applet has multiple views

[jalview.git] / src / jalview / appletgui / APopupMenu.java

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index b3c8f20..f786bde 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
@@ -67,6 +68,7 @@ public class APopupMenu
 \r
   Sequence seq;\r
   MenuItem revealAll = new MenuItem();\r
+  Menu menu1 = new Menu();\r
 \r
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)\r
   {\r
@@ -143,7 +145,6 @@ public class APopupMenu
         else\r
           url = link.substring(link.lastIndexOf("|")+1);\r
 \r
-        System.out.println("add "+url +" "+target);\r
            item.addActionListener(new java.awt.event.ActionListener()\r
            {\r
                public void actionPerformed(ActionEvent e)\r
@@ -234,43 +235,75 @@ public class APopupMenu
       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
+    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
+      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
@@ -279,7 +312,7 @@ public class APopupMenu
 \r
   void outputText(ActionEvent e)\r
   {\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);\r
     Vector vseqs = new Vector();\r
 \r
       String [] selection = ap.av.getViewAsString(true);\r
@@ -348,19 +381,14 @@ public class APopupMenu
     hideSeqs.setLabel("Hide Sequences");\r
     repGroup.setLabel("Represent Group with");\r
     revealAll.setLabel("Reveal All");\r
-\r
+    menu1.setLabel("Group");\r
     add(groupMenu);\r
     this.add(seqMenu);\r
     this.add(hideSeqs);\r
     this.add(revealAll);\r
     groupMenu.add(editMenu);\r
     groupMenu.add(outputmenu);\r
-    groupMenu.addSeparator();\r
-    groupMenu.add(unGroupMenuItem);\r
-    groupMenu.add(colourMenu);\r
-    groupMenu.add(showBoxes);\r
-    groupMenu.add(showText);\r
-    groupMenu.add(showColourText);\r
+    groupMenu.add(menu1);\r
     colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
     colourMenu.add(BLOSUM62Colour);\r
@@ -418,6 +446,11 @@ public class APopupMenu
     editMenu.add(toggleCase);\r
     seqMenu.add(pdb);\r
     seqMenu.add(repGroup);\r
+    menu1.add(unGroupMenuItem);\r
+    menu1.add(colourMenu);\r
+    menu1.add(showBoxes);\r
+    menu1.add(showText);\r
+    menu1.add(showColourText);\r
     toggleCase.addActionListener(this);\r
     pdb.addActionListener(this);\r
     hideSeqs.addActionListener(this);\r