X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=1c9b3cd94091c3bb1a19283843fe2472ba0dfccc;hb=c23f28e21e50f93f6e695bdc86247f2700c35869;hp=a9a0e354b88ec1c5f79136024e85d66a6234d828;hpb=81bf67e64fade340738792bfbcd8b3a3efd3a010;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index a9a0e35..1c9b3cd 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -53,6 +53,12 @@ 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");
+  MenuItem toggleCase = new MenuItem("Toggle Case");
 
   public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
@@ -75,19 +81,25 @@ public class APopupMenu
     }
 
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg != null)
+
+    if (sg != null && sg.getSize()>0)
     {
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
-    }
+      if (!ap.av.alignment.getGroups().contains(sg))
+      {
+        groupMenu.remove(unGroupMenuItem);
+      }
 
-    if (!ap.av.alignment.getGroups().contains(sg))
+    }
+    else
     {
-      groupMenu.remove(unGroupMenuItem);
+      remove(groupMenu);
+      remove(editMenu);
     }
 
-    if (seq != null && links!=null)
+    if (links!=null)
     {
       Menu linkMenu = new Menu("Link");
       MenuItem item;
@@ -97,13 +109,22 @@ public class APopupMenu
         link = links.elementAt(i).toString();
         final String target = link.substring(0, link.indexOf("|"));
         item = new MenuItem(target);
-        String id = seq.getName();
-        if(id.indexOf("|")>-1)
-             id = id.substring(id.lastIndexOf("|")+1);
 
-        final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
-               + id +
-               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+        final String url;
+
+        if (link.indexOf("$SEQUENCE_ID$") > -1)
+        {
+          String id = seq.getName();
+          if (id.indexOf("|") > -1)
+            id = id.substring(id.lastIndexOf("|") + 1);
+
+          url = link.substring(link.indexOf("|") + 1,
+                               link.indexOf("$SEQUENCE_ID$"))
+              + id +
+              link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+        }
+        else
+          url = link.substring(link.lastIndexOf("|")+1);
 
            item.addActionListener(new java.awt.event.ActionListener()
            {
@@ -116,18 +137,19 @@ public class APopupMenu
       }
       add(linkMenu);
 
-      item = new MenuItem("Show PDB Structure");
-      item.addActionListener(new java.awt.event.ActionListener()
-           {
-               public void actionPerformed(ActionEvent e)
-               {
-                  addPDB(seq);
-               }
-           });
-
-      add(item);
-
-
+      if(seq!=null)
+      {
+        item = new MenuItem("Show PDB Structure");
+        item.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            addPDB(seq);
+          }
+        });
+
+        add(item);
+      }
     }
   }
 
@@ -145,45 +167,67 @@ 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 || source==toLower || source==toggleCase)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      if (sg != null)
+      {
+        for (int g = 0; g < sg.getSize(); g++)
+        {
+          if (source == toggleCase)
+            sg.getSequenceAt(g).toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
+          else
+            sg.getSequenceAt(g).changeCase(source == toUpper, 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);
@@ -265,6 +309,18 @@ 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);
+    editMenu.add(toggleCase);
+    toggleCase.addActionListener(this);
+
   }
 
   void refresh()