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Example 1 with Cytopanels

use of org.cytoscape.io.internal.util.session.model.Cytopanels 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");
    }
}
Also used : SessionState(org.cytoscape.io.internal.util.session.model.SessionState) CyNode(org.cytoscape.model.CyNode) Node(org.cytoscape.io.internal.util.session.model.Node) NetworkFrames(org.cytoscape.io.internal.util.session.model.NetworkFrames) ByteArrayInputStream(java.io.ByteArrayInputStream) Cytopanels(org.cytoscape.io.internal.util.session.model.Cytopanels) CyNetwork(org.cytoscape.model.CyNetwork) CySubNetwork(org.cytoscape.model.subnetwork.CySubNetwork) Network(org.cytoscape.io.internal.util.session.model.Network) CyPropertyReader(org.cytoscape.io.read.CyPropertyReader) Edge(org.cytoscape.io.internal.util.session.model.Edge) CyEdge(org.cytoscape.model.CyEdge) NetworkFrame(org.cytoscape.io.internal.util.session.model.NetworkFrame) Cytopanel(org.cytoscape.io.internal.util.session.model.Cytopanel)

Aggregations

ByteArrayInputStream (java.io.ByteArrayInputStream)1 Cytopanel (org.cytoscape.io.internal.util.session.model.Cytopanel)1 Cytopanels (org.cytoscape.io.internal.util.session.model.Cytopanels)1 Edge (org.cytoscape.io.internal.util.session.model.Edge)1 Network (org.cytoscape.io.internal.util.session.model.Network)1 NetworkFrame (org.cytoscape.io.internal.util.session.model.NetworkFrame)1 NetworkFrames (org.cytoscape.io.internal.util.session.model.NetworkFrames)1 Node (org.cytoscape.io.internal.util.session.model.Node)1 SessionState (org.cytoscape.io.internal.util.session.model.SessionState)1 CyPropertyReader (org.cytoscape.io.read.CyPropertyReader)1 CyEdge (org.cytoscape.model.CyEdge)1 CyNetwork (org.cytoscape.model.CyNetwork)1 CyNode (org.cytoscape.model.CyNode)1 CySubNetwork (org.cytoscape.model.subnetwork.CySubNetwork)1