Mapping to PDB added

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index abd76d6..0d1dad3 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -46,7 +46,7 @@ public class APopupMenu
   MenuItem noColourmenuItem = new MenuItem();\r
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
 \r
-  AlignmentPanel ap;\r
+  final AlignmentPanel ap;\r
   MenuItem unGroupMenuItem = new MenuItem();\r
   MenuItem nucleotideMenuItem = new MenuItem();\r
   Menu colourMenu = new Menu();\r
@@ -54,7 +54,7 @@ public class APopupMenu
   CheckboxMenuItem showText = new CheckboxMenuItem();\r
   CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
 \r
-  public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)\r
+  public APopupMenu(AlignmentPanel apanel, Sequence seq, Vector links)\r
   {\r
     ///////////////////////////////////////////////////////////\r
     // If this is activated from the sequence panel, the user may want to\r
@@ -63,7 +63,7 @@ public class APopupMenu
     // If from the IDPanel, we must display the sequence menu\r
     //////////////////////////////////////////////////////////\r
 \r
-    this.ap = ap;\r
+    this.ap = apanel;\r
 \r
     try\r
     {\r
@@ -105,7 +105,7 @@ public class APopupMenu
            {\r
                public void actionPerformed(ActionEvent e)\r
                {\r
-                  jalview.bin.JalviewLite.showURL(url, target);\r
+                  ap.alignFrame.showURL(url, target);\r
                }\r
            });\r
           linkMenu.add(item);\r
@@ -319,6 +319,8 @@ public class APopupMenu
       }\r
         }\r
     ap.seqPanel.seqCanvas.repaint();\r
+    if(ap.overviewPanel!=null)\r
+      ap.overviewPanel.updateOverviewImage();\r
   }\r
 \r
   protected void clustalColour_actionPerformed(ActionEvent e)\r
@@ -379,6 +381,9 @@ public class APopupMenu
   protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
+\r
     if (abovePIDColour.getState())\r
     {\r
       sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
@@ -435,6 +440,8 @@ public class APopupMenu
   protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
   {\r
     SequenceGroup sg = getGroup();\r
+    if(sg.cs==null)\r
+          return;\r
 \r
     if (conservationMenuItem.getState())\r
     {\r
@@ -462,7 +469,7 @@ public class APopupMenu
 \r
   protected void analyze_actionPerformed(ActionEvent e)\r
   {\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);\r
     Frame frame = new Frame();\r
     frame.add(cap);\r
     jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r