Change case new implementation

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index e837ec8..dad22cb 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -26,6 +26,7 @@ import java.util.Vector;
 import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
 import jalview.schemes.*;\r
+import jalview.commands.ChangeCaseCommand;\r
 \r
 public class APopupMenu\r
     extends java.awt.PopupMenu implements ActionListener, ItemListener\r
@@ -234,44 +235,76 @@ public class APopupMenu
     else if(source==cut)\r
       ap.alignFrame.cut_actionPerformed();\r
     else if(source==toUpper || source==toLower || source==toggleCase)\r
-    {/*\r
-      SequenceGroup sg = ap.av.getSelectionGroup();\r
-      if (sg != null)\r
+    {\r
+    SequenceGroup sg = ap.av.getSelectionGroup();\r
+    Vector regions = new Vector();\r
+    if (sg != null)\r
+    {\r
+      int start = sg.getStartRes();\r
+      int end = sg.getEndRes() + 1;\r
+\r
+      do\r
       {\r
-        for (int g = 0; g < sg.getSize(true); g++)\r
+        if (ap.av.hasHiddenColumns)\r
+        {\r
+          if(start==0)\r
+            start = ap.av.colSel.adjustForHiddenColumns(start);\r
+\r
+          end = ap.av.colSel.getHiddenBoundaryRight(start);\r
+          if (start == end)\r
+            end = sg.getEndRes() + 1;\r
+          if (end > sg.getEndRes())\r
+            end = sg.getEndRes() + 1;\r
+        }\r
+\r
+        regions.addElement(new int[]\r
+                           {start, end});\r
+\r
+        if (ap.av.hasHiddenColumns)\r
         {\r
-          int start = sg.getStartRes();\r
-          int end = sg.getEndRes() + 1;\r
-\r
-          do\r
-          {\r
-            if (ap.av.hasHiddenColumns)\r
-            {\r
-              end = ap.av.colSel.getHiddenBoundaryRight(start);\r
-              if (start == end)\r
-                end = sg.getEndRes() + 1;\r
-              if (end > sg.getEndRes())\r
-                end = sg.getEndRes() + 1;\r
-            }\r
-\r
-            if (source == toggleCase)\r
-              ( (SequenceI) sg.getSequences(true).elementAt(g))\r
-                  .toggleCase(start, end);\r
-            else\r
-              ( (SequenceI) sg.getSequences(true).elementAt(g))\r
-                  .changeCase(source == toUpper, start, end);\r
-\r
-            if (ap.av.hasHiddenColumns)\r
-            {\r
-              start = ap.av.colSel.adjustForHiddenColumns(end);\r
-              start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
-            }\r
-\r
-          }\r
-        while (end < sg.getEndRes());\r
+          start = ap.av.colSel.adjustForHiddenColumns(end);\r
+          start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;\r
         }\r
-        ap.seqPanel.seqCanvas.repaint();\r
-      }*/\r
+      }\r
+      while (end < sg.getEndRes());\r
+\r
+      int[][] startEnd = new int[regions.size()][2];\r
+      for (int i = 0; i < regions.size(); i++)\r
+      {\r
+        startEnd[i] = (int[]) regions.elementAt(i);\r
+      }\r
+\r
+\r
+      String description;\r
+      int caseChange;\r
+\r
+      if(source==toggleCase)\r
+      {\r
+        description = "Toggle Case";\r
+        caseChange = ChangeCaseCommand.TOGGLE_CASE;\r
+      }\r
+      else if(source==toUpper)\r
+      {\r
+        description = "To Upper Case";\r
+        caseChange = ChangeCaseCommand.TO_UPPER;\r
+      }\r
+      else\r
+      {\r
+        description = "To Lower Case";\r
+        caseChange = ChangeCaseCommand.TO_LOWER;\r
+      }\r
+\r
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(\r
+          description, sg.getSequencesAsArray(true), startEnd, caseChange\r
+          );\r
+\r
+      ap.alignFrame.addHistoryItem(caseCommand);\r
+\r
+\r
+      ap.av.firePropertyChange("alignment", null,\r
+                                ap.av.getAlignment().getSequences());\r
+\r
+    }\r
     }\r
     else\r
       outputText(evt);\r