X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=f0fdb9f378dbeac0a983fdeafe496f1835661f9f;hb=4a5137b64f7ec23db2a09290bfcd392984a52150;hp=4b0ffad851283468ebb1d2458ac6415f153e9af7;hpb=ba03e96346fceac9d73148d743e523634f5f9539;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 4b0ffad..f0fdb9f 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -38,6 +38,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.AnnotationColourGradient;
@@ -60,7 +61,6 @@ 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;
@@ -2271,28 +2271,7 @@ 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()
@@ -2360,47 +2339,8 @@ public class PopupMenu extends JPopupMenu
     // or we simply trust the user wants
     // wysiwig behaviour
 
-    cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
-            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();
+    FileFormat fileFormat = FileFormat.forName(e.getActionCommand());
+    cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
   }
 
   public void sequenceFeature_actionPerformed()