Author: jm
Date: 2011-09-20 08:41:12 -0700 (Tue, 20 Sep 2011)
New Revision: 26873
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/GroupAttributesLayoutTask.java
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
core3/impl/trunk/layout-cytoscape-impl/src/main/resources/META-INF/spring/bundle-context.xml
Log:
Removed unnecessary references to CyTableManager
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
2011-09-20 15:38:34 UTC (rev 26872)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
2011-09-20 15:41:12 UTC (rev 26873)
@@ -40,7 +40,6 @@
import java.util.List;
import java.util.Set;
-import org.cytoscape.model.CyTableManager;
import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
@@ -84,20 +83,16 @@
//@Tunable(description="The namespace of the attribute to use for the
layout")
public String attributeNamespace;
- private CyTableManager tableMgr;
-
/**
* Creates a new GroupAttributesLayout object.
*/
- public GroupAttributesLayout(UndoSupport undoSupport, CyTableManager
tableMgr) {
+ public GroupAttributesLayout(UndoSupport undoSupport) {
super(undoSupport, "attributes-layout", "Group Attributes
Layout", true);
- this.tableMgr = tableMgr;
-
}
public TaskIterator getTaskIterator() {
return new TaskIterator(new
GroupAttributesLayoutTask(networkView, getName(), selectedOnly, staticNodes,
-
spacingx,spacingy,maxwidth,minrad,radmult,attributeName,attributeNamespace,
tableMgr));
+
spacingx,spacingy,maxwidth,minrad,radmult,attributeName,attributeNamespace));
}
@Override
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/GroupAttributesLayoutTask.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/GroupAttributesLayoutTask.java
2011-09-20 15:38:34 UTC (rev 26872)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/GroupAttributesLayoutTask.java
2011-09-20 15:41:12 UTC (rev 26873)
@@ -11,7 +11,6 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableManager;
import org.cytoscape.view.layout.AbstractBasicLayoutTask;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
@@ -35,12 +34,10 @@
private TaskMonitor taskMonitor;
private CyNetwork network;
- private CyTableManager tableMgr;
public GroupAttributesLayoutTask(final CyNetworkView networkView, final
String name, final boolean selectedOnly,
final Set<View<CyNode>> staticNodes, final double
spacingx, final double spacingy, final double maxwidth,
- final double minrad, final double radmult, final String
attributeName, final String attributeNamespace,
- CyTableManager tableMgr) {
+ final double minrad, final double radmult, final String
attributeName, final String attributeNamespace) {
super(networkView, name, selectedOnly, staticNodes);
@@ -55,7 +52,6 @@
this.attributeName = attributeName;
this.attributeNamespace = attributeNamespace;
- this.tableMgr = tableMgr;
}
@@ -97,7 +93,7 @@
taskMonitor.setStatusMessage("Initializing");
- CyTable dataTable = tableMgr.getTableMap(CyNode.class,
network).get(CyNetwork.DEFAULT_ATTRS);
+ CyTable dataTable = network.getDefaultNodeTable();
Class<?> klass = dataTable.getColumn(attributeName).getType();
if (Comparable.class.isAssignableFrom(klass)){
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2011-09-20 15:38:34 UTC (rev 26872)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2011-09-20 15:41:12 UTC (rev 26873)
@@ -1,29 +1,15 @@
package csplugins.layout.algorithms.graphPartition;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.List;
-
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableManager;
-import org.cytoscape.view.layout.AbstractPartitionLayoutTask;
import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
-import org.cytoscape.view.layout.LayoutNode;
-import org.cytoscape.view.layout.LayoutPartition;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
-import org.cytoscape.work.TunableValidator.ValidationState;
import org.cytoscape.work.undo.UndoSupport;
public class DegreeSortedCircleLayout extends AbstractLayoutAlgorithm
implements TunableValidator {
private static final String DEGREE_ATTR_NAME = "degree";
- private CyTableManager tableMgr;
@Tunable(description="Don't partition graph before layout",
groups="Standard settings")
public boolean singlePartition;
@@ -31,9 +17,8 @@
/**
* Creates a new DegreeSortedCircleLayout object.
*/
- public DegreeSortedCircleLayout(UndoSupport undoSupport, CyTableManager
tableMgr) {
+ public DegreeSortedCircleLayout(UndoSupport undoSupport) {
super(undoSupport, "degree-circle", "Degree Sorted Circle
Layout", true);
- this.tableMgr = tableMgr;
}
@Override // TODO
@@ -44,7 +29,6 @@
public TaskIterator getTaskIterator() {
return new TaskIterator(
new DegreeSortedCircleLayoutTask(networkView,
getName(), selectedOnly,
- staticNodes,
DEGREE_ATTR_NAME,
- tableMgr,
singlePartition));
+ staticNodes,
DEGREE_ATTR_NAME, singlePartition));
}
}
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
2011-09-20 15:38:34 UTC (rev 26872)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayoutTask.java
2011-09-20 15:41:12 UTC (rev 26873)
@@ -10,19 +10,16 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableManager;
import org.cytoscape.model.CyTable;
import org.cytoscape.view.layout.AbstractPartitionLayoutTask;
import org.cytoscape.view.layout.LayoutNode;
import org.cytoscape.view.layout.LayoutPartition;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
-import org.cytoscape.model.CyTableEntry;
public class DegreeSortedCircleLayoutTask extends AbstractPartitionLayoutTask {
private String DEGREE_ATTR_NAME = "degree";
- private CyTableManager tableMgr;
private CyNetwork network;
/**
@@ -31,12 +28,11 @@
public DegreeSortedCircleLayoutTask(
final CyNetworkView networkView, final String name, final
boolean selectedOnly,
final Set<View<CyNode>> staticNodes, final String
DEGREE_ATTR_NAME,
- final CyTableManager tableMgr, final boolean singlePartition)
+ final boolean singlePartition)
{
super(networkView, name, singlePartition, selectedOnly,
staticNodes);
this.DEGREE_ATTR_NAME= DEGREE_ATTR_NAME;
- this.tableMgr = tableMgr;
this.network = networkView.getModel();
}
@@ -47,7 +43,7 @@
*/
public void layoutPartion(LayoutPartition partition) {
// Create attribute
- CyTable table = tableMgr.getTableMap(CyNode.class,
network).get(CyNetwork.DEFAULT_ATTRS);
+ CyTable table = network.getDefaultNodeTable();
if (table.getColumn(DEGREE_ATTR_NAME) == null)
table.createColumn(DEGREE_ATTR_NAME, Double.class,
false);
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-20 15:38:34 UTC (rev 26872)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/resources/META-INF/spring/bundle-context.xml
2011-09-20 15:41:12 UTC (rev 26873)
@@ -33,7 +33,6 @@
<bean id="degreeSortedCircleLayout"
class="csplugins.layout.algorithms.graphPartition.DegreeSortedCircleLayout">
<constructor-arg ref="undoSupportServiceRef"/>
- <constructor-arg ref="cyTableManagerServiceRef"/>
</bean>
<bean id="ISOMLayout"
class="csplugins.layout.algorithms.graphPartition.ISOMLayout">
@@ -62,7 +61,6 @@
<bean id="groupAttributesLayout"
class="csplugins.layout.algorithms.GroupAttributesLayout">
<constructor-arg ref="undoSupportServiceRef"/>
- <constructor-arg ref="cyTableManagerServiceRef"/>
</bean>
</beans>
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