X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=cfffbb9e1bbb57a3746a8c8e5eec82cbab0680d7;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=6c8e0e4e9573b1350249f2bf806649766bd7e4f4;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 6c8e0e4..cfffbb9 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,6 +1,6 @@
- /*
+/*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
@@ -18,19 +18,15 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
+import java.util.*;
 
-import jalview.bin.*;
+import java.awt.*;
 
+import jalview.analysis.*;
+import jalview.bin.*;
 import jalview.datamodel.*;
-
 import jalview.schemes.*;
 
-import java.awt.*;
-
-import java.util.*;
-
-
 /**
  * DOCUMENT ME!
  *
@@ -39,443 +35,258 @@ import java.util.*;
  */
 public class AlignViewport
 {
-    int startRes;
-    int endRes;
-    int startSeq;
-    int endSeq;
-    boolean showJVSuffix = true;
-    boolean showText = true;
-    boolean showColourText = false;
-    boolean showBoxes = true;
-    boolean wrapAlignment = false;
-    boolean renderGaps = true;
-    boolean showSequenceFeatures = false;
-    boolean showAnnotation = true;
-    boolean colourAppliesToAllGroups = true;
-    ColourSchemeI globalColourScheme = null;
-    boolean conservationColourSelected = false;
-    boolean abovePIDThreshold = false;
-    SequenceGroup selectionGroup;
-    int charHeight;
-    int charWidth;
-    boolean validCharWidth;
-    int wrappedWidth;
-    Font font;
-    boolean seqNameItalics;
-    AlignmentI alignment;
-    ColumnSelection colSel = new ColumnSelection();
-    int threshold;
-    int increment;
-    NJTree currentTree = null;
-    boolean scaleAboveWrapped = false;
-    boolean scaleLeftWrapped = true;
-    boolean scaleRightWrapped = true;
-    boolean hasHiddenColumns = false;
-    boolean hasHiddenRows = false;
-    boolean showHiddenMarkers = true;
-
-    boolean cursorMode = false;
-
-    // The following vector holds the features which are
-    // currently visible, in the correct order or rendering
-    Hashtable featuresDisplayed = null;
-
-
-    /** DOCUMENT ME!! */
-    public Hashtable [] hconsensus;
-    AlignmentAnnotation consensus;
-    AlignmentAnnotation conservation;
-    AlignmentAnnotation quality;
-    boolean autoCalculateConsensus = true;
-
-    /** DOCUMENT ME!! */
-    public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
-    // JBPNote Prolly only need this in the applet version.
-    private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
-
-    boolean ignoreGapsInConsensusCalculation = false;
-
-    boolean isDataset = false;
-
-    boolean antiAlias = false;
-
-    boolean padGaps = false;
-
-    Rectangle explodedPosition;
-
-    String viewName;
-
-    String sequenceSetID;
-
-    boolean gatherViewsHere = false;
-
-    Stack historyList = new Stack();
-    Stack redoList = new Stack();
-
-    Hashtable sequenceColours;
-
-    int thresholdTextColour = 0;
-    Color textColour = Color.black;
-    Color textColour2 = Color.white;
-
-    boolean rightAlignIds = false;
-
-    Hashtable hiddenRepSequences;
-
-
-    /**
-     * Creates a new AlignViewport object.
-     *
-     * @param al DOCUMENT ME!
-     */
-    public AlignViewport(AlignmentI al)
-    {
-        setAlignment(al);
-        init();
-    }
-    /**
-     * Create a new AlignViewport with hidden regions
-     * @param al AlignmentI
-     * @param hiddenColumns ColumnSelection
-     */
-    public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) {
-      setAlignment(al);
-      if (hiddenColumns!=null) {
-        this.colSel = hiddenColumns;
-        if (hiddenColumns.getHiddenColumns() != null)
-          hasHiddenColumns = true;
+  int startRes;
+  int endRes;
+  int startSeq;
+  int endSeq;
+  boolean showJVSuffix = true;
+  boolean showText = true;
+  boolean showColourText = false;
+  boolean showBoxes = true;
+  boolean wrapAlignment = false;
+  boolean renderGaps = true;
+  boolean showSequenceFeatures = false;
+  boolean showAnnotation = true;
+  boolean colourAppliesToAllGroups = true;
+  ColourSchemeI globalColourScheme = null;
+  boolean conservationColourSelected = false;
+  boolean abovePIDThreshold = false;
+  SequenceGroup selectionGroup;
+  int charHeight;
+  int charWidth;
+  boolean validCharWidth;
+  int wrappedWidth;
+  Font font;
+  boolean seqNameItalics;
+  AlignmentI alignment;
+  ColumnSelection colSel = new ColumnSelection();
+  int threshold;
+  int increment;
+  NJTree currentTree = null;
+  boolean scaleAboveWrapped = false;
+  boolean scaleLeftWrapped = true;
+  boolean scaleRightWrapped = true;
+  boolean hasHiddenColumns = false;
+  boolean hasHiddenRows = false;
+  boolean showHiddenMarkers = true;
+
+  boolean cursorMode = false;
+
+  // The following vector holds the features which are
+  // currently visible, in the correct order or rendering
+  Hashtable featuresDisplayed = null;
+
+  /** DOCUMENT ME!! */
+  public Hashtable[] hconsensus;
+  AlignmentAnnotation consensus;
+  AlignmentAnnotation conservation;
+  AlignmentAnnotation quality;
+  boolean autoCalculateConsensus = true;
+
+  /** DOCUMENT ME!! */
+  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
+  // JBPNote Prolly only need this in the applet version.
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.
+      PropertyChangeSupport(this);
+
+  boolean ignoreGapsInConsensusCalculation = false;
+
+  boolean isDataset = false;
+
+  boolean antiAlias = false;
+
+  boolean padGaps = false;
+
+  Rectangle explodedPosition;
+
+  String viewName;
+
+  String sequenceSetID;
+
+  boolean gatherViewsHere = false;
+
+  Stack historyList = new Stack();
+  Stack redoList = new Stack();
+
+  Hashtable sequenceColours;
+
+  int thresholdTextColour = 0;
+  Color textColour = Color.black;
+  Color textColour2 = Color.white;
+
+  boolean rightAlignIds = false;
+
+  Hashtable hiddenRepSequences;
+
+  /**
+   * Creates a new AlignViewport object.
+   *
+   * @param al DOCUMENT ME!
+   */
+  public AlignViewport(AlignmentI al)
+  {
+    setAlignment(al);
+    init();
+  }
+
+  /**
+   * Create a new AlignViewport with hidden regions
+   * @param al AlignmentI
+   * @param hiddenColumns ColumnSelection
+   */
+  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+  {
+    setAlignment(al);
+    if (hiddenColumns != null)
+    {
+      this.colSel = hiddenColumns;
+      if (hiddenColumns.getHiddenColumns() != null)
+      {
+        hasHiddenColumns = true;
       }
-      init();
     }
+    init();
+  }
 
-    void init()
-    {
-        this.startRes = 0;
-        this.endRes = alignment.getWidth() - 1;
-        this.startSeq = 0;
-        this.endSeq = alignment.getHeight() - 1;
-
-      antiAlias = Cache.getDefault("ANTI_ALIAS", false);
-
-      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
-      showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
-
-      rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
-
-      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
-
-      padGaps = Cache.getDefault("PAD_GAPS", true);
+  void init()
+  {
+    this.startRes = 0;
+    this.endRes = alignment.getWidth() - 1;
+    this.startSeq = 0;
+    this.endSeq = alignment.getHeight() - 1;
 
-       String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
-       String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
-       String fontSize = Cache.getDefault("FONT_SIZE", "10");
+    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
-       seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+    showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+    showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
 
-       int style = 0;
+    rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
 
-       if (fontStyle.equals("bold"))
-       {
-         style = 1;
-       }
-       else if (fontStyle.equals("italic"))
-       {
-         style = 2;
-       }
+    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
-       setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+    padGaps = Cache.getDefault("PAD_GAPS", true);
 
-       alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
+    String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+    String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
+    String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
+    seqNameItalics = Cache.getDefault("ID_ITALICS", true);
 
-        // We must set conservation and consensus before setting colour,
-        // as Blosum and Clustal require this to be done
-        if(hconsensus==null && !isDataset)
-        {
-          if(!alignment.isNucleotide())
-          {
-            conservation = new AlignmentAnnotation("Conservation",
-                "Conservation of total alignment less than " +
-                ConsPercGaps + "% gaps",
-                new Annotation[1], 0f,
-                11f,
-                AlignmentAnnotation.BAR_GRAPH);
-            conservation.hasText = true;
-            conservation.autoCalculated = true;
+    int style = 0;
 
-
-            if (Cache.getDefault("SHOW_CONSERVATION", true))
-            {
-              alignment.addAnnotation(conservation);
-            }
-
-            if (Cache.getDefault("SHOW_QUALITY", true))
-            {
-              quality = new AlignmentAnnotation("Quality",
-                                                "Alignment Quality based on Blosum62 scores",
-                                                new Annotation[1],
-                                                0f,
-                                                11f,
-                                                AlignmentAnnotation.BAR_GRAPH);
-              quality.hasText = true;
-              quality.autoCalculated = true;
-
-              alignment.addAnnotation(quality);
-            }
-          }
-
-          consensus = new AlignmentAnnotation("Consensus", "PID",
-                                               new Annotation[1], 0f, 100f,
-                                               AlignmentAnnotation.BAR_GRAPH);
-          consensus.hasText = true;
-          consensus.autoCalculated = true;
-
-           if (Cache.getDefault("SHOW_IDENTITY", true))
-           {
-             alignment.addAnnotation(consensus);
-           }
-        }
-
-        if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
-        {
-          globalColourScheme = ColourSchemeProperty.getColour(alignment,
-              jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
-
-            if (globalColourScheme instanceof UserColourScheme)
-            {
-                globalColourScheme = UserDefinedColours.loadDefaultColours();
-                ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());
-            }
-
-            if (globalColourScheme != null)
-            {
-                globalColourScheme.setConsensus(hconsensus);
-            }
-        }
-
-        wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
-    }
-
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowSequenceFeatures(boolean b)
+    if (fontStyle.equals("bold"))
     {
-        showSequenceFeatures = b;
+      style = 1;
     }
-
-    public boolean getShowSequenceFeatures()
+    else if (fontStyle.equals("italic"))
     {
-      return showSequenceFeatures;
+      style = 2;
     }
 
+    setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
 
+    alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
 
-    class ConservationThread extends Thread
+    // We must set conservation and consensus before setting colour,
+    // as Blosum and Clustal require this to be done
+    if (hconsensus == null && !isDataset)
     {
-      AlignmentPanel ap;
-      public ConservationThread(AlignmentPanel ap)
+      if (!alignment.isNucleotide())
       {
-        this.ap = ap;
-      }
-
-      public void run()
-      {
-        try
-        {
-          updatingConservation = true;
-
-          while (UPDATING_CONSERVATION)
-          {
-            try
-            {
-              if (ap != null)
-              {
-                ap.repaint();
-              }
-              Thread.sleep(200);
-            }
-            catch (Exception ex)
-            {
-              ex.printStackTrace();
-            }
-          }
-
-          UPDATING_CONSERVATION = true;
-
-
-          int alWidth = alignment.getWidth();
-          if(alWidth<0)
-            return;
-
-          Conservation cons = new jalview.analysis.Conservation("All",
-              jalview.schemes.ResidueProperties.propHash, 3,
-              alignment.getSequences(), 0, alWidth -1);
-
-          cons.calculate();
-          cons.verdict(false, ConsPercGaps);
-
-          if (quality!=null)
-          {
-            cons.findQuality();
-          }
-
-          char [] sequence = cons.getConsSequence().getSequence();
-          float minR;
-          float minG;
-          float minB;
-          float maxR;
-          float maxG;
-          float maxB;
-          minR = 0.3f;
-          minG = 0.0f;
-          minB = 0f;
-          maxR = 1.0f - minR;
-          maxG = 0.9f - minG;
-          maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
-
-          float min = 0f;
-          float max = 11f;
-          float qmin = 0f;
-          float qmax = 0f;
-
-          char c;
-
-          conservation.annotations = new Annotation[alWidth];
-
-          if (quality!=null)
-          {
-            quality.graphMax = cons.qualityRange[1].floatValue();
-            quality.annotations = new Annotation[alWidth];
-            qmin = cons.qualityRange[0].floatValue();
-            qmax = cons.qualityRange[1].floatValue();
-          }
+        conservation = new AlignmentAnnotation("Conservation",
+                                               "Conservation of total alignment less than " +
+                                               ConsPercGaps + "% gaps",
+                                               new Annotation[1], 0f,
+                                               11f,
+                                               AlignmentAnnotation.BAR_GRAPH);
+        conservation.hasText = true;
+        conservation.autoCalculated = true;
 
-          for (int i = 0; i < alWidth; i++)
-          {
-            float value = 0;
-
-            c = sequence[i];
-
-            if (Character.isDigit(c))
-              value = (int) (c - '0');
-            else if (c == '*')
-              value = 11;
-            else if (c == '+')
-              value = 10;
-
-            float vprop = value - min;
-            vprop /= max;
-            conservation.annotations[i] =
-                new Annotation(String.valueOf(c),
-                               String.valueOf(value), ' ', value,
-                               new Color(minR + (maxR * vprop),
-                                         minG + (maxG * vprop),
-                                         minB + (maxB * vprop)));
-
-            // Quality calc
-            if (quality!=null)
-            {
-              value = ( (Double) cons.quality.get(i)).floatValue();
-              vprop = value - qmin;
-              vprop /= qmax;
-              quality.annotations[i] = new Annotation(" ", String.valueOf(value), ' ',
-                                               value,
-                                               new Color(minR + (maxR * vprop),
-                  minG + (maxG * vprop),
-                  minB + (maxB * vprop)));
-            }
-          }
-        }
-        catch (OutOfMemoryError error)
+        if (Cache.getDefault("SHOW_CONSERVATION", true))
         {
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-
-
-            public void run()
-            {
-              javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  "Out of memory calculating conservation!!"
-                  +
-                  "\nSee help files for increasing Java Virtual Machine memory."
-                  , "Out of memory",
-                  javax.swing.JOptionPane.WARNING_MESSAGE);
-            }
-          });
-
-          conservation = null;
-          quality = null;
-
-          System.out.println("Conservation calculation: " + error);
-          System.gc();
-
+          alignment.addAnnotation(conservation);
         }
 
-        UPDATING_CONSERVATION = false;
-        updatingConservation = false;
-
-        if(ap!=null)
+        if (Cache.getDefault("SHOW_QUALITY", true))
         {
-          ap.repaint();
+          quality = new AlignmentAnnotation("Quality",
+                                            "Alignment Quality based on Blosum62 scores",
+                                            new Annotation[1],
+                                            0f,
+                                            11f,
+                                            AlignmentAnnotation.BAR_GRAPH);
+          quality.hasText = true;
+          quality.autoCalculated = true;
+
+          alignment.addAnnotation(quality);
         }
-
       }
-    }
 
+      consensus = new AlignmentAnnotation("Consensus", "PID",
+                                          new Annotation[1], 0f, 100f,
+                                          AlignmentAnnotation.BAR_GRAPH);
+      consensus.hasText = true;
+      consensus.autoCalculated = true;
 
-    ConservationThread conservationThread;
-
-    ConsensusThread consensusThread;
-
-    boolean consUpdateNeeded = false;
+      if (Cache.getDefault("SHOW_IDENTITY", true))
+      {
+        alignment.addAnnotation(consensus);
+      }
+    }
 
-    static boolean UPDATING_CONSENSUS = false;
+    if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+    {
+      globalColourScheme = ColourSchemeProperty.getColour(alignment,
+          jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
 
-    static boolean UPDATING_CONSERVATION = false;
+      if (globalColourScheme instanceof UserColourScheme)
+      {
+        globalColourScheme = UserDefinedColours.loadDefaultColours();
+        ( (UserColourScheme) globalColourScheme).setThreshold(0,
+            getIgnoreGapsConsensus());
+      }
 
-    boolean updatingConsensus = false;
+      if (globalColourScheme != null)
+      {
+        globalColourScheme.setConsensus(hconsensus);
+      }
+    }
 
-    boolean updatingConservation = false;
+    wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
+  }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateConservation(final AlignmentPanel ap)
-    {
-      if (alignment.isNucleotide() || conservation==null)
-        return;
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setShowSequenceFeatures(boolean b)
+  {
+    showSequenceFeatures = b;
+  }
 
-      conservationThread = new ConservationThread(ap);
-      conservationThread.start();
-    }
+  public boolean getShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateConsensus(final AlignmentPanel ap)
+  class ConservationThread
+      extends Thread
+  {
+    AlignmentPanel ap;
+    public ConservationThread(AlignmentPanel ap)
     {
-      consensusThread = new ConsensusThread(ap);
-      consensusThread.start();
+      this.ap = ap;
     }
 
-
-    class ConsensusThread extends Thread
+    public void run()
     {
-      AlignmentPanel ap;
-      public ConsensusThread(AlignmentPanel ap)
+      try
       {
-        this.ap = ap;
-      }
-      public void run()
-      {
-        updatingConsensus = true;
-        while (UPDATING_CONSENSUS)
+        updatingConservation = true;
+
+        while (UPDATING_CONSERVATION)
         {
           try
           {
@@ -483,7 +294,6 @@ public class AlignViewport
             {
               ap.repaint();
             }
-
             Thread.sleep(200);
           }
           catch (Exception ex)
@@ -492,1182 +302,1458 @@ public class AlignViewport
           }
         }
 
+        UPDATING_CONSERVATION = true;
 
-        UPDATING_CONSENSUS = true;
-
-        try
+        int alWidth = alignment.getWidth();
+        if (alWidth < 0)
         {
-          int aWidth = alignment.getWidth();
-          if(aWidth<0)
-            return;
+          return;
+        }
 
-          consensus.annotations = null;
-          consensus.annotations = new Annotation[aWidth];
+        Conservation cons = new jalview.analysis.Conservation("All",
+            jalview.schemes.ResidueProperties.propHash, 3,
+            alignment.getSequences(), 0, alWidth - 1);
 
+        cons.calculate();
+        cons.verdict(false, ConsPercGaps);
 
-          hconsensus = new Hashtable[aWidth];
-          AAFrequency.calculate(alignment.getSequencesArray(),
-                                0,
-                                alignment.getWidth(),
-                                hconsensus);
+        if (quality != null)
+        {
+          cons.findQuality();
+        }
 
-          for (int i = 0; i < aWidth; i++)
-          {
-            float value = 0;
-            if (ignoreGapsInConsensusCalculation)
-              value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
-                  floatValue();
-            else
-              value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
-                  floatValue();
-
-            String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
-            String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
-
-            if (maxRes.length() > 1)
-            {
-              mouseOver = "[" + maxRes + "] ";
-              maxRes = "+";
-            }
+        char[] sequence = cons.getConsSequence().getSequence();
+        float minR;
+        float minG;
+        float minB;
+        float maxR;
+        float maxG;
+        float maxB;
+        minR = 0.3f;
+        minG = 0.0f;
+        minB = 0f;
+        maxR = 1.0f - minR;
+        maxG = 0.9f - minG;
+        maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
+
+        float min = 0f;
+        float max = 11f;
+        float qmin = 0f;
+        float qmax = 0f;
+
+        char c;
+
+        conservation.annotations = new Annotation[alWidth];
+
+        if (quality != null)
+        {
+          quality.graphMax = cons.qualityRange[1].floatValue();
+          quality.annotations = new Annotation[alWidth];
+          qmin = cons.qualityRange[0].floatValue();
+          qmax = cons.qualityRange[1].floatValue();
+        }
 
-            mouseOver += ( (int) value + "%");
-            consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
-          }
+        for (int i = 0; i < alWidth; i++)
+        {
+          float value = 0;
 
+          c = sequence[i];
 
-          if (globalColourScheme != null)
-            globalColourScheme.setConsensus(hconsensus);
+          if (Character.isDigit(c))
+          {
+            value = (int) (c - '0');
+          }
+          else if (c == '*')
+          {
+            value = 11;
+          }
+          else if (c == '+')
+          {
+            value = 10;
+          }
 
+          float vprop = value - min;
+          vprop /= max;
+          conservation.annotations[i] =
+              new Annotation(String.valueOf(c),
+                             String.valueOf(value), ' ', value,
+                             new Color(minR + (maxR * vprop),
+                                       minG + (maxG * vprop),
+                                       minB + (maxB * vprop)));
+
+          // Quality calc
+          if (quality != null)
+          {
+            value = ( (Double) cons.quality.get(i)).floatValue();
+            vprop = value - qmin;
+            vprop /= qmax;
+            quality.annotations[i] = new Annotation(" ", String.valueOf(value),
+                ' ',
+                value,
+                new Color(minR + (maxR * vprop),
+                          minG + (maxG * vprop),
+                          minB + (maxB * vprop)));
+          }
         }
-        catch (OutOfMemoryError error)
+      }
+      catch (OutOfMemoryError error)
+      {
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
-          alignment.deleteAnnotation(consensus);
 
-          consensus = null;
-          hconsensus = null;
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          public void run()
           {
-            public void run()
-            {
-              javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  "Out of memory calculating consensus!!"
-                  +
-                  "\nSee help files for increasing Java Virtual Machine memory."
-                  , "Out of memory",
-                  javax.swing.JOptionPane.WARNING_MESSAGE);
-            }
-          });
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory calculating conservation!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
 
-          System.out.println("Consensus calculation: " + error);
-          System.gc();
-        }
-        UPDATING_CONSENSUS = false;
-        updatingConsensus = false;
+        conservation = null;
+        quality = null;
+
+        System.out.println("Conservation calculation: " + error);
+        System.gc();
 
-        if (ap != null)
-        {
-          ap.repaint();
-        }
-      }
-    }
-    /**
-     * get the consensus sequence as displayed under the PID consensus annotation row.
-     * @return consensus sequence as a new sequence object
-     */
-    public SequenceI getConsensusSeq() {
-      if (consensus==null)
-        updateConsensus(null);
-      if (consensus==null)
-        return null;
-      StringBuffer seqs=new StringBuffer();
-      for (int i=0; i<consensus.annotations.length; i++) {
-        if (consensus.annotations[i]!=null) {
-          if (consensus.annotations[i].description.charAt(0) == '[')
-            seqs.append(consensus.annotations[i].description.charAt(1));
-          else
-            seqs.append(consensus.annotations[i].displayCharacter);
-        }
       }
 
-      SequenceI sq = new Sequence("Consensus", seqs.toString());
-      sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
-      return sq;
-    }
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceGroup getSelectionGroup()
-    {
-        return selectionGroup;
-    }
+      UPDATING_CONSERVATION = false;
+      updatingConservation = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void setSelectionGroup(SequenceGroup sg)
-    {
-        selectionGroup = sg;
-    }
+      if (ap != null)
+      {
+        ap.repaint();
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getConservationSelected()
-    {
-        return conservationColourSelected;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setConservationSelected(boolean b)
-    {
-        conservationColourSelected = b;
-    }
+  ConservationThread conservationThread;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getAbovePIDThreshold()
-    {
-        return abovePIDThreshold;
-    }
+  ConsensusThread consensusThread;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setAbovePIDThreshold(boolean b)
-    {
-        abovePIDThreshold = b;
-    }
+  boolean consUpdateNeeded = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartRes()
-    {
-        return startRes;
-    }
+  static boolean UPDATING_CONSENSUS = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndRes()
-    {
-        return endRes;
-    }
+  static boolean UPDATING_CONSERVATION = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartSeq()
-    {
-        return startSeq;
-    }
+  boolean updatingConsensus = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     */
-    public void setGlobalColourScheme(ColourSchemeI cs)
-    {
-        globalColourScheme = cs;
-    }
+  boolean updatingConservation = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public ColourSchemeI getGlobalColourScheme()
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateConservation(final AlignmentPanel ap)
+  {
+    if (alignment.isNucleotide() || conservation == null)
     {
-        return globalColourScheme;
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     */
-    public void setStartRes(int res)
-    {
-        this.startRes = res;
-    }
+    conservationThread = new ConservationThread(ap);
+    conservationThread.start();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateConsensus(final AlignmentPanel ap)
+  {
+    consensusThread = new ConsensusThread(ap);
+    consensusThread.start();
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setStartSeq(int seq)
+  class ConsensusThread
+      extends Thread
+  {
+    AlignmentPanel ap;
+    public ConsensusThread(AlignmentPanel ap)
     {
-        this.startSeq = seq;
+      this.ap = ap;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     */
-    public void setEndRes(int res)
+    public void run()
     {
-        if (res > (alignment.getWidth() - 1))
+      updatingConsensus = true;
+      while (UPDATING_CONSENSUS)
+      {
+        try
         {
-            // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-            res = alignment.getWidth() - 1;
-        }
+          if (ap != null)
+          {
+            ap.repaint();
+          }
 
-        if (res < 0)
-        {
-            res = 0;
+          Thread.sleep(200);
         }
-
-        this.endRes = res;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setEndSeq(int seq)
-    {
-        if (seq > alignment.getHeight())
+        catch (Exception ex)
         {
-            seq = alignment.getHeight();
+          ex.printStackTrace();
         }
+      }
+
+      UPDATING_CONSENSUS = true;
 
-        if (seq < 0)
+      try
+      {
+        int aWidth = alignment.getWidth();
+        if (aWidth < 0)
         {
-            seq = 0;
+          return;
         }
 
-        this.endSeq = seq;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndSeq()
-    {
-        return endSeq;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param f DOCUMENT ME!
-     */
-    public void setFont(Font f)
-    {
-        font = f;
-
-        Container c = new Container();
-
-        java.awt.FontMetrics fm = c.getFontMetrics(font);
-        setCharHeight(fm.getHeight());
-        setCharWidth(fm.charWidth('M'));
-        validCharWidth = true;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Font getFont()
-    {
-        return font;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param w DOCUMENT ME!
-     */
-    public void setCharWidth(int w)
-    {
-        this.charWidth = w;
-    }
+        consensus.annotations = null;
+        consensus.annotations = new Annotation[aWidth];
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getCharWidth()
-    {
-        return charWidth;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param h DOCUMENT ME!
-     */
-    public void setCharHeight(int h)
-    {
-        this.charHeight = h;
-    }
+        hconsensus = new Hashtable[aWidth];
+        AAFrequency.calculate(alignment.getSequencesArray(),
+                              0,
+                              alignment.getWidth(),
+                              hconsensus);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getCharHeight()
-    {
-        return charHeight;
-    }
+        for (int i = 0; i < aWidth; i++)
+        {
+          float value = 0;
+          if (ignoreGapsInConsensusCalculation)
+          {
+            value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
+                floatValue();
+          }
+          else
+          {
+            value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
+                floatValue();
+          }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param w DOCUMENT ME!
-     */
-    public void setWrappedWidth(int w)
-    {
-        this.wrappedWidth = w;
-    }
+          String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
+          String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWrappedWidth()
-    {
-        return wrappedWidth;
-    }
+          if (maxRes.length() > 1)
+          {
+            mouseOver = "[" + maxRes + "] ";
+            maxRes = "+";
+          }
 
+          mouseOver += ( (int) value + "%");
+          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+              value);
+        }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public AlignmentI getAlignment()
-    {
-        return alignment;
-    }
+        if (globalColourScheme != null)
+        {
+          globalColourScheme.setConsensus(hconsensus);
+        }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param align DOCUMENT ME!
-     */
-    public void setAlignment(AlignmentI align)
-    {
-        this.alignment = align;
-    }
+      }
+      catch (OutOfMemoryError error)
+      {
+        alignment.deleteAnnotation(consensus);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setWrapAlignment(boolean state)
-    {
-        wrapAlignment = state;
-    }
+        consensus = null;
+        hconsensus = null;
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                "Out of memory calculating consensus!!"
+                +
+                "\nSee help files for increasing Java Virtual Machine memory."
+                , "Out of memory",
+                javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowText(boolean state)
-    {
-        showText = state;
-    }
+        System.out.println("Consensus calculation: " + error);
+        System.gc();
+      }
+      UPDATING_CONSENSUS = false;
+      updatingConsensus = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setRenderGaps(boolean state)
-    {
-        renderGaps = state;
+      if (ap != null)
+      {
+        ap.repaint();
+      }
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourText()
+  /**
+   * get the consensus sequence as displayed under the PID consensus annotation row.
+   * @return consensus sequence as a new sequence object
+   */
+  public SequenceI getConsensusSeq()
+  {
+    if (consensus == null)
     {
-        return showColourText;
+      updateConsensus(null);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setColourText(boolean state)
+    if (consensus == null)
     {
-        showColourText = state;
+      return null;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowBoxes(boolean state)
+    StringBuffer seqs = new StringBuffer();
+    for (int i = 0; i < consensus.annotations.length; i++)
     {
-        showBoxes = state;
+      if (consensus.annotations[i] != null)
+      {
+        if (consensus.annotations[i].description.charAt(0) == '[')
+        {
+          seqs.append(consensus.annotations[i].description.charAt(1));
+        }
+        else
+        {
+          seqs.append(consensus.annotations[i].displayCharacter);
+        }
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getWrapAlignment()
-    {
-        return wrapAlignment;
-    }
+    SequenceI sq = new Sequence("Consensus", seqs.toString());
+    sq.setDescription("Percentage Identity Consensus " +
+                      ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
+                       ""));
+    return sq;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceGroup getSelectionGroup()
+  {
+    return selectionGroup;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param sg DOCUMENT ME!
+   */
+  public void setSelectionGroup(SequenceGroup sg)
+  {
+    selectionGroup = sg;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getConservationSelected()
+  {
+    return conservationColourSelected;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setConservationSelected(boolean b)
+  {
+    conservationColourSelected = b;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getAbovePIDThreshold()
+  {
+    return abovePIDThreshold;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setAbovePIDThreshold(boolean b)
+  {
+    abovePIDThreshold = b;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getStartRes()
+  {
+    return startRes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getEndRes()
+  {
+    return endRes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getStartSeq()
+  {
+    return startSeq;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param cs DOCUMENT ME!
+   */
+  public void setGlobalColourScheme(ColourSchemeI cs)
+  {
+    globalColourScheme = cs;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public ColourSchemeI getGlobalColourScheme()
+  {
+    return globalColourScheme;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param res DOCUMENT ME!
+   */
+  public void setStartRes(int res)
+  {
+    this.startRes = res;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seq DOCUMENT ME!
+   */
+  public void setStartSeq(int seq)
+  {
+    this.startSeq = seq;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param res DOCUMENT ME!
+   */
+  public void setEndRes(int res)
+  {
+    if (res > (alignment.getWidth() - 1))
+    {
+      // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
+      res = alignment.getWidth() - 1;
+    }
+
+    if (res < 0)
+    {
+      res = 0;
+    }
+
+    this.endRes = res;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param seq DOCUMENT ME!
+   */
+  public void setEndSeq(int seq)
+  {
+    if (seq > alignment.getHeight())
+    {
+      seq = alignment.getHeight();
+    }
+
+    if (seq < 0)
+    {
+      seq = 0;
+    }
+
+    this.endSeq = seq;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getEndSeq()
+  {
+    return endSeq;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param f DOCUMENT ME!
+   */
+  public void setFont(Font f)
+  {
+    font = f;
+
+    Container c = new Container();
+
+    java.awt.FontMetrics fm = c.getFontMetrics(font);
+    setCharHeight(fm.getHeight());
+    setCharWidth(fm.charWidth('M'));
+    validCharWidth = true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public Font getFont()
+  {
+    return font;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param w DOCUMENT ME!
+   */
+  public void setCharWidth(int w)
+  {
+    this.charWidth = w;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getCharWidth()
+  {
+    return charWidth;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param h DOCUMENT ME!
+   */
+  public void setCharHeight(int h)
+  {
+    this.charHeight = h;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getCharHeight()
+  {
+    return charHeight;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param w DOCUMENT ME!
+   */
+  public void setWrappedWidth(int w)
+  {
+    this.wrappedWidth = w;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getWrappedWidth()
+  {
+    return wrappedWidth;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public AlignmentI getAlignment()
+  {
+    return alignment;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param align DOCUMENT ME!
+   */
+  public void setAlignment(AlignmentI align)
+  {
+    this.alignment = align;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setWrapAlignment(boolean state)
+  {
+    wrapAlignment = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setShowText(boolean state)
+  {
+    showText = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setRenderGaps(boolean state)
+  {
+    renderGaps = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getColourText()
+  {
+    return showColourText;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setColourText(boolean state)
+  {
+    showColourText = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param state DOCUMENT ME!
+   */
+  public void setShowBoxes(boolean state)
+  {
+    showBoxes = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getWrapAlignment()
+  {
+    return wrapAlignment;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowText()
+  {
+    return showText;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowBoxes()
+  {
+    return showBoxes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public char getGapCharacter()
+  {
+    return getAlignment().getGapCharacter();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param gap DOCUMENT ME!
+   */
+  public void setGapCharacter(char gap)
+  {
+    if (getAlignment() != null)
+    {
+      getAlignment().setGapCharacter(gap);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param thresh DOCUMENT ME!
+   */
+  public void setThreshold(int thresh)
+  {
+    threshold = thresh;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getThreshold()
+  {
+    return threshold;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param inc DOCUMENT ME!
+   */
+  public void setIncrement(int inc)
+  {
+    increment = inc;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public int getIncrement()
+  {
+    return increment;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public ColumnSelection getColumnSelection()
+  {
+    return colSel;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param tree DOCUMENT ME!
+   */
+  public void setCurrentTree(NJTree tree)
+  {
+    currentTree = tree;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public NJTree getCurrentTree()
+  {
+    return currentTree;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setColourAppliesToAllGroups(boolean b)
+  {
+    colourAppliesToAllGroups = b;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getColourAppliesToAllGroups()
+  {
+    return colourAppliesToAllGroups;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowJVSuffix()
+  {
+    return showJVSuffix;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setShowJVSuffix(boolean b)
+  {
+    showJVSuffix = b;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowAnnotation()
+  {
+    return showAnnotation;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setShowAnnotation(boolean b)
+  {
+    showAnnotation = b;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getScaleAboveWrapped()
+  {
+    return scaleAboveWrapped;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getScaleLeftWrapped()
+  {
+    return scaleLeftWrapped;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean getScaleRightWrapped()
+  {
+    return scaleRightWrapped;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setScaleAboveWrapped(boolean b)
+  {
+    scaleAboveWrapped = b;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setScaleLeftWrapped(boolean b)
+  {
+    scaleLeftWrapped = b;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param b DOCUMENT ME!
+   */
+  public void setScaleRightWrapped(boolean b)
+  {
+    scaleRightWrapped = b;
+  }
+
+  /**
+   * Property change listener for changes in alignment
+   *
+   * @param listener DOCUMENT ME!
+   */
+  public void addPropertyChangeListener(
+      java.beans.PropertyChangeListener listener)
+  {
+    changeSupport.addPropertyChangeListener(listener);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param listener DOCUMENT ME!
+   */
+  public void removePropertyChangeListener(
+      java.beans.PropertyChangeListener listener)
+  {
+    changeSupport.removePropertyChangeListener(listener);
+  }
+
+  /**
+   * Property change listener for changes in alignment
+   *
+   * @param prop DOCUMENT ME!
+   * @param oldvalue DOCUMENT ME!
+   * @param newvalue DOCUMENT ME!
+   */
+  public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+  {
+    changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+  }
+
+  public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
+  {
+    ignoreGapsInConsensusCalculation = b;
+    updateConsensus(ap);
+    if (globalColourScheme != null)
+    {
+      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+                                      ignoreGapsInConsensusCalculation);
+    }
+  }
+
+  public boolean getIgnoreGapsConsensus()
+  {
+    return ignoreGapsInConsensusCalculation;
+  }
+
+  public void setDataset(boolean b)
+  {
+    isDataset = b;
+  }
+
+  public boolean isDataset()
+  {
+    return isDataset;
+  }
+
+  public void hideSelectedColumns()
+  {
+    if (colSel.size() < 1)
+    {
+      return;
+    }
+
+    colSel.hideSelectedColumns();
+    setSelectionGroup(null);
+
+    hasHiddenColumns = true;
+  }
+
+  public void hideColumns(int start, int end)
+  {
+    if (start == end)
+    {
+      colSel.hideColumns(start);
+    }
+    else
+    {
+      colSel.hideColumns(start, end);
+    }
+
+    hasHiddenColumns = true;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowText()
+  public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+  {
+    int sSize = sg.getSize();
+    if (sSize < 2)
     {
-        return showText;
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowBoxes()
+    if (hiddenRepSequences == null)
     {
-        return showBoxes;
+      hiddenRepSequences = new Hashtable();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getGapCharacter()
-    {
-        return getAlignment().getGapCharacter();
-    }
+    hiddenRepSequences.put(repSequence, sg);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gap DOCUMENT ME!
-     */
-    public void setGapCharacter(char gap)
+    //Hide all sequences except the repSequence
+    SequenceI[] seqs = new SequenceI[sSize - 1];
+    int index = 0;
+    for (int i = 0; i < sSize; i++)
     {
-        if (getAlignment() != null)
+      if (sg.getSequenceAt(i) != repSequence)
+      {
+        if (index == sSize - 1)
         {
-            getAlignment().setGapCharacter(gap);
+          return;
         }
-    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param thresh DOCUMENT ME!
-     */
-    public void setThreshold(int thresh)
-    {
-        threshold = thresh;
+        seqs[index++] = sg.getSequenceAt(i);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getThreshold()
-    {
-        return threshold;
-    }
+    hideSequence(seqs);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param inc DOCUMENT ME!
-     */
-    public void setIncrement(int inc)
-    {
-        increment = inc;
-    }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getIncrement()
+  public void hideAllSelectedSeqs()
+  {
+    if (selectionGroup == null)
     {
-        return increment;
+      return;
     }
 
+    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public ColumnSelection getColumnSelection()
-    {
-        return colSel;
-    }
+    hideSequence(seqs);
 
+    setSelectionGroup(null);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tree DOCUMENT ME!
-     */
-    public void setCurrentTree(NJTree tree)
-    {
-        currentTree = tree;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public NJTree getCurrentTree()
+  public void hideSequence(SequenceI[] seq)
+  {
+    if (seq != null)
     {
-        return currentTree;
+      for (int i = 0; i < seq.length; i++)
+      {
+        alignment.getHiddenSequences().hideSequence(seq[i]);
+      }
+      hasHiddenRows = true;
+      firePropertyChange("alignment", null, alignment.getSequences());
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setColourAppliesToAllGroups(boolean b)
+  public void showSequence(int index)
+  {
+    Vector tmp = alignment.getHiddenSequences().showSequence(index
+        , hiddenRepSequences);
+    if (tmp.size() > 0)
     {
-        colourAppliesToAllGroups = b;
-    }
+      if (selectionGroup == null)
+      {
+        selectionGroup = new SequenceGroup();
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourAppliesToAllGroups()
-    {
-        return colourAppliesToAllGroups;
+      for (int t = 0; t < tmp.size(); t++)
+      {
+        selectionGroup.addSequence(
+            (SequenceI) tmp.elementAt(t), false
+            );
+      }
+      firePropertyChange("alignment", null, alignment.getSequences());
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowJVSuffix()
+    if (alignment.getHiddenSequences().getSize() < 1)
     {
-        return showJVSuffix;
+      hasHiddenRows = false;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowJVSuffix(boolean b)
+  public void showColumn(int col)
+  {
+    colSel.revealHiddenColumns(col);
+    if (colSel.getHiddenColumns() == null)
     {
-        showJVSuffix = b;
+      hasHiddenColumns = false;
     }
+  }
 
+  public void showAllHiddenColumns()
+  {
+    colSel.revealAllHiddenColumns();
+    hasHiddenColumns = false;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowAnnotation()
-    {
-        return showAnnotation;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowAnnotation(boolean b)
+  public void showAllHiddenSeqs()
+  {
+    if (alignment.getHiddenSequences().getSize() > 0)
     {
-        showAnnotation = b;
+      if (selectionGroup == null)
+      {
+        selectionGroup = new SequenceGroup();
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
+      }
+      Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
+      for (int t = 0; t < tmp.size(); t++)
+      {
+        selectionGroup.addSequence(
+            (SequenceI) tmp.elementAt(t), false
+            );
+      }
+      firePropertyChange("alignment", null, alignment.getSequences());
+      hasHiddenRows = false;
+      hiddenRepSequences = null;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleAboveWrapped()
+  public void invertColumnSelection()
+  {
+    for (int i = 0; i < alignment.getWidth(); i++)
     {
-        return scaleAboveWrapped;
+      if (colSel.contains(i))
+      {
+        colSel.removeElement(i);
+      }
+      else
+      {
+        if (!hasHiddenColumns || colSel.isVisible(i))
+        {
+          colSel.addElement(i);
+        }
+      }
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleLeftWrapped()
-    {
-        return scaleLeftWrapped;
-    }
+  public int adjustForHiddenSeqs(int alignmentIndex)
+  {
+    return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleRightWrapped()
-    {
-        return scaleRightWrapped;
-    }
+  /**
+   * This method returns the a new SequenceI [] with
+   * the selection sequence and start and end points adjusted
+   * @return String[]
+   */
+  public SequenceI[] getSelectionAsNewSequence()
+  {
+    SequenceI[] sequences;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleAboveWrapped(boolean b)
+    if (selectionGroup == null)
     {
-        scaleAboveWrapped = b;
+      sequences = alignment.getSequencesArray();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleLeftWrapped(boolean b)
+    else
     {
-        scaleLeftWrapped = b;
+      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleRightWrapped(boolean b)
-    {
-        scaleRightWrapped = b;
-    }
+    return sequences;
+  }
 
-    /**
-     * Property change listener for changes in alignment
-     *
-     * @param listener DOCUMENT ME!
-     */
-    public void addPropertyChangeListener(
-        java.beans.PropertyChangeListener listener)
+  /**
+   * This method returns the visible alignment as text, as
+   * seen on the GUI, ie if columns are hidden they will not
+   * be returned in the result.
+   * Use this for calculating trees, PCA, redundancy etc on views
+   * which contain hidden columns.
+   * @return String[]
+   */
+  public jalview.datamodel.CigarArray getViewAsCigars(boolean
+      selectedRegionOnly)
+  {
+    CigarArray selection = null;
+    SequenceI[] seqs = null;
+    int i, iSize;
+    int start = 0, end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
     {
-        changeSupport.addPropertyChangeListener(listener);
+      iSize = selectionGroup.getSize();
+      seqs = selectionGroup.getSequencesInOrder(alignment);
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param listener DOCUMENT ME!
-     */
-    public void removePropertyChangeListener(
-        java.beans.PropertyChangeListener listener)
+    else
     {
-        changeSupport.removePropertyChangeListener(listener);
+      iSize = alignment.getHeight();
+      seqs = alignment.getSequencesArray();
+      end = alignment.getWidth() - 1;
     }
-
-    /**
-     * Property change listener for changes in alignment
-     *
-     * @param prop DOCUMENT ME!
-     * @param oldvalue DOCUMENT ME!
-     * @param newvalue DOCUMENT ME!
-     */
-    public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+    SeqCigar[] selseqs = new SeqCigar[iSize];
+    for (i = 0; i < iSize; i++)
     {
-        changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+      selseqs[i] = new SeqCigar(seqs[i], start, end);
     }
-
-    public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
+    selection = new CigarArray(selseqs);
+    // now construct the CigarArray operations
+    if (hasHiddenColumns)
     {
-      ignoreGapsInConsensusCalculation = b;
-      updateConsensus(ap);
-      if(globalColourScheme!=null)
+      Vector regions = colSel.getHiddenColumns();
+      int[] region;
+      int hideStart, hideEnd;
+      int last = start;
+      for (int j = 0; last < end & j < regions.size(); j++)
       {
-        globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);
-      }
-    }
-
-    public boolean getIgnoreGapsConsensus()
-    {
-     return ignoreGapsInConsensusCalculation;
-    }
-
-    public void setDataset(boolean b)
-    {
-      isDataset = b;
-    }
-
-    public boolean isDataset()
-    {
-      return isDataset;
-    }
-
-
-    public void hideSelectedColumns()
-    {
-      if (colSel.size() < 1)
-        return;
-
-      colSel.hideSelectedColumns();
-      setSelectionGroup(null);
-
-      hasHiddenColumns = true;
-    }
-
-
-    public void hideColumns(int start, int end)
-    {
-      if(start==end)
-        colSel.hideColumns(start);
-      else
-        colSel.hideColumns(start, end);
-
-      hasHiddenColumns = true;
-    }
-
-    public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
-    {
-      int sSize = sg.getSize();
-      if(sSize < 2)
-        return;
-
-      if(hiddenRepSequences==null)
-        hiddenRepSequences = new Hashtable();
-
-       hiddenRepSequences.put(repSequence, sg);
-
-      //Hide all sequences except the repSequence
-      SequenceI [] seqs = new SequenceI[sSize-1];
-      int index = 0;
-      for(int i=0; i<sSize; i++)
-        if(sg.getSequenceAt(i)!=repSequence)
+        region = (int[]) regions.elementAt(j);
+        hideStart = region[0];
+        hideEnd = region[1];
+        // edit hidden regions to selection range
+        if (hideStart < last)
         {
-          if(index==sSize-1)
-            return;
-
-          seqs[index++] = sg.getSequenceAt(i);
+          if (hideEnd > last)
+          {
+            hideStart = last;
+          }
+          else
+          {
+            continue;
+          }
         }
 
-      hideSequence(seqs);
-
-    }
-
-    public void hideAllSelectedSeqs()
-    {
-      if (selectionGroup == null)
-        return;
-
-      SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
-
-      hideSequence(seqs);
-
-      setSelectionGroup(null);
-    }
-
-    public void hideSequence(SequenceI [] seq)
-    {
-      if(seq!=null)
-      {
-        for (int i = 0; i < seq.length; i++)
+        if (hideStart > end)
         {
-          alignment.getHiddenSequences().hideSequence(seq[i]);
+          break;
         }
-        hasHiddenRows = true;
-        firePropertyChange("alignment", null, alignment.getSequences());
-      }
-    }
 
-    public void showSequence(int index)
-    {
-      Vector tmp = alignment.getHiddenSequences().showSequence(index
-          , hiddenRepSequences);
-      if(tmp.size()>0)
-      {
-        if(selectionGroup==null)
+        if (hideEnd > end)
         {
-          selectionGroup = new SequenceGroup();
-          selectionGroup.setEndRes(alignment.getWidth()-1);
+          hideEnd = end;
         }
 
-        for (int t = 0; t < tmp.size(); t++)
+        if (hideStart > hideEnd)
+        {
+          break;
+        }
+        /**
+         * form operations...
+         */
+        if (last < hideStart)
         {
-          selectionGroup.addSequence(
-              (SequenceI) tmp.elementAt(t), false
-              );
+          selection.addOperation(CigarArray.M, hideStart - last);
         }
-        firePropertyChange("alignment", null, alignment.getSequences());
+        selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);
+        last = hideEnd + 1;
+      }
+      // Final match if necessary.
+      if (last < end)
+      {
+        selection.addOperation(CigarArray.M, end - last + 1);
+      }
+    }
+    else
+    {
+      selection.addOperation(CigarArray.M, end - start + 1);
+    }
+    return selection;
+  }
+
+  /**
+   * return a compact representation of the current alignment selection to
+   * pass to an analysis function
+   * @param selectedOnly boolean true to just return the selected view
+   * @return AlignmentView
+   */
+  jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+  {
+    // JBPNote:
+    // this is here because the AlignmentView constructor modifies the CigarArray
+    // object. Refactoring of Cigar and alignment view representation should
+    // be done to remove redundancy.
+    CigarArray aligview = getViewAsCigars(selectedOnly);
+    if (aligview != null)
+    {
+      return new AlignmentView(aligview,
+                               (selectedOnly && selectionGroup != null) ?
+                               selectionGroup.getStartRes() : 0);
+    }
+    return null;
+  }
+
+  /**
+   * This method returns the visible alignment as text, as
+   * seen on the GUI, ie if columns are hidden they will not
+   * be returned in the result.
+   * Use this for calculating trees, PCA, redundancy etc on views
+   * which contain hidden columns.
+   * @return String[]
+   */
+  public String[] getViewAsString(boolean selectedRegionOnly)
+  {
+    String[] selection = null;
+    SequenceI[] seqs = null;
+    int i, iSize;
+    int start = 0, end = 0;
+    if (selectedRegionOnly && selectionGroup != null)
+    {
+      iSize = selectionGroup.getSize();
+      seqs = selectionGroup.getSequencesInOrder(alignment);
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes() + 1;
+    }
+    else
+    {
+      iSize = alignment.getHeight();
+      seqs = alignment.getSequencesArray();
+      end = alignment.getWidth();
+    }
+
+    selection = new String[iSize];
+    if (hasHiddenColumns)
+    {
+      selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+    }
+    else
+    {
+      for (i = 0; i < iSize; i++)
+      {
+        selection[i] = seqs[i].getSequenceAsString(start, end);
       }
 
-      if(alignment.getHiddenSequences().getSize()<1)
-        hasHiddenRows = false;
     }
+    return selection;
+  }
+
+  public boolean getShowHiddenMarkers()
+  {
+    return showHiddenMarkers;
+  }
 
-    public void showColumn(int col)
+  public void setShowHiddenMarkers(boolean show)
+  {
+    showHiddenMarkers = show;
+  }
+
+  public String getSequenceSetId()
+  {
+    if (sequenceSetID == null)
     {
-      colSel.revealHiddenColumns(col);
-      if(colSel.getHiddenColumns()==null)
-        hasHiddenColumns = false;
+      sequenceSetID = alignment.hashCode() + "";
     }
 
-    public void showAllHiddenColumns()
+    return sequenceSetID;
+  }
+
+  public void alignmentChanged(AlignmentPanel ap)
+  {
+    if (padGaps)
     {
-      colSel.revealAllHiddenColumns();
-      hasHiddenColumns = false;
+      alignment.padGaps();
     }
 
-    public void showAllHiddenSeqs()
+    if (hconsensus != null && autoCalculateConsensus)
     {
-      if(alignment.getHiddenSequences().getSize()>0)
-      {
-        if(selectionGroup==null)
-        {
-          selectionGroup = new SequenceGroup();
-          selectionGroup.setEndRes(alignment.getWidth()-1);
-        }
-        Vector tmp = alignment.getHiddenSequences().showAll(hiddenRepSequences);
-        for(int t=0; t<tmp.size(); t++)
-        {
-          selectionGroup.addSequence(
-              (SequenceI)tmp.elementAt(t), false
-              );
-        }
-        firePropertyChange("alignment", null, alignment.getSequences());
-        hasHiddenRows = false;
-        hiddenRepSequences = null;
-      }
+      updateConsensus(ap);
+      updateConservation(ap);
     }
 
-
-
-    public void invertColumnSelection()
+    //Reset endRes of groups if beyond alignment width
+    int alWidth = alignment.getWidth();
+    Vector groups = alignment.getGroups();
+    if (groups != null)
     {
-      for(int i=0; i<alignment.getWidth(); i++)
+      for (int i = 0; i < groups.size(); i++)
       {
-        if(colSel.contains(i))
-          colSel.removeElement(i);
-        else
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+        if (sg.getEndRes() > alWidth)
         {
-          if (!hasHiddenColumns || colSel.isVisible(i))
-          {
-            colSel.addElement(i);
-          }
+          sg.setEndRes(alWidth - 1);
         }
       }
     }
 
-    public int adjustForHiddenSeqs(int alignmentIndex)
+    if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
     {
-      return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+      selectionGroup.setEndRes(alWidth - 1);
     }
 
-    /**
-     * This method returns the a new SequenceI [] with
-     * the selection sequence and start and end points adjusted
-     * @return String[]
-     */
-    public SequenceI[] getSelectionAsNewSequence()
-    {
-      SequenceI[] sequences;
+    resetAllColourSchemes();
 
-      if (selectionGroup == null)
-        sequences = alignment.getSequencesArray();
-      else
-        sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+    // alignment.adjustSequenceAnnotations();
+  }
 
-      return sequences;
-    }
-
-    /**
-     * This method returns the visible alignment as text, as
-     * seen on the GUI, ie if columns are hidden they will not
-     * be returned in the result.
-     * Use this for calculating trees, PCA, redundancy etc on views
-     * which contain hidden columns.
-     * @return String[]
-     */
-    public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = globalColourScheme;
+    if (cs != null)
     {
-      CigarArray selection=null;
-      SequenceI [] seqs= null;
-      int i, iSize;
-      int start = 0, end = 0;
-      if(selectedRegionOnly && selectionGroup!=null)
+      if (cs instanceof ClustalxColourScheme)
       {
-        iSize = selectionGroup.getSize();
-        seqs = selectionGroup.getSequencesInOrder(alignment);
-        start = selectionGroup.getStartRes();
-        end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
+        ( (ClustalxColourScheme) cs).
+            resetClustalX(alignment.getSequences(),
+                          alignment.getWidth());
       }
-      else
-      {
-        iSize = alignment.getHeight();
-        seqs = alignment.getSequencesArray();
-        end = alignment.getWidth()-1;
-      }
-      SeqCigar[] selseqs = new SeqCigar[iSize];
-      for(i=0; i<iSize; i++)
-      {
-        selseqs[i] = new SeqCigar(seqs[i], start, end);
-      }
-      selection=new CigarArray(selseqs);
-      // now construct the CigarArray operations
-      if (hasHiddenColumns) {
-        Vector regions = colSel.getHiddenColumns();
-        int [] region;
-        int hideStart, hideEnd;
-        int last=start;
-        for (int j = 0; last<end & j < regions.size(); j++)
-        {
-          region = (int[]) regions.elementAt(j);
-          hideStart = region[0];
-          hideEnd = region[1];
-          // edit hidden regions to selection range
-          if(hideStart<last) {
-            if (hideEnd > last)
-            {
-              hideStart = last;
-            } else
-              continue;
-          }
 
-          if (hideStart>end)
-            break;
-
-          if (hideEnd>end)
-            hideEnd=end;
-
-          if (hideStart>hideEnd)
-            break;
-          /**
-           * form operations...
-           */
-          if (last<hideStart)
-            selection.addOperation(CigarArray.M, hideStart-last);
-          selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
-          last = hideEnd+1;
-        }
-        // Final match if necessary.
-        if (last<end)
-          selection.addOperation(CigarArray.M, end-last+1);
-      } else {
-        selection.addOperation(CigarArray.M, end-start+1);
-      }
-      return selection;
-    }
-    /**
-     * return a compact representation of the current alignment selection to
-     * pass to an analysis function
-     * @param selectedOnly boolean true to just return the selected view
-     * @return AlignmentView
-     */
-    jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
-      // JBPNote:
-      // this is here because the AlignmentView constructor modifies the CigarArray
-      // object. Refactoring of Cigar and alignment view representation should
-      // be done to remove redundancy.
-      CigarArray aligview = getViewAsCigars(selectedOnly);
-      if (aligview!=null) {
-        return new AlignmentView(aligview,
-            (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
-      }
-      return null;
-    }
-    /**
-     * This method returns the visible alignment as text, as
-     * seen on the GUI, ie if columns are hidden they will not
-     * be returned in the result.
-     * Use this for calculating trees, PCA, redundancy etc on views
-     * which contain hidden columns.
-     * @return String[]
-     */
-    public String [] getViewAsString(boolean selectedRegionOnly)
-    {
-      String [] selection = null;
-      SequenceI [] seqs= null;
-      int i, iSize;
-      int start = 0, end = 0;
-      if(selectedRegionOnly && selectionGroup!=null)
-      {
-        iSize = selectionGroup.getSize();
-        seqs = selectionGroup.getSequencesInOrder(alignment);
-        start = selectionGroup.getStartRes();
-        end = selectionGroup.getEndRes()+1;
-      }
-      else
+      cs.setConsensus(hconsensus);
+      if (cs.conservationApplied())
       {
-        iSize = alignment.getHeight();
-        seqs = alignment.getSequencesArray();
-        end = alignment.getWidth();
+        Alignment al = (Alignment) alignment;
+        Conservation c = new Conservation("All",
+                                          ResidueProperties.propHash, 3,
+                                          al.getSequences(), 0,
+                                          al.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, ConsPercGaps);
+
+        cs.setConservation(c);
       }
-
-      selection = new String[iSize];
-      if (hasHiddenColumns) {
-        selection = colSel.getVisibleSequenceStrings(start, end, seqs);
-      } else {
-        for(i=0; i<iSize; i++)
-        {
-          selection[i] = seqs[i].getSequenceAsString(start, end);
-        }
-
-      }
-      return selection;
     }
 
-    public boolean getShowHiddenMarkers()
+    int s, sSize = alignment.getGroups().size();
+    for (s = 0; s < sSize; s++)
     {
-      return showHiddenMarkers;
+      SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
+      if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
+      {
+        ( (ClustalxColourScheme) sg.cs).resetClustalX(
+            sg.getSequences(hiddenRepSequences), sg.getWidth());
+      }
+      sg.recalcConservation();
     }
+  }
 
-    public void setShowHiddenMarkers(boolean show)
+  public Color getSequenceColour(SequenceI seq)
+  {
+    if (sequenceColours == null || !sequenceColours.containsKey(seq))
     {
-      showHiddenMarkers = show;
+      return Color.white;
     }
-
-    public String getSequenceSetId()
+    else
     {
-      if(sequenceSetID==null)
-        sequenceSetID =  alignment.hashCode()+"";
-
-      return sequenceSetID;
-    }
-
-    public void alignmentChanged(AlignmentPanel ap)
-    {
-        if (padGaps)
-          alignment.padGaps();
-
-        if (hconsensus != null && autoCalculateConsensus)
-        {
-          updateConsensus(ap);
-          updateConservation(ap);
-        }
-
-        //Reset endRes of groups if beyond alignment width
-        int alWidth = alignment.getWidth();
-        Vector groups = alignment.getGroups();
-        if(groups!=null)
-        {
-          for(int i=0; i<groups.size(); i++)
-          {
-            SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-            if(sg.getEndRes()>alWidth)
-              sg.setEndRes(alWidth-1);
-          }
-        }
-
-        if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
-          selectionGroup.setEndRes(alWidth-1);
-
-        resetAllColourSchemes();
-
-       // alignment.adjustSequenceAnnotations();
+      return (Color) sequenceColours.get(seq);
     }
+  }
 
-
-    void resetAllColourSchemes()
+  public void setSequenceColour(SequenceI seq, Color col)
+  {
+    if (sequenceColours == null)
     {
-      ColourSchemeI cs = globalColourScheme;
-      if(cs!=null)
-      {
-        if (cs instanceof ClustalxColourScheme)
-        {
-          ( (ClustalxColourScheme) cs).
-              resetClustalX(alignment.getSequences(),
-                            alignment.getWidth());
-        }
-
-        cs.setConsensus(hconsensus);
-        if (cs.conservationApplied())
-        {
-          Alignment al = (Alignment) alignment;
-          Conservation c = new Conservation("All",
-                                            ResidueProperties.propHash, 3,
-                                            al.getSequences(), 0,
-                                            al.getWidth() - 1);
-          c.calculate();
-          c.verdict(false, ConsPercGaps);
-
-          cs.setConservation(c);
-        }
-      }
-
-      int s, sSize = alignment.getGroups().size();
-      for(s=0; s<sSize; s++)
-      {
-        SequenceGroup sg = (SequenceGroup)alignment.getGroups().elementAt(s);
-        if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
-        {
-          ((ClustalxColourScheme)sg.cs).resetClustalX(
-              sg.getSequences(hiddenRepSequences), sg.getWidth());
-        }
-        sg.recalcConservation();
-      }
+      sequenceColours = new Hashtable();
     }
 
-
-    public Color getSequenceColour(SequenceI seq)
+    if (col == null)
     {
-      if(sequenceColours==null || !sequenceColours.containsKey(seq))
-        return Color.white;
-      else
-        return (Color)sequenceColours.get(seq);
+      sequenceColours.remove(seq);
     }
-
-    public void setSequenceColour(SequenceI seq, Color col)
+    else
     {
-      if(sequenceColours==null)
-        sequenceColours = new Hashtable();
-
-      if(col == null)
-        sequenceColours.remove(seq);
-      else
-        sequenceColours.put(seq, col);
+      sequenceColours.put(seq, col);
     }
-
+  }
 
 }