Author: pwang
Date: 2010-08-17 17:17:32 -0700 (Tue, 17 Aug 2010)
New Revision: 21433
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/ssf/SSFReader.javax
Log:
Not needed
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/ssf/SSFReader.javax
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/ssf/SSFReader.javax
(rev 0)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/ssf/SSFReader.javax
2010-08-18 00:17:32 UTC (rev 21433)
@@ -0,0 +1,58 @@
+package org.cytoscape.io.internal.read.ssf;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.cytoscape.io.internal.read.AbstractNetworkReader;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.subnetwork.CyRootNetwork;
+import org.cytoscape.model.subnetwork.CyRootNetworkFactory;
+
+public class SSFReader extends AbstractNetworkReader {
+
+
+
+ private final SSFParser parser;
+
+ private final CyRootNetworkFactory rnFactory;
+
+ public SSFReader(CyRootNetworkFactory rnFactory) {
+ super();
+ this.rnFactory = rnFactory;
+ parser = new SSFParser();
+ }
+
+ public void read() throws IOException {
+ Map<Class<?>, Object> result = new HashMap<Class<?>, Object>();
+
+ // Create buffered reader from given InputStream
+ final BufferedReader in = new BufferedReader(new
InputStreamReader(
+ inputStream));
+
+ final CyNetwork network = cyNetworkFactory.getInstance();
+ final CyRootNetwork rootNet = rnFactory.convert(network);
+
+ String line = null;
+ try {
+
+ while ((line = in.readLine()) != null) {
+ parser.parse(rootNet, line);
+ }
+
+ } finally {
+ try {
+ in.close();
+ } catch (IOException e) {
+ throw e;
+ }
+ }
+
+ result.put(CyRootNetwork.class, rootNet);
+ parser.flush();
+
+ }
+
+}
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