Author: rozagh
Date: 2012-05-01 17:51:44 -0700 (Tue, 01 May 2012)
New Revision: 29071
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayout.java
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayoutContext.java
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutContext.java
core3/impl/trunk/layout-impl/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/DynamicLayoutMenu.java
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
Log:
fixes #929 added an unweighted option for the attributes list of layouts (for
both setting panel and layout menu) . Corrected layout context for Group layout
and implemented missing getSupportSelectedOnly method for some of the layouts
(based on 2.8.2).
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayout.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayout.java
2012-05-02 00:26:50 UTC (rev 29070)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayout.java
2012-05-02 00:51:44 UTC (rev 29071)
@@ -88,4 +88,10 @@
public GroupAttributesLayoutContext createLayoutContext() {
return new GroupAttributesLayoutContext();
}
+
+ @Override
+ public boolean getSupportsSelectedOnly() {
+ return true;
+ }
+
}
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayoutContext.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayoutContext.java
2012-05-02 00:26:50 UTC (rev 29070)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayoutContext.java
2012-05-02 00:51:44 UTC (rev 29071)
@@ -1,12 +1,11 @@
package csapps.layout.algorithms.graphPartition;
-import org.cytoscape.model.CyNetwork;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
public class AttributeCircleLayoutContext implements TunableValidator {
- @Tunable(description = "The attribute to use for the layout")
- public String attribute = CyNetwork.NAME;
+// @Tunable(description = "The attribute to use for the layout")
+// public String attribute = CyNetwork.NAME;
// @Tunable(description="Node attribute to be use")
// public ListSingleSelection<Integer> attrName;
@@ -19,7 +18,8 @@
@Override
public ValidationState getValidationState(final Appendable errMsg) {
- return attribute.length() > 0 && spacing > 0.0 ?
ValidationState.OK : ValidationState.INVALID;
+ // return attribute.length() > 0 && spacing > 0.0 ?
ValidationState.OK : ValidationState.INVALID;
+ return ValidationState.OK;
}
/**
@@ -27,10 +27,4 @@
*
* @param value the name of the attribute
*/
- public void setLayoutAttribute(String value) {
- if (value.equals("(none)"))
- this.attribute = null;
- else
- this.attribute = value;
- }
}
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
2012-05-02 00:26:50 UTC (rev 29070)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
2012-05-02 00:51:44 UTC (rev 29071)
@@ -46,8 +46,8 @@
int r = (int) Math.sqrt(count);
r *= context.spacing;
- if (context.attribute != null && count > 0) {
- final CyColumn column =
nodes.get(0).getRow().getTable().getColumn(context.attribute);
+ if (layoutAttribute!= null && count > 0) {
+ final CyColumn column =
nodes.get(0).getRow().getTable().getColumn(layoutAttribute);
Class<?> klass = (column == null) ? null :
column.getType();
if (klass != null &&
Comparable.class.isAssignableFrom(klass)){
// FIXME: I assume this would be better, but
get type errors if I try:
@@ -82,8 +82,8 @@
}
public int compare(LayoutNode o1, LayoutNode o2) {
- T v1 = o1.getRow().get(context.attribute, klass);
- T v2 = o2.getRow().get(context.attribute, klass);
+ T v1 = o1.getRow().get(layoutAttribute, klass);
+ T v2 = o2.getRow().get(layoutAttribute, klass);
if (String.class.isAssignableFrom(klass)){ // i.e. if
klass _is_ String.class
String s1 = String.class.cast(v1);
String s2 = String.class.cast(v2);
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2012-05-02 00:26:50 UTC (rev 29070)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2012-05-02 00:51:44 UTC (rev 29071)
@@ -89,4 +89,10 @@
public Object createLayoutContext() {
return new HierarchicalLayoutContext();
}
+
+ @Override
+ public boolean getSupportsSelectedOnly() {
+ return true;
+ }
+
}
Modified:
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutContext.java
===================================================================
---
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutContext.java
2012-05-02 00:26:50 UTC (rev 29070)
+++
core3/impl/trunk/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutContext.java
2012-05-02 00:51:44 UTC (rev 29071)
@@ -18,8 +18,6 @@
public int topEdge = 32;
@Tunable(description="Right edge margin")
public int rightMargin = 7000;
- @Tunable(description="layout selected nodes only")
- public boolean selected_only = false;
@Override // TODO
public ValidationState getValidationState(final Appendable errMsg) {
Modified:
core3/impl/trunk/layout-impl/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
===================================================================
---
core3/impl/trunk/layout-impl/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
2012-05-02 00:26:50 UTC (rev 29070)
+++
core3/impl/trunk/layout-impl/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
2012-05-02 00:51:44 UTC (rev 29071)
@@ -63,4 +63,10 @@
public Object createLayoutContext() {
return new GridNodeLayoutContext();
}
+
+ @Override
+ public boolean getSupportsSelectedOnly() {
+ return true;
+ }
+
}
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/DynamicLayoutMenu.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/DynamicLayoutMenu.java
2012-05-02 00:26:50 UTC (rev 29070)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/DynamicLayoutMenu.java
2012-05-02 00:51:44 UTC (rev 29071)
@@ -32,6 +32,7 @@
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.rmi.UnexpectedException;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -72,7 +73,9 @@
private final CyNetwork network;
private final CyApplicationManager appMgr;
+ private static final String UNWEIGHTED = "(none)";
+
/**
* Creates a new DynamicLayoutMenu object.
*
@@ -125,7 +128,8 @@
}
private void addAttributeMenus(JMenu parent, CyTable attributes,
Set<Class<?>> typeSet, boolean selectedOnly) {
- for (final CyColumn column : attributes.getColumns())
+ parent.add(new LayoutAttributeMenuItem(UNWEIGHTED, selectedOnly));
+ for (final CyColumn column : attributes.getColumns())
if (typeSet.contains(column.getType()))
parent.add(new LayoutAttributeMenuItem(column.getName(),
selectedOnly));
}
@@ -137,7 +141,7 @@
if (usesNodeAttrs || usesEdgeAttrs) {
allNodes = new JMenu("All Nodes");
selNodes = new JMenu("Selected Nodes Only");
-
+
if (usesNodeAttrs) {
addNodeAttributeMenus((JMenu) allNodes, false);
addNodeAttributeMenus((JMenu) selNodes, true);
@@ -175,9 +179,11 @@
nodeViews = CyLayoutAlgorithm.ALL_NODE_VIEWS;
String layoutAttribute = null;
- if (layout.getSupportedNodeAttributeTypes().size() > 0 ||
layout.getSupportedEdgeAttributeTypes().size() > 0)
- layoutAttribute = e.getActionCommand();
-
+ if (layout.getSupportedNodeAttributeTypes().size() > 0 ||
layout.getSupportedEdgeAttributeTypes().size() > 0){
+ layoutAttribute = e.getActionCommand();
+ if (layoutAttribute.equals(UNWEIGHTED))
+ layoutAttribute = null;
+ }
tm.execute(layout.createTaskIterator(netView,layout.getDefaultLayoutContext(),nodeViews,layoutAttribute));
}
}
Modified:
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
===================================================================
---
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
2012-05-02 00:26:50 UTC (rev 29070)
+++
core3/impl/trunk/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
2012-05-02 00:51:44 UTC (rev 29071)
@@ -108,6 +108,8 @@
private LayoutAttributeTunable layoutAttributeTunable;
private JPanel layoutAttributePanel;
private final SelectedTunable selectedTunable;
+
+ private static final String UNWEIGHTED = "(none)";
/**
* Creates a new LayoutSettingsDialog object.
@@ -418,8 +420,8 @@
CyNetworkView view =
appMgr.getCurrentNetworkView();
setNetworkView(view);
- if (currentLayout.getSupportsSelectedOnly()) {
- selectedTunable.selectedNodesOnly =
hasSelectedNodes(view);
+ if (currentLayout.getSupportsSelectedOnly() &&
hasSelectedNodes(view)) {
+ selectedTunable.selectedNodesOnly =
true;
JPanel panel =
taskManager.getConfiguration(null, selectedTunable);
algorithmPanel.add(panel, new
GridBagConstraints(0, row++, 1, 1, 1, 1, GridBagConstraints.PAGE_START,
GridBagConstraints.HORIZONTAL, new Insets(0, 0, 0, 0), 0, 0));
}
@@ -445,6 +447,7 @@
panel.invalidate();
}
}
+
}
private boolean hasSelectedNodes(CyNetworkView view) {
@@ -476,6 +479,9 @@
attributes.add(column.getName());
}
}
+
+ if (attributes.size()>0)
+ attributes.add(0, UNWEIGHTED);
return attributes;
}
@@ -483,6 +489,8 @@
if (layoutAttributeTunable == null ||
layoutAttributeTunable.layoutAttribute == null) {
return null;
}
+
if(layoutAttributeTunable.layoutAttribute.getSelectedValue().equals(UNWEIGHTED))
+ return null;
return
layoutAttributeTunable.layoutAttribute.getSelectedValue();
}
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