Author: ruschein
Date: 2011-01-25 10:03:20 -0800 (Tue, 25 Jan 2011)
New Revision: 23602
Added:
core3/core-task-api/trunk/src/main/java/org/cytoscape/task/table/
core3/core-task-api/trunk/src/main/java/org/cytoscape/task/table/MapNetworkAttrTask.java
Removed:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/attrs/MapNetworkAttrTask.java
Modified:
core3/core-task-api/trunk/pom.xml
core3/io-impl/trunk/pom.xml
Log:
Moved MapNetworkAttrTask.java from io-impl to core-task-api.
Modified: core3/core-task-api/trunk/pom.xml
===================================================================
--- core3/core-task-api/trunk/pom.xml 2011-01-25 17:25:20 UTC (rev 23601)
+++ core3/core-task-api/trunk/pom.xml 2011-01-25 18:03:20 UTC (rev 23602)
@@ -107,9 +107,14 @@
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>work-api</artifactId>
- <version>3.0.0-alpha1</version>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
</dependency>
<dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>session-api</artifactId>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
+ </dependency>
+ <dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
Copied:
core3/core-task-api/trunk/src/main/java/org/cytoscape/task/table/MapNetworkAttrTask.java
(from rev 23599,
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/attrs/MapNetworkAttrTask.java)
===================================================================
---
core3/core-task-api/trunk/src/main/java/org/cytoscape/task/table/MapNetworkAttrTask.java
(rev 0)
+++
core3/core-task-api/trunk/src/main/java/org/cytoscape/task/table/MapNetworkAttrTask.java
2011-01-25 18:03:20 UTC (rev 23602)
@@ -0,0 +1,74 @@
+package org.cytoscape.task.table;
+
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.session.CyApplicationManager;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+
+
+public final class MapNetworkAttrTask extends AbstractTask {
+ @Tunable(description="Map to current network only")
+ public boolean currentNetworkOnly = true;
+
+ private final Class<? extends CyTableEntry> type; // Must be node or
edge!
+ private final CyTable newGlobalTable;
+ private final CyNetworkManager networkManager;
+ final private CyApplicationManager applicationManager;
+
+ public MapNetworkAttrTask(final Class<? extends CyTableEntry> type,
final CyTable newGlobalTable,
+ final CyNetworkManager networkManager,
+ final CyApplicationManager applicationManager)
+ {
+ this.type = type;
+ this.newGlobalTable = newGlobalTable;
+ this.networkManager = networkManager;
+ this.applicationManager = applicationManager;
+
+ if (type != CyNode.class && type != CyEdge.class)
+ throw new IllegalArgumentException("\"type\" must be
CyNode.class or CyEdge.class!");
+ }
+
+ public void run(final TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setTitle("Mapping virtual columns");
+
+ final List<CyTable> targetTables = new ArrayList<CyTable>();
+ if (currentNetworkOnly) {
+ final CyNetwork currentNetwork =
applicationManager.getCurrentNetwork();
+ targetTables.add(type == CyNode.class ?
currentNetwork.getDefaultNodeTable()
+ :
currentNetwork.getDefaultEdgeTable());
+ } else {
+ final Set<CyNetwork> networks =
networkManager.getNetworkSet();
+ for (final CyNetwork network : networks)
+ targetTables.add(type == CyNode.class ?
network.getDefaultNodeTable()
+ :
network.getDefaultEdgeTable());
+ }
+
+ mapAll(targetTables);
+ }
+
+ private void mapAll(final List<CyTable> targetTables) {
+ if (targetTables.isEmpty())
+ return;
+
+ if (newGlobalTable.getPrimaryKeyType() != String.class)
+ throw new IllegalStateException("The new table's
primary key is not of type String!");
+ final String sourceTableJoinColumn =
newGlobalTable.getPrimaryKey();
+
+ for (final CyTable targetTable : targetTables) {
+ if (cancelled)
+ return;
+ targetTable.addVirtualColumns(newGlobalTable,
sourceTableJoinColumn, CyTableEntry.NAME);
+ }
+ }
+}
\ No newline at end of file
Modified: core3/io-impl/trunk/pom.xml
===================================================================
--- core3/io-impl/trunk/pom.xml 2011-01-25 17:25:20 UTC (rev 23601)
+++ core3/io-impl/trunk/pom.xml 2011-01-25 18:03:20 UTC (rev 23602)
@@ -90,16 +90,6 @@
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
- <artifactId>session-api</artifactId>
- <version>3.0.0-alpha2-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>org.cytoscape</groupId>
- <artifactId>work-api</artifactId>
- <version>3.0.0-alpha2-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>org.cytoscape</groupId>
<artifactId>default-mappings</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
Deleted:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/attrs/MapNetworkAttrTask.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/attrs/MapNetworkAttrTask.java
2011-01-25 17:25:20 UTC (rev 23601)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/attrs/MapNetworkAttrTask.java
2011-01-25 18:03:20 UTC (rev 23602)
@@ -1,74 +0,0 @@
-package org.cytoscape.io.internal.read.attrs;
-
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Set;
-
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
-import org.cytoscape.session.CyApplicationManager;
-import org.cytoscape.work.AbstractTask;
-import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.Tunable;
-
-
-public final class MapNetworkAttrTask extends AbstractTask {
- @Tunable(description="Map to current network only")
- public boolean currentNetworkOnly = true;
-
- private final Class<? extends CyTableEntry> type; // Must be node or
edge!
- private final CyTable newGlobalTable;
- private final CyNetworkManager networkManager;
- final private CyApplicationManager applicationManager;
-
- public MapNetworkAttrTask(final Class<? extends CyTableEntry> type,
final CyTable newGlobalTable,
- final CyNetworkManager networkManager,
- final CyApplicationManager applicationManager)
- {
- this.type = type;
- this.newGlobalTable = newGlobalTable;
- this.networkManager = networkManager;
- this.applicationManager = applicationManager;
-
- if (type != CyNode.class && type != CyEdge.class)
- throw new IllegalArgumentException("\"type\" must be
CyNode.class or CyEdge.class!");
- }
-
- public void run(final TaskMonitor taskMonitor) throws Exception {
- taskMonitor.setTitle("Mapping virtual columns");
-
- final List<CyTable> targetTables = new ArrayList<CyTable>();
- if (currentNetworkOnly) {
- final CyNetwork currentNetwork =
applicationManager.getCurrentNetwork();
- targetTables.add(type == CyNode.class ?
currentNetwork.getDefaultNodeTable()
- :
currentNetwork.getDefaultEdgeTable());
- } else {
- final Set<CyNetwork> networks =
networkManager.getNetworkSet();
- for (final CyNetwork network : networks)
- targetTables.add(type == CyNode.class ?
network.getDefaultNodeTable()
- :
network.getDefaultEdgeTable());
- }
-
- mapAll(targetTables);
- }
-
- private void mapAll(final List<CyTable> targetTables) {
- if (targetTables.isEmpty())
- return;
-
- if (newGlobalTable.getPrimaryKeyType() != String.class)
- throw new IllegalStateException("The new table's
primary key is not of type String!");
- final String sourceTableJoinColumn =
newGlobalTable.getPrimaryKey();
-
- for (final CyTable targetTable : targetTables) {
- if (cancelled)
- return;
- targetTable.addVirtualColumns(newGlobalTable,
sourceTableJoinColumn, CyTableEntry.NAME);
- }
- }
-}
\ No newline at end of file
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