FileFormatI further tweaks, clean compile

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1e0772a..4d9dc4d 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -38,6 +38,8 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.AnnotationColourGradient;
@@ -91,8 +93,6 @@ import javax.swing.JRadioButtonMenuItem;
  */
 public class PopupMenu extends JPopupMenu
 {
-  private static final String ALL_ANNOTATIONS = "All";
-
   JMenu groupMenu = new JMenu();
 
   JMenuItem groupName = new JMenuItem();
@@ -258,10 +258,9 @@ public class PopupMenu extends JPopupMenu
     colours.add(purinePyrimidineColour);
     colours.add(RNAInteractionColour);
 
-    for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (String ff : FileFormat.getWritableFormats())
     {
-      JMenuItem item = new JMenuItem(
-              jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+      JMenuItem item = new JMenuItem(ff);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
@@ -478,8 +477,6 @@ 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"));
 
@@ -756,7 +753,8 @@ 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);
@@ -1098,7 +1096,6 @@ 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()
@@ -2270,28 +2267,7 @@ 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()
@@ -2359,47 +2335,8 @@ 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 isNuclueotide = ap.alignFrame.getViewport().getAlignment()
-                .isNucleotide();
-
-        new jalview.ws.DBRefFetcher(sequences, ap.alignFrame, null,
-                ap.alignFrame.featureSettings, isNuclueotide)
-                .fetchDBRefs(false);
-
-      }
-
-    });
-    discpdb.start();
+    FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
+    cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
   }
 
   public void sequenceFeature_actionPerformed()