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

Example 1 with Cytopanel

use of org.cytoscape.io.internal.util.session.model.Cytopanel 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");
    }
}