/**
* 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 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;
}
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);
}