X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=dca9da4a84e744d2f704510390172c8bc4009d25;hb=c97c8a9e4fd58a4927e040e314c5be3c5356745e;hp=a932d66fc4ab8208f50bd23665e12cfd94ff18b8;hpb=6d6d6bc08bca95676a8175c634c03c163fb88684;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index a932d66..dca9da4 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -1,12 +1,34 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
 package jalview.appletgui;
 
-import jalview.datamodel.*;
-import jalview.analysis.*;
-import jalview.schemes.*;
 import java.awt.*;
 import java.awt.event.*;
+import java.util.Vector;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
 
-public class APopupMenu extends java.awt.PopupMenu
+public class APopupMenu
+    extends java.awt.PopupMenu implements ActionListener, ItemListener
 {
   Menu groupMenu = new Menu();
   protected MenuItem clustalColour = new MenuItem();
@@ -24,19 +46,29 @@ public class APopupMenu extends java.awt.PopupMenu
   MenuItem noColourmenuItem = new MenuItem();
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
 
-
-  AlignmentPanel ap;
-  Menu sequenceMenu = new Menu();
-  MenuItem sequenceName = new MenuItem();
-  Sequence sequence;
+  final AlignmentPanel ap;
   MenuItem unGroupMenuItem = new MenuItem();
   MenuItem nucleotideMenuItem = new MenuItem();
   Menu colourMenu = new Menu();
   CheckboxMenuItem showBoxes = new CheckboxMenuItem();
   CheckboxMenuItem showText = new CheckboxMenuItem();
   CheckboxMenuItem showColourText = new CheckboxMenuItem();
-
-  public APopupMenu(AlignmentPanel ap, Sequence seq)
+  Menu editMenu = new Menu("Edit");
+  MenuItem copy = new MenuItem("Copy (Jalview Only)");
+  MenuItem cut = new MenuItem("Cut (Jalview Only)");
+  MenuItem toUpper = new MenuItem("To Upper Case");
+  MenuItem toLower = new MenuItem("To Lower Case");
+  MenuItem toggleCase = new MenuItem("Toggle Case");
+  Menu outputmenu = new Menu();
+  Menu seqMenu = new Menu();
+  MenuItem pdb = new MenuItem();
+  MenuItem hideSeqs = new MenuItem();
+  MenuItem repGroup = new MenuItem();
+
+  Sequence seq;
+  MenuItem revealAll = new MenuItem();
+
+  public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -45,107 +77,290 @@ public class APopupMenu extends java.awt.PopupMenu
     // If from the IDPanel, we must display the sequence menu
     //////////////////////////////////////////////////////////
 
-    this.ap = ap;
-    sequence = seq;
+    this.ap = apanel;
+    this.seq = seq;
 
     try
-    {     jbInit();   }
-    catch(Exception e)
-    {    e.printStackTrace();    }
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
 
+    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+    {
+      MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );
+
+      item.addActionListener(this);
+      outputmenu.add(item);
+    }
 
     SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg!=null)
+
+    if (sg != null && sg.getSize(false)>0)
     {
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
-    }
-
-    if( !ap.av.alignment.getGroups().contains(sg))
+      if (!ap.av.alignment.getGroups().contains(sg))
+      {
         groupMenu.remove(unGroupMenuItem);
+      }
 
-    if(seq==null)
-       remove(sequenceMenu);
-
-
-  }
-  private void jbInit() throws Exception
-  {
-    groupMenu.setLabel("Group");
-    groupMenu.setLabel("Define");
+    }
+    else
+    {
+      remove(hideSeqs);
+      remove(groupMenu);
+    }
 
-    sequenceMenu.setLabel("Sequence");
-    sequenceName.setLabel("Edit name");
-    unGroupMenuItem.setLabel("Remove Group");
-    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    if (links!=null)
     {
-      public void actionPerformed(ActionEvent e)
+      Menu linkMenu = new Menu("Link");
+      MenuItem item;
+      String link;
+      for(int i=0; i<links.size(); i++)
       {
-        unGroupMenuItem_actionPerformed(e);
+        link = links.elementAt(i).toString();
+        final String target = link.substring(0, link.indexOf("|"));
+        item = new MenuItem(target);
+
+        final String url;
+
+        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);
+
+        System.out.println("add "+url +" "+target);
+           item.addActionListener(new java.awt.event.ActionListener()
+           {
+               public void actionPerformed(ActionEvent e)
+               {
+                  ap.alignFrame.showURL(url, target);
+               }
+           });
+          linkMenu.add(item);
       }
-    });
+      if(seq!=null)
+        seqMenu.add(linkMenu);
+      else
+        add(linkMenu);
+    }
+    if(seq!=null)
+    {
+      seqMenu.setLabel(seq.getName());
+      repGroup.setLabel("Represent Group with " + seq.getName());
+    }
+    else
+      remove(seqMenu);
 
+    if(!ap.av.hasHiddenRows)
+      remove(revealAll);
+  }
 
-    nucleotideMenuItem.setLabel("Nucleotide");
-    nucleotideMenuItem.addActionListener(new ActionListener()
+  public void itemStateChanged(ItemEvent evt)
+  {
+    if(evt.getSource()==abovePIDColour)
+      abovePIDColour_itemStateChanged();
+    else if(evt.getSource()==showColourText)
+      showColourText_itemStateChanged();
+    else if(evt.getSource()==showText)
+      showText_itemStateChanged();
+    else if(evt.getSource()==showBoxes)
+       showBoxes_itemStateChanged()   ;
+  }
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    Object source = evt.getSource();
+    if(source==clustalColour)
+      clustalColour_actionPerformed();
+    else if(source==zappoColour)
+      zappoColour_actionPerformed();
+    else if(source==taylorColour)
+      taylorColour_actionPerformed();
+    else if(source==hydrophobicityColour)
+      hydrophobicityColour_actionPerformed();
+    else if(source==helixColour)
+      helixColour_actionPerformed();
+    else if(source==strandColour)
+      strandColour_actionPerformed();
+    else if(source==turnColour)
+      turnColour_actionPerformed();
+    else if(source==buriedColour)
+      buriedColour_actionPerformed();
+    else if(source==nucleotideMenuItem)
+      nucleotideMenuItem_actionPerformed();
+
+    else if (source == userDefinedColour)
+      userDefinedColour_actionPerformed();
+    else if (source == PIDColour)
+      PIDColour_actionPerformed();
+    else if (source == BLOSUM62Colour)
+      BLOSUM62Colour_actionPerformed();
+    else if (source == noColourmenuItem)
+      noColourmenuItem_actionPerformed();
+    else if (source == conservationMenuItem)
+      conservationMenuItem_itemStateChanged();
+    else if (source == unGroupMenuItem)
+      unGroupMenuItem_actionPerformed();
+
+    else if(source == pdb)
+      addPDB();
+    else if(source == hideSeqs)
+      hideSequences(false);
+    else if(source == repGroup)
+      hideSequences(true);
+    else if(source == revealAll)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        nucleotideMenuItem_actionPerformed(e);
-      }
-    });
-    conservationMenuItem.addItemListener(new ItemListener()
+        ap.av.showAllHiddenSeqs();
+    }
+
+    else if(source==copy)
+      ap.alignFrame.copy_actionPerformed();
+    else if(source==cut)
+      ap.alignFrame.cut_actionPerformed();
+    else if(source==toUpper || source==toLower || source==toggleCase)
     {
-      public void itemStateChanged(ItemEvent itemEvent)
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      if (sg != null)
       {
-        conservationMenuItem_itemStateChanged(itemEvent);
+        for (int g = 0; g < sg.getSize(true); g++)
+        {
+          int start = sg.getStartRes();
+          int end = sg.getEndRes() + 1;
+
+          do
+          {
+            if (ap.av.hasHiddenColumns)
+            {
+              end = ap.av.colSel.getHiddenBoundaryRight(start);
+              if (start == end)
+                end = sg.getEndRes() + 1;
+              if (end > sg.getEndRes())
+                end = sg.getEndRes() + 1;
+            }
+
+            if (source == toggleCase)
+              ( (SequenceI) sg.getSequences(true).elementAt(g))
+                  .toggleCase(start, end);
+            else
+              ( (SequenceI) sg.getSequences(true).elementAt(g))
+                  .changeCase(source == toUpper, start, end);
+
+            if (ap.av.hasHiddenColumns)
+            {
+              start = ap.av.colSel.adjustForHiddenColumns(end);
+              start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+            }
+
+          }
+        while (end < sg.getEndRes());
+        }
+        ap.seqPanel.seqCanvas.repaint();
       }
-    });
-    abovePIDColour.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
+    }
+    else
+      outputText(evt);
+
+  }
+
+  void outputText(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+    Vector vseqs = new Vector();
+
+      String [] selection = ap.av.getViewAsString(true);
+      SequenceI [] seqs = ap.av.getSelectionAsNewSequence();
+      if (selection != null)
       {
-        abovePIDColour_itemStateChanged(itemEvent);
+        for (int i = 0; i < selection.length; i++)
+        {
+          Sequence seq = new Sequence(
+              seqs[i].getName(),
+              selection[i],
+              seqs[i].getStart(), seqs[i].getEnd());
+          seq.setDescription(seqs[i].getDescription());
+          vseqs.addElement( seq );
       }
-    });
+    }
+
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame,
+                                     "Selection output - " + e.getActionCommand(),
+                                     600, 500);
+
+    cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
+        e.getActionCommand(),
+        vseqs,
+        ap.av.showJVSuffix));
+
+  }
+
+  void addPDB()
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+    cap.setText("Paste your PDB file here.");
+    cap.setPDBImport(seq);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+    groupMenu.setLabel("Group");
+    groupMenu.setLabel("Selection");
+
+    unGroupMenuItem.setLabel("Remove Group");
+    unGroupMenuItem.addActionListener(this);
+
+    nucleotideMenuItem.setLabel("Nucleotide");
+    nucleotideMenuItem.addActionListener(this);
+    conservationMenuItem.addItemListener(this);
+    abovePIDColour.addItemListener(this);
     colourMenu.setLabel("Group Colour");
     showBoxes.setLabel("Boxes");
     showBoxes.setState(true);
-    showBoxes.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        showBoxes_itemStateChanged(itemEvent);
-      }
-    });
+    showBoxes.addItemListener(this);
 
     showText.setLabel("Text");
-    showText.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        showText_itemStateChanged(itemEvent);
-      }
-    });
+    showText.addItemListener(this);
     showColourText.setLabel("Colour Text");
-    showColourText.addItemListener(new ItemListener()
-    {
-      public void itemStateChanged(ItemEvent itemEvent)
-      {
-        showColourText_itemStateChanged(itemEvent);
-      }
-    });
+    showColourText.addItemListener(this);
+    outputmenu.setLabel("Output to Textbox...");
+    seqMenu.setLabel("Sequence");
+    pdb.setLabel("View PDB Structure");
+    hideSeqs.setLabel("Hide Sequences");
+    repGroup.setLabel("Represent Group with");
+    revealAll.setLabel("Reveal All");
 
     add(groupMenu);
-    this.add(sequenceMenu);
+    this.add(seqMenu);
+    this.add(hideSeqs);
+    this.add(revealAll);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputmenu);
+    groupMenu.addSeparator();
     groupMenu.add(unGroupMenuItem);
     groupMenu.add(colourMenu);
-    groupMenu.addSeparator();
     groupMenu.add(showBoxes);
     groupMenu.add(showText);
     groupMenu.add(showColourText);
-    sequenceMenu.add(sequenceName);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
@@ -164,327 +379,273 @@ public class APopupMenu extends java.awt.PopupMenu
     colourMenu.add(conservationMenuItem);
 
     noColourmenuItem.setLabel("None");
-    noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        noColourmenuItem_actionPerformed(e);
-      }
-    });
+    noColourmenuItem.addActionListener(this);
 
     clustalColour.setLabel("Clustalx colours");
-    clustalColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        clustalColour_actionPerformed(e);
-      }
-    });
+    clustalColour.addActionListener(this);
     zappoColour.setLabel("Zappo");
-    zappoColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        zappoColour_actionPerformed(e);
-      }
-    });
+    zappoColour.addActionListener(this);
     taylorColour.setLabel("Taylor");
-    taylorColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        taylorColour_actionPerformed(e);
-      }
-    });
+    taylorColour.addActionListener(this);
     hydrophobicityColour.setLabel("Hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed(e);
-      }
-    });
+    hydrophobicityColour.addActionListener(this);
     helixColour.setLabel("Helix propensity");
-    helixColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        helixColour_actionPerformed(e);
-      }
-    });
+    helixColour.addActionListener(this);
     strandColour.setLabel("Strand propensity");
-    strandColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        strandColour_actionPerformed(e);
-      }
-    });
+    strandColour.addActionListener(this);
     turnColour.setLabel("Turn propensity");
-    turnColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        turnColour_actionPerformed(e);
-      }
-    });
+    turnColour.addActionListener(this);
     buriedColour.setLabel("Buried Index");
-    buriedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        buriedColour_actionPerformed(e);
-      }
-    });
+    buriedColour.addActionListener(this);
     abovePIDColour.setLabel("Above % Identity");
 
     userDefinedColour.setLabel("User Defined");
-    userDefinedColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        userDefinedColour_actionPerformed(e);
-      }
-    });
+    userDefinedColour.addActionListener(this);
     PIDColour.setLabel("Percentage Identity");
-    PIDColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        PIDColour_actionPerformed(e);
-      }
-    });
+    PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel("BLOSUM62");
-    BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        BLOSUM62Colour_actionPerformed(e);
-      }
-    });
+    BLOSUM62Colour.addActionListener(this);
     conservationMenuItem.setLabel("Conservation");
 
+    editMenu.add(copy);
+    copy.addActionListener(this);
+    editMenu.add(cut);
+    cut.addActionListener(this);
+    editMenu.add(toUpper);
+    toUpper.addActionListener(this);
+    editMenu.add(toLower);
+    toLower.addActionListener(this);
+    editMenu.add(toggleCase);
+    seqMenu.add(pdb);
+    seqMenu.add(repGroup);
+    toggleCase.addActionListener(this);
+    pdb.addActionListener(this);
+    hideSeqs.addActionListener(this);
+    repGroup.addActionListener(this);
+    revealAll.addActionListener(this);
 
   }
 
   void refresh()
   {
-    SequenceGroup sg = getGroup();
-    SuperGroup superG = ap.av.alignment.getSuperGroup( sg );
-    if( superG !=null)
-      superG.setSuperGroupProperties( sg );
-
     ap.seqPanel.seqCanvas.repaint();
+    if(ap.overviewPanel!=null)
+      ap.overviewPanel.updateOverviewImage();
   }
 
-  protected void clustalColour_actionPerformed(ActionEvent e)
+  protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
+    sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());
     refresh();
   }
 
-  protected void zappoColour_actionPerformed(ActionEvent e)
+  protected void zappoColour_actionPerformed()
   {
     getGroup().cs = new ZappoColourScheme();
     refresh();
   }
 
-  protected void taylorColour_actionPerformed(ActionEvent e)
+  protected void taylorColour_actionPerformed()
   {
     getGroup().cs = new TaylorColourScheme();
     refresh();
   }
 
-
-  protected void hydrophobicityColour_actionPerformed(ActionEvent e)
+  protected void hydrophobicityColour_actionPerformed()
   {
     getGroup().cs = new HydrophobicColourScheme();
     refresh();
   }
 
-  protected void helixColour_actionPerformed(ActionEvent e)
+  protected void helixColour_actionPerformed()
   {
     getGroup().cs = new HelixColourScheme();
     refresh();
   }
 
-  protected void strandColour_actionPerformed(ActionEvent e)
+  protected void strandColour_actionPerformed()
   {
     getGroup().cs = new StrandColourScheme();
     refresh();
   }
 
-  protected void turnColour_actionPerformed(ActionEvent e)
+  protected void turnColour_actionPerformed()
   {
     getGroup().cs = new TurnColourScheme();
     refresh();
   }
 
-  protected void buriedColour_actionPerformed(ActionEvent e)
+  protected void buriedColour_actionPerformed()
   {
     getGroup().cs = new BuriedColourScheme();
     refresh();
   }
 
-  public void nucleotideMenuItem_actionPerformed(ActionEvent e)
+  public void nucleotideMenuItem_actionPerformed()
   {
     getGroup().cs = new NucleotideColourScheme();
     refresh();
   }
 
-
-
-  protected void abovePIDColour_itemStateChanged(ItemEvent ie)
+  protected void abovePIDColour_itemStateChanged()
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
+
     if (abovePIDColour.getState())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
+      sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
                                                ap.av.alignment.getWidth()));
-      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
-      if (sg.cs instanceof ResidueColourScheme)
-        ( (ResidueColourScheme)sg. cs).setThreshold(threshold);
-      else if (sg.cs instanceof ScoreColourScheme)
-        ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+          getGroup().getName());
 
-      SliderPanel.showPIDSlider();
+      sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
+      SliderPanel.showPIDSlider();
 
     }
     else // remove PIDColouring
     {
-      ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
-      rcs.setThreshold(0);
-      sg.cs = rcs;
+      sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
     }
 
     refresh();
 
   }
 
-
-  protected void userDefinedColour_actionPerformed(ActionEvent e)
+  protected void userDefinedColour_actionPerformed()
   {
-    new UserDefinedColours( ap, getGroup());
+    new UserDefinedColours(ap, getGroup());
   }
 
-  protected void PIDColour_actionPerformed(ActionEvent e)
+  protected void PIDColour_actionPerformed()
   {
     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(true), 0,
+                                             ap.av.alignment.getWidth()));
     refresh();
   }
 
-  protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
+  protected void BLOSUM62Colour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
-                                               ap.av.alignment.getWidth()));
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
+                                             ap.av.alignment.getWidth()));
 
     refresh();
   }
 
-
-  protected void noColourmenuItem_actionPerformed(ActionEvent e)
+  protected void noColourmenuItem_actionPerformed()
   {
     getGroup().cs = null;
     refresh();
   }
 
-  protected  void conservationMenuItem_itemStateChanged(ItemEvent ie)
+  protected void conservationMenuItem_itemStateChanged()
   {
     SequenceGroup sg = getGroup();
+    if(sg.cs==null)
+          return;
 
-    if(conservationMenuItem.getState())
+    if (conservationMenuItem.getState())
     {
 
-        Conservation c = new Conservation("Group",
-                                          ResidueProperties.propHash, 3,
-                                          sg.sequences, 0,
-                                          ap.av.alignment.getWidth());
-
-        c.calculate();
-        c.verdict(false, ap.av.ConsPercGaps);
-        ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
+      Conservation c = new Conservation("Group",
+                                        ResidueProperties.propHash, 3,
+                                        sg.getSequences(true), 0,
+                                        ap.av.alignment.getWidth());
 
+      c.calculate();
+      c.verdict(false, ap.av.ConsPercGaps);
 
-      sg.cs = ccs;
+      sg.cs.setConservation(c);
 
-      SliderPanel.setConservationSlider(ap, ccs, sg.getName());
+      SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
     else // remove ConservationColouring
     {
-        ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-        sg.cs = ccs.cs;
+      sg.cs.setConservation(null);
     }
 
-     refresh();
+    refresh();
   }
 
 
-  protected void analyze_actionPerformed(ActionEvent e)
-  {
-     CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
-     Frame frame = new Frame();
-     frame.add(cap);
-     jalview.bin.JalviewLite.addFrame(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.elementAt(i);
-       sb.append(  tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
-       sb.append("\n");
-     }
-
-     sb.append("Something amazing will happen soon");
-     cap.setText( sb.toString() );
-
-  }
-
   SequenceGroup getGroup()
   {
     SequenceGroup sg = ap.av.getSelectionGroup();
 
     // this method won't add a new group if it already exists
-    ap.av.alignment.addGroup(sg);
+    if(sg!=null)
+      ap.av.alignment.addGroup(sg);
 
     return sg;
   }
 
-  void unGroupMenuItem_actionPerformed(ActionEvent e)
+  void unGroupMenuItem_actionPerformed()
   {
-     SequenceGroup sg = ap.av.getSelectionGroup();
-     ap.av.alignment.deleteGroup(sg);
-     ap.av.setSelectionGroup(null);
-     ap.repaint();
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ap.av.alignment.deleteGroup(sg);
+    ap.av.setSelectionGroup(null);
+    ap.repaint();
   }
 
-
-  public void showColourText_itemStateChanged(ItemEvent itemEvent)
+  public void showColourText_itemStateChanged()
   {
     getGroup().setColourText(showColourText.getState());
     refresh();
   }
 
-  public void showText_itemStateChanged(ItemEvent itemEvent)
+  public void showText_itemStateChanged()
   {
     getGroup().setDisplayText(showText.getState());
     refresh();
   }
 
-  public void showBoxes_itemStateChanged(ItemEvent itemEvent)
+  public void showBoxes_itemStateChanged()
   {
     getGroup().setDisplayBoxes(showBoxes.getState());
     refresh();
   }
 
+  void hideSequences(boolean representGroup)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null || sg.getSize(false)<1)
+    {
+      ap.av.hideSequence(new SequenceI[]{seq});
+      return;
+    }
+
+    int gsize = sg.getSize(false);
+    SequenceI [] hseqs;
+
+    hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
+
+      int index = 0;
+      for(int i=0; i<gsize; i++)
+      {
+        if(representGroup && sg.getSequenceAt(i)!=seq)
+        {
+          seq.addHiddenSequence(sg.getSequenceAt(i));
+          hseqs[index++] = sg.getSequenceAt(i);
+        }
+        else if(!representGroup)
+        {
+          hseqs[index++] = sg.getSequenceAt(index);
+        }
+        }
+
+      ap.av.hideSequence(hseqs);
+
+      ap.av.setSelectionGroup(null);
+    }
+
 }