Author: mes
Date: 2010-08-20 14:43:30 -0700 (Fri, 20 Aug 2010)
New Revision: 21504
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducer.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducerFactory.java
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/InteractionTest.java
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducerTest.java
core3/io-impl/trunk/src/test/resources/testData/sif/
core3/io-impl/trunk/src/test/resources/testData/sif/degenerate.sif
core3/io-impl/trunk/src/test/resources/testData/sif/multiWordProteins.sif
core3/io-impl/trunk/src/test/resources/testData/sif/multiWordProteinsFileTrailingSpaces.sif
core3/io-impl/trunk/src/test/resources/testData/sif/sample.sif
Removed:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerFactoryImpl.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetwotkViewProducer.java
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/BeanIntegrationTest.java
core3/io-impl/trunk/src/test/java/org/cytoscape/io/read/
Modified:
core3/io-impl/trunk/pom.xml
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewProducer.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerManagerImpl.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/Interaction.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewProducer.java
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
Log:
fixed things to work propertly with new api
Modified: core3/io-impl/trunk/pom.xml
===================================================================
--- core3/io-impl/trunk/pom.xml 2010-08-20 21:41:59 UTC (rev 21503)
+++ core3/io-impl/trunk/pom.xml 2010-08-20 21:43:30 UTC (rev 21504)
@@ -218,13 +218,29 @@
<artifactId>work-api</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
-
<dependency>
<groupId>org.cytoscape</groupId>
+ <artifactId>core-task-api</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
<artifactId>session-api</artifactId>
<version>1.0-SNAPSHOT</version>
<scope>provided</scope>
</dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>test-support</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>1.8.1</version>
+ <scope>test</scope>
+ </dependency>
</dependencies>
</project>
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewProducer.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewProducer.java
2010-08-20 21:41:59 UTC (rev 21503)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/AbstractNetworkViewProducer.java
2010-08-20 21:43:30 UTC (rev 21504)
@@ -5,63 +5,40 @@
import org.cytoscape.io.read.CyNetworkViewProducer;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.vizmap.VisualStyle;
-import org.cytoscape.view.layout.CyLayouts;
-import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.view.vizmap.VisualStyle;
+import org.cytoscape.task.AbstractTask;
-public abstract class AbstractNetworkViewProducer implements
CyNetworkViewProducer{
+public abstract class AbstractNetworkViewProducer extends AbstractTask
+ implements CyNetworkViewProducer {
- protected static final String NODE_NAME_ATTR_LABEL = "name";
protected CyNetworkView[] cyNetworkViews;
protected VisualStyle[] visualstyles;
- protected boolean cancel = false;
protected InputStream inputStream;
- protected CyNetworkFactory cyNetworkFactory;
- protected CyNetworkViewFactory cyNetworkViewFactory;
- protected CyLayouts layouts;
+ protected final CyNetworkViewFactory cyNetworkViewFactory;
+ protected final CyNetworkFactory cyNetworkFactory;
- public CyNetworkView[] getNetworkViews() {
- return cyNetworkViews;
- }
+ // TODO this should come from model-api
+ public static final String NODE_NAME_ATTR_LABEL = "name";
- public VisualStyle[] getVisualStyles() {
- return visualstyles;
- }
-
- public void setInputStream(InputStream is) {
- if (is == null)
+ public AbstractNetworkViewProducer(InputStream inputStream,
+ CyNetworkViewFactory
cyNetworkViewFactory,
+ CyNetworkFactory cyNetworkFactory) {
+ if (inputStream == null)
throw new NullPointerException("Input stream is null");
- inputStream = is;
- cancel = false;
- }
-
- public void setCyNetworkFactory(CyNetworkFactory cyNetworkFactory) {
+ this.inputStream = inputStream;
+ this.cyNetworkViewFactory = cyNetworkViewFactory;
this.cyNetworkFactory = cyNetworkFactory;
}
- public void setCyNetworkViewFactory(CyNetworkViewFactory
cyNetworkViewFactory) {
- this.cyNetworkViewFactory = cyNetworkViewFactory;
+ public CyNetworkView[] getNetworkViews() {
+ return cyNetworkViews;
}
- public void setLayouts(CyLayouts layouts) {
- this.layouts = layouts;
+ public VisualStyle[] getVisualStyles() {
+ return visualstyles;
}
-
- public void cancel()
- {
- if (cancel)
- throw new
IllegalStateException("AbstractNetworkViewProducer has already been cancelled");
-
- cancel = true;
- try
- {
- inputStream.close();
- }
- catch (IOException e) {}
- inputStream = null;
- }
-
}
Deleted:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerFactoryImpl.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerFactoryImpl.java
2010-08-20 21:41:59 UTC (rev 21503)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerFactoryImpl.java
2010-08-20 21:43:30 UTC (rev 21504)
@@ -1,71 +0,0 @@
-package org.cytoscape.io.internal.read;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.Proxy;
-import java.net.URI;
-
-import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.read.CyNetworkViewProducer;
-import org.cytoscape.io.read.CyNetworkViewProducerFactory;
-import org.cytoscape.io.util.StreamUtil;
-
-public class CyNetworkViewProducerFactoryImpl implements
CyNetworkViewProducerFactory {
-
- private CyFileFilter filter;
- private CyNetworkViewProducer producer;
- private StreamUtil streamUtil;
- private InputStream is;
-
- // This should be an OSGi service.
- private Proxy proxy;
-
- public CyNetworkViewProducerFactoryImpl(CyFileFilter filter,
CyNetworkViewProducer producer, StreamUtil streamUtil)
- throws IllegalArgumentException {
- this.filter = filter;
- this.producer = producer;
-
- if (this.producer == null) {
- throw new IllegalArgumentException("Reader cannot be
null.");
- } else if (this.producer == null) {
- throw new IllegalArgumentException("CyFileFilter cannot
be null.");
- }
- this.streamUtil = streamUtil;
- }
-
- public void setProxy(Proxy proxy) {
- this.proxy = proxy;
- }
-
- public CyNetworkViewProducer getTask(){
- ///?????
- return null;
- }
- public void setInputStream(InputStream is) {
- //????
- this.is = is;
- }
-
-
- /**
- * Gets Graph Reader.
- *
- * @param fileName
- * File name.
- * @return GraphReader Object.
- * @throws IOException
- */
- public CyNetworkViewProducer getNetworkViewProducer(URI uri) throws
IOException {
- InputStream is = streamUtil.getInputStream(uri.toURL());
- return getNetworkViewProducer(is);
- }
-
- public CyNetworkViewProducer getNetworkViewProducer(InputStream stream)
throws IOException {
- producer.setInputStream(stream);
- return producer;
- }
-
- public CyFileFilter getCyFileFilter() {
- return filter;
- }
-}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerManagerImpl.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerManagerImpl.java
2010-08-20 21:41:59 UTC (rev 21503)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/CyNetworkViewProducerManagerImpl.java
2010-08-20 21:43:30 UTC (rev 21504)
@@ -13,36 +13,17 @@
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.DataCategory;
+import org.slf4j.LoggerFactory;
+import org.slf4j.Logger;
+
public class CyNetworkViewProducerManagerImpl implements
CyNetworkViewProducerManager{
- private DataCategory category = DataCategory.NETWORK;
-
- /*
- * Not generic because Spring does not support it now.
- */
- @SuppressWarnings("unchecked")
- public void addInputStreamFactory(CyNetworkViewProducerFactory factory,
Map props){
-
- }
+ private final DataCategory category = DataCategory.NETWORK;
+ private final Set<CyNetworkViewProducerFactory> factories =
+ new HashSet<CyNetworkViewProducerFactory>();
+ private final Logger logger =
LoggerFactory.getLogger(CyNetworkViewProducerManagerImpl.class);
- @SuppressWarnings("unchecked")
- public void removeInputStreamFactory(CyNetworkViewProducerFactory
factory, Map props){
-
- }
-
-
- //////////////////
-
- private Set<CyNetworkViewProducerFactory> factories;
-
/**
- * Constructor.
- */
- public CyNetworkViewProducerManagerImpl() {
- factories = new HashSet<CyNetworkViewProducerFactory>();
- }
-
- /**
* Listener for OSGi service
*
* @param factory
@@ -71,79 +52,50 @@
* File name or null if no reader is capable of reading the
file.
* @return GraphReader capable of reading the specified file.
*/
- public CyNetworkViewProducer getProducer(URI fileLocation)
- throws IllegalArgumentException {
- return getProducer(fileLocation, null);
- }
-
- public CyNetworkViewProducer getProducer(InputStream stream)
- throws IllegalArgumentException {
- return getProducer(null, stream);
- }
-
- private CyNetworkViewProducer getProducer(URI uri, InputStream stream) {
-
- CyFileFilter cff;
- CyNetworkViewProducer networkViewProducer = null;
-
-
+ public CyNetworkViewProducer getProducer(URI uri) {
for (CyNetworkViewProducerFactory factory : factories) {
- System.out.println("Checking factory #################
" + factory.getCyFileFilter().getDescription());
-
-
- cff = factory.getCyFileFilter();
+ CyFileFilter cff = factory.getCyFileFilter();
if (uri != null) {
boolean accept = false;
- try
- {
+ try {
accept = cff.accept(uri, category);
+ } catch (IOException e) {
+ logger.warn("Failed to check file's
contents: " + uri.toString(), e);
}
- catch (IOException e)
- {
- throw new
IllegalArgumentException("Failed to check file's contents: " + uri.toString(),
e);
- }
- if (accept)
- {
- try
- {
- networkViewProducer =
factory.getNetworkViewProducer(uri);
+
+ if (accept) {
+ try {
+ factory.setInputStream(
uri.toURL().openStream() );
+ return factory.getTask();
+ } catch (IOException e) {
+ logger.error("Could not get
proper reader for the file: " + uri.toString(), e);
}
- catch (IOException e)
- {
- throw new
IllegalArgumentException("Could not get proper reader for the file.", e);
- }
}
- } else {
- System.out.println("################# " +
cff.getClass());
- //if (cff.accept(stream, category))
- try
- {
- networkViewProducer =
factory.getNetworkViewProducer(stream);
- }
- catch (IOException e)
- {
- throw new
IllegalArgumentException("Could not get proper reader for the file.", e);
- }
}
}
- if (networkViewProducer == null) {
- throw new IllegalArgumentException("File type is not
supported.");
- }
-
- System.out.println("### Producer found: " +
networkViewProducer);
- return networkViewProducer;
+ return null;
}
-
-
-
-
-
-
-
-
+ public CyNetworkViewProducer getProducer(InputStream stream) {
+
+ for (CyNetworkViewProducerFactory factory : factories) {
+
+ CyFileFilter cff = factory.getCyFileFilter();
+
+ try {
+ if (cff.accept(stream, category)) {
+ factory.setInputStream(stream);
+ return factory.getTask();
+ }
+ } catch (IOException e) {
+ logger.warn("Failed to check streams's
contents: ", e);
+ }
+ }
+
+ return null;
+ }
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/Interaction.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/Interaction.java
2010-08-20 21:41:59 UTC (rev 21503)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/Interaction.java
2010-08-20 21:43:30 UTC (rev 21504)
@@ -43,7 +43,7 @@
/**
* Utility class for representing one line of SIF file.
*/
-public class Interaction {
+class Interaction {
private String source;
private List<String> targets = new ArrayList<String>();
@@ -57,7 +57,7 @@
* @param delimiter
* DOCUMENT ME!
*/
- public Interaction(final String rawText, final String delimiter) {
+ Interaction(final String rawText, final String delimiter) {
final StringTokenizer strtok = new StringTokenizer(rawText,
delimiter);
int counter = 0;
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducer.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducer.java
(rev 0)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducer.java
2010-08-20 21:43:30 UTC (rev 21504)
@@ -0,0 +1,179 @@
+/*
+ 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.io.InputStream;
+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.model.CyNetworkFactory;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.view.layout.CyLayouts;
+
+/**
+ * Reader for graphs in the interactions file format. Given the filename,
+ * provides the graph and attributes objects constructed from the file.
+ */
+public class SIFNetworkViewProducer 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 final Set<Interaction> interactions = new
HashSet<Interaction>();
+ private final ReadUtils readUtil;
+ private final CyLayouts layouts;
+
+ public SIFNetworkViewProducer(InputStream is, ReadUtils readUtil,
CyLayouts layouts, CyNetworkViewFactory cyNetworkViewFactory, CyNetworkFactory
cyNetworkFactory) {
+ super(is,cyNetworkViewFactory, cyNetworkFactory);
+ this.readUtil = readUtil;
+ this.layouts = layouts;
+ }
+
+ public void run(TaskMonitor tm) throws IOException {
+ try {
+ readInput(tm);
+ createNetwork(tm);
+ } finally {
+ if (inputStream != null) {
+ inputStream.close();
+ inputStream = null;
+ }
+ }
+ }
+
+ private void readInput(TaskMonitor tm) throws IOException {
+ tm.setProgress(0.00);
+ String delimiter = DEF_DELIMITER;
+
+ final String rawText = readUtil.getInputString(inputStream);
+
+ tm.setProgress(0.10);
+ if (rawText.indexOf("\t") >= 0)
+ delimiter = "\t";
+
+ final String[] lines = rawText.split(LINE_SEP);
+
+ tm.setProgress(0.15);
+ 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));
+ }
+ tm.setProgress(0.20);
+ }
+
+ private void createNetwork(TaskMonitor tm) {
+
+ 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(0.25);
+
+ for (String nodeName : nodeMap.keySet()) {
+ if (cancelTask){
+ return;
+ }
+
+ //tm.setProgress(progress);
+
+ CyNode node = network.addNode();
+ node.attrs().set(NODE_NAME_ATTR_LABEL, nodeName);
+ nodeMap.put(nodeName, node);
+ }
+
+ tm.setProgress(0.65);
+
+ // 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) {
+
+ if (cancelTask){
+ return;
+ }
+
+ //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);
+
+ // SIF always creates only one network.
+ this.cyNetworkViews = new CyNetworkView[] { view };
+
+ nodeMap.clear();
+ nodeMap = null;
+
+ tm.setProgress(1.0);
+ }
+}
Added:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducerFactory.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducerFactory.java
(rev 0)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducerFactory.java
2010-08-20 21:43:30 UTC (rev 21504)
@@ -0,0 +1,91 @@
+/*
+ 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.io.InputStream;
+
+import org.cytoscape.io.internal.util.ReadUtils;
+import org.cytoscape.io.read.CyNetworkViewProducer;
+import org.cytoscape.io.read.CyNetworkViewProducerFactory;
+import org.cytoscape.io.CyFileFilter;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.layout.CyLayouts;
+
+/**
+ */
+public class SIFNetworkViewProducerFactory implements
CyNetworkViewProducerFactory {
+
+ private final ReadUtils readUtil;
+ private final CyFileFilter filter;
+ private final CyLayouts layouts;
+ private final CyNetworkViewFactory cyNetworkViewFactory;
+ private final CyNetworkFactory cyNetworkFactory;
+
+ private InputStream inputStream;
+
+ public SIFNetworkViewProducerFactory(ReadUtils readUtil,
+ CyFileFilter filter,
+ CyLayouts layouts,
+ CyNetworkViewFactory
cyNetworkViewFactory,
+ CyNetworkFactory cyNetworkFactory)
{
+ this.readUtil = readUtil;
+ this.filter = filter;
+ this.layouts = layouts;
+ this.cyNetworkViewFactory = cyNetworkViewFactory;
+ this.cyNetworkFactory = cyNetworkFactory;
+ }
+
+ public void setInputStream(InputStream is) {
+ if ( is == null )
+ throw new NullPointerException("Input stream is null");
+ inputStream = is;
+ }
+
+ public CyNetworkViewProducer getTask() {
+ return new SIFNetworkViewProducer(inputStream, readUtil,
layouts,
+ cyNetworkViewFactory,
cyNetworkFactory);
+ }
+
+ public CyFileFilter getCyFileFilter() {
+ return filter;
+ }
+}
Deleted:
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
2010-08-20 21:41:59 UTC (rev 21503)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetwotkViewProducer.java
2010-08-20 21:43:30 UTC (rev 21504)
@@ -1,182 +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.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);
-
- 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;
-
- 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);
-
- // SIF always creates only one network.
- this.cyNetworkViews = new CyNetworkView[1];
- this.cyNetworkViews[0] = view;
-
- tm.setProgress(0.99);
-
- nodeMap.clear();
- nodeMap = null;
-
- }
-
-}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewProducer.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewProducer.java
2010-08-20 21:41:59 UTC (rev 21503)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/XGMMLNetworkViewProducer.java
2010-08-20 21:43:30 UTC (rev 21504)
@@ -90,7 +90,7 @@
* Constructor.
*/
public XGMMLNetworkViewProducer() {
- super();
+ super(null,null,null);
}
public void run(TaskMonitor tm) throws IOException {
Modified:
core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
--- core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2010-08-20 21:41:59 UTC (rev 21503)
+++ core3/io-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2010-08-20 21:43:30 UTC (rev 21504)
@@ -25,14 +25,6 @@
</bean>
-->
- <bean id="sifNetworkViewProducerFactory"
class="org.cytoscape.io.internal.read.CyNetworkViewProducerFactoryImpl">
- <constructor-arg ref="sifFilter" />
- <constructor-arg ref="sifNetworkViewProducer" />
- <constructor-arg type="org.cytoscape.io.util.StreamUtil">
- <ref bean="streamUtil"/>
- </constructor-arg>
- </bean>
-
<bean id="xgmmlNetworkViewProducerFactory"
class="org.cytoscape.io.internal.read.CyNetworkViewProducerFactoryImpl">
<constructor-arg ref="xgmmlFilter" />
<constructor-arg ref="xgmmlReader" />
@@ -104,11 +96,12 @@
</bean>
<!-- Network Readers -->
- <bean id="sifNetworkViewProducer"
class="org.cytoscape.io.internal.read.sif.SIFNetwotkViewProducer">
+ <bean id="sifNetworkViewProducerFactory"
class="org.cytoscape.io.internal.read.sif.SIFNetwotkViewProducerFactory">
<constructor-arg ref="readUtil" />
- <property name="cyNetworkFactory"
ref="cyNetworkFactoryServiceRef" />
- <property name="cyNetworkViewFactory"
ref="cyNetworkViewFactoryServiceRef" />
- <property name="layouts" ref="cyLayoutsServiceRef" />
+ <constructor-arg ref="sifFilter" />
+ <constructor-arg ref="cyLayoutsServiceRef" />
+ <constructor-arg ref="cyNetworkViewFactoryServiceRef" />
+ <constructor-arg ref="cyNetworkFactoryServiceRef" />
</bean>
Deleted:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/BeanIntegrationTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/BeanIntegrationTest.java
2010-08-20 21:41:59 UTC (rev 21503)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/BeanIntegrationTest.java
2010-08-20 21:43:30 UTC (rev 21504)
@@ -1,112 +0,0 @@
-package org.cytoscape.io.internal;
-
-import static org.easymock.EasyMock.*;
-import static org.junit.Assert.assertEquals;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.URI;
-import java.net.URL;
-
-import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.io.DataCategory;
-//import org.cytoscape.io.read.CyReader;
-//import org.cytoscape.io.read.CyReaderFactory;
-//import org.cytoscape.io.read.CyReaderManager;
-//import org.cytoscape.io.internal.read.AbstractNetworkReader;
-//import org.cytoscape.io.internal.read.sif.InteractionsReader;
-//import org.cytoscape.io.internal.read.xgmml.XGMMLReader;
-import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.test.context.ContextConfiguration;
-import
org.springframework.test.context.junit4.AbstractJUnit4SpringContextTests;
-
-
-/**
- * Integration test the bundle locally (outside of OSGi). Use AbstractOsgiTests
- * and a separate integration test project for testing inside of OSGi.
- */
-//@ContextConfiguration(locations =
"classpath:META-INF/spring/bundle-context.xml")
-//public class BeanIntegrationTest extends AbstractJUnit4SpringContextTests {
-public class BeanIntegrationTest {
-
-// @Autowired
-// private CyReaderManager manager;
-
-// private CyReader sifReader;
-// private CyReader xgmmlReader;
-
- private CyNetworkFactory factoryMock;
- private CyNetworkViewFactory viewFactoryMock;
-
- private CyFileFilter sifFilter;
-
- //private CyReaderFactory sifFactory;
-
- private URI sifFileLocation;
- private URL xgmmlFile;
- private URL xgmmlURL;
-
- //private CyReaderFactory xgmmlFactory;
-
-
- @Before public void initializeTest1() throws Exception {
-/*
- sifFileLocation = new
URI("http://chianti.ucsd.edu/kono/data/galFiltered.sif";);
- final File xFile = new
File("src/test/resources/testData/galFiltered.xgmml");
- xgmmlURL = new
URL("http://chianti.ucsd.edu/kono/data/galFiltered.xgmml";);
-
- xgmmlFile = xFile.toURI().toURL();
- sifReader = (CyReader) applicationContext.getBean("sifReader");
- xgmmlReader = (CyReader)
applicationContext.getBean("xgmmlReader");
- sifFilter = (CyFileFilter)
applicationContext.getBean("sifFilter");
- sifFactory = (CyReaderFactory)
applicationContext.getBean("sifReaderFactory");
- xgmmlFactory = (CyReaderFactory)
applicationContext.getBean("xgmmlReaderFactory");
-
- factoryMock = createMock(CyNetworkFactory.class);
- viewFactoryMock = createMock(CyNetworkViewFactory.class);
-
- expect(factoryMock.getInstance()).andReturn(null).times(2);
-
-
-
((AbstractNetworkReader)sifReader).setCyNetworkFactory(factoryMock);
-
((AbstractNetworkReader)xgmmlReader).setCyNetworkFactory(factoryMock);
-
- System.out.println("--------------------------------------- SIF
Description = " + sifFilter.getDescription());
- */
- }
-
-
- /**
- * Test using mock service objects.
- * @throws Exception
- * @throws IllegalArgumentException
- */
- @Test public void readerManagerTest() throws Exception {
- System.out.println("---------------------------------------
Reader Manager Test Begins");
-
-/*
- // Register factories
- manager.addReaderFactory(sifFactory, null);
- manager.addReaderFactory(xgmmlFactory, null);
-
-// CyReader reader1 = manager.getReader(sifFileLocation,
DataCategory.NETWORK);
-
-// assertEquals(InteractionsReader.class, reader1.getClass());
- // TODO these keep returning sif readers - probably because
CyFileFilters is
- // broken for input streams.
- replay(factoryMock);
- CyReader reader2 = manager.getReader(xgmmlFile.openStream(),
DataCategory.NETWORK);
- assertEquals(XGMMLReader.class, reader2.getClass());
-
- CyReader reader3 = manager.getReader(xgmmlURL.openStream(),
DataCategory.NETWORK);
- assertEquals(XGMMLReader.class, reader3.getClass());
- verify(factoryMock);
-*/
-
- System.out.println("--------------------------------------- End
of reader manager test");
- }
-}
Added:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/InteractionTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/InteractionTest.java
(rev 0)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/InteractionTest.java
2010-08-20 21:43:30 UTC (rev 21504)
@@ -0,0 +1,94 @@
+/*
+ File: InteractionTest.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 static org.junit.Assert.*;
+import org.junit.Test;
+
+public class InteractionTest {
+ private String delim = " ";
+
+ @Test
+ public void test3ArgCtor() throws Exception {
+
+ String source = "YNL312W";
+ String type = "pd";
+ String target = "YPL111W";
+ String raw = source + " " + type + " " + target;
+
+ Interaction inter0 = new Interaction(raw, delim);
+ assertTrue(inter0.getSource().equals(source));
+ assertTrue(inter0.getType().equals(type));
+ assertTrue(inter0.numberOfTargets() == 1);
+ assertTrue(inter0.getTargets()[0].equals(target));
+ }
+
+ @Test
+ public void test1ArgCtor() throws Exception {
+
+ String rawText0 = "YNL312W pp YPL111W";
+ Interaction inter0 = new Interaction(rawText0, delim);
+ assertTrue(inter0.getSource().equals("YNL312W"));
+ assertTrue(inter0.getType().equals("pp"));
+ assertTrue(inter0.numberOfTargets() == 1);
+ assertTrue(inter0.getTargets()[0].equals("YPL111W"));
+
+ String rawText1 = "YPL075W pd YDR050C YGR254W YHR174W";
+ Interaction inter1 = new Interaction(rawText1, delim);
+ assertTrue(inter1.getSource().equals("YPL075W"));
+ assertTrue(inter1.getType().equals("pd"));
+ assertTrue(inter1.numberOfTargets() == 3);
+ assertTrue(inter1.getTargets()[0].equals("YDR050C"));
+ assertTrue(inter1.getTargets()[1].equals("YGR254W"));
+ assertTrue(inter1.getTargets()[2].equals("YHR174W"));
+ }
+
+ /** a degenerate form has -only- a source node: no interaction type
+ * and no target node
+ */
+ @Test
+ public void test1ArgCtorOnDegenerateFrom() throws Exception {
+ String rawText0 = "YNL312W";
+ Interaction inter0 = new Interaction(rawText0, delim);
+ assertTrue(inter0.getSource().equals("YNL312W"));
+ assertTrue(inter0.getType() == null);
+ assertTrue(inter0.numberOfTargets() == 0);
+ }
+
+}
Added:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducerTest.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducerTest.java
(rev 0)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewProducerTest.java
2010-08-20 21:43:30 UTC (rev 21504)
@@ -0,0 +1,160 @@
+package org.cytoscape.io.internal.read.sif;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.io.FileInputStream;
+
+import java.util.List;
+
+import static org.mockito.Mockito.*;
+
+
+import org.cytoscape.test.support.NetworkTestSupport;
+import org.cytoscape.test.support.NetworkViewTestSupport;
+
+import org.cytoscape.io.internal.util.ReadUtils;
+import org.cytoscape.io.internal.util.StreamUtilImpl;
+
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
+
+public class SIFNetworkViewProducerTest {
+
+ TaskMonitor taskMonitor;
+ CyNetworkFactory netFactory;
+ CyNetworkViewFactory viewFactory;
+ ReadUtils readUtil;
+ CyLayouts layouts;
+
+ @Before
+ public void setUp() throws Exception {
+ taskMonitor = mock(TaskMonitor.class);
+
+ CyLayoutAlgorithm def = mock(CyLayoutAlgorithm.class);
+
+ layouts = mock(CyLayouts.class);
+ when(layouts.getDefaultLayout()).thenReturn(def);
+
+ NetworkTestSupport nts = new NetworkTestSupport();
+ netFactory = nts.getNetworkFactory();
+
+ NetworkViewTestSupport nvts = new NetworkViewTestSupport();
+ viewFactory = nvts.getNetworkViewFactory();
+
+ readUtil = new ReadUtils( new StreamUtilImpl() );
+ }
+
+ /**
+ * 'typical' means that all lines have the form "node1 pd node2 [node3
node4 ...]
+ */
+ @Test
+ public void testReadFromTypicalFile() throws Exception {
+
+ CyNetworkView[] views = getViews("sample.sif");
+
+ CyNetwork net = checkNetwork(views, 31, 27);
+
+ findInteraction(net, "YNL312W", "YPL111W", "pd", 1);
+ }
+
+ /** all lines have the degenerate form "node1"
+ * that is, with no interaction type and no target
+ */
+ @Test
+ public void testReadFileWithNoInteractions() throws Exception {
+ CyNetworkView[] views = getViews("degenerate.sif");
+
+ CyNetwork net = checkNetwork(views, 9, 0);
+
+ for ( CyNode n : net.getNodeList() )
+ assertTrue(
n.attrs().get("name",String.class).startsWith("Y") );
+ }
+
+ @Test
+ public void testReadMultiWordProteinsFile() throws Exception {
+
+ CyNetworkView[] views = getViews("multiWordProteins.sif");
+
+ CyNetwork net = checkNetwork(views, 28, 31);
+
+ findInteraction(net,"26S ubiquitin dependent proteasome",
+ "I-kappa-B-alpha",
"interactsWith", 1);
+ findInteraction(net,"TRAF6", "RIP2", "interactsWith", 13);
+ findInteraction(net,"TRAF6", "ABCDE oopah", "interactsWith",
13);
+ findInteraction(net,"TRAF6", "HJKOL coltrane",
"interactsWith", 13);
+
+ }
+
+ @Test
+ public void testReadMultiWordProteinsFileWithErrantSpaces() throws
Exception {
+
+ CyNetworkView[] views =
getViews("multiWordProteinsFileTrailingSpaces.sif");
+
+ CyNetwork net = checkNetwork(views, 28, 31);
+
+ findInteraction(net,"26S ubiquitin dependent proteasome",
+ "I-kappa-B-alpha",
"interactsWith", 1);
+ findInteraction(net,"TRAF6", "RIP2", "interactsWith", 13);
+ findInteraction(net,"TRAF6", "ABCDE oopah", "interactsWith",
13);
+ findInteraction(net,"TRAF6", "HJKOL coltrane",
"interactsWith", 13);
+ }
+
+
+ // will fail if it doesn't find the specified interaction
+ private void findInteraction(CyNetwork net, String source, String
target,
+ String interaction, int count) {
+ for ( CyNode n : net.getNodeList() ) {
+ if ( n.attrs().get("name",String.class).equals(source)
) {
+ List<CyNode> neigh =
net.getNeighborList(n,CyEdge.Type.ANY);
+ assertEquals(count,neigh.size());
+ for ( CyNode nn : neigh ) {
+ if (
nn.attrs().get("name",String.class).equals(target) ) {
+ List<CyEdge> con =
net.getConnectingEdgeList(n,nn, CyEdge.Type.ANY);
+ for ( CyEdge e : con ) {
+ if (
e.attrs().get("interaction",String.class).equals(interaction) ) {
+ return;
+ }
+ }
+ }
+ }
+ }
+ }
+ fail("couldn't find interaction: " + source + " " + interaction
+ " " + target );
+ }
+
+ // in the SIF world, we only ever create one view for one network
+ private CyNetwork checkNetwork(CyNetworkView[] views, int numNodes, int
numEdges) {
+ assertNotNull(views);
+ assertEquals(1,views.length);
+
+ CyNetwork net = views[0].getModel();
+
+ assertNotNull( net );
+
+ assertEquals( numNodes, net.getNodeCount() );
+ assertEquals( numEdges, net.getEdgeCount() );
+
+ return net;
+ }
+
+ private CyNetworkView[] getViews(String file) throws Exception {
+ File f = new File("./src/test/resources/testData/sif/" + file);
+ SIFNetworkViewProducer snvp = new SIFNetworkViewProducer(new
FileInputStream(f),
+ readUtil,
layouts, viewFactory, netFactory);
+ snvp.run(taskMonitor);
+
+ return snvp.getNetworkViews();
+ }
+}
Added: core3/io-impl/trunk/src/test/resources/testData/sif/degenerate.sif
===================================================================
--- core3/io-impl/trunk/src/test/resources/testData/sif/degenerate.sif
(rev 0)
+++ core3/io-impl/trunk/src/test/resources/testData/sif/degenerate.sif
2010-08-20 21:43:30 UTC (rev 21504)
@@ -0,0 +1,9 @@
+YNL312W
+YNL314W
+YOL051W
+YOR194C
+YOR377W
+YPL075W
+YPL248C
+YPL259C
+YPR065W
Added: core3/io-impl/trunk/src/test/resources/testData/sif/multiWordProteins.sif
===================================================================
--- core3/io-impl/trunk/src/test/resources/testData/sif/multiWordProteins.sif
(rev 0)
+++ core3/io-impl/trunk/src/test/resources/testData/sif/multiWordProteins.sif
2010-08-20 21:43:30 UTC (rev 21504)
@@ -0,0 +1,30 @@
+LPS interactsWith TLR4
+LPS interactsWith MD-2
+LPS interactsWith TLR4
+ADOH interactsWith LPS
+TLR4 interactsWith MyD88
+TLR4 interactsWith IRAK Complex
+TLR4 interactsWith TIRAP
+TRAF6 interactsWith IRAK Complex
+Uev1a/UBc13 Ubiquitin-conjugating Complex interactsWith TRAF6
+TRAF6 interactsWith TAK1
+A20 interactsWith TRAF6
+TAK1 interactsWith IKK-beta
+IKK-beta interactsWith I-kappa-B-alpha
+I-kappa-B-alpha interactsWith p50
+I-kappa-B-alpha interactsWith p65
+SCF Ubiquitin Ligase interactsWith I-kappa-B-alpha
+26S ubiquitin dependent proteasome interactsWith I-kappa-B-alpha
+TLR4 interactsWith TRIF
+TRIF interactsWith IRF3
+IRAK4 interactsWith MyD88
+IRAK4 interactsWith IRAK1
+IRAK1 interactsWith MyD88
+IRAK1 interactsWith TRAF6
+TRAF6 interactsWith CD40
+TRAF6 interactsWith RANK
+TRAF6 interactsWith IRAK1
+TRAF6 interactsWith IRAK2
+TRAF6 interactsWith IRAKM
+TRAF6 interactsWith RIP2 ABCDE oopah HJKOL coltrane
+
Added:
core3/io-impl/trunk/src/test/resources/testData/sif/multiWordProteinsFileTrailingSpaces.sif
===================================================================
---
core3/io-impl/trunk/src/test/resources/testData/sif/multiWordProteinsFileTrailingSpaces.sif
(rev 0)
+++
core3/io-impl/trunk/src/test/resources/testData/sif/multiWordProteinsFileTrailingSpaces.sif
2010-08-20 21:43:30 UTC (rev 21504)
@@ -0,0 +1,30 @@
+LPS interactsWith TLR4
+LPS interactsWith MD-2
+LPS interactsWith TLR4
+ADOH interactsWith LPS
+TLR4 interactsWith MyD88
+TLR4 interactsWith IRAK Complex
+TLR4 interactsWith TIRAP
+TRAF6 interactsWith IRAK Complex
+Uev1a/UBc13 Ubiquitin-conjugating Complex interactsWith TRAF6
+TRAF6 interactsWith TAK1
+A20 interactsWith TRAF6
+TAK1 interactsWith IKK-beta
+IKK-beta interactsWith I-kappa-B-alpha
+I-kappa-B-alpha interactsWith p50
+I-kappa-B-alpha interactsWith p65
+SCF Ubiquitin Ligase interactsWith I-kappa-B-alpha
+26S ubiquitin dependent proteasome interactsWith I-kappa-B-alpha
+TLR4 interactsWith TRIF
+TRIF interactsWith IRF3
+IRAK4 interactsWith MyD88
+IRAK4 interactsWith IRAK1
+IRAK1 interactsWith MyD88
+IRAK1 interactsWith TRAF6
+TRAF6 interactsWith CD40
+TRAF6 interactsWith RANK
+TRAF6 interactsWith IRAK1
+TRAF6 interactsWith IRAK2
+TRAF6 interactsWith IRAKM
+TRAF6 interactsWith RIP2 ABCDE oopah HJKOL coltrane
+
Added: core3/io-impl/trunk/src/test/resources/testData/sif/sample.sif
===================================================================
--- core3/io-impl/trunk/src/test/resources/testData/sif/sample.sif
(rev 0)
+++ core3/io-impl/trunk/src/test/resources/testData/sif/sample.sif
2010-08-20 21:43:30 UTC (rev 21504)
@@ -0,0 +1,25 @@
+YNL312W pd YPL111W
+YNL314W pd YIR028W
+YNL314W pd YIR031C
+YOL051W pd YBR018C
+YOL051W pd YBR019C
+YOL051W pd YBR020W
+YOL051W pd YLR081W
+YOR194C pd YCL018W
+YOR377W pd YFL018C
+YPL075W pd YAL038W
+YPL075W pd YCR012W
+YPL075W pd YDR050C YGR254W YHR174W
+YPL075W pd YOL086C
+YPL248C pd MEL1
+YPL248C pd YBR018C
+YPL248C pd YBR019C
+YPL248C pd YBR020W
+YPL248C pd YJR048W
+YPL248C pd YLR081W
+YPL248C pd YML051W
+YPL248C pd YOR120W
+YPL259C pd YGR209C
+YPR065W pd YDR044W
+YPR065W pd YJR047C
+YPR065W pd YPR065W
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