private void addLinks(LinkTriple[] links) {
CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
// CyAttributes edgeAttr = Cytoscape.getEdgeAttributes();
Map<CyNode, Boolean> updateList = new HashMap<CyNode, Boolean>();
CyNetwork net = Cytoscape.getCurrentNetwork();
for (LinkTriple link : links) {
CyNode src = Cytoscape.getCyNode(link.subj.toString());
CyNode dst = Cytoscape.getCyNode(link.obj.toString());
if (src == null) {
src = net.addNode(Cytoscape.getCyNode(link.subj.toString(), true));
if (link.subj.getType() != null)
nodeAttr.setAttribute(src.getIdentifier(), "NodeType", link.subj.getType());
}
if (dst == null) {
dst = net.addNode(Cytoscape.getCyNode(link.obj.toString(), true));
if (link.obj.getType() != null)
nodeAttr.setAttribute(dst.getIdentifier(), "NodeType", link.obj.getType());
}
CyEdge edge =
Cytoscape.getCyEdge(
link.subj.toString(), "link", link.obj.toString(), link.pred.toString());
// if ( link.pred != null )
// edgeAttr.setAttribute(edge.getIdentifier(), "EdgeType", link.pred.toString() );
net.addEdge(edge);
updateList.put(src, true);
updateList.put(dst, true);
}
Cytoscape.getCurrentNetworkView()
.applyLayout(new GridNodeLayout(), updateList.keySet().toArray(new CyNode[0]), null);
Cytoscape.getCurrentNetworkView().redrawGraph(true, true);
}
/**
* Write out the state for the given attributes
*
* @param selectedRows
* @return number of files successfully saved, the better way to do this would just be to throw
* the error and display a specific message for each failure, but oh well.
* @throws IOException
*/
public void writeAttributes() throws IOException {
final String className;
final byte dataType =
cyAttributes.getMultiHashMapDefinition().getAttributeValueType(attributeName);
if ((dataType == CyAttributes.TYPE_COMPLEX)
|| (dataType == CyAttributes.TYPE_SIMPLE_MAP)
|| (dataType == CyAttributes.TYPE_UNDEFINED))
throw new IOException("Unsupported Datatype.");
if (dataType == MultiHashMapDefinition.TYPE_BOOLEAN) className = "java.lang.Boolean";
else if (dataType == MultiHashMapDefinition.TYPE_INTEGER) className = "java.lang.Integer";
else if (dataType == MultiHashMapDefinition.TYPE_FLOATING_POINT) className = "java.lang.Double";
else className = "java.lang.String";
try {
fileWriter.write(attributeName + " (class=" + className + ")" + newline);
final MultiHashMap attributeMap = cyAttributes.getMultiHashMap();
if (attributeMap != null) {
final Iterator<String> keys = cyAttributes.getMultiHashMap().getObjectKeys(attributeName);
String key;
Object value;
Iterator objIt;
String vs;
StringBuilder result = new StringBuilder();
while (keys.hasNext()) {
key = keys.next();
if (cyAttributes.getType(attributeName) == CyAttributes.TYPE_SIMPLE_LIST)
value = cyAttributes.getListAttribute(key, attributeName);
else value = cyAttributes.getAttribute(key, attributeName);
key = encodeString(key);
if (value != null) {
if (value instanceof List) {
result.append(key + " = ");
if (((Collection) value).size() > 0) {
Object o;
objIt = ((Collection) value).iterator();
result.append("(");
o = objIt.next();
vs = o.toString();
vs = slashEncodeString(vs);
vs = encodeString(vs);
result.append(vs);
while (objIt.hasNext()) {
o = objIt.next();
vs = o.toString();
vs = slashEncodeString(vs);
vs = encodeString(vs);
result.append("::" + vs);
}
result.append(")" + newline);
fileWriter.write(result.toString());
result = new StringBuilder();
}
} else {
vs = value.toString();
vs = slashEncodeString(vs);
vs = encodeString(vs);
fileWriter.write(key + " = " + vs + newline);
}
}
}
fileWriter.flush();
}
} finally {
if (fileWriter != null) {
fileWriter.close();
}
}
}
@SuppressWarnings("unchecked")
@Override
public void actionPerformed(ActionEvent ae) {
String action = ae.getActionCommand();
LinkTriple[] addNodes = null;
if (action.equals("Fetch")) {
addNodes = iSparql.ExploreURI(urlText.getText());
addLinks(addNodes);
// Cytoscape.getCurrentNetwork().addNode( Cytoscape.getCyNode( urlText.getText(), true ) );
}
if (action.equals("Fetch Selected")) {
CyNetwork network = Cytoscape.getCurrentNetwork();
Set nodeset = network.getSelectedNodes();
java.util.List<LinkTriple> nodeList = new LinkedList<LinkTriple>();
for (Object o : nodeset) {
CyNode node = (CyNode) o;
for (LinkTriple newNode : iSparql.ExploreURI(node.getIdentifier())) {
nodeList.add(newNode);
}
}
if (filterCheckbox.getState())
addLinks(iSparql.NodeFilter(null, nodeList.toArray(new LinkTriple[0])));
else addLinks(nodeList.toArray(new LinkTriple[0]));
}
if (action.equals("Find Nodes")) {
CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
CyNetwork network = Cytoscape.getCurrentNetwork();
Set nodeset = network.getSelectedNodes();
java.util.List<Map<String, Object>> nodeList = new LinkedList<Map<String, Object>>();
for (Object o : nodeset) {
CyNode node = (CyNode) o;
Map<String, Object> map = new HashMap<String, Object>();
String id = node.getIdentifier();
map.put("ID", id);
for (String attr : nodeAttr.getAttributeNames()) {
if (nodeAttr.hasAttribute(id, attr)) {
System.out.println(id + " " + attr + " " + nodeAttr.getType(attr));
if (nodeAttr.getType(attr) == CyAttributes.TYPE_STRING) {
Object iAttr = nodeAttr.getAttribute(id, attr);
map.put(attr, iAttr);
}
}
}
nodeList.add(map);
}
LinkTriple[] links = iSparql.NodeSearch(null, nodeList, "ID");
addLinks(links);
}
if (action.equals("Edit Namespaces")) {
Map<String, String> nameMap = prefs.getNameSpaces();
Map<String, String> newMap = NameSpaceEditor.EditDialog(nameMap);
for (String key : nameMap.keySet()) {
prefs.removeNameSpace(key);
}
for (String key : newMap.keySet()) {
prefs.addNameSpace(key, newMap.get(key));
}
}
}
public gpClique[] creategpClique() {
gpClique[] gps = new gpClique[2];
gps[0] = new gpClique();
gps[1] = new gpClique();
Iterator<Edge> edgeIt = nw.edgesIterator();
CyAttributes edgeAtt = Cytoscape.getEdgeAttributes();
ArrayList largeALNodes = new ArrayList();
ArrayList targetALNodes = new ArrayList();
ArrayList matchALNodes = new ArrayList();
while (edgeIt.hasNext()) {
Edge edge = edgeIt.next();
if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("p2")) {
largeALNodes.add(new Integer(nw.getEdgeSourceIndex(edge.getRootGraphIndex())));
largeALNodes.add(new Integer(nw.getEdgeTargetIndex(edge.getRootGraphIndex())));
continue; // go directly next step
}
if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("p1")) {
targetALNodes.add(new Integer(nw.getEdgeSourceIndex(edge.getRootGraphIndex())));
targetALNodes.add(new Integer(nw.getEdgeTargetIndex(edge.getRootGraphIndex())));
continue;
}
if (edgeAtt.getStringAttribute(edge.getIdentifier(), "interaction").equals("pd")) {
matchALNodes.add(
new Integer(
nw.getEdgeSourceIndex(
edge
.getRootGraphIndex()))); // the matched node(containing "-") of target
// network
matchALNodes.add(
new Integer(
nw.getEdgeTargetIndex(
edge
.getRootGraphIndex()))); // the matched node(containing "-") of large
// network
continue;
}
JOptionPane.showMessageDialog(Cytoscape.getDesktop(), "File Format error!");
return null;
}
Iterator matchALNIt = matchALNodes.iterator();
CyNode node;
Integer it;
while (matchALNIt.hasNext()) {
it = (Integer) matchALNIt.next();
node =
Cytoscape.getCyNode(
nw.getNode(it.intValue()).getIdentifier().substring(1),
true); // get node according to its identifier
matchNodes.add(node);
if (!targetALNodes.contains(
node.getRootGraphIndex())) // matched node,but not a node of network
{
nw.addNode(node);
targetALNodes.add(node.getRootGraphIndex()); // add to network
}
it = (Integer) matchALNIt.next();
node =
Cytoscape.getCyNode(
nw.getNode(it.intValue()).getIdentifier().substring(1),
true); // get node according to its identifier
matchNodes.add(node);
if (!largeALNodes.contains(node.getRootGraphIndex())) {
nw.addNode(node);
largeALNodes.add(node.getRootGraphIndex());
}
}
gps[0].setgpNodes(largeALNodes);
gps[1].setgpNodes(targetALNodes);
return gps;
}
/**
* DOCUMENT ME!
*
* @throws Exception DOCUMENT ME!
*/
public void testReadTable() throws Exception {
InputStream is = null;
POIFSFileSystem excelIn;
try {
is = getClass().getResource(NETWORK_FILE).openStream();
excelIn = new POIFSFileSystem(is);
} finally {
if (is != null) {
is.close();
}
}
HSSFWorkbook wb = new HSSFWorkbook(excelIn);
HSSFSheet sheet = wb.getSheetAt(0);
List<String> delimiters = new ArrayList<String>();
delimiters.add(TextFileDelimiters.TAB.toString());
String[] galAttrName = {
"Source", "Target", "Interaction", "edge bool attr", "edge string attr", "edge float attr"
};
Byte[] galAttrTypes = {
CyAttributes.TYPE_STRING, CyAttributes.TYPE_STRING,
CyAttributes.TYPE_STRING, CyAttributes.TYPE_BOOLEAN,
CyAttributes.TYPE_STRING, CyAttributes.TYPE_FLOATING
};
NetworkTableMappingParameters mapping =
new NetworkTableMappingParameters(
delimiters,
TextFileDelimiters.PIPE.toString(),
galAttrName,
galAttrTypes,
null,
null,
0,
1,
2,
null);
reader = new ExcelNetworkSheetReader(wb.getSheetName(0), sheet, mapping);
CyNetwork net = Cytoscape.createNetwork(reader, false, null);
/*
* test cases
*/
assertEquals("Yeast Network Sheet 1", net.getTitle());
assertEquals(331, net.getNodeCount());
assertEquals(362, net.getEdgeCount());
CyAttributes attr = Cytoscape.getEdgeAttributes();
assertTrue(attr.getBooleanAttribute("YGL122C (pp) YOL123W", "edge bool attr"));
assertFalse(attr.getBooleanAttribute("YKR026C (pp) YGL122C", "edge bool attr"));
assertEquals(1.2344543, attr.getDoubleAttribute("YBL026W (pp) YOR167C", "edge float attr"));
assertEquals("abcd12706", attr.getStringAttribute("YBL026W (pp) YOR167C", "edge string attr"));
assertEquals("abcd12584", attr.getStringAttribute("YPL248C (pd) ?", "edge string attr"));
Cytoscape.destroyNetwork(net);
}
public void testReadTableWithEmptyRows() throws Exception {
String network = "/empty_attr_row.xls";
InputStream is = null;
POIFSFileSystem excelIn;
try {
is = getClass().getResource(network).openStream();
excelIn = new POIFSFileSystem(is);
} finally {
if (is != null) {
is.close();
}
}
HSSFWorkbook wb = new HSSFWorkbook(excelIn);
HSSFSheet sheet = wb.getSheetAt(0);
List<String> delimiters = new ArrayList<String>();
delimiters.add(TextFileDelimiters.TAB.toString());
String[] galAttrName = {"Gene 1", "Gene 2", "Interaction Type", "Gene", "GO Group"};
Byte[] galAttrTypes = {
CyAttributes.TYPE_STRING,
CyAttributes.TYPE_STRING,
CyAttributes.TYPE_STRING,
CyAttributes.TYPE_STRING,
CyAttributes.TYPE_STRING
};
NetworkTableMappingParameters mapping =
new NetworkTableMappingParameters(
delimiters,
TextFileDelimiters.PIPE.toString(),
galAttrName,
galAttrTypes,
null,
null,
0,
1,
2,
null);
CyNetwork net = null;
try {
reader = new ExcelNetworkSheetReader(wb.getSheetName(0), sheet, mapping, 1);
net = Cytoscape.createNetwork(reader, false, null);
} catch (Exception ee) {
ee.printStackTrace();
fail("Caught exception");
}
assertEquals(222, net.getNodeCount());
assertEquals(443, net.getEdgeCount());
CyAttributes attr = Cytoscape.getEdgeAttributes();
// test some random edges
assertEquals("cc", attr.getStringAttribute("YDR459C (cc) YNL271C", "interaction"));
assertEquals("Transport", attr.getStringAttribute("YDR459C (cc) YNL271C", "GO Group"));
assertEquals("YPR011C", attr.getStringAttribute("YDR459C (cc) YNL271C", "Gene"));
assertNull(attr.getStringAttribute("YEL040W (cc) YER016W", "GO Group"));
assertNull(attr.getStringAttribute("YEL040W (cc) YER016W", "Gene"));
Cytoscape.destroyNetwork(net);
}
