Author: rodche
Date: 2010-01-30 20:16:37 -0800 (Sat, 30 Jan 2010)
New Revision: 19084
Added:
coreplugins/trunk/BioPAX/resources/log4j.properties
Removed:
coreplugins/trunk/BioPAX/sampleData/
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/LayoutUtil.java
Modified:
coreplugins/trunk/BioPAX/
coreplugins/trunk/BioPAX/build.xml
coreplugins/trunk/BioPAX/resources/COPYING.LESSER
coreplugins/trunk/BioPAX/resources/plugin.props
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/BioPaxGraphReader.java
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/BiopaxPlugin.java
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/MapBioPaxToCytoscape.java
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxVisualStyleUtil.java
coreplugins/trunk/BioPAX/test/cytoscape/coreplugins/biopax/TestBioPaxUtil.java
Log:
BioPAX plugin: authors line (plugin.props) - syntax fixed; less deprecated and
old things; "polishing"
Property changes on: coreplugins/trunk/BioPAX
___________________________________________________________________
Name: svn:ignore
- .project
.classpath
.settings
.externalToolBuilders
+ .project
.classpath
.settings
.externalToolBuilders
build
Modified: coreplugins/trunk/BioPAX/build.xml
===================================================================
--- coreplugins/trunk/BioPAX/build.xml 2010-01-31 02:18:44 UTC (rev 19083)
+++ coreplugins/trunk/BioPAX/build.xml 2010-01-31 04:16:37 UTC (rev 19084)
@@ -70,6 +70,9 @@
<path id="test.classpath">
<pathelement path="${build.test.classes}"/>
+ <fileset dir="${cytoscape.dir}/lib/build-libs">
+ <include name="*.jar"/>
+ </fileset>
<path refid="classpath.without.yfiles"/>
</path>
@@ -180,7 +183,7 @@
</target>
<!-- target to run cytoscape with biopax plugin -->
- <target depends="check.yfiles,set.classpath,jar" description="Runs
Cytoscape with BioPAX Data."
+ <target depends="all" description="Runs Cytoscape with BioPAX Data."
name="run">
<copy file="${jars.dir}/${jar_file}" todir="${cytoscape.dir}/plugins"
overwrite="true" />
<java classname="cytoscape.CyMain" classpathref="runtime.classpath"
Modified: coreplugins/trunk/BioPAX/resources/COPYING.LESSER
===================================================================
--- coreplugins/trunk/BioPAX/resources/COPYING.LESSER 2010-01-31 02:18:44 UTC
(rev 19083)
+++ coreplugins/trunk/BioPAX/resources/COPYING.LESSER 2010-01-31 04:16:37 UTC
(rev 19084)
@@ -1,3 +1,31 @@
+/** BioPAX Plugin for Cytoscape
+ **
+ ** Copyright (c) 2010 University of Toronto (UofT)
+ ** and Memorial Sloan-Kettering Cancer Center (MSKCC).
+ **
+ ** This 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
+ ** both UofT and MSKCC have no obligations to provide maintenance,
+ ** support, updates, enhancements or modifications. In no event shall
+ ** UofT or MSKCC 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
+ ** UofT or MSKCC 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 software; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA;
+ ** or find it at http://www.fsf.org/ or http://www.gnu.org.
+ **/
+
GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Added: coreplugins/trunk/BioPAX/resources/log4j.properties
===================================================================
--- coreplugins/trunk/BioPAX/resources/log4j.properties
(rev 0)
+++ coreplugins/trunk/BioPAX/resources/log4j.properties 2010-01-31 04:16:37 UTC
(rev 19084)
@@ -0,0 +1,12 @@
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=INFO, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
+
+log4j.logger.org.biopax.paxtools = WARN
+log4j.logger.cytoscape.coreplugins.biopax = INFO
Property changes on: coreplugins/trunk/BioPAX/resources/log4j.properties
___________________________________________________________________
Name: svn:mime-type
+ text/plain
Modified: coreplugins/trunk/BioPAX/resources/plugin.props
===================================================================
--- coreplugins/trunk/BioPAX/resources/plugin.props 2010-01-31 02:18:44 UTC
(rev 19083)
+++ coreplugins/trunk/BioPAX/resources/plugin.props 2010-01-31 04:16:37 UTC
(rev 19084)
@@ -17,11 +17,11 @@
cytoscapeVersion=2.7
# Category, use one of the categories listed on the website or create your own
-pluginCategory=Network and Attribute I/O
+pluginCategory=Core
# List of authors. Note each author and institution pair are separated by a :
(colon)
# each additional author institution pair must be separated from other pairs
by a ; (semicolon)
-pluginAuthorsIntsitutions=Ethan Cerami, Benjamin Gross, Chris Sander:Memorial
Sloan-Kettering Cancer Center;B. Arman Aksoy; Rex Dwyer:Singenta;Gary Bader,
Igor Rodchenkov:Uniersity of Toronto
+pluginAuthorsIntsitutions=Ethan Cerami, Benjamin Gross and Chris
Sander:Memorial Sloan-Kettering Cancer Center;B. Arman Aksoy:Gerstner
Sloan-Kettering Graduate School;Rex Dwyer:Singenta;Gary Bader and Igor
Rodchenkov:University of Toronto
# Date this plugin/plugin version was released
releaseDate=January 29, 2010
Modified:
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/BioPaxGraphReader.java
===================================================================
---
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/BioPaxGraphReader.java
2010-01-31 02:18:44 UTC (rev 19083)
+++
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/BioPaxGraphReader.java
2010-01-31 04:16:37 UTC (rev 19084)
@@ -1,37 +1,5 @@
-// $Id: TestExternalLinkUtil.java,v 1.11 2006/06/15 22:07:49 grossb Exp $
-//------------------------------------------------------------------------------
-/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
- **
- ** Code written by: Ethan Cerami, Benjamin Gross.
- ** Authors: Ethan Cerami, Gary Bader, Chris Sander
- **
- ** 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
- ** Memorial Sloan-Kettering Cancer Center
- ** has no obligations to provide maintenance, support,
- ** updates, enhancements or modifications. In no event shall
- ** Memorial Sloan-Kettering Cancer Center
- ** 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
- ** Memorial Sloan-Kettering Cancer Center
- ** has 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 cytoscape.coreplugins.biopax;
-
import giny.model.RootGraph;
import giny.view.GraphView;
@@ -250,6 +218,7 @@
// Repair Canonical Name
repairCanonicalName(cyNetwork);
+
// repair network name
if (!validNetworkName) {
repairNetworkName(cyNetwork);
@@ -298,6 +267,8 @@
BioPaxContainer bpContainer = BioPaxContainer.getInstance();
bpContainer.showLegend();
+ BioPaxVisualStyleUtil.setNodeToolTips(view);
+
// add network listener
NetworkListener networkListener = bpContainer.getNetworkListener();
networkListener.registerNetwork(cyNetwork);
@@ -306,9 +277,6 @@
BiopaxNodeCtxMenuListener nodeCtxMenuListener = new
BiopaxNodeCtxMenuListener();
view.addNodeContextMenuListener(nodeCtxMenuListener);
-
- BioPaxVisualStyleUtil.setNodeToolTips(view);
-
}
/**
@@ -349,6 +317,7 @@
/**
+ *
* Repairs Network Name. Temporary fix to automatically set network
* name to match BioPAX Pathway name.
*
Modified:
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/BiopaxPlugin.java
===================================================================
--- coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/BiopaxPlugin.java
2010-01-31 02:18:44 UTC (rev 19083)
+++ coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/BiopaxPlugin.java
2010-01-31 04:16:37 UTC (rev 19084)
@@ -1,11 +1,9 @@
-// $Id: BiopaxPlugin.java,v 1.11 2006/06/15 22:06:02 grossb Exp $
-//------------------------------------------------------------------------------
-/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+/** BioPAX Plugin for Cytoscape
**
- ** Code written by: Ethan Cerami
- ** Authors: Ethan Cerami, Gary Bader, Chris Sander
+ ** Copyright (c) 2010 University of Toronto (UofT)
+ ** and Memorial Sloan-Kettering Cancer Center (MSKCC).
**
- ** This library is free software; you can redistribute it and/or modify it
+ ** This 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.
@@ -14,20 +12,18 @@
** 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
- ** Memorial Sloan-Kettering Cancer Center
- ** has no obligations to provide maintenance, support,
- ** updates, enhancements or modifications. In no event shall
- ** Memorial Sloan-Kettering Cancer Center
- ** be liable to any party for direct, indirect, special,
+ ** both UofT and MSKCC have no obligations to provide maintenance,
+ ** support, updates, enhancements or modifications. In no event shall
+ ** UofT or MSKCC 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
- ** Memorial Sloan-Kettering Cancer Center
- ** has been advised of the possibility of such damage. See
- ** the GNU Lesser General Public License for more details.
+ ** UofT or MSKCC 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.
+ ** along with this software; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA;
+ ** or find it at http://www.fsf.org/ or http://www.gnu.org.
**/
package cytoscape.coreplugins.biopax;
Modified:
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/MapBioPaxToCytoscape.java
===================================================================
---
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/MapBioPaxToCytoscape.java
2010-01-31 02:18:44 UTC (rev 19083)
+++
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/MapBioPaxToCytoscape.java
2010-01-31 04:16:37 UTC (rev 19084)
@@ -1,34 +1,3 @@
-// $Id: MapBioPaxToCytoscape.java,v 1.38 2006/10/09 20:48:20 cerami Exp $
-//------------------------------------------------------------------------------
-/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
- **
- ** Code written by: Ethan Cerami
- ** Authors: Ethan Cerami, Gary Bader, Chris Sander
- **
- ** 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
- ** Memorial Sloan-Kettering Cancer Center
- ** has no obligations to provide maintenance, support,
- ** updates, enhancements or modifications. In no event shall
- ** Memorial Sloan-Kettering Cancer Center
- ** 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
- ** Memorial Sloan-Kettering Cancer Center
- ** has 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 cytoscape.coreplugins.biopax;
import cytoscape.CyEdge;
@@ -69,7 +38,6 @@
import ding.view.DNodeView;
-
import java.awt.Paint;
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
@@ -79,13 +47,9 @@
/**
* Maps a BioPAX Model to Cytoscape Nodes/Edges.
*
- * @author Ethan Cerami.
- * @author Igor Rodchenkov (re-factoring using PaxTools API)
+ * @author Ethan Cerami, Igor Rodchenkov (re-factoring using PaxTools API)
*
- *
- * TODO This probably must be re-written from scratch -
- * - using PaxTools 'AbstractTraverser' class, so that
- * all the properties will be mapped...
+ * TODO later, re-write from scratch using 'AbstractTraverser'
*/
public class MapBioPaxToCytoscape {
@@ -661,7 +625,7 @@
if (controlledList.size() > 1)
{
log.warn("Warning! Control Interaction: " +
interactionId
- + "has more than one CONTROLLED
Element.");
+ + " has more than one CONTROLLED
Element.");
}
else if (controlledList != null && !controlledList.isEmpty())
{
@@ -693,7 +657,7 @@
}
else
{
- log.warn(interactionId + "has no CONTROLLED Elements");
+ log.warn(interactionId + " has no CONTROLLED Elements");
}
// Create Edges from the Controller(s) to the
@@ -707,7 +671,7 @@
(BioPAXElement)
controllerElement, CONTROLLER);
}
} else {
- log.warn(interactionId + "has no CONTROLLER Elements");
+ log.warn(interactionId + " has no CONTROLLER Elements");
}
mapCoFactors(interactionElement);
Modified:
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
===================================================================
---
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
2010-01-31 02:18:44 UTC (rev 19083)
+++
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxUtil.java
2010-01-31 04:16:37 UTC (rev 19084)
@@ -1,11 +1,7 @@
-// $Id: BioPaxUtil.java,v 1.6 2006/06/20 19:40:01 cerami Exp $
-//------------------------------------------------------------------------------
-/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
+/** Copyright (c) 2010 University of Toronto (UofT)
+ ** and Memorial Sloan-Kettering Cancer Center (MSKCC).
**
- ** Code written by: Ethan Cerami
- ** Authors: Ethan Cerami, Gary Bader, Chris Sander
- **
- ** This library is free software; you can redistribute it and/or modify it
+ ** This 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.
@@ -14,20 +10,18 @@
** 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
- ** Memorial Sloan-Kettering Cancer Center
- ** has no obligations to provide maintenance, support,
- ** updates, enhancements or modifications. In no event shall
- ** Memorial Sloan-Kettering Cancer Center
- ** be liable to any party for direct, indirect, special,
+ ** both UofT and MSKCC have no obligations to provide maintenance,
+ ** support, updates, enhancements or modifications. In no event shall
+ ** UofT or MSKCC 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
- ** Memorial Sloan-Kettering Cancer Center
- ** has been advised of the possibility of such damage. See
- ** the GNU Lesser General Public License for more details.
+ ** UofT or MSKCC 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.
+ ** along with this software; if not, write to the Free Software Foundation,
+ ** Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA;
+ ** or find it at http://www.fsf.org/ or http://www.gnu.org.
**/
package cytoscape.coreplugins.biopax.util;
@@ -58,8 +52,7 @@
* BioPax Utility Class - is a BioPAX Model Adapter
* that also defines additional constants.
*
- * @author Ethan Cerami,
- * @author Igor Rodchenkov (re-factoring using PaxTools API), Arman, Rex
+ * @author Ethan Cerami, Rex, Arman and Igor Rodchenkov
*/
public class BioPaxUtil {
private static final Map<String,String> plainEnglishMap;
@@ -786,13 +779,25 @@
Set<String> pathwayNames = new HashSet<String>();
Set<? extends BioPAXElement> procs =
BioPaxUtil.getObjects(model, pathway.class, Pathway.class);
- Set<BioPAXElement> pathways = fetchParentNodeNames(bpe, procs);
- //if(pathways.isEmpty()) {
- // // then find interactions
- // procs = BioPaxUtil.getObjects(model, interaction.class,
Interaction.class);
- // pathways = fetchParentNodeNames(bpe, procs);
- //}
+ // remove sub-pathways (finding all parents is sacrificed to
performance...)
+ Set<BioPAXElement> topPathways = new HashSet<BioPAXElement>();
+ for(BioPAXElement p : procs ) {
+ if( (p instanceof pathway
+ &&
((pathway)p).isPATHWAY_COMPONENTSof().isEmpty()
+ && ((pathway)p).isPARTICIPANTSof().isEmpty()
+ && ((pathway)p).isCONTROLLEDOf().isEmpty())
+ ||
+ (p instanceof Pathway
+ &&
((Pathway)p).getPathwayComponentsOf().isEmpty()
+ && ((Pathway)p).getParticipantsOf().isEmpty()
+ && ((Pathway)p).getControlledOf().isEmpty()))
+ {
+ topPathways.add(p);
+ }
+ }
+
+ Set<BioPAXElement> pathways = fetchParentNodeNames(bpe,
topPathways);
if(!pathways.isEmpty()) {
for(BioPAXElement pw : pathways) {
Modified:
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxVisualStyleUtil.java
===================================================================
---
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxVisualStyleUtil.java
2010-01-31 02:18:44 UTC (rev 19083)
+++
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/BioPaxVisualStyleUtil.java
2010-01-31 04:16:37 UTC (rev 19084)
@@ -156,10 +156,10 @@
if (bioPaxVisualStyle == null) {
bioPaxVisualStyle = new
VisualStyle(BIO_PAX_VISUAL_STYLE);
- NodeAppearanceCalculator nac = new
NodeAppearanceCalculator();
- nac.setNodeSizeLocked(false);
+ NodeAppearanceCalculator nac =
bioPaxVisualStyle.getNodeAppearanceCalculator();
+
bioPaxVisualStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,false);
- EdgeAppearanceCalculator eac = new
EdgeAppearanceCalculator();
+ EdgeAppearanceCalculator eac =
bioPaxVisualStyle.getEdgeAppearanceCalculator();
createNodeShape(nac);
createNodeSize(nac);
@@ -361,10 +361,8 @@
while (nodesIt.hasNext()) {
NodeView nodeView = nodesIt.next();
String id = nodeView.getNode().getIdentifier();
- String tip = "He-he-he!";
-
- /*
- + nodeAttributes.getAttribute(id,
MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE)
+ String tip =
+ nodeAttributes.getAttribute(id,
MapBioPaxToCytoscape.BIOPAX_ENTITY_TYPE)
+ "\n" +
nodeAttributes.getAttribute(id,
MapBioPaxToCytoscape.BIOPAX_AVAILABILITY)
+ "\n" +
@@ -375,7 +373,7 @@
nodeAttributes.getAttribute(id,
MapBioPaxToCytoscape.BIOPAX_PATHWAY_NAME)
+ "\n" +
nodeAttributes.getAttribute(id,
MapBioPaxToCytoscape.BIOPAX_RDF_ID);
- */
+
nodeView.setToolTip(tip);
if(log.isDebugging())
Deleted:
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/LayoutUtil.java
===================================================================
---
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/LayoutUtil.java
2010-01-31 02:18:44 UTC (rev 19083)
+++
coreplugins/trunk/BioPAX/src/cytoscape/coreplugins/biopax/util/LayoutUtil.java
2010-01-31 04:16:37 UTC (rev 19084)
@@ -1,200 +0,0 @@
-//
-// WARNING - THIS FILE IS AUTO-GENERATED - ANY CHANGES YOU MAKE HERE WILL BE
LOST
-//
-//------------------------------------------------------------------------------
-/** Copyright (c) 2007 Memorial Sloan-Kettering Cancer Center.
- **
- ** Code written by: Ethan Cerami, Benjamin Gross
- ** Authors: Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross
- **
- ** 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
- ** Memorial Sloan-Kettering Cancer Center
- ** has no obligations to provide maintenance, support,
- ** updates, enhancements or modifications. In no event shall
- ** Memorial Sloan-Kettering Cancer Center
- ** 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
- ** Memorial Sloan-Kettering Cancer Center
- ** has 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 cytoscape.coreplugins.biopax.util;
-
-// imports
-import giny.view.NodeView;
-import java.util.Iterator;
-import cytoscape.Cytoscape;
-import cytoscape.task.TaskMonitor;
-import cytoscape.view.CyNetworkView;
-import cytoscape.layout.CyLayoutAlgorithm;
-import cytoscape.layout.LayoutProperties;
-
-import java.util.List;
-import java.util.ArrayList;
-import javax.swing.JPanel;
-
-/**
- * This class implements CyLayoutAlgorithim. Used to layout BioPAX graphs.
- *
- * @author Benjamin Gross
- */
-public class LayoutUtil implements CyLayoutAlgorithm {
-
- /**
- * Our implementation of LayoutAlgorithm.doLayout().
- */
- public void doLayout() {
- doLayout(Cytoscape.getCurrentNetworkView(), null);
- }
-
- /**
- * Our implementation of LayoutAlgorithm.doLayout(..).
- */
- public void doLayout(CyNetworkView networkView) {
- doLayout(networkView, null);
- }
-
- /**
- * Our implementation of LayoutAlgorithm.doLayout(..,..).
- */
- public void doLayout(CyNetworkView networkView, TaskMonitor monitor) {
-
- double distanceBetweenNodes = 50.0d;
- int columns = (int) Math.sqrt(networkView.nodeCount());
- Iterator nodeViews = networkView.getNodeViewsIterator();
- double currX = 0.0d;
- double currY = 0.0d;
- int count = 0;
-
- while (nodeViews.hasNext()) {
- NodeView nView = (NodeView) nodeViews.next();
- nView.setOffset(currX, currY);
- count++;
-
- if (count == columns) {
- count = 0;
- currX = 0.0d;
- currY += distanceBetweenNodes;
- } else {
- currX += distanceBetweenNodes;
- }
- }
- }
-
- /**
- * Our implementation of LayoutAlgorithm.supportsSelectedOnly().
- */
- public boolean supportsSelectedOnly() {
- return false;
- }
-
- /**
- * Our implementation of LayoutAlgorithm.setSelectedOnly(..).
- */
- public void setSelectedOnly(boolean selectedOnly) {
- }
-
- /**
- * Our implementation of LayoutAlgorithm.supportsNodeAttributes().
- */
- public byte[] supportsNodeAttributes() {
- return null;
- }
-
- /**
- * Our implementation of LayoutAlgorithm.supportsEdgeAttributes().
- */
- public byte[] supportsEdgeAttributes() {
- return null;
- }
-
- /**
- * Our implementation of LayoutAlgorithm.setLayoutAttribute(..).
- */
- public void setLayoutAttribute(String attributeName) {
- }
-
- /**
- * Our implementation of LayoutAlgorithm.getInitialAttributeList().
- */
- public List<String> getInitialAttributeList() {
- return new ArrayList<String>();
- }
-
- /**
- * Our implementation of LayoutAlgorithm.getSettingsPanel().
- */
- public JPanel getSettingsPanel() {
- return null;
- }
-
- /**
- * Our implementation of LayoutAlgorithm.revertSettings().
- */
- public void revertSettings() {
- }
-
- /**
- * Our implementation of LayoutAlgorithm.updateSettings().
- */
- public void updateSettings() {
- }
-
- /**
- * Our implementation of LayoutAlgorithm.getSettings().
- */
- public LayoutProperties getSettings() {
- return null;
- }
-
- /**
- * Our implementation of LayoutAlgorithm.getName().
- */
- public String getName() {
- return "BioPax Plugin Layout Algorithm";
- }
-
- /**
- * Our implementation of LayoutAlgorithm.lockNodes(..).
- */
- public void lockNodes(NodeView[] nodes) {
- }
-
- /**
- * Our implementation of LayoutAlgorithm.lockNode(..).
- */
- public void lockNode(NodeView v) {
- }
-
- /**
- * Our implementation of LayoutAlgorithm.unlockNode(..).
- */
- public void unlockNode(NodeView v) {
- }
-
- /**
- * Our implementation of LayoutAlgorithm.unlockAllNodes().
- */
- public void unlockAllNodes() {
- }
-
- /**
- * Our implementation of LayoutAlgorithm.halt().
- */
- public void halt() {
- }
-}
-
Modified:
coreplugins/trunk/BioPAX/test/cytoscape/coreplugins/biopax/TestBioPaxUtil.java
===================================================================
---
coreplugins/trunk/BioPAX/test/cytoscape/coreplugins/biopax/TestBioPaxUtil.java
2010-01-31 02:18:44 UTC (rev 19083)
+++
coreplugins/trunk/BioPAX/test/cytoscape/coreplugins/biopax/TestBioPaxUtil.java
2010-01-31 04:16:37 UTC (rev 19084)
@@ -35,7 +35,6 @@
import junit.framework.TestCase;
-import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.model.Model;
import org.biopax.paxtools.model.level2.interaction;
import org.biopax.paxtools.model.level2.pathway;
@@ -82,7 +81,7 @@
*/
public void testUtil2() throws Exception {
Model model =
BioPaxUtil.readFile("test-resources/biopax_complex.owl");
- Set pathways = BioPaxUtil.getParentPathwayName(
+ Set<String> pathways = BioPaxUtil.getParentPathwayName(
model.getByID("http://cbio.mskcc.org/cpath#CPATH-124";), model);
System.out.println("PARENT PROCESSes NAMES: " + pathways);
assertTrue(pathways.size()==0);
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
