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

Example 71 with CySubNetwork

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

the class HandleEdge method handle.

@Override
public ParseState handle(final String tag, final Attributes atts, final ParseState current) throws SAXException {
    // Get the label, id, source and target
    Object id = null;
    String href = atts.getValue(ReadDataManager.XLINK, "href");
    if (href == null) {
        // Create the edge:
        id = getId(atts);
        String label = getLabel(atts);
        Object sourceId = asLongOrString(atts.getValue("source"));
        Object targetId = asLongOrString(atts.getValue("target"));
        String isDirected = atts.getValue("cy:directed");
        String sourceAlias = null;
        String targetAlias = null;
        // no longer users
        String interaction = "";
        if (label != null) {
            // Parse out the interaction (if this is from Cytoscape)
            // parts[0] = source alias
            // parts[1] = interaction
            // parts[2] = target alias
            final String[] parts = SPLIT.split(label);
            if (parts.length == 3) {
                sourceAlias = parts[0];
                interaction = parts[1];
                targetAlias = parts[2];
            }
        }
        final boolean directed;
        if (isDirected == null) {
            // xgmml files made by pre-3.0 cytoscape and strictly
            // upstream-XGMML conforming files
            // won't have directedness flag, in which case use the
            // graph-global directedness setting.
            // 
            // (org.xml.sax.Attributes.getValue() returns null if attribute
            // does not exists)
            // 
            // This is the correct way to read the edge-directionality of
            // non-cytoscape xgmml files as well.
            directed = manager.currentNetworkIsDirected;
        } else {
            // parse directedness flag
            directed = ObjectTypeMap.fromXGMMLBoolean(isDirected);
        }
        CyNode sourceNode = null;
        CyNode targetNode = null;
        if (sourceId != null)
            sourceNode = manager.getCache().getNode(sourceId);
        if (targetId != null)
            targetNode = manager.getCache().getNode(targetId);
        if (sourceNode == null && sourceAlias != null)
            sourceNode = manager.getCache().getNode(sourceAlias);
        if (targetNode == null && targetAlias != null)
            targetNode = manager.getCache().getNode(targetAlias);
        if (label == null || label.isEmpty())
            label = String.format("%s (%s) %s", sourceId, (directed ? "directed" : "undirected"), targetId);
        CyNetwork net = manager.getCurrentNetwork();
        CyEdge edge = null;
        if (sourceNode != null && targetNode != null) {
            // We need to do this because of groups that are exported from
            // Cytoscape 2.x.
            // The problem is that internal edges are duplicated in the
            // document when the group is expanded,
            // but we don't want to create them twice.
            boolean checkDuplicate = manager.getCache().hasNetworkPointers() && manager.getDocumentVersion() > 0.0 && manager.getDocumentVersion() < 3.0;
            edge = checkDuplicate ? manager.getCache().getEdge(id) : null;
            if (edge == null) {
                edge = manager.createEdge(sourceNode, targetNode, id, label, directed, net);
            } else if (net instanceof CySubNetwork && !net.containsEdge(edge)) {
                ((CySubNetwork) net).addEdge(edge);
            }
        } else {
            edge = manager.createEdge(sourceId, targetId, id, label, directed, net);
        }
        if (edge != null) {
            if (!manager.isSessionFormat() || manager.getDocumentVersion() < 3.0) {
                // the root-network only.
                if (!net.containsEdge(edge))
                    net = manager.getRootNetwork();
                if (net != null && net.containsEdge(edge)) {
                    CyRow row = net.getRow(edge);
                    row.set(CyNetwork.NAME, label);
                    row.set(CyEdge.INTERACTION, interaction);
                }
                if (manager.getRootNetwork() != null && !manager.getRootNetwork().equals(net)) {
                    CyRow row = manager.getRootNetwork().getRow(edge);
                    row.set(CyNetwork.NAME, label);
                    row.set(CyEdge.INTERACTION, interaction);
                }
            }
            manager.setCurrentElement(edge);
        } else {
            throw new SAXException("Cannot create edge from XGMML (id=" + id + " label=" + label + " source=" + sourceId + " target=" + targetId + "): source or target node not found");
        }
    } else {
        // The edge might not have been created yet!
        // Save the reference so it can be added to the network after the
        // whole graph is parsed.
        manager.addElementLink(href, CyEdge.class);
    }
    return current;
}

Example 72 with CySubNetwork

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

the class HandleNode method handle.

@Override
public ParseState handle(final String tag, final Attributes atts, final ParseState current) throws SAXException {
    final String href = atts.getValue(ReadDataManager.XLINK, "href");
    Object id = null;
    String label = null;
    CyNode node = null;
    final CyNetwork curNet = manager.getCurrentNetwork();
    final CyNetwork rootNet = manager.getRootNetwork();
    if (href == null) {
        // Create the node
        id = getId(atts);
        label = atts.getValue("label");
        if (label == null)
            // For backwards compatibility
            label = atts.getValue("name");
        node = manager.getCache().getNode(id);
        if (node == null)
            node = manager.createNode(id, label, curNet);
        else if (curNet instanceof CySubNetwork)
            manager.addNode(node, label, (CySubNetwork) curNet);
        if (label != null && (!manager.isSessionFormat() || manager.getDocumentVersion() < 3.0)) {
            if (!manager.isSessionFormat()) {
                if (!curNet.containsNode(node) && curNet instanceof CySubNetwork) {
                    // The node should be node in root network, it does not exist in current subnetwork yet
                    CySubNetwork subnet = (CySubNetwork) curNet;
                    subnet.addNode(node);
                    node = subnet.getNode(node.getSUID());
                }
            }
            curNet.getRow(node).set(CyNetwork.NAME, label);
            if (rootNet != null && curNet != rootNet)
                rootNet.getRow(node).set(CyNetwork.NAME, label);
        }
    } else {
        // Try to get the node from the internal cache
        id = XGMMLParseUtil.getIdFromXLink(href);
        node = manager.getCache().getNode(id);
        if (node != null) {
            if (curNet instanceof CySubNetwork)
                ((CySubNetwork) curNet).addNode(node);
            else
                logger.error("Cannot add existing node \"" + id + "\" to a network which is not a CySubNetwork");
        } else {
            // The node might not have been created yet!
            // So just save the reference so it can be added to the network after the whole graph is parsed.
            manager.addElementLink(href, CyNode.class);
        }
    }
    if (node != null)
        manager.setCurrentElement(node);
    return current;
}

Example 73 with CySubNetwork

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

the class SessionXGMMLNetworkWriterTest method testRegisteredSubNetworkSavedIfSessionSavePolicy.

@Test
public void testRegisteredSubNetworkSavedIfSessionSavePolicy() throws UnsupportedEncodingException {
    CySubNetwork sn = rootNet.addSubNetwork();
    // It doesn't matter
    setRegistered(sn, true);
    write(rootNet);
    assertEquals("1", evalString("/x:graph/x:att/x:graph[@id=" + sn.getSUID() + "]/@cy:registered"));
}

Example 74 with CySubNetwork

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

the class SessionXGMMLNetworkWriterTest method testRegisteredNetworkPointerSavedUnderRootGraph.

@Test
public void testRegisteredNetworkPointerSavedUnderRootGraph() throws UnsupportedEncodingException {
    CySubNetwork sn = rootNet.addSubNetwork();
    setRegistered(sn, true);
    CyNode n = net.getNodeList().get(0);
    n.setNetworkPointer(sn);
    write(rootNet);
    // The subnetwork is saved under the root graph, because it is registered
    assertEquals(0, evalNumber("count(/x:graph/x:att/x:graph[@id=" + n.getSUID() + "])"));
    // The nested node graph (network pointer) is an XLink to that graph
    assertEquals("#" + sn.getSUID(), evalString("//x:node[@id=" + n.getSUID() + "]/x:att/x:graph/@xlink:href"));
}

Example 75 with CySubNetwork

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

the class SessionXGMMLNetworkWriterTest method testSubNetworkIgnoredIfNotSessionSavePolicy.

@Test
public void testSubNetworkIgnoredIfNotSessionSavePolicy() throws UnsupportedEncodingException {
    CySubNetwork sn = rootNet.addSubNetwork(SavePolicy.DO_NOT_SAVE);
    // It doesn't matter
    setRegistered(sn, true);
    write(rootNet);
    assertEquals(2, evalNumber("count(//x:graph)"));
    assertEquals(0, evalNumber("count(//x:graph[@id=" + sn.getSUID() + "])"));
}