X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=eba1200927c74c02b3e7eb2c4e4b2a8e304f7db8;hb=d6802cb21c694ab6a971fa568f6686660559a5d5;hp=ce1bae28ec14176db131160b0f38833bbd32f5bc;hpb=21c29b20790ac555b2e2a124a034f6c6b4486270;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index ce1bae2..eba1200 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,19 +1,22 @@
 /*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * 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/>.
+ * 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;
 
@@ -70,6 +73,8 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   MenuItem unGroupMenuItem = new MenuItem();
 
+  MenuItem createGroupMenuItem = new MenuItem();
+
   MenuItem nucleotideMenuItem = new MenuItem();
 
   Menu colourMenu = new Menu();
@@ -84,15 +89,19 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   Menu editMenu = new Menu(MessageManager.getString("action.edit"));
 
-  MenuItem copy = new MenuItem(MessageManager.getString("label.jalview_copy"));
+  MenuItem copy = new MenuItem(
+          MessageManager.getString("label.jalview_copy"));
 
   MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
 
-  MenuItem toUpper = new MenuItem(MessageManager.getString("label.to_upper_case"));
+  MenuItem toUpper = new MenuItem(
+          MessageManager.getString("label.to_upper_case"));
 
-  MenuItem toLower = new MenuItem(MessageManager.getString("label.to_lower_case"));
+  MenuItem toLower = new MenuItem(
+          MessageManager.getString("label.to_lower_case"));
 
-  MenuItem toggleCase = new MenuItem(MessageManager.getString("label.toggle_case"));
+  MenuItem toggleCase = new MenuItem(
+          MessageManager.getString("label.toggle_case"));
 
   Menu outputmenu = new Menu();
 
@@ -104,15 +113,20 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
   MenuItem repGroup = new MenuItem();
 
-  MenuItem sequenceName = new MenuItem(MessageManager.getString("label.edit_name_description"));
+  MenuItem sequenceName = new MenuItem(
+          MessageManager.getString("label.edit_name_description"));
 
-  MenuItem sequenceFeature = new MenuItem(MessageManager.getString("label.create_sequence_feature"));
+  MenuItem sequenceFeature = new MenuItem(
+          MessageManager.getString("label.create_sequence_feature"));
 
-  MenuItem editSequence = new MenuItem(MessageManager.getString("label.edit_sequence"));
+  MenuItem editSequence = new MenuItem(
+          MessageManager.getString("label.edit_sequence"));
 
-  MenuItem sequenceDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
+  MenuItem sequenceDetails = new MenuItem(
+          MessageManager.getString("label.sequence_details") + "...");
 
-  MenuItem selSeqDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
+  MenuItem selSeqDetails = new MenuItem(
+          MessageManager.getString("label.sequence_details") + "...");
 
   Sequence seq;
 
@@ -160,15 +174,23 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     if (sg != null && sg.getSize() > 0)
     {
-      editGroupName.setLabel(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
+      editGroupName.setLabel(MessageManager.formatMessage(
+              "label.name_param", new String[]
+              { sg.getName() }));
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
       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);
+      }
 
     }
     else
@@ -301,7 +323,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
     if (seq != null)
     {
       seqMenu.setLabel(seq.getName());
-      repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));
+      repGroup.setLabel(MessageManager.formatMessage(
+              "label.represent_group_with", new String[]
+              { seq.getName() }));
     }
     else
     {
@@ -458,6 +482,11 @@ public class APopupMenu extends java.awt.PopupMenu implements
       unGroupMenuItem_actionPerformed();
     }
 
+    else if (source == createGroupMenuItem)
+    {
+      createGroupMenuItem_actionPerformed();
+    }
+
     else if (source == sequenceName)
     {
       editName();
@@ -530,7 +559,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
         if (dialog.accept)
         {
-          EditCommand editCommand = new EditCommand("Edit Sequences",
+          EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
                   EditCommand.REPLACE, dialog.getName().replace(' ',
                           ap.av.getGapCharacter()),
                   sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
@@ -635,16 +664,16 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
-    		MessageManager.formatMessage("label.selection_output_command", new String[]{e.getActionCommand()}),600, 500);
+    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+            "label.selection_output_command", new String[]
+            { e.getActionCommand() }), 600, 500);
     // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
     // now returns a full copy of sequence data
     // TODO consider using getSequenceSelection instead here
 
     cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
-            e.getActionCommand(),
-            new Alignment(ap.av.getSelectionAsNewSequence()),
-            ap.av.showJVSuffix));
+            e.getActionCommand(), 
+            ap.av.showJVSuffix, ap.av, true));
 
   }
 
@@ -667,7 +696,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
     StringBuffer contents = new StringBuffer();
     for (SequenceI seq : sequences)
     {
-      contents.append(MessageManager.formatMessage("label.annotation_for_displayid",new String[]{seq.getDisplayId(true)}));
+      contents.append(MessageManager.formatMessage(
+              "label.annotation_for_displayid", new String[]
+              { seq.getDisplayId(true) }));
       new SequenceAnnotationReport(null)
               .createSequenceAnnotationReport(
                       contents,
@@ -684,7 +715,9 @@ public class APopupMenu extends java.awt.PopupMenu implements
     jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
             + (sequences.length == 1 ? sequences[0].getDisplayId(true)
                     : "Selection"), 600, 500);
-    cap.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
+    cap.setText(MessageManager.formatMessage("label.html_content",
+            new String[]
+            { contents.toString() }));
   }
 
   void editName()
@@ -723,36 +756,43 @@ public class APopupMenu extends java.awt.PopupMenu implements
       cap.setPDBImport(seq);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
-              MessageManager.formatMessage("label.paste_pdb_file_for_sequence",  new String[]{seq.getName()}), 400, 300);
+      jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+              "label.paste_pdb_file_for_sequence", new String[]
+              { seq.getName() }), 400, 300);
     }
   }
 
   private void jbInit() throws Exception
   {
-    groupMenu.setLabel(MessageManager.getString("label.group"));
     groupMenu.setLabel(MessageManager.getString("label.selection"));
     sequenceFeature.addActionListener(this);
 
     editGroupName.addActionListener(this);
-    unGroupMenuItem.setLabel(MessageManager.getString("action.remove_group"));
+    unGroupMenuItem.setLabel(MessageManager
+            .getString("action.remove_group"));
     unGroupMenuItem.addActionListener(this);
 
-    nucleotideMenuItem.setLabel(MessageManager.getString("label.nucleotide"));
+    createGroupMenuItem.setLabel(MessageManager
+            .getString("action.create_group"));
+    createGroupMenuItem.addActionListener(this);
+
+    nucleotideMenuItem.setLabel(MessageManager
+            .getString("label.nucleotide"));
     nucleotideMenuItem.addActionListener(this);
     conservationMenuItem.addItemListener(this);
     abovePIDColour.addItemListener(this);
     colourMenu.setLabel(MessageManager.getString("label.group_colour"));
-    showBoxes.setLabel(MessageManager.getString("label.boxes"));
+    showBoxes.setLabel(MessageManager.getString("action.boxes"));
     showBoxes.setState(true);
     showBoxes.addItemListener(this);
     sequenceName.addActionListener(this);
     sequenceDetails.addActionListener(this);
     selSeqDetails.addActionListener(this);
-    displayNonconserved.setLabel(MessageManager.getString("label.show_non_conversed"));
+    displayNonconserved.setLabel(MessageManager
+            .getString("label.show_non_conversed"));
     displayNonconserved.setState(false);
     displayNonconserved.addItemListener(this);
-    showText.setLabel(MessageManager.getString("label.text"));
+    showText.setLabel(MessageManager.getString("action.text"));
     showText.addItemListener(this);
     showColourText.setLabel(MessageManager.getString("label.colour_text"));
     showColourText.addItemListener(this);
@@ -760,20 +800,23 @@ 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);
@@ -793,34 +836,34 @@ public class APopupMenu extends java.awt.PopupMenu implements
     colourMenu.add(abovePIDColour);
     colourMenu.add(conservationMenuItem);
 
-    noColourmenuItem.setLabel("None");
+    noColourmenuItem.setLabel(MessageManager.getString("label.none"));
     noColourmenuItem.addActionListener(this);
 
-    clustalColour.setLabel("Clustalx colours");
+    clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));
     clustalColour.addActionListener(this);
-    zappoColour.setLabel("Zappo");
+    zappoColour.setLabel(MessageManager.getString("label.zappo"));
     zappoColour.addActionListener(this);
-    taylorColour.setLabel("Taylor");
+    taylorColour.setLabel(MessageManager.getString("label.taylor"));
     taylorColour.addActionListener(this);
-    hydrophobicityColour.setLabel("Hydrophobicity");
+    hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
     hydrophobicityColour.addActionListener(this);
-    helixColour.setLabel("Helix propensity");
+    helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
     helixColour.addActionListener(this);
-    strandColour.setLabel("Strand propensity");
+    strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
     strandColour.addActionListener(this);
-    turnColour.setLabel("Turn propensity");
+    turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
     turnColour.addActionListener(this);
-    buriedColour.setLabel("Buried Index");
+    buriedColour.setLabel(MessageManager.getString("label.buried_index"));
     buriedColour.addActionListener(this);
-    abovePIDColour.setLabel("Above % Identity");
+    abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));
 
-    userDefinedColour.setLabel("User Defined");
+    userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
     userDefinedColour.addActionListener(this);
-    PIDColour.setLabel("Percentage Identity");
+    PIDColour.setLabel(MessageManager.getString("action.percentage_identity"));
     PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel("BLOSUM62");
     BLOSUM62Colour.addActionListener(this);
-    conservationMenuItem.setLabel("Conservation");
+    conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));
 
     editMenu.add(copy);
     copy.addActionListener(this);
@@ -843,7 +886,7 @@ 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);
@@ -1027,6 +1070,12 @@ 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());