showConservation, quality, identity not used

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 82477ea..4972874 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -143,7 +143,6 @@ public class APopupMenu
         else\r
           url = link.substring(link.lastIndexOf("|")+1);\r
 \r
-        System.out.println("add "+url +" "+target);\r
            item.addActionListener(new java.awt.event.ActionListener()\r
            {\r
                public void actionPerformed(ActionEvent e)\r
@@ -197,7 +196,7 @@ public class APopupMenu
       helixColour_actionPerformed();\r
     else if(source==strandColour)\r
       strandColour_actionPerformed();\r
-    else if(source==clustalColour)\r
+    else if(source==turnColour)\r
       turnColour_actionPerformed();\r
     else if(source==buriedColour)\r
       buriedColour_actionPerformed();\r
@@ -233,7 +232,7 @@ public class APopupMenu
     else if(source==cut)\r
       ap.alignFrame.cut_actionPerformed();\r
     else if(source==toUpper || source==toLower || source==toggleCase)\r
-    {\r
+    {/*\r
       SequenceGroup sg = ap.av.getSelectionGroup();\r
       if (sg != null)\r
       {\r
@@ -270,7 +269,7 @@ public class APopupMenu
         while (end < sg.getEndRes());\r
         }\r
         ap.seqPanel.seqCanvas.repaint();\r
-      }\r
+      }*/\r
     }\r
     else\r
       outputText(evt);\r
@@ -620,24 +619,30 @@ public class APopupMenu
     SequenceGroup sg = ap.av.getSelectionGroup();\r
     if(sg==null || sg.getSize(false)<1)\r
     {\r
-      ap.av.hideSequence(seq);\r
+      ap.av.hideSequence(new SequenceI[]{seq});\r
       return;\r
     }\r
 \r
+    int gsize = sg.getSize(false);\r
+    SequenceI [] hseqs;\r
+\r
+    hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];\r
+\r
       int index = 0;\r
-      while(index < sg.getSize(false))\r
+      for(int i=0; i<gsize; i++)\r
       {\r
-        if(representGroup && sg.getSequenceAt(index)!=seq)\r
+        if(representGroup && sg.getSequenceAt(i)!=seq)\r
         {\r
-          seq.addHiddenSequence(sg.getSequenceAt(index));\r
-          ap.av.hideSequence(sg.getSequenceAt(index));\r
+          seq.addHiddenSequence(sg.getSequenceAt(i));\r
+          hseqs[index++] = sg.getSequenceAt(i);\r
         }\r
         else if(!representGroup)\r
         {\r
-          ap.av.hideSequence(sg.getSequenceAt(index));\r
+          hseqs[index++] = sg.getSequenceAt(i);\r
         }\r
-        index ++;\r
-      }\r
+        }\r
+\r
+      ap.av.hideSequence(hseqs);\r
 \r
       ap.av.setSelectionGroup(null);\r
     }\r