Author: pwang
Date: 2011-01-20 16:40:24 -0800 (Thu, 20 Jan 2011)
New Revision: 23532
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/NetworkTableReader.java
Log:
Clean up
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/NetworkTableReader.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/NetworkTableReader.java
2011-01-21 00:39:25 UTC (rev 23531)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/NetworkTableReader.java
2011-01-21 00:40:24 UTC (rev 23532)
@@ -77,7 +77,7 @@
protected final int startLineNumber;
protected final String commentChar;
- private CyNetwork network;
+ protected CyNetwork network;
private static final Logger logger =
LoggerFactory.getLogger(NetworkTableReader.class);
@@ -128,8 +128,7 @@
InputStream is = null;
String line;
- network.getCyRow().set("name",
CytoscapeServices.cyNetworkNaming.getSuggestedNetworkTitle(sourceURL.toString()));
-
+ network.getCyRow().set("name", this.getNetworkName());
parser.setNetwork(network);
try {
@@ -146,7 +145,7 @@
while ((line = bufRd.readLine()) != null) {
/*
- * Ignore Empty & Commnet lines.
+ * Ignore Empty & Comment lines.
*/
if ((commentChar != null) &&
(commentChar.trim().length() != 0)
&&
line.startsWith(commentChar)) {
@@ -176,41 +175,10 @@
}
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- //@Override
- public Long[] getNodeIndicesArray() {
- final Long[] nodeArray = new Long[nodeList.size()];
- for (int i = 0; i < nodeArray.length; i++) {
- nodeArray[i] = nodeList.get(i);
- }
-
- return nodeArray;
- }
-
/**
* DOCUMENT ME!
*
- * @return DOCUMENT ME!
- */
- //@Override
- public Long[] getEdgeIndicesArray() {
- final Long[] edgeArray = new Long[edgeList.size()];
-
- for (int i = 0; i < edgeArray.length; i++) {
- edgeArray[i] = edgeList.get(i);
- }
-
- return edgeArray;
- }
-
- /**
- * DOCUMENT ME!
- *
* @throws IOException DOCUMENT ME!
*/
//@Override
@@ -226,17 +194,11 @@
*/
public String getReport() {
- return null;
- /*
final StringBuffer sb = new StringBuffer();
- final Set<Integer> uniqueNodes = new TreeSet<Integer>(nodeList);
- final Set<Integer> uniqueEdges = new TreeSet<Integer>(edgeList);
+ sb.append(network.getNodeCount() + " nodes and " +
network.getEdgeCount() + " edges are loaded.\n");
+ sb.append("New network name is " + super.getNetworkName() +
"\n\n");
- sb.append(uniqueNodes.size() + " nodes and " +
uniqueEdges.size() + " edges are loaded.\n");
- //sb.append("New network name is " + super.getNetworkName() +
"\n\n");
-
- return sb.toString();
- */
+ return sb.toString();
}
public void setNetwork(CyNetwork network){
--
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