
                    sb.append("            <panelState>" + state + "</panelState>\n");
                    sb.append("            <selectedPanel>" + selection + "</selectedPanel>\n");
                    sb.append("        </cytopanel>\n");
                }
            }
        }
        sb.append("    </cytopanels>\n");
        sb.append("</sessionState>");
        // Extract it as an app file now:
        ByteArrayInputStream bais = new ByteArrayInputStream(sb.toString().getBytes("UTF-8"));
        extractPluginEntry(bais, cysession.getId() + "/" + PLUGINS_FOLDER + "org.cytoscape.swing-application/session_state.xml");
    }
}

Example 2 with Node

use of org.cytoscape.io.internal.util.session.model.Node in project cytoscape-impl by cytoscape.

the class Cy2SessionReaderImpl method extractNetworksAndViews.

/**
 * @param is
 * @param entryName
 * @param parent
 * @param createView
 * @return The top-level network that was extracted from the XGMML file.
 * @throws Exception
 */
private CyNetwork extractNetworksAndViews(final InputStream is, final String entryName, final CyNetwork parent, final boolean createView) throws Exception {
    CyNetwork topNetwork = null;
    final CyNetworkReader reader = networkReaderMgr.getReader(is, entryName);
    if (parent != null) {
        if (reader instanceof SessionXGMMLNetworkReader) {
            ((SessionXGMMLNetworkReader) reader).setParent(parent);
        } else {
            logger.error("CyNetworkReader should be an instance of XGMMLNetworkReader. " + "Cannot extract network as sub-nertwork of: " + entryName);
        }
    }
    reader.run(taskMonitor);
    final CyNetwork[] netArray = reader.getNetworks();
    if (netArray != null && netArray.length > 0) {
        topNetwork = netArray[0];
        for (int i = 0; i < netArray.length; i++) {
            // Process each CyNetwork
            final CyNetwork net = netArray[i];
            final String netName = net.getRow(net).get(CyNetwork.NAME, String.class);
            networkLookup.put(netName, net);
            // Add parent network attribute to a column in the hidden table,
            // to preserve the network hierarchy info from Cytoscape 2.x
            final CyRow hRow = net.getRow(net, CyNetwork.HIDDEN_ATTRS);
            final CyTable hTbl = hRow.getTable();
            if (parent instanceof CySubNetwork) {
                if (hTbl.getColumn(CY3_PARENT_NETWORK_COLUMN) == null)
                    hTbl.createColumn(CY3_PARENT_NETWORK_COLUMN, Long.class, false);
                hRow.set(CY3_PARENT_NETWORK_COLUMN, parent.getSUID());
            }
            final CyTable tbl = net.getRow(net, CyNetwork.LOCAL_ATTRS).getTable();
            // (e.g. the user imported a Cy3 XGMML that contains this attribute into Cy2)
            if (tbl.getColumn(CY2_PARENT_NETWORK_COLUMN) != null && parent instanceof CySubNetwork == false)
                tbl.deleteColumn(CY2_PARENT_NETWORK_COLUMN);
            // Restore node/edge selection
            List<Node> selNodes = nodeSelectionLookup.get(netName);
            List<Edge> selEdges = edgeSelectionLookup.get(netName);
            if (selNodes != null)
                setBooleanNodeAttr(net, selNodes, SELECTED, DEFAULT_ATTRS);
            if (selEdges != null)
                setBooleanEdgeAttr(net, selEdges, SELECTED, DEFAULT_ATTRS);
            networks.add(net);
            if (!cancelled && i == 0 && createView) {
                // Create a network view for the first network only,
                // which is supposed to be the top-level one
                final CyNetworkView view = reader.buildCyNetworkView(net);
                networkViewLookup.put(netName, view);
                networkViews.add(view);
                cache.cache(netName, view);
            }
        }
    }
    return topNetwork;
}

Example 3 with Node

use of org.cytoscape.io.internal.util.session.model.Node in project cytoscape-impl by cytoscape.

the class Cy2SessionReaderImpl method setBooleanNodeAttr.

private void setBooleanNodeAttr(final CyNetwork net, final List<Node> nodes, final String attrName, final String tableName) {
    if (net != null && nodes != null) {
        // set attr values based on ids
        for (final Node nodeObject : nodes) {
            if (cancelled)
                return;
            String name = nodeObject.getId();
            // The XGMML node "id" is only used internally, by the XGMML parser--the name is the real ID.
            CyNode n = cache.getNodeByName(name);
            if (n != null)
                net.getRow(n, tableName).set(attrName, true);
            else
                logger.error("Cannot restore boolean node attr \"" + name + "\": node not found.");
        }
    }
}

Example 4 with Node

use of org.cytoscape.io.internal.util.session.model.Node in project cytoscape-impl by cytoscape.

the class Cy2SessionReaderImpl method processNetworks.

private void processNetworks() throws Exception {
    if (cysession == null)
        return;
    // Network attributes and visual styles
    if (cysession.getNetworkTree() != null) {
        for (final Network net : cysession.getNetworkTree().getNetwork()) {
            if (cancelled)
                return;
            // so let's ignore a network with that name.
            if (net.getId().equals(NETWORK_ROOT))
                continue;
            final String netName = net.getId();
            final CyNetworkView view = getNetworkView(netName);
            if (view != null) {
                // Populate the visual style map
                String vsName = net.getVisualStyle();
                if (vsName != null)
                    visualStyleMap.put(view, vsName);
                // Convert 2.x hidden state (cysession.xml) to 3.x visual properties
                if (net.getHiddenEdges() != null) {
                    for (final Edge edgeObject : net.getHiddenEdges().getEdge()) {
                        if (cancelled)
                            return;
                        final String name = edgeObject.getId();
                        final CyEdge e = cache.getEdge(name);
                        if (e != null) {
                            final View<CyEdge> ev = view.getEdgeView(e);
                            if (ev != null)
                                ev.setLockedValue(BasicVisualLexicon.EDGE_VISIBLE, false);
                            else
                                logger.error("Cannot restore hidden state of edge \"" + name + "\": Edge view not found.");
                        } else {
                            logger.error("Cannot restore hidden state of edge \"" + name + "\": Edge not found.");
                        }
                    }
                }
                if (net.getHiddenNodes() != null) {
                    for (final Node nodeObject : net.getHiddenNodes().getNode()) {
                        if (cancelled)
                            return;
                        final String name = nodeObject.getId();
                        final CyNode n = cache.getNodeByName(name);
                        if (n != null) {
                            final View<CyNode> nv = view.getNodeView(n);
                            if (nv != null)
                                nv.setLockedValue(BasicVisualLexicon.NODE_VISIBLE, false);
                            else
                                logger.error("Cannot restore hidden state of node \"" + name + "\": Node view not found.");
                        } else {
                            logger.error("Cannot restore hidden state of node \"" + name + "\": Node not found.");
                        }
                    }
                }
            }
        }
    }
    // Network view sizes
    if (cysession.getSessionState() != null) {
        Desktop desktop = cysession.getSessionState().getDesktop();
        if (desktop != null && desktop.getNetworkFrames() != null) {
            List<NetworkFrame> frames = desktop.getNetworkFrames().getNetworkFrame();
            for (final NetworkFrame nf : frames) {
                if (cancelled)
                    return;
                // Set sizes
                final CyNetworkView view = getNetworkView(nf.getFrameID());
                if (view != null) {
                    BigInteger w = nf.getWidth();
                    BigInteger h = nf.getHeight();
                    if (w != null)
                        view.setVisualProperty(BasicVisualLexicon.NETWORK_WIDTH, w.doubleValue());
                    if (h != null)
                        view.setVisualProperty(BasicVisualLexicon.NETWORK_HEIGHT, h.doubleValue());
                }
            }
        }
    }
    if (!networks.isEmpty()) {
        // Select the last network that has a view, since Cy2 files do not contain the network selection info
        final CyNetwork[] array = networks.toArray(new CyNetwork[networks.size()]);
        for (int i = array.length - 1; i >= 0; i--) {
            final CyNetwork net = array[i];
            final CyRow row = net.getRow(net);
            final String netName = row.get(CyNetwork.NAME, String.class);
            final CyNetworkView view = networkViewLookup.get(netName);
            if (view != null) {
                row.set(CyNetwork.SELECTED, true);
                break;
            }
        }
    }
}