Merge branch 'bug/JAL-1486_flatfile' into Release_2_8_2_Branch

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

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 44860a1..0957d28 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,23 +20,58 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.commands.ChangeCaseCommand;
+import jalview.commands.EditCommand;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.io.SequenceAnnotationReport;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.HelixColourScheme;
+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;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
+
 /**
  * DOCUMENT ME!
  * 
@@ -256,8 +291,8 @@ public class PopupMenu extends JPopupMenu
             {
               // TODO re JAL-860: optionally open dialog or provide a menu entry
               // allowing user to open just one structure per sequence
-              //new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
-              //{ pdb })[0], null, ap);
+              // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
+              // { pdb })[0], null, ap);
               new StructureViewer(ap.getStructureSelectionManager())
                       .viewStructures(pdb,
                               ap.av.collateForPDB(new PDBEntry[]
@@ -522,7 +557,7 @@ public class PopupMenu extends JPopupMenu
       {
         Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
                 .getPDBId();
-        if (pes != null && pes.size()>0)
+        if (pes != null && pes.size() > 0)
         {
           reppdb.put(pes.get(0).getId(), pes.get(0));
           for (PDBEntry pe : pes)
@@ -561,7 +596,8 @@ public class PopupMenu extends JPopupMenu
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pe, ap.av.collateForPDB(pe));
+            new StructureViewer(ap.getStructureSelectionManager())
+                    .viewStructures(ap, pe, ap.av.collateForPDB(pe));
           }
         });
         if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
@@ -579,7 +615,8 @@ public class PopupMenu extends JPopupMenu
             @Override
             public void actionPerformed(ActionEvent e)
             {
-              new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pr, ap.av.collateForPDB(pr));
+              new StructureViewer(ap.getStructureSelectionManager())
+                      .viewStructures(ap, pr, ap.av.collateForPDB(pr));
             }
           });
         }
@@ -2071,23 +2108,8 @@ public class PopupMenu extends JPopupMenu
     System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
     // or we simply trust the user wants
     // wysiwig behaviour
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
-    omitHidden = ap.av.getViewAsString(true);
-    Alignment oal = new Alignment(ap.av.getSequenceSelection());
-    AlignmentAnnotation[] nala = ap.av.getAlignment()
-            .getAlignmentAnnotation();
-    if (nala != null)
-    {
-      for (int i = 0; i < nala.length; i++)
-      {
-        AlignmentAnnotation na = nala[i];
-        oal.addAnnotation(na);
-      }
-    }
-    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
-            oal, omitHidden, csel, sg));
-    oal = null;
+
+    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), ap.av, true));
   }
 
   public void pdbFromFile_actionPerformed()