From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 21 Nov 2006 17:14:28 +0000 (+0000)
Subject: Change case new implementation
X-Git-Tag: Release_2_2~66
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=07c1edb779cfa11d19ea6e5dc731333e5dfd2250;p=jalview.git

Change case new implementation
---

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index e837ec8..dad22cb 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
@@ -234,44 +235,76 @@ 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)
+    {
+    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);