X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=b3c8f20b4218df1a5296db67f27108a8e7f95234;hb=8797ce6a98df4aa29eefecb25b10fed4f2ab9e86;hp=be4a599e748fff68acfd4eb65e4690c85cc7d4b1;hpb=19795496c99500c7ea09dcadb39140566478a97b;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index be4a599..b3c8f20 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -89,11 +89,10 @@ public class APopupMenu
       e.printStackTrace();
     }
 
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size()-1; i++)
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
-      MenuItem item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats.
-                                     elementAt(
-                                         i));
+      MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );
+
       item.addActionListener(this);
       outputmenu.add(item);
     }
@@ -198,7 +197,7 @@ public class APopupMenu
       helixColour_actionPerformed();
     else if(source==strandColour)
       strandColour_actionPerformed();
-    else if(source==clustalColour)
+    else if(source==turnColour)
       turnColour_actionPerformed();
     else if(source==buriedColour)
       buriedColour_actionPerformed();
@@ -227,7 +226,6 @@ public class APopupMenu
     else if(source == revealAll)
     {
         ap.av.showAllHiddenSeqs();
-        ap.repaint();
     }
 
     else if(source==copy)
@@ -241,13 +239,35 @@ public class APopupMenu
       {
         for (int g = 0; g < sg.getSize(true); g++)
         {
-          if (source == toggleCase)
-           ((SequenceI) sg.getSequences(true).elementAt(g))
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
-          else
-            ((SequenceI) sg.getSequences(true).elementAt(g))
-                .changeCase(source == toUpper, sg.getStartRes(),
-                                           sg.getEndRes() + 1);
+          int start = sg.getStartRes();
+          int end = sg.getEndRes() + 1;
+
+          do
+          {
+            if (ap.av.hasHiddenColumns)
+            {
+              end = ap.av.colSel.getHiddenBoundaryRight(start);
+              if (start == end)
+                end = sg.getEndRes() + 1;
+              if (end > sg.getEndRes())
+                end = sg.getEndRes() + 1;
+            }
+
+            if (source == toggleCase)
+              ( (SequenceI) sg.getSequences(true).elementAt(g))
+                  .toggleCase(start, end);
+            else
+              ( (SequenceI) sg.getSequences(true).elementAt(g))
+                  .changeCase(source == toUpper, start, end);
+
+            if (ap.av.hasHiddenColumns)
+            {
+              start = ap.av.colSel.adjustForHiddenColumns(end);
+              start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+            }
+
+          }
+        while (end < sg.getEndRes());
         }
         ap.seqPanel.seqCanvas.repaint();
       }
@@ -600,28 +620,32 @@ public class APopupMenu
     SequenceGroup sg = ap.av.getSelectionGroup();
     if(sg==null || sg.getSize(false)<1)
     {
-      ap.av.hideSequence(seq);
+      ap.av.hideSequence(new SequenceI[]{seq});
       return;
     }
 
+    int gsize = sg.getSize(false);
+    SequenceI [] hseqs;
+
+    hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
+
       int index = 0;
-      while(index < sg.getSize(false))
+      for(int i=0; i<gsize; i++)
       {
-        if(representGroup && sg.getSequenceAt(index)!=seq)
+        if(representGroup && sg.getSequenceAt(i)!=seq)
         {
-          seq.addHiddenSequence(sg.getSequenceAt(index));
-          ap.av.hideSequence(sg.getSequenceAt(index));
+          seq.addHiddenSequence(sg.getSequenceAt(i));
+          hseqs[index++] = sg.getSequenceAt(i);
         }
         else if(!representGroup)
         {
-          ap.av.hideSequence(sg.getSequenceAt(index));
+          hseqs[index++] = sg.getSequenceAt(i);
         }
-        index ++;
-      }
+        }
+
+      ap.av.hideSequence(hseqs);
 
       ap.av.setSelectionGroup(null);
-      ap.repaint();
-      refresh();
     }
 
 }