X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=9ed81abb1cb5984c3603944798777a07342f4f66;hb=3e6b14950a06bb87c147493e4dfff0c4491ea25b;hp=f9e0d19d262ed88f4e7bfdfba5c8f19c079c5aa4;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index f9e0d19..9ed81ab 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -21,17 +21,18 @@ package jalview.gui;
 import MCview.*;
 
 import jalview.analysis.*;
-
 import jalview.datamodel.*;
-
-
 import jalview.schemes.*;
+import jalview.commands.ChangeCaseCommand;
 
 import java.awt.*;
 import java.awt.event.*;
 
 import javax.swing.*;
 
+import java.util.Vector;
+import jalview.io.FormatAdapter;
+
 
 /**
  * DOCUMENT ME!
@@ -68,14 +69,28 @@ public class PopupMenu extends JPopupMenu
     JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
     JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
     JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
-
-    /**
+  JMenu editMenu = new JMenu();
+  JMenuItem cut = new JMenuItem();
+  JMenuItem copy = new JMenuItem();
+  JMenuItem upperCase = new JMenuItem();
+  JMenuItem lowerCase = new JMenuItem();
+  JMenuItem toggle = new JMenuItem();
+  JMenu pdbMenu = new JMenu();
+  JMenuItem pdbFromFile = new JMenuItem();
+  JMenuItem enterPDB = new JMenuItem();
+  JMenuItem discoverPDB = new JMenuItem();
+  JMenu outputMenu = new JMenu();
+  JMenuItem sequenceFeature = new JMenuItem();
+  JMenuItem textColour = new JMenuItem();
+  JMenu jMenu1 = new JMenu();
+
+  /**
      * Creates a new PopupMenu object.
      *
      * @param ap DOCUMENT ME!
      * @param seq DOCUMENT ME!
      */
-    public PopupMenu(final AlignmentPanel ap, Sequence seq)
+    public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
     {
         ///////////////////////////////////////////////////////////
         // If this is activated from the sequence panel, the user may want to
@@ -101,6 +116,22 @@ public class PopupMenu extends JPopupMenu
         colours.add(PIDColour);
         colours.add(BLOSUM62Colour);
 
+        for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+        {
+          JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
+
+          item.addActionListener(new java.awt.event.ActionListener()
+          {
+            public void actionPerformed(ActionEvent e)
+            {
+              outputText_actionPerformed(e);
+            }
+          });
+
+          outputMenu.add(item);
+        }
+
+
         try
         {
             jbInit();
@@ -111,28 +142,96 @@ public class PopupMenu extends JPopupMenu
         }
 
 
-        if ((seq != null)
-            && seq.getDatasetSequence().getPDBId() != null)
+        if (seq != null)
         {
-          java.util.Enumeration e = seq.getDatasetSequence().getPDBId().elements();
-          while(e.hasMoreElements())
+          sequenceMenu.setText(sequence.getName());
+
+          JMenuItem menuItem;
+          if( seq.getDatasetSequence().getPDBId() != null)
           {
-            final PDBEntry pdb = (PDBEntry)e.nextElement();
+            java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
+                elements();
 
-            JMenuItem pdbMenuItem = new JMenuItem();
-            pdbMenuItem.setText("View PDB entry: "+pdb.getId());
-            pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
+            while (e.hasMoreElements())
             {
+              final PDBEntry pdb = (PDBEntry) e.nextElement();
+
+              menuItem = new JMenuItem();
+              menuItem.setText("View PDB entry: " + pdb.getId());
+              menuItem.addActionListener(new java.awt.event.ActionListener()
+              {
                 public void actionPerformed(ActionEvent e)
                 {
                   new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
                 }
+              });
+              sequenceMenu.add(menuItem);
+            }
+          }
+
+          menuItem = new JMenuItem("Hide Sequences");
+          menuItem.addActionListener(new java.awt.event.ActionListener()
+              {
+                public void actionPerformed(ActionEvent e)
+                {
+                  hideSequences(false);
+                }
+              });
+          add(menuItem);
+
+          if(ap.av.getSelectionGroup() !=null
+             && ap.av.getSelectionGroup().getSize()>1)
+          {
+            menuItem = new JMenuItem("Represent Group with " + seq.getName());
+            menuItem.addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                hideSequences(true);
+              }
             });
-            sequenceMenu.add(pdbMenuItem);
+            sequenceMenu.add(menuItem);
           }
 
+          if (ap.av.hasHiddenRows)
+          {
+            final int index = ap.av.alignment.findIndex(seq);
+
+            if (ap.av.adjustForHiddenSeqs(index) -
+                ap.av.adjustForHiddenSeqs(index - 1) > 1)
+            {
+              menuItem = new JMenuItem("Reveal Sequences");
+              menuItem.addActionListener(new ActionListener()
+              {
+                public void actionPerformed(ActionEvent e)
+                {
+                  ap.av.showSequence(index);
+                  if (ap.overviewPanel != null)
+                    ap.overviewPanel.updateOverviewImage();
+                }
+              });
+              add(menuItem);
+            }
+
+            menuItem = new JMenuItem("Reveal All");
+            menuItem.addActionListener(new ActionListener()
+                {
+                  public void actionPerformed(ActionEvent e)
+                  {
+                    ap.av.showAllHiddenSeqs();
+                    if (ap.overviewPanel != null)
+                      ap.overviewPanel.updateOverviewImage();
+                    }
+                });
+
+            add(menuItem);
+          }
+
+
         }
 
+
+
         SequenceGroup sg = ap.av.getSelectionGroup();
 
         if (sg != null)
@@ -197,38 +296,48 @@ public class PopupMenu extends JPopupMenu
             showColourText.setSelected(sg.getColourText());
             showBoxes.setSelected(sg.getDisplayBoxes());
         }
+        else
+        {
+          groupMenu.setVisible(false);
+          editMenu.setVisible(false);
+        }
 
         if (!ap.av.alignment.getGroups().contains(sg))
         {
             unGroupMenuItem.setVisible(false);
         }
-        else
-        {
-            groupMenu.insertSeparator(3);
-        }
+
 
         if (seq == null)
         {
             sequenceMenu.setVisible(false);
+            pdbMenu.setVisible(false);
         }
-        else
-        {
-          java.util.Vector links = Preferences.sequenceURLLinks;
 
+        if(links != null && links.size()>0)
+        {
           JMenu linkMenu = new JMenu("Link");
           JMenuItem item;
           for(int i=0; i<links.size(); i++)
           {
             String link = links.elementAt(i).toString();
+            final String label = link.substring(0, link.indexOf("|"));
+            item = new JMenuItem(label);
+            final String url;
 
-            item = new JMenuItem(link.substring(0, link.indexOf("|")));
-            String id = sequence.getName();
-            if(id.indexOf("|")>-1)
-              id = id.substring(id.lastIndexOf("|")+1);
-
-            final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
-                + id +
-                link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+            if (link.indexOf("$SEQUENCE_ID$") > -1)
+            {
+              String id = seq.getName();
+              if (id.indexOf("|") > -1)
+                id = id.substring(id.lastIndexOf("|") + 1);
+
+              url = link.substring(link.indexOf("|") + 1,
+                                   link.indexOf("$SEQUENCE_ID$"))
+                  + id +
+                  link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+            }
+            else
+              url = link.substring(link.lastIndexOf("|")+1);
 
 
             item.addActionListener(new java.awt.event.ActionListener()
@@ -241,10 +350,14 @@ public class PopupMenu extends JPopupMenu
 
             linkMenu.add(item);
           }
-          add(linkMenu);
+          if(sequence!=null)
+            sequenceMenu.add(linkMenu);
+          else
+            add(linkMenu);
         }
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -253,7 +366,7 @@ public class PopupMenu extends JPopupMenu
     private void jbInit() throws Exception
     {
         groupMenu.setText("Group");
-        groupMenu.setText("Define");
+        groupMenu.setText("Selection");
         groupName.setText("Name");
         groupName.addActionListener(new java.awt.event.ActionListener()
             {
@@ -263,7 +376,7 @@ public class PopupMenu extends JPopupMenu
                 }
             });
         sequenceMenu.setText("Sequence");
-        sequenceName.setText("Edit name");
+        sequenceName.setText("Edit Name/Description");
         sequenceName.addActionListener(new java.awt.event.ActionListener()
             {
                 public void actionPerformed(ActionEvent e)
@@ -324,20 +437,101 @@ public class PopupMenu extends JPopupMenu
                     showColourText_actionPerformed(e);
                 }
             });
-        add(groupMenu);
-        add(sequenceMenu);
-        groupMenu.add(groupName);
-        groupMenu.addSeparator();
-        groupMenu.add(unGroupMenuItem);
-        groupMenu.add(colourMenu);
-        groupMenu.addSeparator();
-        groupMenu.add(showBoxes);
-        groupMenu.add(showText);
-        groupMenu.add(showColourText);
-        groupMenu.addSeparator();
-        groupMenu.add(outline);
-        sequenceMenu.add(sequenceName);
-        colourMenu.add(noColourmenuItem);
+    editMenu.setText("Edit");
+    cut.setText("Cut");
+    cut.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        cut_actionPerformed(e);
+      }
+    });
+    upperCase.setText("To Upper Case");
+    upperCase.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        changeCase(e);
+      }
+    });
+    copy.setText("Copy");
+    copy.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        copy_actionPerformed(e);
+      }
+    });
+    lowerCase.setText("To Lower Case");
+    lowerCase.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        changeCase(e);
+      }
+    });
+    toggle.setText("Toggle Case");
+    toggle.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        changeCase(e);
+      }
+    });
+    pdbMenu.setText("Associate Structure with Sequence");
+    pdbFromFile.setText("From File");
+    pdbFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pdbFromFile_actionPerformed(e);
+      }
+    });
+    enterPDB.setText("Enter PDB Id");
+    enterPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        enterPDB_actionPerformed(e);
+      }
+    });
+    discoverPDB.setText("Discover PDB ids");
+    discoverPDB.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        discoverPDB_actionPerformed(e);
+      }
+    });
+    outputMenu.setText("Output to Textbox...");
+    sequenceFeature.setText("Create Sequence Feature");
+    sequenceFeature.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceFeature_actionPerformed(e);
+      }
+    });
+    textColour.setText("Text Colour");
+    textColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        textColour_actionPerformed(e);
+      }
+    });
+    jMenu1.setText("Group");
+    add(groupMenu);
+
+    add(sequenceMenu);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputMenu);
+    groupMenu.add(sequenceFeature);
+    groupMenu.add(jMenu1);
+    sequenceMenu.add(sequenceName);
+    sequenceMenu.add(pdbMenu);
+    colourMenu.add(textColour);
+    colourMenu.add(noColourmenuItem);
         colourMenu.add(clustalColour);
         colourMenu.add(BLOSUM62Colour);
         colourMenu.add(PIDColour);
@@ -375,7 +569,22 @@ public class PopupMenu extends JPopupMenu
         colourMenu.addSeparator();
         colourMenu.add(abovePIDColour);
         colourMenu.add(conservationMenuItem);
-        noColourmenuItem.setText("None");
+    editMenu.add(copy);
+    editMenu.add(cut);
+    editMenu.add(upperCase);
+    editMenu.add(lowerCase);
+    editMenu.add(toggle);
+    pdbMenu.add(pdbFromFile);
+    pdbMenu.add(enterPDB);
+    pdbMenu.add(discoverPDB);
+    jMenu1.add(groupName);
+    jMenu1.add(unGroupMenuItem);
+    jMenu1.add(colourMenu);
+    jMenu1.add(showBoxes);
+    jMenu1.add(showText);
+    jMenu1.add(showColourText);
+    jMenu1.add(outline);
+    noColourmenuItem.setText("None");
         noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
             {
                 public void actionPerformed(ActionEvent e)
@@ -495,20 +704,10 @@ public class PopupMenu extends JPopupMenu
      */
     void refresh()
     {
-        SequenceGroup sg = getGroup();
-        if(sg!=null)
-        {
-          SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
-
-          if (superG != null)
-          {
-            superG.setSuperGroupProperties(sg);
-          }
-        }
         if (ap.overviewPanel != null)
           ap.overviewPanel.updateOverviewImage();
 
-        ap.seqPanel.repaint();
+        PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
     }
 
     /**
@@ -519,7 +718,7 @@ public class PopupMenu extends JPopupMenu
     protected void clustalColour_actionPerformed(ActionEvent e)
     {
         SequenceGroup sg = getGroup();
-        sg.cs = new ClustalxColourScheme(sg.sequences,
+        sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
                 ap.av.alignment.getWidth());
         refresh();
     }
@@ -625,8 +824,9 @@ public class PopupMenu extends JPopupMenu
 
         if (abovePIDColour.isSelected())
         {
-            sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                    ap.av.alignment.getWidth()));
+          sg.cs.setConsensus(AAFrequency.calculate(
+              sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
+              sg.getEndRes() + 1));
 
             int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
                     getGroup().getName());
@@ -661,6 +861,7 @@ public class PopupMenu extends JPopupMenu
 
          sg.cs = udc;
        }
+       refresh();
      }
     /**
      * DOCUMENT ME!
@@ -671,8 +872,9 @@ public class PopupMenu extends JPopupMenu
     {
         SequenceGroup sg = getGroup();
         sg.cs = new PIDColourScheme();
-        sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
         refresh();
     }
 
@@ -687,8 +889,9 @@ public class PopupMenu extends JPopupMenu
 
         sg.cs = new Blosum62ColourScheme();
 
-        sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                ap.av.alignment.getWidth()));
+        sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.hiddenRepSequences),
+                                                 sg.getStartRes(),
+                                                 sg.getEndRes() + 1));
 
         refresh();
     }
@@ -718,8 +921,10 @@ public class PopupMenu extends JPopupMenu
         if (conservationMenuItem.isSelected())
         {
             Conservation c = new Conservation("Group",
-                    ResidueProperties.propHash, 3, sg.sequences, 0,
-                    ap.av.alignment.getWidth());
+                    ResidueProperties.propHash, 3,
+                    sg.getSequences(ap.av.hiddenRepSequences),
+                    sg.getStartRes(),
+                    sg.getEndRes() + 1);
 
             c.calculate();
             c.verdict(false, ap.av.ConsPercGaps);
@@ -758,31 +963,6 @@ public class PopupMenu extends JPopupMenu
         groupName.setText(reply);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    protected void analyze_actionPerformed(ActionEvent e)
-    {
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        JInternalFrame frame = new JInternalFrame();
-        frame.setContentPane(cap);
-        Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
-
-        SequenceGroup sg = getGroup();
-        StringBuffer sb = new StringBuffer();
-
-        for (int i = 0; i < sg.sequences.size(); i++)
-        {
-            Sequence tmp = (Sequence) sg.sequences.get(i);
-            sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
-            sb.append("\n");
-        }
-
-        sb.append("Something amazing will happen soon");
-        cap.setText(sb.toString());
-    }
 
     /**
      * DOCUMENT ME!
@@ -806,11 +986,34 @@ public class PopupMenu extends JPopupMenu
      */
     void sequenceName_actionPerformed(ActionEvent e)
     {
-        String id = sequence.getName();
-        String s = (String) JOptionPane.showInternalInputDialog(ap,
-                "Edit sequence name",
-                "Edit sequence name (" + sequence.getName() + ")",
-                JOptionPane.PLAIN_MESSAGE, null, null, id);
+      JLabel idlabel = new JLabel(  "       Sequence Name ");
+      JLabel desclabel = new JLabel("Sequence Description ");
+      idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
+      desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
+      JTextField id = new JTextField(sequence.getName(), 40);
+      JTextField description = new JTextField(sequence.getDescription(), 40);
+      JPanel panel = new JPanel(new BorderLayout());
+      JPanel panel2 = new JPanel(new BorderLayout());
+      panel2.add(idlabel, BorderLayout.WEST);
+      panel2.add(id, BorderLayout.CENTER);
+      panel.add(panel2, BorderLayout.NORTH);
+      panel2 = new JPanel(new BorderLayout());
+      panel2.add(desclabel, BorderLayout.WEST);
+      panel2.add(description, BorderLayout.CENTER);
+      panel.add(panel2, BorderLayout.SOUTH);
+
+
+       int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+          panel, "Edit Sequence Name/Description",
+          JOptionPane.OK_CANCEL_OPTION );
+
+
+        if (reply != JOptionPane.OK_OPTION )
+        {
+            return;
+        }
+
+        String s = id.getText();
 
         if (s != null)
         {
@@ -826,6 +1029,12 @@ public class PopupMenu extends JPopupMenu
             sequence.setName(s);
             ap.repaint();
         }
+
+        sequence.setDescription(description.getText());
+
+        ap.av.firePropertyChange("alignment", null,
+                                  ap.av.getAlignment().getSequences());
+
     }
 
     /**
@@ -911,4 +1120,246 @@ public class PopupMenu extends JPopupMenu
         ex.printStackTrace();
       }
     }
+
+    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;
+
+      hseqs = new SequenceI[gsize];
+
+      int index = 0;
+      for (int i = 0; i < gsize; i++)
+      {
+        hseqs[index++] = sg.getSequenceAt(i);
+      }
+
+      ap.av.hideSequence(hseqs);
+    }
+
+  public void copy_actionPerformed(ActionEvent e)
+  {
+    ap.alignFrame.copy_actionPerformed(null);
+  }
+
+  public void cut_actionPerformed(ActionEvent e)
+  {
+    ap.alignFrame.cut_actionPerformed(null);
+  }
+
+  void changeCase(ActionEvent e)
+  {
+    Object source = e.getSource();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    Vector regions = new Vector();
+    if (sg != null)
+    {
+      int start = sg.getStartRes();
+      int end = sg.getEndRes() + 1;
+
+      do
+      {
+        if (ap.av.hasHiddenColumns)
+        {
+          if(start==0)
+            start = ap.av.colSel.adjustForHiddenColumns(start);
+
+          end = ap.av.colSel.getHiddenBoundaryRight(start);
+          if (start == end)
+            end = sg.getEndRes() + 1;
+          if (end > sg.getEndRes())
+            end = sg.getEndRes() + 1;
+        }
+
+        regions.addElement(new int[]
+                           {start, end});
+
+        if (ap.av.hasHiddenColumns)
+        {
+          start = ap.av.colSel.adjustForHiddenColumns(end);
+          start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+        }
+      }
+      while (end < sg.getEndRes());
+
+      int[][] startEnd = new int[regions.size()][2];
+      for (int i = 0; i < regions.size(); i++)
+      {
+        startEnd[i] = (int[]) regions.elementAt(i);
+      }
+
+
+      String description;
+      int caseChange;
+
+      if(source==toggle)
+      {
+        description = "Toggle Case";
+        caseChange = ChangeCaseCommand.TOGGLE_CASE;
+      }
+      else if(source==upperCase)
+      {
+        description = "To Upper Case";
+        caseChange = ChangeCaseCommand.TO_UPPER;
+      }
+      else
+      {
+        description = "To Lower Case";
+        caseChange = ChangeCaseCommand.TO_LOWER;
+      }
+
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(
+          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
+          startEnd, caseChange
+          );
+
+      ap.alignFrame.addHistoryItem(caseCommand);
+
+
+      ap.av.firePropertyChange("alignment", null,
+                                ap.av.getAlignment().getSequences());
+
+    }
+  }
+
+  public void outputText_actionPerformed(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
+    cap.setForInput(null);
+    Desktop.addInternalFrame(cap,
+                             "Alignment output - " + e.getActionCommand(), 600,
+                             500);
+
+    String [] omitHidden = null;
+
+    if(ap.av.hasHiddenColumns)
+    {
+      System.out.println("PROMPT USER HERE");
+      omitHidden = ap.av.getViewAsString(true);
+    }
+
+    cap.setText(new FormatAdapter().formatSequences(
+        e.getActionCommand(),
+        ap.av.getSelectionAsNewSequence(),
+        omitHidden));
+  }
+
+
+  public void pdbFromFile_actionPerformed(ActionEvent e)
+  {
+     jalview.io.JalviewFileChooser chooser
+         = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
+         getProperty(
+             "LAST_DIRECTORY"));
+     chooser.setFileView(new jalview.io.JalviewFileView());
+     chooser.setDialogTitle("Select a PDB file");
+     chooser.setToolTipText("Load a PDB file");
+
+     int value = chooser.showOpenDialog(null);
+
+     if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+     {
+       PDBEntry entry = new PDBEntry();
+       String choice = chooser.getSelectedFile().getPath();
+       jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+       try
+       {
+         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
+                                       jalview.io.AppletFormatAdapter.FILE);
+
+         if (pdbfile.id == null)
+         {
+           String reply = JOptionPane.showInternalInputDialog(
+               Desktop.desktop,
+               "Couldn't find a PDB id in the file supplied."
+               + "Please enter an Id to identify this structure.",
+               "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
+           if (reply == null)
+             return;
+
+           entry.setId(reply);
+         }
+         else
+           entry.setId(pdbfile.id);
+       }
+       catch (java.io.IOException ex)
+       {
+         ex.printStackTrace();
+       }
+
+       entry.setFile(choice);
+       sequence.getDatasetSequence().addPDBId(entry);
+     }
+
+  }
+
+  public void enterPDB_actionPerformed(ActionEvent e)
+  {
+    String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
+        "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+
+    if (id != null && id.length() > 0)
+    {
+      PDBEntry entry = new PDBEntry();
+      entry.setId(id);
+      sequence.getDatasetSequence()
+          .addPDBId(entry);
+    }
+  }
+
+  public void discoverPDB_actionPerformed(ActionEvent e)
+  {
+    new jalview.io.DBRefFetcher(
+             ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
+  }
+
+  public void sequenceFeature_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null)
+      return;
+
+    int gSize= sg.getSize();
+    SequenceI [] seqs = new SequenceI[gSize];
+    SequenceFeature [] features = new SequenceFeature[gSize];
+
+    for (int i = 0; i < gSize; i++)
+    {
+      seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
+      int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+      int end = sg.findEndRes(sg.getSequenceAt(i));
+      features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");
+    }
+
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+        .createNewFeatures(seqs, features))
+    {
+      ap.alignFrame.showSeqFeatures.setSelected(true);
+      ap.av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
+  }
+
+  public void textColour_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = getGroup();
+    if (sg != null)
+      new TextColourChooser().chooseColour(ap, sg);
+  }
 }