X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=f786bde5dfaba8b787b6363c7f4c7b6539b81bbd;hb=2e699d341f8e64868e3c279f9c02af617c4e9b44;hp=28e40eb1ea7591de061b72b0b36bf6dca98c7357;hpb=5cd5b6e7864fe435ceb3f5c2f339a436ea0aac93;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 28e40eb..f786bde 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
@@ -26,6 +26,7 @@ import java.util.Vector;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.commands.ChangeCaseCommand;
 
 public class APopupMenu
     extends java.awt.PopupMenu implements ActionListener, ItemListener
@@ -67,6 +68,7 @@ public class APopupMenu
 
   Sequence seq;
   MenuItem revealAll = new MenuItem();
+  Menu menu1 = new Menu();
 
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
@@ -89,11 +91,10 @@ 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);
     }
@@ -113,6 +114,7 @@ public class APopupMenu
     }
     else
     {
+      remove(hideSeqs);
       remove(groupMenu);
     }
 
@@ -152,7 +154,10 @@ public class APopupMenu
            });
           linkMenu.add(item);
       }
-      seqMenu.add(linkMenu);
+      if(seq!=null)
+        seqMenu.add(linkMenu);
+      else
+        add(linkMenu);
     }
     if(seq!=null)
     {
@@ -193,7 +198,7 @@ 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();
@@ -222,7 +227,6 @@ public class APopupMenu
     else if(source == revealAll)
     {
         ap.av.showAllHiddenSeqs();
-        ap.repaint();
     }
 
     else if(source==copy)
@@ -231,21 +235,75 @@ public class APopupMenu
       ap.alignFrame.cut_actionPerformed();
     else if(source==toUpper || source==toLower || source==toggleCase)
     {
-      SequenceGroup sg = ap.av.getSelectionGroup();
-      if (sg != null)
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    Vector regions = new Vector();
+    if (sg != null)
+    {
+      int start = sg.getStartRes();
+      int end = sg.getEndRes() + 1;
+
+      do
       {
-        for (int g = 0; g < sg.getSize(true); g++)
+        if (ap.av.hasHiddenColumns)
         {
-          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);
+          if(start==0)
+            start = ap.av.colSel.adjustForHiddenColumns(start);
+
+          end = ap.av.colSel.getHiddenBoundaryRight(start);
+          if (start == end)
+            end = sg.getEndRes() + 1;
+          if (end > sg.getEndRes())
+            end = sg.getEndRes() + 1;
+        }
+
+        regions.addElement(new int[]
+                           {start, end});
+
+        if (ap.av.hasHiddenColumns)
+        {
+          start = ap.av.colSel.adjustForHiddenColumns(end);
+          start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
         }
-        ap.seqPanel.seqCanvas.repaint();
       }
+      while (end < sg.getEndRes());
+
+      int[][] startEnd = new int[regions.size()][2];
+      for (int i = 0; i < regions.size(); i++)
+      {
+        startEnd[i] = (int[]) regions.elementAt(i);
+      }
+
+
+      String description;
+      int caseChange;
+
+      if(source==toggleCase)
+      {
+        description = "Toggle Case";
+        caseChange = ChangeCaseCommand.TOGGLE_CASE;
+      }
+      else if(source==toUpper)
+      {
+        description = "To Upper Case";
+        caseChange = ChangeCaseCommand.TO_UPPER;
+      }
+      else
+      {
+        description = "To Lower Case";
+        caseChange = ChangeCaseCommand.TO_LOWER;
+      }
+
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(
+          description, sg.getSequencesAsArray(true), startEnd, caseChange
+          );
+
+      ap.alignFrame.addHistoryItem(caseCommand);
+
+
+      ap.av.firePropertyChange("alignment", null,
+                                ap.av.getAlignment().getSequences());
+
+    }
     }
     else
       outputText(evt);
@@ -254,7 +312,7 @@ public class APopupMenu
 
   void outputText(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
     Vector vseqs = new Vector();
 
       String [] selection = ap.av.getViewAsString(true);
@@ -323,19 +381,14 @@ public class APopupMenu
     hideSeqs.setLabel("Hide Sequences");
     repGroup.setLabel("Represent Group with");
     revealAll.setLabel("Reveal All");
-
+    menu1.setLabel("Group");
     add(groupMenu);
     this.add(seqMenu);
     this.add(hideSeqs);
     this.add(revealAll);
     groupMenu.add(editMenu);
     groupMenu.add(outputmenu);
-    groupMenu.addSeparator();
-    groupMenu.add(unGroupMenuItem);
-    groupMenu.add(colourMenu);
-    groupMenu.add(showBoxes);
-    groupMenu.add(showText);
-    groupMenu.add(showColourText);
+    groupMenu.add(menu1);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
@@ -393,6 +446,11 @@ public class APopupMenu
     editMenu.add(toggleCase);
     seqMenu.add(pdb);
     seqMenu.add(repGroup);
+    menu1.add(unGroupMenuItem);
+    menu1.add(colourMenu);
+    menu1.add(showBoxes);
+    menu1.add(showText);
+    menu1.add(showColourText);
     toggleCase.addActionListener(this);
     pdb.addActionListener(this);
     hideSeqs.addActionListener(this);
@@ -595,28 +653,32 @@ 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();
     }
 
 }