Author: scooter
Date: 2010-08-04 11:18:06 -0700 (Wed, 04 Aug 2010)
New Revision: 21189
Added:
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/Columns.java
Modified:
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/CreateByAttributeDialog.java
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/GroupTableModel.java
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/GroupToolDialog.java
Log:
Additions for 2.8 network-specific groups
Added: csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/Columns.java
===================================================================
--- csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/Columns.java
(rev 0)
+++ csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/Columns.java
2010-08-04 18:18:06 UTC (rev 21189)
@@ -0,0 +1,76 @@
+/* vim: set ts=2: */
+/**
+ * Copyright (c) 2006 The Regents of the University of California.
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions, and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above
+ * copyright notice, this list of conditions, and the following
+ * disclaimer in the documentation and/or other materials provided
+ * with the distribution.
+ * 3. Redistributions must acknowledge that this software was
+ * originally developed by the UCSF Computer Graphics Laboratory
+ * under support by the NIH National Center for Research Resources,
+ * grant P41-RR01081.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
+ * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+ * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
+ * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+ * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+ * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ */
+package groupTool.ui;
+
+// System imports
+import java.util.List;
+import java.util.ArrayList;
+
+public enum Columns {
+ NAME("Group Name", String.class),
+ NETWORK("Network", String.class),
+ NODES("Nodes", Integer.class),
+ INTERNAL("Internal Edges", Integer.class),
+ EXTERNAL("External Edges", Integer.class),
+ VIEWER("Viewer", String.class);
+
+ protected static List<Columns> columnList;
+
+ protected static void addColumn(Columns column) {
+ if (columnList == null) columnList = new ArrayList<Columns>();
+ columnList.add(column);
+ }
+
+ public static int columnCount() { return columnList.size(); }
+
+ public static String getColumnName(int col) { return
columnList.get(col).toString(); }
+ public static Columns getColumn(int col) { return columnList.get(col); }
+ public static int getColumnNumber(Columns column) {
+ for (int i = 0; i < columnList.size(); i++) {
+ if (columnList.get(i).equals(column)) return i;
+ }
+ return -1;
+ }
+
+ private String columnName = null;
+ private Class columnClass = null;
+
+ Columns(String name, Class classType) {
+ columnName = name;
+ columnClass = classType;
+ Columns.addColumn(this);
+ }
+
+ public String toString() {return columnName;}
+ public Class getColumnClass() { return columnClass; }
+}
Modified:
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/CreateByAttributeDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/CreateByAttributeDialog.java
2010-08-04 18:04:14 UTC (rev 21188)
+++
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/CreateByAttributeDialog.java
2010-08-04 18:18:06 UTC (rev 21189)
@@ -226,7 +226,7 @@
CyGroupManager.removeGroup(group);
}
- group = CyGroupManager.createGroup(groupName,
nodeList, viewer);
+ group = CyGroupManager.createGroup(groupName,
nodeList, viewer, network);
// nodeAttributes.setAttribute(groupName,
attribute, groupName);
CyGroupViewer groupViewer =
CyGroupManager.getGroupViewer(viewer);
groupViewer.groupCreated(group);
Modified:
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/GroupTableModel.java
===================================================================
---
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/GroupTableModel.java
2010-08-04 18:04:14 UTC (rev 21188)
+++
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/GroupTableModel.java
2010-08-04 18:18:06 UTC (rev 21189)
@@ -32,29 +32,18 @@
*/
package groupTool.ui;
+import javax.swing.table.AbstractTableModel;
+
// System imports
import java.util.List;
import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.HashMap;
-import javax.swing.*;
-import javax.swing.table.*;
-import javax.swing.event.*;
-import javax.swing.text.Position;
-
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.event.*;
-
// Cytoscape imports
import cytoscape.CyNetwork;
-import cytoscape.CyNode;
-import cytoscape.view.CyNetworkView;
-import cytoscape.groups.*;
+import cytoscape.groups.CyGroup;
+import cytoscape.groups.CyGroupManager;
+
/**
* The GroupTableModel class provides the table model used by the
GroupToolDialog
*
@@ -64,8 +53,6 @@
public class GroupTableModel
extends AbstractTableModel {
- private static final String[] columnNames = {"Group Name", "Nodes",
"Internal Edges", "External Edges", "Viewer"};
-
private GroupToolDialog groupDialog = null;
private List<CyGroup> groupList = null;
@@ -93,7 +80,7 @@
*
* @return 5
*/
- public int getColumnCount() { return columnNames.length; }
+ public int getColumnCount() { return Columns.columnCount(); }
/**
* Return the value at the requested row and column. In our case
@@ -107,17 +94,28 @@
*/
public Object getValueAt(int row, int col) {
CyGroup group = groupList.get(row);
- if (col == 0) {
+
+ Columns column = Columns.getColumn(col);
+ switch (column) {
+
+ case NAME:
return group.getGroupName();
- } else if (col == 1) {
- return new Integer(group.getNodes().size());
- } else if (col == 2) {
+ case NETWORK:
+ CyNetwork net = group.getNetwork();
+ if (net != null)
+ return net.getTitle();
+ return "Global";
+ case INTERNAL:
return new Integer(group.getInnerEdges().size());
- } else if (col == 3) {
+ case EXTERNAL:
return new Integer(group.getOuterEdges().size());
- } else if (col == 4) {
+ case NODES:
+ return new Integer(group.getNodes().size());
+ case VIEWER:
return group.getViewer();
+
}
+
return null;
}
@@ -129,7 +127,8 @@
* @return false
*/
public boolean isCellEditable(int row, int col) {
- if (col == 4)
+ Columns column = Columns.getColumn(col);
+ if (column == Columns.VIEWER || column == Columns.NETWORK)
return true;
return false;
@@ -142,7 +141,7 @@
* @return column name as a String
*/
public String getColumnName(int col) {
- return columnNames[col];
+ return Columns.getColumnName(col);
}
/**
@@ -153,9 +152,7 @@
* @return object Class of this column
*/
public Class getColumnClass(int c) {
- if (c == 0 || c == 4) return String.class;
-
- return Integer.class;
+ return Columns.getColumn(c).getColumnClass();
}
public CyGroup getGroupAtRow(int row) {
Modified:
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/GroupToolDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/GroupToolDialog.java
2010-08-04 18:04:14 UTC (rev 21188)
+++
csplugins/trunk/ucsf/scooter/groupTool/src/groupTool/ui/GroupToolDialog.java
2010-08-04 18:18:06 UTC (rev 21189)
@@ -35,8 +35,6 @@
import java.util.ArrayList;
import java.util.List;
import java.util.Collection;
-import java.util.Iterator;
-import java.util.HashMap;
import javax.swing.*;
import javax.swing.tree.*;
@@ -53,7 +51,10 @@
import java.awt.GridBagLayout;
import java.awt.event.*;
-import cytoscape.groups.*;
+import cytoscape.groups.CyGroup;
+import cytoscape.groups.CyGroupChangeListener;
+import cytoscape.groups.CyGroupManager;
+import cytoscape.groups.CyGroupViewer;
import cytoscape.Cytoscape;
import cytoscape.CyNetwork;
import cytoscape.CyNode;
@@ -115,7 +116,8 @@
this.groupTable = new JTable(sorter);
sorter.setTableHeader(groupTable.getTableHeader());
- setUpViewerRenderer(groupTable,
groupTable.getColumnModel().getColumn(4));
+ setUpViewerRenderer(groupTable);
+ setUpNetworkRenderer(groupTable);
groupTable.setCellSelectionEnabled(true);
ListSelectionModel lsm = groupTable.getSelectionModel();
lsm.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
@@ -189,13 +191,14 @@
List<CyGroup> groupList = CyGroupManager.getGroupList();
String groupName = JOptionPane.showInputDialog("Please
enter a name for this group");
if (groupName == null) return;
- CyGroup group = CyGroupManager.createGroup(groupName,
currentNodes, null);
+ CyGroup group = CyGroupManager.createGroup(groupName,
currentNodes, null, network);
} else if ("delete".equals(e.getActionCommand())) {
// Don't listen until we're done
CyGroupManager.removeGroupChangeListener(this);
int rows[] = groupTable.getSelectedRows();
for (int row = 0; row < rows.length; row++) {
- String groupName = (String)
groupTable.getValueAt(rows[row], 0);
+ String groupName = (String)
groupTable.getValueAt(rows[row],
+
Columns.getColumnNumber(Columns.NAME));
CyGroup group =
CyGroupManager.findGroup(groupName);
if (group == null) continue;
CyGroupManager.removeGroup(group);
@@ -214,7 +217,8 @@
if (rows == null) return;
int cols[] = groupTable.getSelectedColumns();
for (int row = 0; row < rows.length; row++) {
- String groupName = (String)
groupTable.getValueAt(rows[row], 0);
+ String groupName = (String)
groupTable.getValueAt(rows[row],
+
Columns.getColumnNumber(Columns.NAME));
CyGroup group =
CyGroupManager.findGroup(groupName);
if (group == null) continue;
@@ -224,14 +228,30 @@
if
("clear".equals(e.getActionCommand()))
state = false;
- if (cols[col] == 1 || cols[col] == 0) {
+ Columns column =
Columns.getColumn(cols[col]);
+
+ switch (column) {
+ case NAME:
Cytoscape.getCurrentNetwork().setSelectedNodeState(group.getGroupNode(), state);
Cytoscape.getCurrentNetwork().setSelectedNodeState(group.getNodes(), state);
- }
- if (cols[col] == 2 || cols[col] == 0)
Cytoscape.getCurrentNetwork().setSelectedEdgeState(group.getInnerEdges(),
state);
- if (cols[col] == 3 || cols[col] == 0)
Cytoscape.getCurrentNetwork().setSelectedEdgeState(group.getOuterEdges(),
state);
+ break;
+
+ case NODES:
+
Cytoscape.getCurrentNetwork().setSelectedNodeState(group.getGroupNode(), state);
+
Cytoscape.getCurrentNetwork().setSelectedNodeState(group.getNodes(), state);
+ break;
+
+ case INTERNAL:
+
Cytoscape.getCurrentNetwork().setSelectedEdgeState(group.getInnerEdges(),
state);
+ break;
+
+ case EXTERNAL:
+
Cytoscape.getCurrentNetwork().setSelectedEdgeState(group.getOuterEdges(),
state);
+ break;
+ }
+
}
}
Cytoscape.getCurrentNetworkView().updateView();
@@ -242,12 +262,12 @@
}
}
- private void setUpViewerRenderer(JTable table, TableColumn
viewerColumn) {
+ private void setUpViewerRenderer(JTable table) {
+ int viewerCol = Columns.getColumnNumber(Columns.VIEWER);
+ TableColumn viewerColumn =
groupTable.getColumnModel().getColumn(viewerCol);
JComboBox vBox = new JComboBox();
Collection<CyGroupViewer> viewers =
CyGroupManager.getGroupViewers();
- Iterator <CyGroupViewer> vIter = viewers.iterator();
- while (vIter.hasNext()) {
- CyGroupViewer gv = vIter.next();
+ for (CyGroupViewer gv: viewers) {
vBox.addItem(gv.getViewerName());
}
DefaultCellEditor editor = new DefaultCellEditor(vBox);
@@ -255,21 +275,65 @@
viewerColumn.setCellEditor(editor);
}
+ private void setUpNetworkRenderer(JTable table) {
+ int netCol = Columns.getColumnNumber(Columns.NETWORK);
+ TableColumn networkColumn =
groupTable.getColumnModel().getColumn(netCol);
+ JComboBox vBox = new JComboBox();
+ // Get the list of networks
+ Collection<CyNetwork> networks = Cytoscape.getNetworkSet();
+ for (CyNetwork net: networks) {
+ vBox.addItem(net.getTitle());
+ }
+ vBox.addItem("Global");
+ DefaultCellEditor editor = new DefaultCellEditor(vBox);
+ editor.addCellEditorListener(this);
+ networkColumn.setCellEditor(editor);
+ }
+
public void editingCanceled(ChangeEvent e) { }
public void editingStopped(ChangeEvent e) {
int row = groupTable.getSelectedRow();
int col = groupTable.getSelectedColumn();
- if (row == -1 || col != 4) return;
+ if (row == -1) return;
+ Columns column = Columns.getColumn(col);
+ CyGroup group = tableModel.getGroupAtRow(row);
DefaultCellEditor editor = (DefaultCellEditor)e.getSource();
- String viewerName = (String) editor.getCellEditorValue();
- String oldViewerName = (String)groupTable.getValueAt(row,col);
- if (viewerName.equals(oldViewerName)) return;
- CyGroup group = tableModel.getGroupAtRow(row);
- // Set the new viewer
- CyGroupManager.setGroupViewer(group, viewerName,
Cytoscape.getCurrentNetworkView(), true);
+ switch (column) {
+ case VIEWER:
+ String viewerName = (String)
editor.getCellEditorValue();
+ String oldViewerName =
(String)groupTable.getValueAt(row,col);
+ if (viewerName.equals(oldViewerName)) return;
+
+ // Set the new viewer
+ CyGroupManager.setGroupViewer(group,
viewerName, Cytoscape.getCurrentNetworkView(), true);
+ break;
+
+ case NETWORK:
+ String networkName = (String)
editor.getCellEditorValue();
+ String oldNetworkName =
(String)groupTable.getValueAt(row,col);
+ if (networkName.equals(oldNetworkName)) return;
+
+ // OK, update the network
+
+ if (networkName.equals("Global")) {
+ group.setNetwork(null, true);
+ return;
+ }
+
+ Collection<CyNetwork> networks =
Cytoscape.getNetworkSet();
+ for (CyNetwork network: networks) {
+ if
(network.getTitle().equals(networkName)) {
+ group.setNetwork(network, true);
+ return;
+ }
+ }
+ break;
+
+ }
+ return;
}
public void valueChanged (ListSelectionEvent e) {
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
