Merge branch 'Release_2_8_1_Branch' into JAL-1372_referenceseq

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index ce1bae2..75cb494 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,11 +14,11 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
 import java.util.*;
-
 import java.awt.*;
 import java.awt.event.*;
 
@@ -70,6 +70,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   MenuItem unGroupMenuItem = new MenuItem();
 
+  MenuItem createGroupMenuItem = new MenuItem();
+
   MenuItem nucleotideMenuItem = new MenuItem();
 
   Menu colourMenu = new Menu();
@@ -114,6 +116,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   MenuItem selSeqDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
 
+  MenuItem makeReferenceSeq = new MenuItem();
+  
   Sequence seq;
 
   MenuItem revealAll = new MenuItem();
@@ -167,7 +171,11 @@ public class APopupMenu extends java.awt.PopupMenu implements
       displayNonconserved.setState(sg.getShowNonconserved());
       if (!ap.av.getAlignment().getGroups().contains(sg))
       {
+        menu1.setLabel(MessageManager.getString("action.edit_new_group"));
         groupMenu.remove(unGroupMenuItem);
+      } else {
+        menu1.setLabel(MessageManager.getString("action.edit_group"));
+        groupMenu.remove(createGroupMenuItem);
       }
 
     }
@@ -301,6 +309,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
     if (seq != null)
     {
       seqMenu.setLabel(seq.getName());
+      if (seq == ap.av.getAlignment().getSeqrep())
+      {
+        makeReferenceSeq.setLabel(MessageManager.getString("action.unmark_as_reference"));// Unmark representative");
+      } else {
+        makeReferenceSeq.setLabel(MessageManager.getString("action.set_as_reference")); // );
+      }
       repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));
     }
     else
@@ -458,10 +472,19 @@ public class APopupMenu extends java.awt.PopupMenu implements
       unGroupMenuItem_actionPerformed();
     }
 
+    else if (source == createGroupMenuItem)
+    {
+      createGroupMenuItem_actionPerformed();
+    }
+
     else if (source == sequenceName)
     {
       editName();
     }
+    else if (source == makeReferenceSeq)
+    {
+      makeReferenceSeq_actionPerformed();
+    }
     else if (source == sequenceDetails)
     {
       showSequenceDetails();
@@ -730,7 +753,6 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   private void jbInit() throws Exception
   {
-    groupMenu.setLabel(MessageManager.getString("label.group"));
     groupMenu.setLabel(MessageManager.getString("label.selection"));
     sequenceFeature.addActionListener(this);
 
@@ -738,6 +760,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
     unGroupMenuItem.setLabel(MessageManager.getString("action.remove_group"));
     unGroupMenuItem.addActionListener(this);
 
+    createGroupMenuItem.setLabel(MessageManager.getString("action.create_group"));
+    createGroupMenuItem.addActionListener(this);
+
     nucleotideMenuItem.setLabel(MessageManager.getString("label.nucleotide"));
     nucleotideMenuItem.addActionListener(this);
     conservationMenuItem.addItemListener(this);
@@ -760,20 +785,21 @@ public class APopupMenu extends java.awt.PopupMenu implements
     seqMenu.setLabel(MessageManager.getString("label.sequence"));
     pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
     hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
-    repGroup.setLabel(MessageManager.getString("label.represent_group_with"));
+    repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{""}));
     revealAll.setLabel(MessageManager.getString("action.reveal_all"));
     revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
-    menu1.setLabel(MessageManager.getString("label.group"));
+    menu1.setLabel(MessageManager.getString("label.group")+":");
     add(groupMenu);
     this.add(seqMenu);
     this.add(hideSeqs);
     this.add(revealSeq);
     this.add(revealAll);
     // groupMenu.add(selSeqDetails);
-    groupMenu.add(editGroupName);
     groupMenu.add(editMenu);
     groupMenu.add(outputmenu);
     groupMenu.add(sequenceFeature);
+    groupMenu.add(createGroupMenuItem);
+    groupMenu.add(unGroupMenuItem);
     groupMenu.add(menu1);
 
     colourMenu.add(noColourmenuItem);
@@ -836,6 +862,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     toLower.addActionListener(this);
     editMenu.add(toggleCase);
     seqMenu.add(sequenceName);
+    seqMenu.add(makeReferenceSeq);
     // seqMenu.add(sequenceDetails);
 
     if (!ap.av.applet.useXtrnalSviewer)
@@ -843,7 +870,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       seqMenu.add(pdb);
     }
     seqMenu.add(repGroup);
-    menu1.add(unGroupMenuItem);
+    menu1.add(editGroupName);
     menu1.add(colourMenu);
     menu1.add(showBoxes);
     menu1.add(showText);
@@ -855,6 +882,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     repGroup.addActionListener(this);
     revealAll.addActionListener(this);
     revealSeq.addActionListener(this);
+    makeReferenceSeq.addActionListener(this);
   }
 
   void refresh()
@@ -1027,6 +1055,12 @@ public class APopupMenu extends java.awt.PopupMenu implements
     ap.paintAlignment(true);
   }
 
+  void createGroupMenuItem_actionPerformed()
+  {
+    getGroup(); // implicitly create group
+    refresh();
+  }
+
   public void showColourText_itemStateChanged()
   {
     getGroup().setColourText(showColourText.getState());
@@ -1038,6 +1072,28 @@ public class APopupMenu extends java.awt.PopupMenu implements
     getGroup().setDisplayText(showText.getState());
     refresh();
   }
+  public void makeReferenceSeq_actionPerformed()
+  {
+    if (!ap.av.getAlignment().hasSeqrep())
+    {
+      // initialise the display flags so the user sees something happen
+      ap.av.setDisplayReferenceSeq(true);
+      ap.av.setColourByReferenceSeq(true);
+      ap.av.getAlignment().setSeqrep(seq);
+    }
+    else
+    {
+      if (ap.av.getAlignment().getSeqrep() == seq)
+      {
+        ap.av.getAlignment().setSeqrep(null);
+      }
+      else
+      {
+        ap.av.getAlignment().setSeqrep(seq);
+      }
+    }
+    refresh();
+  }
 
   public void showNonconserved_itemStateChanged()
   {