X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=1d5eacec0d18ceafc2afdf0f84f50131b49357a1;hb=3b5ad2b93c9765e2f381ef66dc755184657d7d71;hp=c90af984025276dc36a318d75c90791cbfdb79b0;hpb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index c90af98..1d5eace 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -53,6 +53,11 @@ public class APopupMenu
   CheckboxMenuItem showBoxes = new CheckboxMenuItem();
   CheckboxMenuItem showText = new CheckboxMenuItem();
   CheckboxMenuItem showColourText = new CheckboxMenuItem();
+  Menu editMenu = new Menu("Edit");
+  MenuItem copy = new MenuItem("Copy (Jalview Only)");
+  MenuItem cut = new MenuItem("Cut (Jalview Only)");
+  MenuItem toUpper = new MenuItem("To Upper Case");
+  MenuItem toLower = new MenuItem("To Lower Case");
 
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
@@ -145,45 +150,77 @@ public class APopupMenu
 
   public void actionPerformed(ActionEvent evt)
   {
-    if(evt.getSource()==clustalColour)
+    Object source = evt.getSource();
+    if(source==clustalColour)
       clustalColour_actionPerformed();
-    else if(evt.getSource()==zappoColour)
+    else if(source==zappoColour)
       zappoColour_actionPerformed();
-    else if(evt.getSource()==taylorColour)
+    else if(source==taylorColour)
       taylorColour_actionPerformed();
-    else if(evt.getSource()==hydrophobicityColour)
+    else if(source==hydrophobicityColour)
       hydrophobicityColour_actionPerformed();
-    else if(evt.getSource()==helixColour)
+    else if(source==helixColour)
       helixColour_actionPerformed();
-    else if(evt.getSource()==strandColour)
+    else if(source==strandColour)
       strandColour_actionPerformed();
-    else if(evt.getSource()==clustalColour)
+    else if(source==clustalColour)
       turnColour_actionPerformed();
-    else if(evt.getSource()==buriedColour)
+    else if(source==buriedColour)
       buriedColour_actionPerformed();
-    else if(evt.getSource()==nucleotideMenuItem)
+    else if(source==nucleotideMenuItem)
       nucleotideMenuItem_actionPerformed();
 
-    else if(evt.getSource()==userDefinedColour)
+    else if(source==userDefinedColour)
           userDefinedColour_actionPerformed();
-        else if(evt.getSource()==PIDColour)
+        else if(source==PIDColour)
        PIDColour_actionPerformed();
-     else if(evt.getSource()==BLOSUM62Colour)
+     else if(source==BLOSUM62Colour)
       BLOSUM62Colour_actionPerformed();
-    else if(evt.getSource()==noColourmenuItem)
+    else if(source==noColourmenuItem)
       noColourmenuItem_actionPerformed();
-    else if(evt.getSource()==conservationMenuItem)
+    else if(source==conservationMenuItem)
         conservationMenuItem_itemStateChanged();
-      else if(evt.getSource()==unGroupMenuItem)
+      else if(source==unGroupMenuItem)
       unGroupMenuItem_actionPerformed();
 
+    else if(source==copy)
+      ap.alignFrame.copy_actionPerformed();
+    else if(source==cut)
+      ap.alignFrame.cut_actionPerformed();
+    else if(source==toUpper)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      if (sg != null)
+      {
+        for (int g = 0; g < sg.getSize(); g++)
+        {
+          sg.getSequenceAt(g).changeCase(true, sg.getStartRes(),
+                                         sg.getEndRes() + 1);
+        }
+        ap.seqPanel.seqCanvas.repaint();
+      }
+    }
+    else if(source==toLower)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      if (sg != null)
+      {
+        for (int g = 0; g < sg.getSize(); g++)
+        {
+          sg.getSequenceAt(g).changeCase(false, sg.getStartRes(),
+                                         sg.getEndRes() + 1);
+        }
+        ap.seqPanel.seqCanvas.repaint();
+      }
+    }
+
   }
 
   void addPDB(Sequence seq)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame.applet);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
     cap.setText("Paste your PDB file here.");
-    cap.setPDBImport(seq, ap.seqPanel.seqCanvas);
+    cap.setPDBImport(seq);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
@@ -265,20 +302,20 @@ public class APopupMenu
     BLOSUM62Colour.addActionListener(this);
     conservationMenuItem.setLabel("Conservation");
 
+    add(editMenu);
+    editMenu.add(copy);
+    copy.addActionListener(this);
+    editMenu.add(cut);
+    cut.addActionListener(this);
+    editMenu.add(toUpper);
+    toUpper.addActionListener(this);
+    editMenu.add(toLower);
+    toLower.addActionListener(this);
+
   }
 
   void refresh()
   {
-    SequenceGroup sg = getGroup();
-    if(sg!=null)
-    {
-      SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
-
-      if (superG != null)
-      {
-        superG.setSuperGroupProperties(sg);
-      }
-        }
     ap.seqPanel.seqCanvas.repaint();
     if(ap.overviewPanel!=null)
       ap.overviewPanel.updateOverviewImage();