Author: pwang
Date: 2010-08-17 17:16:48 -0700 (Tue, 17 Aug 2010)
New Revision: 21432
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetwotkViewProducer.java
Removed:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/InteractionsReader.java
Log:
Renamed
Deleted:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/InteractionsReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/InteractionsReader.java
2010-08-18 00:15:10 UTC (rev 21431)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/InteractionsReader.java
2010-08-18 00:16:48 UTC (rev 21432)
@@ -1,160 +0,0 @@
-/*
- File: InteractionsReader.java
-
- Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
- */
-
-package org.cytoscape.io.internal.read.sif;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import org.cytoscape.io.internal.util.ReadUtils;
-import org.cytoscape.io.internal.read.AbstractNetworkReader;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.view.model.CyNetworkView;
-
-/**
- * Reader for graphs in the interactions file format. Given the filename,
- * provides the graph and attributes objects constructed from the file.
- */
-public class InteractionsReader extends AbstractNetworkReader {
-
- private static final String DEF_DELIMITER = " ";
- private static final String LINE_SEP =
System.getProperty("line.separator");
-
- private static final String INTERACTION = "interaction";
-
- private ReadUtils readUtil;
-
- private Set<Interaction> interactions;
-
- public InteractionsReader(ReadUtils readUtil) {
- super();
- this.interactions = new HashSet<Interaction>();
- this.readUtil = readUtil;
- }
-
- public Map<Class<?>, Object> read() throws IOException {
- refresh();
-
- String delimiter = DEF_DELIMITER;
-
- final String rawText = readUtil.getInputString(inputStream);
-
- if (rawText.indexOf("\t") >= 0)
- delimiter = "\t";
-
- final String[] lines = rawText.split(LINE_SEP);
-
- final int size = lines.length;
- for (int i = 0; i < size; i++) {
- if (lines[i].length() <= 0)
- continue;
- interactions.add(new Interaction(lines[i], delimiter));
- }
-
- if (inputStream != null) {
- inputStream.close();
- inputStream = null;
- }
-
- createNetwork();
-
- return readObjects;
- }
-
- private void refresh() {
- readObjects.clear();
- interactions.clear();
- interactions = new HashSet<Interaction>();
- readObjects = new HashMap<Class<?>, Object>();
- }
-
- private void createNetwork() {
-
- final CyNetwork network = cyNetworkFactory.getInstance();
-
- Map<String, CyNode> nodeMap = new HashMap<String, CyNode>();
-
- // put all node names in the Set
- for (Interaction interaction : interactions) {
- nodeMap.put(interaction.getSource(), null);
- for (String target : interaction.getTargets())
- nodeMap.put(target, null);
- }
-
- CyNode node;
- for (String nodeName : nodeMap.keySet()) {
- node = network.addNode();
- node.attrs().set(NODE_NAME_ATTR_LABEL, nodeName);
- nodeMap.put(nodeName, node);
- }
-
- // Now loop over the interactions again, this time creating
edges
- // between
- // all sources and each of their respective targets.
- String srcName;
- String interactionType;
- CyEdge edge;
-
- for (Interaction interaction : interactions) {
-
- srcName = interaction.getSource();
- interactionType = interaction.getType();
-
- for (String tgtName : interaction.getTargets()) {
- edge = network.addEdge(nodeMap.get(srcName),
nodeMap
- .get(tgtName), true);
- edge.attrs().set(NODE_NAME_ATTR_LABEL,
- srcName + " (" +
interactionType + ") " + tgtName);
- edge.attrs().set(INTERACTION, interactionType);
- }
- }
-
- readObjects.put(CyNetwork.class, network);
-
- final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(network);
- layouts.getDefaultLayout().doLayout(view);
- readObjects.put(CyNetworkView.class, view);
-
- nodeMap.clear();
- nodeMap = null;
- }
-}
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetwotkViewProducer.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetwotkViewProducer.java
(rev 0)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetwotkViewProducer.java
2010-08-18 00:16:48 UTC (rev 21432)
@@ -0,0 +1,185 @@
+/*
+ File: InteractionsReader.java
+
+ Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+
+package org.cytoscape.io.internal.read.sif;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import org.cytoscape.io.internal.util.ReadUtils;
+import org.cytoscape.io.internal.read.AbstractNetworkViewProducer;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.work.TaskMonitor;
+
+/**
+ * Reader for graphs in the interactions file format. Given the filename,
+ * provides the graph and attributes objects constructed from the file.
+ */
+public class SIFNetwotkViewProducer extends AbstractNetworkViewProducer {
+
+ private static final String DEF_DELIMITER = " ";
+ private static final String LINE_SEP =
System.getProperty("line.separator");
+ private static final String INTERACTION = "interaction";
+ private ReadUtils readUtil;
+ private Set<Interaction> interactions;
+
+ public SIFNetwotkViewProducer(ReadUtils readUtil) {
+ super();
+ this.interactions = new HashSet<Interaction>();
+ this.readUtil = readUtil;
+ }
+
+ public void run(TaskMonitor tm) throws IOException {
+ refresh();
+
+ String delimiter = DEF_DELIMITER;
+
+ final String rawText = readUtil.getInputString(inputStream);
+
+ if (rawText.indexOf("\t") >= 0)
+ delimiter = "\t";
+
+ final String[] lines = rawText.split(LINE_SEP);
+
+ final int size = lines.length;
+ for (int i = 0; i < size; i++) {
+ if (lines[i].length() <= 0)
+ continue;
+ interactions.add(new Interaction(lines[i], delimiter));
+ }
+
+ if (inputStream != null) {
+ inputStream.close();
+ inputStream = null;
+ }
+
+ createNetwork(tm);
+
+ }
+
+
+ private void refresh() {
+ interactions.clear();
+ interactions = new HashSet<Interaction>();
+ this.cyNetworkViews = null;
+ }
+
+ private void createNetwork(TaskMonitor tm) {
+
+ double progress = 0.01;
+
+ final CyNetwork network = cyNetworkFactory.getInstance();
+
+ Map<String, CyNode> nodeMap = new HashMap<String, CyNode>();
+
+ // put all node names in the Set
+ for (Interaction interaction : interactions) {
+ nodeMap.put(interaction.getSource(), null);
+ for (String target : interaction.getTargets())
+ nodeMap.put(target, null);
+ }
+
+ tm.setProgress(0.05);
+
+ int nodeCount = nodeMap.size();
+
+ CyNode node;
+ for (String nodeName : nodeMap.keySet()) {
+ if (this.cancel){
+ return;
+ }
+
+ //progress = (??)/nodeCount;
+ tm.setProgress(progress);
+
+ node = network.addNode();
+ node.attrs().set(NODE_NAME_ATTR_LABEL, nodeName);
+ nodeMap.put(nodeName, node);
+ }
+
+ tm.setProgress(0.20);
+
+ // Now loop over the interactions again, this time creating
edges
+ // between
+ // all sources and each of their respective targets.
+ String srcName;
+ String interactionType;
+ CyEdge edge;
+
+ int edgeCount = interactions.size();
+
+ for (Interaction interaction : interactions) {
+
+ if (this.cancel){
+ return;
+ }
+ //progress = (??)/edgeCount;
+ tm.setProgress(progress);
+
+ srcName = interaction.getSource();
+ interactionType = interaction.getType();
+
+ for (String tgtName : interaction.getTargets()) {
+ edge = network.addEdge(nodeMap.get(srcName),
nodeMap
+ .get(tgtName), true);
+ edge.attrs().set(NODE_NAME_ATTR_LABEL,
+ srcName + " (" +
interactionType + ") " + tgtName);
+ edge.attrs().set(INTERACTION, interactionType);
+ }
+ }
+
+ tm.setProgress(0.90);
+
+ final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(network);
+ layouts.getDefaultLayout().doLayout(view);
+
+ this.cyNetworkViews[0] = view;
+
+ tm.setProgress(0.99);
+
+ nodeMap.clear();
+ nodeMap = null;
+
+ }
+
+}
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