Author: scooter
Date: 2013-03-24 07:51:03 -0700 (Sun, 24 Mar 2013)
New Revision: 31164
Added:
csplugins/trunk/ucsf/scooter/chemViz/lib/SMSD.jar
Removed:
csplugins/trunk/ucsf/scooter/chemViz/tools/TestMCSS.class
Modified:
csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-1.5.1.git.jar
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/AttributesMenu.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/MCSSMenus.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/SearchMenu.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/SimilarityMenu.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/StructureMenus.java
Log:
Fix up menus and move to latest cdk and SMSD
Added: csplugins/trunk/ucsf/scooter/chemViz/lib/SMSD.jar
===================================================================
(Binary files differ)
Property changes on: csplugins/trunk/ucsf/scooter/chemViz/lib/SMSD.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-1.5.1.git.jar
===================================================================
(Binary files differ)
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/AttributesMenu.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/AttributesMenu.java
2013-03-21 23:59:41 UTC (rev 31163)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/AttributesMenu.java
2013-03-24 14:51:03 UTC (rev 31164)
@@ -73,8 +73,8 @@
if (context == null) {
JMenu create = new JMenu("Create attributes from
compound descriptors");
+ addNodeAttributesMenus(create, null);
addEdgeAttributesMenus(create, null);
- addNodeAttributesMenus(create, null);
menu.add(create);
} else if (context instanceof NodeView) {
addNodeAttributesMenus(menu, (NodeView)context);
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/MCSSMenus.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/MCSSMenus.java
2013-03-21 23:59:41 UTC (rev 31163)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/MCSSMenus.java
2013-03-24 14:51:03 UTC (rev 31164)
@@ -106,6 +106,8 @@
if (edgeContext == null) {
// Populating main menu
JMenuItem item = buildMenuItem("of all edges",
"allEdges");
+ if (!settingsDialog.hasEdgeCompounds(null))
+ item.setEnabled(false);
menu.add(item);
if (selectedEdges != null && selectedEdges.size() > 0) {
JMenuItem item2 = buildMenuItem("of selected
edges", "selectedEdges");
@@ -140,6 +142,8 @@
if (nodeContext == null) {
JMenuItem item = buildMenuItem("of all nodes",
"allNodes");
+ if (!settingsDialog.hasNodeCompounds(null))
+ item.setEnabled(false);
menu.add(item);
if (selectedNodes != null && selectedNodes.size() > 0) {
JMenuItem item2 = buildMenuItem("of selected
nodes", "selectedNodes");
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/SearchMenu.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/SearchMenu.java
2013-03-21 23:59:41 UTC (rev 31163)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/SearchMenu.java
2013-03-24 14:51:03 UTC (rev 31164)
@@ -106,7 +106,10 @@
if (edgeContext == null) {
// Populating main menu
JMenuItem item = buildMenuItem("all edges", "allEdges");
+ if (!settingsDialog.hasEdgeCompounds(null))
+ item.setEnabled(false);
menu.add(item);
+ menu.add(item);
if (selectedEdges != null && selectedEdges.size() > 0) {
JMenuItem item2 = buildMenuItem("selected
edges", "selectedEdges");
if
(!settingsDialog.hasEdgeCompounds(selectedEdges)) {
@@ -140,6 +143,8 @@
if (nodeContext == null) {
JMenuItem item = buildMenuItem("all nodes", "allNodes");
+ if (!settingsDialog.hasNodeCompounds(null))
+ item.setEnabled(false);
menu.add(item);
if (selectedNodes != null && selectedNodes.size() > 0) {
JMenuItem item2 = buildMenuItem("selected
nodes", "selectedNodes");
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/SimilarityMenu.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/SimilarityMenu.java
2013-03-21 23:59:41 UTC (rev 31163)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/SimilarityMenu.java
2013-03-24 14:51:03 UTC (rev 31164)
@@ -69,7 +69,10 @@
JMenu simMenu = new JMenu("Create similarity network");
menu.add(simMenu);
- simMenu.add(buildMenuItem("for all nodes",
"allNodeSimilarity"));
+ JMenuItem item = buildMenuItem("for all nodes",
"allNodeSimilarity");
+ if (!settingsDialog.hasNodeCompounds(null))
+ item.setEnabled(false);
+ simMenu.add(item);
Set<GraphObject> selectedNodes =
Cytoscape.getCurrentNetwork().getSelectedNodes();
if (selectedNodes != null && selectedNodes.size() > 1) {
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/StructureMenus.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/StructureMenus.java
2013-03-21 23:59:41 UTC (rev 31163)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/menus/StructureMenus.java
2013-03-24 14:51:03 UTC (rev 31164)
@@ -101,7 +101,10 @@
if (edgeContext == null) {
// Populating main menu
- menu.add(buildMenuItem("for all edges",
"clearAllEdges"));
+ JMenuItem item = buildMenuItem("for all edges",
"clearAllEdges");
+ if (!settingsDialog.hasEdgeCompounds(null))
+ item.setEnabled(false);
+ menu.add(item);
if (selectedEdges != null && selectedEdges.size() > 0) {
JMenuItem item2 = buildMenuItem("for selected
edges", "clearSelectedEdges");
if
(!settingsDialog.hasEdgeCompounds(selectedEdges)) {
@@ -136,7 +139,10 @@
if (nodeContext == null) {
// Populating main menu
- menu.add(buildMenuItem("for all nodes",
"clearAllNodes"));
+ JMenuItem item = buildMenuItem("for all nodes",
"clearAllNodes");
+ if (!settingsDialog.hasNodeCompounds(null))
+ item.setEnabled(false);
+ menu.add(item);
if (selectedNodes != null && selectedNodes.size() > 0) {
JMenuItem item2 = buildMenuItem("for selected
nodes", "clearSelectedNodes");
if
(!settingsDialog.hasNodeCompounds(selectedNodes)) {
Deleted: csplugins/trunk/ucsf/scooter/chemViz/tools/TestMCSS.class
===================================================================
(Binary files differ)
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