JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 4b0ffad..7ab6022 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -49,7 +49,6 @@ import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
@@ -60,7 +59,6 @@ import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
-import jalview.ws.DBRefFetcher;
 
 import java.awt.Color;
 import java.awt.event.ActionEvent;
@@ -92,8 +90,6 @@ import javax.swing.JRadioButtonMenuItem;
  */
 public class PopupMenu extends JPopupMenu
 {
-  private static final String ALL_ANNOTATIONS = "All";
-
   JMenu groupMenu = new JMenu();
 
   JMenuItem groupName = new JMenuItem();
@@ -479,8 +475,6 @@ public class PopupMenu extends JPopupMenu
 
     if (sg != null && sg.getSize() > 0)
     {
-      groupName.setText(MessageManager.formatMessage("label.name_param",
-              new Object[] { sg.getName() }));
       groupName.setText(MessageManager
               .getString("label.edit_name_and_description_current_group"));
 
@@ -757,7 +751,8 @@ public class PopupMenu extends JPopupMenu
     showMenu.removeAll();
     hideMenu.removeAll();
 
-    final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
+    final List<String> all = Arrays.asList(new String[] { MessageManager
+            .getString("label.all") });
     addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
     addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
             false);
@@ -933,8 +928,7 @@ public class PopupMenu extends JPopupMenu
         urlLink = new GroupUrlLink(link);
       } catch (Exception foo)
       {
-        Cache.log.error("Exception for GroupURLLink '" + link
-                + "'", foo);
+        Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
         continue;
       }
       ;
@@ -1099,7 +1093,6 @@ public class PopupMenu extends JPopupMenu
    */
   private void jbInit() throws Exception
   {
-    groupMenu.setText(MessageManager.getString("label.group"));
     groupMenu.setText(MessageManager.getString("label.selection"));
     groupName.setText(MessageManager.getString("label.name"));
     groupName.addActionListener(new java.awt.event.ActionListener()
@@ -2044,9 +2037,8 @@ public class PopupMenu extends JPopupMenu
     if (conservationMenuItem.isSelected())
     {
       // JBPNote: Conservation name shouldn't be i18n translated
-      Conservation c = new Conservation("Group",
-              ResidueProperties.propHash, 3, sg.getSequences(ap.av
-                      .getHiddenRepSequences()), sg.getStartRes(),
+      Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av
+              .getHiddenRepSequences()), sg.getStartRes(),
               sg.getEndRes() + 1);
 
       c.calculate();
@@ -2271,28 +2263,7 @@ public class PopupMenu extends JPopupMenu
 
   void hideSequences(boolean representGroup)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg == null || sg.getSize() < 1)
-    {
-      ap.av.hideSequence(new SequenceI[] { sequence });
-      return;
-    }
-
-    ap.av.setSelectionGroup(null);
-
-    if (representGroup)
-    {
-      ap.av.hideRepSequences(sequence, sg);
-
-      return;
-    }
-
-    int gsize = sg.getSize();
-    SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
-
-    ap.av.hideSequence(hseqs);
-    // refresh(); TODO: ? needed ?
-    ap.av.sendSelection();
+    ap.av.hideSequences(sequence, representGroup);
   }
 
   public void copy_actionPerformed()
@@ -2364,45 +2335,6 @@ public class PopupMenu extends JPopupMenu
             ap, true));
   }
 
-  public void enterPDB_actionPerformed()
-  {
-    String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
-            MessageManager.getString("label.enter_pdb_id"),
-            MessageManager.getString("label.enter_pdb_id"),
-            JOptionPane.QUESTION_MESSAGE);
-
-    if (id != null && id.length() > 0)
-    {
-      PDBEntry entry = new PDBEntry();
-      entry.setId(id.toUpperCase());
-      sequence.getDatasetSequence().addPDBId(entry);
-    }
-  }
-
-  public void discoverPDB_actionPerformed()
-  {
-
-    final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
-    { sequence }
-            : ap.av.getSequenceSelection());
-    Thread discpdb = new Thread(new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        boolean isNucleotide = ap.alignFrame.getViewport().getAlignment()
-                .isNucleotide();
-
-        new DBRefFetcher(sequences, ap.alignFrame, null,
-                ap.alignFrame.featureSettings, isNucleotide)
-                .fetchDBRefs(false);
-
-      }
-
-    });
-    discpdb.start();
-  }
-
   public void sequenceFeature_actionPerformed()
   {
     SequenceGroup sg = ap.av.getSelectionGroup();