X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=a103073895c00f6a88aedbec6eeec04a872f140d;hb=890bd0eac47a4b0f55bd062a359c16a43c3780a0;hp=cf854b0d797ea6e4004be4902b02a2fb9fb2acc1;hpb=5fbe7c141f482121b3f7f04570ab84bf6203ebf6;p=jalview.git

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index cf854b0..a103073 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.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) 2007 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
@@ -19,17 +19,21 @@
 
 package jalview.appletgui;
 
+import java.util.*;
+
 import java.awt.*;
 import java.awt.event.*;
 
 import jalview.analysis.*;
+import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 
 public class APopupMenu
-    extends java.awt.PopupMenu
+    extends java.awt.PopupMenu implements ActionListener, ItemListener
 {
   Menu groupMenu = new Menu();
+  MenuItem editGroupName = new MenuItem();
   protected MenuItem clustalColour = new MenuItem();
   protected MenuItem zappoColour = new MenuItem();
   protected MenuItem taylorColour = new MenuItem();
@@ -45,18 +49,31 @@ public class APopupMenu
   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();
+  MenuItem sequenceName = new MenuItem("Edit Name/Description");
+
+  Sequence seq;
+  MenuItem revealAll = new MenuItem();
+  Menu menu1 = new Menu();
+
+  public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -65,8 +82,8 @@ public class APopupMenu
     // If from the IDPanel, we must display the sequence menu
     //////////////////////////////////////////////////////////
 
-    this.ap = ap;
-    sequence = seq;
+    this.ap = apanel;
+    this.seq = seq;
 
     try
     {
@@ -77,102 +94,401 @@ public class APopupMenu
       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() > 0)
     {
+      editGroupName.setLabel(sg.getName());
       showText.setState(sg.getDisplayText());
       showColourText.setState(sg.getColourText());
       showBoxes.setState(sg.getDisplayBoxes());
+      if (!ap.av.alignment.getGroups().contains(sg))
+      {
+        groupMenu.remove(unGroupMenuItem);
+      }
+
+    }
+    else
+    {
+      remove(hideSeqs);
+      remove(groupMenu);
     }
 
-    if (!ap.av.alignment.getGroups().contains(sg))
+    if (links != null)
     {
-      groupMenu.remove(unGroupMenuItem);
+      Menu linkMenu = new Menu("Link");
+      MenuItem item;
+      String link;
+      for (int i = 0; i < links.size(); i++)
+      {
+        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);
+        }
+
+        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 (seq == null)
+    if (!ap.av.hasHiddenRows)
     {
-      remove(sequenceMenu);
+      remove(revealAll);
     }
+  }
 
+  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();
+    }
   }
 
-  private void jbInit()
-      throws Exception
+  public void actionPerformed(ActionEvent evt)
   {
-    groupMenu.setLabel("Group");
-    groupMenu.setLabel("Define");
+    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();
+    }
 
-    sequenceMenu.setLabel("Sequence");
-    sequenceName.setLabel("Edit name");
-    unGroupMenuItem.setLabel("Remove Group");
-    unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+    else if (source == userDefinedColour)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        unGroupMenuItem_actionPerformed(e);
-      }
-    });
+      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();
+    }
 
-    nucleotideMenuItem.setLabel("Nucleotide");
-    nucleotideMenuItem.addActionListener(new ActionListener()
+    else if (source == sequenceName)
     {
-      public void actionPerformed(ActionEvent e)
-      {
-        nucleotideMenuItem_actionPerformed(e);
-      }
-    });
-    conservationMenuItem.addItemListener(new ItemListener()
+      editName();
+    }
+    else if (source == pdb)
+    {
+      addPDB();
+    }
+    else if (source == hideSeqs)
+    {
+      hideSequences(false);
+    }
+    else if (source == repGroup)
+    {
+      hideSequences(true);
+    }
+    else if (source == revealAll)
+    {
+      ap.av.showAllHiddenSeqs();
+    }
+
+    else if (source == editGroupName)
     {
-      public void itemStateChanged(ItemEvent itemEvent)
+      EditNameDialog dialog = new EditNameDialog(
+          getGroup().getName(),
+          getGroup().getDescription(),
+          "       Group Name",
+          "Group Description",
+          ap,
+          "Edit Group Name / Description");
+
+      if (dialog.accept)
       {
-        conservationMenuItem_itemStateChanged(itemEvent);
+
+        getGroup().setName(dialog.getName().replace(' ', '_'));
+        getGroup().setDescription(dialog.getDescription());
       }
-    });
-    abovePIDColour.addItemListener(new ItemListener()
+
+    }
+    else if (source == copy)
     {
-      public void itemStateChanged(ItemEvent itemEvent)
+      ap.alignFrame.copy_actionPerformed();
+    }
+    else if (source == cut)
+    {
+      ap.alignFrame.cut_actionPerformed();
+    }
+    else if (source == toUpper || source == toLower || source == toggleCase)
+    {
+      SequenceGroup sg = ap.av.getSelectionGroup();
+      Vector regions = new Vector();
+      if (sg != null)
       {
-        abovePIDColour_itemStateChanged(itemEvent);
+        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 == toggleCase)
+        {
+          description = "Toggle Case";
+          caseChange = ChangeCaseCommand.TOGGLE_CASE;
+        }
+        else if (source == toUpper)
+        {
+          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());
+
       }
-    });
+    }
+    else
+    {
+      outputText(evt);
+    }
+
+  }
+
+  void outputText(ActionEvent e)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
+
+    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(),
+        new Alignment(ap.av.getSelectionAsNewSequence()),
+        ap.av.showJVSuffix));
+
+  }
+
+  void editName()
+  {
+    EditNameDialog dialog = new EditNameDialog(
+        seq.getName(),
+        seq.getDescription(),
+        "       Sequence Name",
+        "Sequence Description",
+        ap,
+        "Edit Sequence Name / Description");
+
+    if (dialog.accept)
+    {
+      seq.setName(dialog.getName());
+      seq.setDescription(dialog.getDescription());
+      ap.paintAlignment(false);
+    }
+  }
+
+  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");
+
+    editGroupName.addActionListener(this);
+    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);
+    sequenceName.addActionListener(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");
+    menu1.setLabel("Group");
     add(groupMenu);
-    this.add(sequenceMenu);
-    groupMenu.add(unGroupMenuItem);
-    groupMenu.add(colourMenu);
-    groupMenu.addSeparator();
-    groupMenu.add(showBoxes);
-    groupMenu.add(showText);
-    groupMenu.add(showColourText);
-    sequenceMenu.add(sequenceName);
+    this.add(seqMenu);
+    this.add(hideSeqs);
+    this.add(revealAll);
+    groupMenu.add(editGroupName);
+    groupMenu.add(editMenu);
+    groupMenu.add(outputmenu);
+    groupMenu.add(menu1);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
@@ -191,328 +507,286 @@ public class APopupMenu
     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(sequenceName);
+    seqMenu.add(pdb);
+    seqMenu.add(repGroup);
+    menu1.add(unGroupMenuItem);
+    menu1.add(colourMenu);
+    menu1.add(showBoxes);
+    menu1.add(showText);
+    menu1.add(showColourText);
+    toggleCase.addActionListener(this);
+    pdb.addActionListener(this);
+    hideSeqs.addActionListener(this);
+    repGroup.addActionListener(this);
+    revealAll.addActionListener(this);
   }
 
   void refresh()
   {
-    SequenceGroup sg = getGroup();
-    if(sg!=null)
-    {
-      SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
-
-      if (superG != null)
-      {
-        superG.setSuperGroupProperties(sg);
-      }
-        }
-    ap.seqPanel.seqCanvas.repaint();
+    ap.paintAlignment(true);
   }
 
-  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(ap.av.hiddenRepSequences),
+                                     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(ap.av.
+          hiddenRepSequences), 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);
-      }
+
+      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());
   }
 
-  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,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences), 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,
+    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
+        hiddenRepSequences), 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())
     {
 
       Conservation c = new Conservation("Group",
                                         ResidueProperties.propHash, 3,
-                                        sg.sequences, 0,
+                                        sg.getSequences(ap.av.
+          hiddenRepSequences), 0,
                                         ap.av.alignment.getWidth());
 
       c.calculate();
       c.verdict(false, ap.av.ConsPercGaps);
-      ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
 
-      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();
   }
 
-  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
-    if(sg!=null)
+    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();
+    ap.paintAlignment(true);
   }
 
-  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() < 1)
+    {
+      ap.av.hideSequence(new SequenceI[]
+                         {seq});
+      return;
+    }
+
+    ap.av.setSelectionGroup(null);
+
+    if (representGroup)
+    {
+      ap.av.hideRepSequences(seq, 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);
+  }
+
 }