X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=f786bde5dfaba8b787b6363c7f4c7b6539b81bbd;hb=74f2c25a0ad46ce7286cca6d976f3592952d36ad;hp=b3c8f20b4218df1a5296db67f27108a8e7f95234;hpb=8797ce6a98df4aa29eefecb25b10fed4f2ab9e86;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index b3c8f20..f786bde 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -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)
   {
@@ -143,7 +145,6 @@ 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)
@@ -234,43 +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(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)
         {
-          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());
+          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);
@@ -279,7 +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);
@@ -348,19 +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);
@@ -418,6 +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);