Author: jm
Date: 2010-12-20 09:20:31 -0800 (Mon, 20 Dec 2010)
New Revision: 23244
Modified:
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/ApplyFilterThread.java
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/FilterUtil.java
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/SelectUtil.java
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/quickfind/plugin/QuickFindPlugIn.java
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/quickfind/util/CyAttributesUtil.java
Log:
Implemented stubs in FilterUtil and SelectUtil
Modified:
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/ApplyFilterThread.java
===================================================================
---
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/ApplyFilterThread.java
2010-12-18 21:38:58 UTC (rev 23243)
+++
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/ApplyFilterThread.java
2010-12-20 17:20:31 UTC (rev 23244)
@@ -210,7 +210,7 @@
}
//System.out.println("\tpassedNodes.size()
="+passedNodes.size());
- SelectUtil.setSelectedNodeState(network, passedNodes,
true);
+ SelectUtil.setSelectedNodeState(passedNodes, true);
}
if (pCompositeFilter.getAdvancedSetting().isEdgeChecked()) {
@@ -229,7 +229,7 @@
}
//System.out.println("\tpassedEdges.size()
="+passedEdges.size());
- SelectUtil.setSelectedEdgeState(network, passedEdges,
true);
+ SelectUtil.setSelectedEdgeState(passedEdges, true);
}
} //testObjects
}
Modified:
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/FilterUtil.java
===================================================================
---
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/FilterUtil.java
2010-12-18 21:38:58 UTC (rev 23243)
+++
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/FilterUtil.java
2010-12-20 17:20:31 UTC (rev 23244)
@@ -1,6 +1,5 @@
package org.cytoscape.filter.internal.filters.util;
-import java.awt.Cursor;
import java.util.ArrayList;
import java.util.List;
@@ -63,7 +62,7 @@
passedNodes.add(node);
i = next_set_bit;
}
- SelectUtil.setSelectedNodeState(network, passedNodes,
true);
+ SelectUtil.setSelectedNodeState(passedNodes, true);
}
if (pFilter.getAdvancedSetting().isEdgeChecked()&&
(pFilter.getEdgeBits() != null)) {
// Select edges
@@ -79,7 +78,7 @@
passedEdges.add(edge);
i = next_set_bit;
}
- SelectUtil.setSelectedEdgeState(network, passedEdges,
true);
+ SelectUtil.setSelectedEdgeState(passedEdges, true);
}
applicationManager.getCurrentNetworkView().updateView();
Modified:
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/SelectUtil.java
===================================================================
---
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/SelectUtil.java
2010-12-18 21:38:58 UTC (rev 23243)
+++
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/filters/util/SelectUtil.java
2010-12-20 17:20:31 UTC (rev 23244)
@@ -1,44 +1,73 @@
package org.cytoscape.filter.internal.filters.util;
import java.util.Collection;
+import java.util.HashSet;
import java.util.Set;
+import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTableEntry;
public class SelectUtil {
public static void unselectAllNodes(CyNetwork network) {
-
+ setSelectedState(network.getNodeList(), Boolean.FALSE);
}
public static void unselectAllEdges(CyNetwork network) {
-
+ setSelectedState(network.getEdgeList(), Boolean.FALSE);
}
- public static void setSelectedNodeState(CyNetwork network, Collection
list, boolean b) {
- // TODO Auto-generated method stub
-
+ public static void setSelectedNodeState(Collection<CyNode> list,
boolean selected) {
+ setSelectedState(list, selected);
}
- public static void setSelectedEdgeState(CyNetwork network, Collection
list, boolean b) {
- // TODO Auto-generated method stub
-
+ public static void setSelectedEdgeState(Collection<CyEdge> list,
boolean selected) {
+ setSelectedState(list, selected);
}
- public static Set getSelectedNodes(CyNetwork cyNetwork) {
- // TODO Auto-generated method stub
- return null;
+ static void setSelectedState(Collection<? extends CyTableEntry> list,
Boolean selected) {
+ for (CyTableEntry edge : list) {
+ CyRow row = edge.getCyRow();
+ row.set(CyTableEntry.SELECTED, selected);
+ }
+
}
+
+ public static Set<CyNode> getSelectedNodes(CyNetwork cyNetwork) {
+ return getSelected(cyNetwork.getNodeList());
+ }
- public static Set getSelectedEdges(CyNetwork cyNetwork) {
- // TODO Auto-generated method stub
- return null;
+ public static Set<CyEdge> getSelectedEdges(CyNetwork cyNetwork) {
+ return getSelected(cyNetwork.getEdgeList());
}
+ static <T extends CyTableEntry> Set<T> getSelected(Collection<T> items)
{
+ Set<T> entries = new HashSet<T>();
+ for (T item : items) {
+ CyRow row = item.getCyRow();
+ if (row.get(CyTableEntry.SELECTED, Boolean.class)) {
+ entries.add(item);
+ }
+ }
+ return entries;
+ }
+
public static void selectAllNodes(CyNetwork cyNetwork) {
- // TODO Auto-generated method stub
+ selectAll(cyNetwork.getNodeList());
}
public static void selectAllEdges(CyNetwork cyNetwork) {
- // TODO Auto-generated method stub
+ selectAll(cyNetwork.getEdgeList());
}
+
+ static <T extends CyTableEntry> void selectAll(Collection<T> items) {
+ for (T item : items) {
+ CyRow row = item.getCyRow();
+ if (!row.get(CyTableEntry.SELECTED, Boolean.class)) {
+ row.set(CyTableEntry.SELECTED, Boolean.TRUE);
+ }
+ }
+ }
}
Modified:
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/quickfind/plugin/QuickFindPlugIn.java
===================================================================
---
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/quickfind/plugin/QuickFindPlugIn.java
2010-12-18 21:38:58 UTC (rev 23243)
+++
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/quickfind/plugin/QuickFindPlugIn.java
2010-12-20 17:20:31 UTC (rev 23244)
@@ -41,6 +41,7 @@
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.List;
import java.util.Set;
@@ -274,7 +275,7 @@
// Assemble Hit Objects
final Object[] graphObjects = hit.getAssociatedObjects();
- final List<Object> list = new ArrayList<Object>();
+ final List list = new ArrayList();
for (int i = 0; i < graphObjects.length; i++) {
list.add(graphObjects[i]);
@@ -289,10 +290,10 @@
GenericIndex index =
quickFind.getIndex(cyNetwork);
if (index.getIndexType() ==
QuickFind.INDEX_NODES) {
-
SelectUtil.setSelectedNodeState(network, list, true);
+
SelectUtil.setSelectedNodeState(list, true);
applicationManager.getCurrentNetworkView().fitSelected();
} else {
-
SelectUtil.setSelectedEdgeState(network, list, true);
+
SelectUtil.setSelectedEdgeState(list, true);
List<CyNode> nodeList = new
ArrayList<CyNode>();
@@ -304,7 +305,7 @@
nodeList.add(targetNode);
}
-
SelectUtil.setSelectedNodeState(network, nodeList, true);
+
SelectUtil.setSelectedNodeState(nodeList, true);
networkView.fitSelected();
}
@@ -370,7 +371,7 @@
Set selectedEdgeSet = SelectUtil.getSelectedEdges(cyNetwork);
if (selectedEdgeSet.size() > 0) {
- SelectUtil.setSelectedEdgeState(cyNetwork,
selectedEdgeSet, false);
+ SelectUtil.setSelectedEdgeState(selectedEdgeSet, false);
}
// Then, determine the current set of selected nodes
@@ -390,8 +391,8 @@
SwingUtilities.invokeLater(new Runnable() {
public void run() {
-
SelectUtil.setSelectedNodeState(cyNetwork, toBeSelected, true);
-
SelectUtil.setSelectedNodeState(cyNetwork, toBeUnselected, false);
+
SelectUtil.setSelectedNodeState(toBeSelected, true);
+
SelectUtil.setSelectedNodeState(toBeUnselected, false);
applicationManager.getCurrentNetworkView().updateView();
}
});
@@ -402,7 +403,7 @@
Set selectedNodeSet = SelectUtil.getSelectedNodes(cyNetwork);
if (selectedNodeSet.size() > 0) {
- SelectUtil.setSelectedNodeState(cyNetwork,
selectedNodeSet, false);
+ SelectUtil.setSelectedNodeState(selectedNodeSet, false);
}
// Then, determine the current set of selected edge
@@ -422,8 +423,8 @@
SwingUtilities.invokeLater(new Runnable() {
public void run() {
-
SelectUtil.setSelectedEdgeState(cyNetwork, toBeSelected, true);
-
SelectUtil.setSelectedEdgeState(cyNetwork, toBeUnselected, false);
+
SelectUtil.setSelectedEdgeState(toBeSelected, true);
+
SelectUtil.setSelectedEdgeState(toBeUnselected, false);
applicationManager.getCurrentNetworkView().updateView();
}
});
Modified:
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/quickfind/util/CyAttributesUtil.java
===================================================================
---
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/quickfind/util/CyAttributesUtil.java
2010-12-18 21:38:58 UTC (rev 23243)
+++
core3/filter-impl/trunk/src/main/java/org/cytoscape/filter/internal/quickfind/util/CyAttributesUtil.java
2010-12-20 17:20:31 UTC (rev 23244)
@@ -36,6 +36,7 @@
package org.cytoscape.filter.internal.quickfind.util;
+import java.util.Collection;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
@@ -178,7 +179,24 @@
}
public static boolean isNullAttribute(CyNetwork cyNetwork, String
indexType, String attributeName) {
- // TODO Auto-generated method stub
- return false;
+ Collection<? extends CyTableEntry> entries;
+ if (indexType.equals("node")) {
+ entries = cyNetwork.getNodeList();
+ } else if (indexType.equals("edge")) {
+ entries = cyNetwork.getEdgeList();
+ } else {
+ return true;
+ }
+ if (entries.size() == 0) {
+ return true;
+ }
+ for (CyTableEntry entry : entries) {
+ CyRow row = entry.getCyRow();
+ Class<?> type = row.getType(attributeName);
+ if (row.get(attributeName, type) != null) {
+ return false;
+ }
+ }
+ return true;
}
}
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