X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=4972874549554961b7a9a79a1c41f93815e1cddb;hb=e3a5770d5844eb5cf183424643605611d3545726;hp=94296719dd6a7ede0dc9ce9a7566c59645cf9149;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 9429671..4972874 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -143,7 +143,6 @@ public class APopupMenu
         else
           url = link.substring(link.lastIndexOf("|")+1);
 
-        System.out.println("add "+url +" "+target);
            item.addActionListener(new java.awt.event.ActionListener()
            {
                public void actionPerformed(ActionEvent e)
@@ -197,7 +196,7 @@ 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();
@@ -233,22 +232,44 @@ public class APopupMenu
     else if(source==cut)
       ap.alignFrame.cut_actionPerformed();
     else if(source==toUpper || source==toLower || source==toggleCase)
-    {
+    {/*
       SequenceGroup sg = ap.av.getSelectionGroup();
       if (sg != null)
       {
         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();
-      }
+      }*/
     }
     else
       outputText(evt);
@@ -598,24 +619,30 @@ 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);
     }