From: jprocter <Jim Procter>
Date: Mon, 19 Mar 2007 14:36:47 +0000 (+0000)
Subject: convenience method to get visible selected region.
X-Git-Tag: Release_2_3~323
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8b873826900aa9a453515b6055ff1976a33c1aa5;p=jalview.git

convenience method to get visible selected region.
---

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fa458a6..96c1f67 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,4 +1,4 @@
-/*
+ /*
  * Jalview - A Sequence Alignment Editor and Viewer
  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
@@ -23,8 +23,11 @@ import java.util.*;
 import java.awt.*;
 
 import jalview.analysis.*;
+
 import jalview.bin.*;
+
 import jalview.datamodel.*;
+
 import jalview.schemes.*;
 
 /**
@@ -35,1599 +38,1613 @@ import jalview.schemes.*;
  */
 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.
+    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 ignoreGapsInConsensusCalculation = false;
 
-  boolean isDataset = false;
+    boolean isDataset = false;
 
-  boolean antiAlias = false;
+    boolean antiAlias = false;
 
-  boolean padGaps = false;
+    boolean padGaps = false;
 
-  Rectangle explodedPosition;
+    Rectangle explodedPosition;
 
-  String viewName;
+    String viewName;
 
-  String sequenceSetID;
+    String sequenceSetID;
 
-  boolean gatherViewsHere = false;
+    boolean gatherViewsHere = false;
 
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
+    Stack historyList = new Stack();
+    Stack redoList = new Stack();
 
-  Hashtable sequenceColours;
+    Hashtable sequenceColours;
 
-  int thresholdTextColour = 0;
-  Color textColour = Color.black;
-  Color textColour2 = Color.white;
+    int thresholdTextColour = 0;
+    Color textColour = Color.black;
+    Color textColour2 = Color.white;
 
-  boolean rightAlignIds = false;
+    boolean rightAlignIds = false;
 
-  Hashtable hiddenRepSequences;
+    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
-   */
+    /**
+     * 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);
+      setAlignment(al);
     if (hiddenColumns != null)
     {
-      this.colSel = hiddenColumns;
-      if (hiddenColumns.getHiddenColumns() != null)
+        this.colSel = hiddenColumns;
+        if (hiddenColumns.getHiddenColumns() != null)
       {
-        hasHiddenColumns = true;
+          hasHiddenColumns = true;
       }
     }
-    init();
-  }
+      init();
+    }
 
-  void init()
-  {
-    this.startRes = 0;
-    this.endRes = alignment.getWidth() - 1;
-    this.startSeq = 0;
-    this.endSeq = alignment.getHeight() - 1;
+    void init()
+    {
+        this.startRes = 0;
+        this.endRes = alignment.getWidth() - 1;
+        this.startSeq = 0;
+        this.endSeq = alignment.getHeight() - 1;
 
-    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+      antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
-    showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
-    showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+      showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
 
-    rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+      rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
 
-    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
-    padGaps = Cache.getDefault("PAD_GAPS", true);
+      padGaps = Cache.getDefault("PAD_GAPS", true);
 
-    String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
-    String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
-    String fontSize = Cache.getDefault("FONT_SIZE", "10");
+       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);
+       seqNameItalics = Cache.getDefault("ID_ITALICS", true);
 
-    int style = 0;
+       int style = 0;
 
-    if (fontStyle.equals("bold"))
-    {
-      style = 1;
-    }
-    else if (fontStyle.equals("italic"))
-    {
-      style = 2;
-    }
+       if (fontStyle.equals("bold"))
+       {
+         style = 1;
+       }
+       else if (fontStyle.equals("italic"))
+       {
+         style = 2;
+       }
 
-    setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+       setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
 
-    alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+       alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
 
-    // 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;
 
-        if (Cache.getDefault("SHOW_CONSERVATION", true))
+        // We must set conservation and consensus before setting colour,
+        // as Blosum and Clustal require this to be done
+        if(hconsensus==null && !isDataset)
         {
-          alignment.addAnnotation(conservation);
-        }
+          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;
 
-        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_CONSERVATION", true))
+            {
+              alignment.addAnnotation(conservation);
+            }
 
-      if (Cache.getDefault("SHOW_IDENTITY", true))
-      {
-        alignment.addAnnotation(consensus);
-      }
-    }
+            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);
+            }
+          }
 
-    if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
-    {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-          jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+          consensus = new AlignmentAnnotation("Consensus", "PID",
+                                               new Annotation[1], 0f, 100f,
+                                               AlignmentAnnotation.BAR_GRAPH);
+          consensus.hasText = true;
+          consensus.autoCalculated = true;
 
-      if (globalColourScheme instanceof UserColourScheme)
-      {
-        globalColourScheme = UserDefinedColours.loadDefaultColours();
+           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);
-      }
+            if (globalColourScheme != null)
+            {
+                globalColourScheme.setConsensus(hconsensus);
+            }
+        }
+
+        wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
     }
 
-    wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
-  }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void setShowSequenceFeatures(boolean b)
-  {
-    showSequenceFeatures = b;
-  }
 
-  public boolean getShowSequenceFeatures()
-  {
-    return showSequenceFeatures;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setShowSequenceFeatures(boolean b)
+    {
+        showSequenceFeatures = b;
+    }
 
-  class ConservationThread
-      extends Thread
-  {
-    AlignmentPanel ap;
-    public ConservationThread(AlignmentPanel ap)
+    public boolean getShowSequenceFeatures()
     {
-      this.ap = ap;
+      return showSequenceFeatures;
     }
 
-    public void run()
+  class ConservationThread
+      extends Thread
     {
-      try
+      AlignmentPanel ap;
+      public ConservationThread(AlignmentPanel ap)
       {
-        updatingConservation = true;
+        this.ap = ap;
+      }
 
-        while (UPDATING_CONSERVATION)
+      public void run()
+      {
+        try
         {
-          try
+          updatingConservation = true;
+
+          while (UPDATING_CONSERVATION)
           {
-            if (ap != null)
+            try
             {
+              if (ap != null)
+              {
               ap.paintAlignment(true);
+              }
+              Thread.sleep(200);
+            }
+            catch (Exception ex)
+            {
+              ex.printStackTrace();
             }
-            Thread.sleep(200);
-          }
-          catch (Exception ex)
-          {
-            ex.printStackTrace();
           }
-        }
 
-        UPDATING_CONSERVATION = true;
+          UPDATING_CONSERVATION = true;
 
-        int alWidth = alignment.getWidth();
-        if (alWidth < 0)
+
+          int alWidth = alignment.getWidth();
+          if(alWidth<0)
         {
-          return;
+            return;
         }
 
-        Conservation cons = new jalview.analysis.Conservation("All",
-            jalview.schemes.ResidueProperties.propHash, 3,
-            alignment.getSequences(), 0, alWidth - 1);
+          Conservation cons = new jalview.analysis.Conservation("All",
+              jalview.schemes.ResidueProperties.propHash, 3,
+              alignment.getSequences(), 0, alWidth -1);
 
-        cons.calculate();
-        cons.verdict(false, ConsPercGaps);
+          cons.calculate();
+          cons.verdict(false, ConsPercGaps);
 
-        if (quality != null)
-        {
-          cons.findQuality();
-        }
+          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();
-        }
+          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();
+          }
 
-        for (int i = 0; i < alWidth; i++)
-        {
-          float value = 0;
+          for (int i = 0; i < alWidth; i++)
+          {
+            float value = 0;
 
-          c = sequence[i];
+            c = sequence[i];
 
-          if (Character.isDigit(c))
+            if (Character.isDigit(c))
           {
-            value = (int) (c - '0');
+              value = (int) (c - '0');
           }
-          else if (c == '*')
+            else if (c == '*')
           {
-            value = 11;
+              value = 11;
           }
-          else if (c == '+')
+            else if (c == '+')
           {
-            value = 10;
+              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;
+            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)));
+                                               value,
+                                               new Color(minR + (maxR * vprop),
+                  minG + (maxG * vprop),
+                  minB + (maxB * vprop)));
+            }
           }
         }
-      }
-      catch (OutOfMemoryError error)
-      {
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        catch (OutOfMemoryError error)
         {
-
-          public void run()
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
-            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();
+            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;
 
-      UPDATING_CONSERVATION = false;
-      updatingConservation = false;
+          System.out.println("Conservation calculation: " + error);
+          System.gc();
 
-      if (ap != null)
-      {
+        }
+
+        UPDATING_CONSERVATION = false;
+        updatingConservation = false;
+
+        if(ap!=null)
+        {
         ap.paintAlignment(true);
-      }
+        }
 
+      }
     }
-  }
 
-  ConservationThread conservationThread;
 
-  ConsensusThread consensusThread;
+    ConservationThread conservationThread;
 
-  boolean consUpdateNeeded = false;
+    ConsensusThread consensusThread;
 
-  static boolean UPDATING_CONSENSUS = false;
+    boolean consUpdateNeeded = false;
 
-  static boolean UPDATING_CONSERVATION = false;
+    static boolean UPDATING_CONSENSUS = false;
 
-  boolean updatingConsensus = false;
+    static boolean UPDATING_CONSERVATION = false;
 
-  boolean updatingConservation = false;
+    boolean updatingConsensus = false;
 
-  /**
-   * DOCUMENT ME!
-   */
-  public void updateConservation(final AlignmentPanel ap)
-  {
-    if (alignment.isNucleotide() || conservation == null)
+    boolean updatingConservation = false;
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void updateConservation(final AlignmentPanel ap)
+    {
+      if (alignment.isNucleotide() || conservation==null)
     {
-      return;
+        return;
     }
 
-    conservationThread = new ConservationThread(ap);
-    conservationThread.start();
-  }
-
-  /**
-   * DOCUMENT ME!
-   */
-  public void updateConsensus(final AlignmentPanel ap)
-  {
-    consensusThread = new ConsensusThread(ap);
-    consensusThread.start();
-  }
+      conservationThread = new ConservationThread(ap);
+      conservationThread.start();
+    }
 
-  class ConsensusThread
-      extends Thread
-  {
-    AlignmentPanel ap;
-    public ConsensusThread(AlignmentPanel ap)
+    /**
+     * DOCUMENT ME!
+     */
+    public void updateConsensus(final AlignmentPanel ap)
     {
-      this.ap = ap;
+      consensusThread = new ConsensusThread(ap);
+      consensusThread.start();
     }
 
-    public void run()
+  class ConsensusThread
+      extends Thread
     {
-      updatingConsensus = true;
-      while (UPDATING_CONSENSUS)
+      AlignmentPanel ap;
+      public ConsensusThread(AlignmentPanel ap)
       {
-        try
+        this.ap = ap;
+      }
+      public void run()
+      {
+        updatingConsensus = true;
+        while (UPDATING_CONSENSUS)
         {
-          if (ap != null)
+          try
           {
+            if (ap != null)
+            {
             ap.paintAlignment(true);
-          }
+            }
 
-          Thread.sleep(200);
-        }
-        catch (Exception ex)
-        {
-          ex.printStackTrace();
+            Thread.sleep(200);
+          }
+          catch (Exception ex)
+          {
+            ex.printStackTrace();
+          }
         }
-      }
 
-      UPDATING_CONSENSUS = true;
 
-      try
-      {
-        int aWidth = alignment.getWidth();
-        if (aWidth < 0)
+        UPDATING_CONSENSUS = true;
+
+        try
+        {
+          int aWidth = alignment.getWidth();
+          if(aWidth<0)
         {
-          return;
+            return;
         }
 
-        consensus.annotations = null;
-        consensus.annotations = new Annotation[aWidth];
+          consensus.annotations = null;
+          consensus.annotations = new Annotation[aWidth];
 
-        hconsensus = new Hashtable[aWidth];
-        AAFrequency.calculate(alignment.getSequencesArray(),
-                              0,
-                              alignment.getWidth(),
-                              hconsensus);
 
-        for (int i = 0; i < aWidth; i++)
-        {
-          float value = 0;
-          if (ignoreGapsInConsensusCalculation)
+          hconsensus = new Hashtable[aWidth];
+          AAFrequency.calculate(alignment.getSequencesArray(),
+                                0,
+                                alignment.getWidth(),
+                                hconsensus);
+
+          for (int i = 0; i < aWidth; i++)
+          {
+            float value = 0;
+            if (ignoreGapsInConsensusCalculation)
           {
-            value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
-                floatValue();
+              value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
+                  floatValue();
           }
-          else
+            else
           {
-            value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
-                floatValue();
+              value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
+                  floatValue();
           }
 
-          String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
-          String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
+            String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
+            String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
 
-          if (maxRes.length() > 1)
-          {
-            mouseOver = "[" + maxRes + "] ";
-            maxRes = "+";
-          }
+            if (maxRes.length() > 1)
+            {
+              mouseOver = "[" + maxRes + "] ";
+              maxRes = "+";
+            }
 
-          mouseOver += ( (int) value + "%");
+            mouseOver += ( (int) value + "%");
           consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
               value);
-        }
+          }
+
 
-        if (globalColourScheme != null)
+          if (globalColourScheme != null)
         {
-          globalColourScheme.setConsensus(hconsensus);
+            globalColourScheme.setConsensus(hconsensus);
         }
 
-      }
-      catch (OutOfMemoryError error)
-      {
-        alignment.deleteAnnotation(consensus);
-
-        consensus = null;
-        hconsensus = null;
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        }
+        catch (OutOfMemoryError error)
         {
-          public void run()
+          alignment.deleteAnnotation(consensus);
+
+          consensus = null;
+          hconsensus = null;
+          javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
-            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);
-          }
-        });
+            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);
+            }
+          });
 
-        System.out.println("Consensus calculation: " + error);
-        System.gc();
-      }
-      UPDATING_CONSENSUS = false;
-      updatingConsensus = false;
+          System.out.println("Consensus calculation: " + error);
+          System.gc();
+        }
+        UPDATING_CONSENSUS = false;
+        updatingConsensus = false;
 
-      if (ap != null)
-      {
+        if (ap != null)
+        {
         ap.paintAlignment(true);
+        }
       }
     }
-  }
-
-  /**
-   * get the consensus sequence as displayed under the PID consensus annotation row.
-   * @return consensus sequence as a new sequence object
-   */
+    /**
+     * 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)
+      if (consensus==null)
     {
-      updateConsensus(null);
+        updateConsensus(null);
     }
-    if (consensus == null)
+      if (consensus==null)
     {
-      return null;
+        return null;
     }
-    StringBuffer seqs = new StringBuffer();
+      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) == '[')
+          if (consensus.annotations[i].description.charAt(0) == '[')
         {
-          seqs.append(consensus.annotations[i].description.charAt(1));
+            seqs.append(consensus.annotations[i].description.charAt(1));
         }
-        else
+          else
         {
-          seqs.append(consensus.annotations[i].displayCharacter);
+            seqs.append(consensus.annotations[i].displayCharacter);
         }
       }
     }
 
-    SequenceI sq = new Sequence("Consensus", seqs.toString());
+      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;
-  }
+      return sq;
+    }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceGroup getSelectionGroup()
+    {
+        return selectionGroup;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void setConservationSelected(boolean b)
-  {
-    conservationColourSelected = b;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param sg DOCUMENT ME!
+     */
+    public void setSelectionGroup(SequenceGroup sg)
+    {
+        selectionGroup = sg;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public boolean getAbovePIDThreshold()
-  {
-    return abovePIDThreshold;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getConservationSelected()
+    {
+        return conservationColourSelected;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void setAbovePIDThreshold(boolean b)
-  {
-    abovePIDThreshold = b;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setConservationSelected(boolean b)
+    {
+        conservationColourSelected = b;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getStartRes()
-  {
-    return startRes;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getAbovePIDThreshold()
+    {
+        return abovePIDThreshold;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getEndRes()
-  {
-    return endRes;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param b DOCUMENT ME!
+     */
+    public void setAbovePIDThreshold(boolean b)
+    {
+        abovePIDThreshold = b;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getStartSeq()
-  {
-    return startSeq;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartRes()
+    {
+        return startRes;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param cs DOCUMENT ME!
-   */
-  public void setGlobalColourScheme(ColourSchemeI cs)
-  {
-    globalColourScheme = cs;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEndRes()
+    {
+        return endRes;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public ColourSchemeI getGlobalColourScheme()
-  {
-    return globalColourScheme;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getStartSeq()
+    {
+        return startSeq;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param res DOCUMENT ME!
-   */
-  public void setStartRes(int res)
-  {
-    this.startRes = res;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param cs DOCUMENT ME!
+     */
+    public void setGlobalColourScheme(ColourSchemeI cs)
+    {
+        globalColourScheme = cs;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
-   */
-  public void setStartSeq(int seq)
-  {
-    this.startSeq = seq;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public ColourSchemeI getGlobalColourScheme()
+    {
+        return globalColourScheme;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param res DOCUMENT ME!
-   */
-  public void setEndRes(int res)
-  {
-    if (res > (alignment.getWidth() - 1))
+    /**
+     * DOCUMENT ME!
+     *
+     * @param res DOCUMENT ME!
+     */
+    public void setStartRes(int res)
     {
-      // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-      res = alignment.getWidth() - 1;
+        this.startRes = res;
     }
 
-    if (res < 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void setStartSeq(int seq)
     {
-      res = 0;
+        this.startSeq = seq;
     }
 
-    this.endRes = res;
-  }
+    /**
+     * 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;
+        }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
-   */
-  public void setEndSeq(int seq)
-  {
-    if (seq > alignment.getHeight())
+        if (res < 0)
+        {
+            res = 0;
+        }
+
+        this.endRes = res;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void setEndSeq(int seq)
     {
-      seq = alignment.getHeight();
+        if (seq > alignment.getHeight())
+        {
+            seq = alignment.getHeight();
+        }
+
+        if (seq < 0)
+        {
+            seq = 0;
+        }
+
+        this.endSeq = seq;
     }
 
-    if (seq < 0)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getEndSeq()
     {
-      seq = 0;
+        return endSeq;
     }
 
-    this.endSeq = seq;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param f DOCUMENT ME!
+     */
+    public void setFont(Font f)
+    {
+        font = f;
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getEndSeq()
-  {
-    return endSeq;
-  }
+        Container c = new Container();
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param f DOCUMENT ME!
-   */
-  public void setFont(Font f)
-  {
-    font = f;
+        java.awt.FontMetrics fm = c.getFontMetrics(font);
+        setCharHeight(fm.getHeight());
+        setCharWidth(fm.charWidth('M'));
+        validCharWidth = true;
+    }
 
-    Container c = new Container();
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Font getFont()
+    {
+        return font;
+    }
 
-    java.awt.FontMetrics fm = c.getFontMetrics(font);
-    setCharHeight(fm.getHeight());
-    setCharWidth(fm.charWidth('M'));
-    validCharWidth = true;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param w DOCUMENT ME!
+     */
+    public void setCharWidth(int w)
+    {
+        this.charWidth = w;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public Font getFont()
-  {
-    return font;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getCharWidth()
+    {
+        return charWidth;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param w DOCUMENT ME!
-   */
-  public void setCharWidth(int w)
-  {
-    this.charWidth = w;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param h DOCUMENT ME!
+     */
+    public void setCharHeight(int h)
+    {
+        this.charHeight = h;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getCharWidth()
-  {
-    return charWidth;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getCharHeight()
+    {
+        return charHeight;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param h DOCUMENT ME!
-   */
-  public void setCharHeight(int h)
-  {
-    this.charHeight = h;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param w DOCUMENT ME!
+     */
+    public void setWrappedWidth(int w)
+    {
+        this.wrappedWidth = w;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getCharHeight()
-  {
-    return charHeight;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getWrappedWidth()
+    {
+        return wrappedWidth;
+    }
 
-  /**
-   * 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!
-   *
-   * @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 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 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 setShowText(boolean state)
-  {
-    showText = state;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setRenderGaps(boolean state)
+    {
+        renderGaps = 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!
-   *
-   * @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 setColourText(boolean state)
-  {
-    showColourText = state;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param state DOCUMENT ME!
+     */
+    public void setShowBoxes(boolean state)
+    {
+        showBoxes = 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 getWrapAlignment()
-  {
-    return wrapAlignment;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getShowText()
+    {
+        return showText;
+    }
 
-  /**
-   * 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 boolean getShowBoxes()
-  {
-    return showBoxes;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char getGapCharacter()
+    {
+        return getAlignment().getGapCharacter();
+    }
 
-  /**
-   * 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 gap DOCUMENT ME!
-   */
-  public void setGapCharacter(char gap)
-  {
-    if (getAlignment() != null)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param thresh DOCUMENT ME!
+     */
+    public void setThreshold(int thresh)
     {
-      getAlignment().setGapCharacter(gap);
+        threshold = thresh;
     }
-  }
 
-  /**
-   * 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!
-   *
-   * @return DOCUMENT ME!
-   */
-  public int getThreshold()
-  {
-    return threshold;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param inc DOCUMENT ME!
+     */
+    public void setIncrement(int inc)
+    {
+        increment = inc;
+    }
 
-  /**
-   * 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 int getIncrement()
-  {
-    return increment;
-  }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public ColumnSelection getColumnSelection()
-  {
-    return colSel;
-  }
+    /**
+     * 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 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!
-   *
-   * @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 getColourAppliesToAllGroups()
-  {
-    return colourAppliesToAllGroups;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getShowJVSuffix()
+    {
+        return showJVSuffix;
+    }
 
-  /**
-   * 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!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void setShowJVSuffix(boolean b)
-  {
-    showJVSuffix = b;
-  }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public boolean getShowAnnotation()
-  {
-    return showAnnotation;
-  }
+    /**
+     * 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!
+     *
+     * @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 getScaleAboveWrapped()
+    {
+        return scaleAboveWrapped;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public boolean getScaleLeftWrapped()
-  {
-    return scaleLeftWrapped;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean getScaleLeftWrapped()
+    {
+        return scaleLeftWrapped;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public boolean getScaleRightWrapped()
-  {
-    return scaleRightWrapped;
-  }
+    /**
+     * 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 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 setScaleLeftWrapped(boolean b)
+    {
+        scaleLeftWrapped = b;
+    }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param b DOCUMENT ME!
-   */
-  public void setScaleRightWrapped(boolean b)
-  {
-    scaleRightWrapped = 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);
-  }
+    /**
+     * 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);
-  }
+    /**
+     * 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);
-  }
+    /**
+     * 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)
+    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 boolean getIgnoreGapsConsensus()
+    {
+     return ignoreGapsInConsensusCalculation;
+    }
 
-  public void setDataset(boolean b)
-  {
-    isDataset = b;
-  }
+    public void setDataset(boolean b)
+    {
+      isDataset = b;
+    }
 
-  public boolean isDataset()
-  {
-    return isDataset;
-  }
+    public boolean isDataset()
+    {
+      return isDataset;
+    }
 
-  public void hideSelectedColumns()
-  {
-    if (colSel.size() < 1)
+
+    public void hideSelectedColumns()
+    {
+      if (colSel.size() < 1)
     {
-      return;
+        return;
     }
 
-    colSel.hideSelectedColumns();
-    setSelectionGroup(null);
+      colSel.hideSelectedColumns();
+      setSelectionGroup(null);
 
-    hasHiddenColumns = true;
-  }
+      hasHiddenColumns = true;
+    }
 
-  public void hideColumns(int start, int end)
-  {
-    if (start == end)
+
+    public void hideColumns(int start, int end)
     {
-      colSel.hideColumns(start);
+      if(start==end)
+    {
+        colSel.hideColumns(start);
     }
-    else
+      else
     {
-      colSel.hideColumns(start, end);
+        colSel.hideColumns(start, end);
     }
 
-    hasHiddenColumns = true;
-  }
+      hasHiddenColumns = true;
+    }
 
-  public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
-  {
-    int sSize = sg.getSize();
-    if (sSize < 2)
+    public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
     {
-      return;
+      int sSize = sg.getSize();
+      if(sSize < 2)
+    {
+        return;
     }
 
-    if (hiddenRepSequences == null)
+      if(hiddenRepSequences==null)
     {
-      hiddenRepSequences = new Hashtable();
+        hiddenRepSequences = new Hashtable();
     }
 
-    hiddenRepSequences.put(repSequence, sg);
+       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++)
+      //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)
-      {
-        if (index == sSize - 1)
+        if(sg.getSequenceAt(i)!=repSequence)
         {
-          return;
+          if(index==sSize-1)
+        {
+            return;
         }
 
-        seqs[index++] = sg.getSequenceAt(i);
-      }
+          seqs[index++] = sg.getSequenceAt(i);
+        }
     }
 
-    hideSequence(seqs);
+      hideSequence(seqs);
 
-  }
+    }
 
-  public void hideAllSelectedSeqs()
-  {
+    public void hideAllSelectedSeqs()
+    {
     if (selectionGroup == null || selectionGroup.getSize()<1)
     {
-      return;
+        return;
     }
 
-    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
+      SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
 
-    hideSequence(seqs);
+      hideSequence(seqs);
 
-    setSelectionGroup(null);
-  }
+      setSelectionGroup(null);
+    }
 
-  public void hideSequence(SequenceI[] seq)
-  {
-    if (seq != null)
+    public void hideSequence(SequenceI [] seq)
     {
-      for (int i = 0; i < seq.length; i++)
+      if(seq!=null)
       {
-        alignment.getHiddenSequences().hideSequence(seq[i]);
+        for (int i = 0; i < seq.length; i++)
+        {
+          alignment.getHiddenSequences().hideSequence(seq[i]);
+        }
+        hasHiddenRows = true;
+        firePropertyChange("alignment", null, alignment.getSequences());
       }
-      hasHiddenRows = true;
-      firePropertyChange("alignment", null, alignment.getSequences());
     }
-  }
 
-  public void showSequence(int index)
-  {
-    Vector tmp = alignment.getHiddenSequences().showSequence(index
-        , hiddenRepSequences);
-    if (tmp.size() > 0)
+    public void showSequence(int index)
     {
-      if (selectionGroup == null)
+      Vector tmp = alignment.getHiddenSequences().showSequence(index
+          , hiddenRepSequences);
+      if(tmp.size()>0)
       {
-        selectionGroup = new SequenceGroup();
-        selectionGroup.setEndRes(alignment.getWidth() - 1);
-      }
+        if(selectionGroup==null)
+        {
+          selectionGroup = new SequenceGroup();
+          selectionGroup.setEndRes(alignment.getWidth()-1);
+        }
 
-      for (int t = 0; t < tmp.size(); t++)
-      {
-        selectionGroup.addSequence(
-            (SequenceI) tmp.elementAt(t), false
-            );
+        for (int t = 0; t < tmp.size(); t++)
+        {
+          selectionGroup.addSequence(
+              (SequenceI) tmp.elementAt(t), false
+              );
+        }
+        firePropertyChange("alignment", null, alignment.getSequences());
       }
-      firePropertyChange("alignment", null, alignment.getSequences());
-    }
 
-    if (alignment.getHiddenSequences().getSize() < 1)
+      if(alignment.getHiddenSequences().getSize()<1)
     {
-      hasHiddenRows = false;
+        hasHiddenRows = false;
     }
   }
 
-  public void showColumn(int col)
-  {
-    colSel.revealHiddenColumns(col);
-    if (colSel.getHiddenColumns() == null)
+    public void showColumn(int col)
     {
-      hasHiddenColumns = false;
+      colSel.revealHiddenColumns(col);
+      if(colSel.getHiddenColumns()==null)
+    {
+        hasHiddenColumns = false;
     }
   }
 
-  public void showAllHiddenColumns()
-  {
-    colSel.revealAllHiddenColumns();
-    hasHiddenColumns = false;
-  }
+    public void showAllHiddenColumns()
+    {
+      colSel.revealAllHiddenColumns();
+      hasHiddenColumns = false;
+    }
 
-  public void showAllHiddenSeqs()
-  {
-    if (alignment.getHiddenSequences().getSize() > 0)
+    public void showAllHiddenSeqs()
     {
-      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++)
+      if(alignment.getHiddenSequences().getSize()>0)
       {
-        selectionGroup.addSequence(
-            (SequenceI) tmp.elementAt(t), false
-            );
+        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;
       }
-      firePropertyChange("alignment", null, alignment.getSequences());
-      hasHiddenRows = false;
-      hiddenRepSequences = null;
     }
-  }
 
-  public void invertColumnSelection()
-  {
-    for (int i = 0; i < alignment.getWidth(); i++)
+
+
+    public void invertColumnSelection()
     {
-      if (colSel.contains(i))
+      for(int i=0; i<alignment.getWidth(); i++)
       {
-        colSel.removeElement(i);
-      }
-      else
+        if(colSel.contains(i))
       {
-        if (!hasHiddenColumns || colSel.isVisible(i))
+          colSel.removeElement(i);
+      }
+        else
         {
-          colSel.addElement(i);
+          if (!hasHiddenColumns || colSel.isVisible(i))
+          {
+            colSel.addElement(i);
+          }
         }
       }
     }
-  }
 
-  public int adjustForHiddenSeqs(int alignmentIndex)
-  {
-    return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
-  }
+    public int adjustForHiddenSeqs(int alignmentIndex)
+    {
+      return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+    }
 
-  /**
-   * This method returns the a new SequenceI [] with
-   * the selection sequence and start and end points adjusted
-   * @return String[]
-   */
-  public SequenceI[] getSelectionAsNewSequence()
-  {
-    SequenceI[] sequences;
+    /**
+     * This method returns the a new SequenceI [] with
+     * the selection sequence and start and end points adjusted
+     * @return String[]
+     */
+    public SequenceI[] getSelectionAsNewSequence()
+    {
+      SequenceI[] sequences;
 
-    if (selectionGroup == null)
+      if (selectionGroup == null)
     {
-      sequences = alignment.getSequencesArray();
+        sequences = alignment.getSequencesArray();
     }
-    else
+      else
     {
-      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+        sequences = selectionGroup.getSelectionAsNewSequences(alignment);
     }
 
-    return sequences;
-  }
+      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[]
-   */
+    /**
+     * 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)
-    {
-      iSize = selectionGroup.getSize();
-      seqs = selectionGroup.getSequencesInOrder(alignment);
-      start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
-    }
-    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
+      CigarArray 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(); // inclusive for start and end in SeqCigar constructor
+      }
+      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
+        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;
+            if (hideEnd > last)
+            {
+              hideStart = last;
           }
           else
           {
-            continue;
+              continue;
           }
         }
 
-        if (hideStart > end)
+          if (hideStart>end)
         {
-          break;
+            break;
         }
 
-        if (hideEnd > end)
+          if (hideEnd>end)
         {
-          hideEnd = end;
+            hideEnd=end;
         }
 
-        if (hideStart > hideEnd)
+          if (hideStart>hideEnd)
         {
-          break;
+            break;
         }
-        /**
-         * form operations...
-         */
-        if (last < hideStart)
+          /**
+           * form operations...
+           */
+          if (last<hideStart)
         {
-          selection.addOperation(CigarArray.M, hideStart - last);
+            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.D, 1+hideEnd-hideStart);
+          last = hideEnd+1;
+        }
+        // Final match if necessary.
+        if (last<end)
       {
-        selection.addOperation(CigarArray.M, end - last + 1);
+          selection.addOperation(CigarArray.M, end-last+1);
       }
     }
     else
     {
-      selection.addOperation(CigarArray.M, end - start + 1);
+        selection.addOperation(CigarArray.M, end-start+1);
+      }
+      return selection;
     }
-    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
-   */
+    /**
+     * 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);
+      // 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,
+        return new AlignmentView(aligview,
                                (selectedOnly && selectionGroup != null) ?
                                selectionGroup.getStartRes() : 0);
+      }
+      return null;
     }
-    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
+    /**
+     * 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)
     {
-      iSize = alignment.getHeight();
-      seqs = alignment.getSequencesArray();
-      end = alignment.getWidth();
-    }
+      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];
+      selection = new String[iSize];
     if (hasHiddenColumns)
     {
-      selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+        selection = colSel.getVisibleSequenceStrings(start, end, seqs);
     }
     else
     {
-      for (i = 0; i < iSize; i++)
-      {
-        selection[i] = seqs[i].getSequenceAsString(start, end);
-      }
+        for(i=0; i<iSize; i++)
+        {
+          selection[i] = seqs[i].getSequenceAsString(start, end);
+        }
 
+      }
+      return selection;
     }
-    return selection;
-  }
 
   public int [][] getVisibleRegionBoundaries(int min, int max)
   {
@@ -1674,131 +1691,154 @@ public class AlignViewport
 
   }
 
-  public boolean getShowHiddenMarkers()
-  {
-    return showHiddenMarkers;
-  }
-
-  public void setShowHiddenMarkers(boolean show)
-  {
-    showHiddenMarkers = show;
-  }
-
-  public String getSequenceSetId()
-  {
-    if (sequenceSetID == null)
+    public boolean getShowHiddenMarkers()
     {
-      sequenceSetID = alignment.hashCode() + "";
+      return showHiddenMarkers;
     }
 
-    return sequenceSetID;
-  }
-
-  public void alignmentChanged(AlignmentPanel ap)
-  {
-    if (padGaps)
+    public void setShowHiddenMarkers(boolean show)
     {
-      alignment.padGaps();
+      showHiddenMarkers = show;
     }
 
-    if (hconsensus != null && autoCalculateConsensus)
+    public String getSequenceSetId()
     {
-      updateConsensus(ap);
-      updateConservation(ap);
+      if(sequenceSetID==null)
+    {
+        sequenceSetID =  alignment.hashCode()+"";
+    }
+
+      return sequenceSetID;
     }
 
-    //Reset endRes of groups if beyond alignment width
-    int alWidth = alignment.getWidth();
-    Vector groups = alignment.getGroups();
-    if (groups != null)
+    public void alignmentChanged(AlignmentPanel ap)
     {
-      for (int i = 0; i < groups.size(); i++)
-      {
-        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-        if (sg.getEndRes() > alWidth)
+        if (padGaps)
+    {
+          alignment.padGaps();
+    }
+
+        if (hconsensus != null && autoCalculateConsensus)
         {
-          sg.setEndRes(alWidth - 1);
+          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)
+        if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
     {
-      selectionGroup.setEndRes(alWidth - 1);
+          selectionGroup.setEndRes(alWidth-1);
     }
 
-    resetAllColourSchemes();
+        resetAllColourSchemes();
 
-    // alignment.adjustSequenceAnnotations();
-  }
+       // alignment.adjustSequenceAnnotations();
+    }
 
-  void resetAllColourSchemes()
-  {
-    ColourSchemeI cs = globalColourScheme;
-    if (cs != null)
+
+    void resetAllColourSchemes()
     {
-      if (cs instanceof ClustalxColourScheme)
+      ColourSchemeI cs = globalColourScheme;
+      if(cs!=null)
       {
-        ( (ClustalxColourScheme) cs).
-            resetClustalX(alignment.getSequences(),
-                          alignment.getWidth());
-      }
+        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);
+        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)
+      int s, sSize = alignment.getGroups().size();
+      for(s=0; s<sSize; s++)
       {
-        ( (ClustalxColourScheme) sg.cs).resetClustalX(
-            sg.getSequences(hiddenRepSequences), sg.getWidth());
+        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();
       }
-      sg.recalcConservation();
     }
-  }
 
-  public Color getSequenceColour(SequenceI seq)
-  {
-    if (sequenceColours == null || !sequenceColours.containsKey(seq))
+
+    public Color getSequenceColour(SequenceI seq)
     {
-      return Color.white;
+      if(sequenceColours==null || !sequenceColours.containsKey(seq))
+    {
+        return Color.white;
     }
-    else
+      else
     {
-      return (Color) sequenceColours.get(seq);
+        return (Color)sequenceColours.get(seq);
     }
   }
 
-  public void setSequenceColour(SequenceI seq, Color col)
-  {
-    if (sequenceColours == null)
+    public void setSequenceColour(SequenceI seq, Color col)
     {
-      sequenceColours = new Hashtable();
+      if(sequenceColours==null)
+    {
+        sequenceColours = new Hashtable();
     }
 
-    if (col == null)
+      if(col == null)
     {
-      sequenceColours.remove(seq);
+        sequenceColours.remove(seq);
     }
-    else
+      else
     {
-      sequenceColours.put(seq, col);
+        sequenceColours.put(seq, col);
     }
-  }
+    }
+    /**
+     * returns the visible column regions of the alignment
+     * @param selectedRegionOnly true to just return the contigs intersecting with the selected area
+     * @return
+     */
+    public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) {
+      int[] viscontigs=null;
+      int start = 0, end = 0;
+      if(selectedRegionOnly && selectionGroup!=null)
+      {
+        start = selectionGroup.getStartRes();
+        end = selectionGroup.getEndRes()+1;
+      }
+      else
+      {
+        end = alignment.getWidth();
+      }
+      viscontigs = colSel.getVisibleContigs(start, end);
+      return viscontigs;
+    }
+
 
 }