Author: mes
Date: 2012-06-11 11:13:29 -0700 (Mon, 11 Jun 2012)
New Revision: 29525
Modified:
core3/gui-distribution/trunk/features/src/main/resources/features.xml
core3/impl/trunk/layout-cytoscape-impl/pom.xml
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayoutTask.java
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/Layout.java
Log:
Removed use of colt in favor of parallel colt. This is important because colt
uses a library that is only free for non-commercial use, which could become a
problem for many users.
Modified: core3/gui-distribution/trunk/features/src/main/resources/features.xml
===================================================================
--- core3/gui-distribution/trunk/features/src/main/resources/features.xml
2012-06-11 17:57:41 UTC (rev 29524)
+++ core3/gui-distribution/trunk/features/src/main/resources/features.xml
2012-06-11 18:13:29 UTC (rev 29525)
@@ -13,7 +13,6 @@
<bundle start-level="103">wrap:mvn:net.sf.opencsv/opencsv/2.1</bundle>
<bundle start-level="103">mvn:cytoscape-sun/jhall/1.0</bundle>
<bundle
start-level="103">mvn:org.apache.commons/com.springsource.org.apache.commons.collections/3.2.1</bundle>
- <bundle start-level="103">mvn:cytoscape-temp/colt/1.2.0</bundle>
<bundle start-level="103">mvn:cytoscape-temp/parallelcolt/0.9.4</bundle>
<bundle start-level="103">mvn:cytoscape-temp/prefuse/20071021</bundle>
<bundle
start-level="103">mvn:cytoscape-temp/org.apache.lucene/3.0.2</bundle>
Modified: core3/impl/trunk/layout-cytoscape-impl/pom.xml
===================================================================
--- core3/impl/trunk/layout-cytoscape-impl/pom.xml 2012-06-11 17:57:41 UTC
(rev 29524)
+++ core3/impl/trunk/layout-cytoscape-impl/pom.xml 2012-06-11 18:13:29 UTC
(rev 29525)
@@ -89,11 +89,6 @@
</dependency>
<dependency>
<groupId>cytoscape-temp</groupId>
- <artifactId>colt</artifactId>
- <version>1.2.0</version>
- </dependency>
- <dependency>
- <groupId>cytoscape-temp</groupId>
<artifactId>parallelcolt</artifactId>
<version>0.9.4</version>
</dependency>
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayoutTask.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayoutTask.java
2012-06-11 17:57:41 UTC (rev 29524)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayoutTask.java
2012-06-11 18:13:29 UTC (rev 29525)
@@ -15,11 +15,11 @@
import org.cytoscape.work.undo.UndoSupport;
import cern.colt.list.tlong.LongArrayList;
-import cern.colt.map.OpenLongObjectHashMap;
+import cern.colt.map.tobject.OpenLongObjectHashMap;
import cern.colt.map.PrimeFinder;
import cern.colt.map.tlong.OpenLongIntHashMap;
-import cern.colt.matrix.DoubleMatrix1D;
-import cern.colt.matrix.impl.DenseDoubleMatrix1D;
+import cern.colt.matrix.tdouble.DoubleMatrix1D;
+import cern.colt.matrix.tdouble.impl.DenseDoubleMatrix1D;
public class ISOMLayoutTask extends AbstractPartitionLayoutTask {
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/Layout.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/Layout.java
2012-06-11 17:57:41 UTC (rev 29524)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/Layout.java
2012-06-11 18:13:29 UTC (rev 29525)
@@ -44,8 +44,6 @@
import java.util.HashMap;
import java.util.Map;
-// import cern.colt.map.OpenIntDoubleHashMap;
-// import cern.colt.map.tlong.OpenLongDoubleHashMap;
import cern.colt.map.PrimeFinder;
/**
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