X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=13f66d973ffeaf84e2085f32bd7e07f85db678c4;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=88a6e37fab493ce38f6f9506039fd0ce4f24c705;hpb=1b5ee75e7538b6229da397b28a91296e612d23e8;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
old mode 100755
new mode 100644
index 88a6e37..13f66d9
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,4 +1,21 @@
- /*
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+/*
  * Jalview - A Sequence Alignment Editor and Viewer
  * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
@@ -23,1652 +40,1606 @@ import java.util.*;
 import java.awt.*;
 
 import jalview.analysis.*;
+import jalview.api.StructureSelectionManagerProvider;
 
 import jalview.bin.*;
 
 import jalview.datamodel.*;
 
 import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
- * @version $Revision$
+ * @version $Revision: 1.141 $
  */
-public class AlignViewport
+public class AlignViewport implements SelectionSource, VamsasSource
 {
-    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;
+  private static final int RIGHT_JUSTIFY = 1;
 
-    boolean cursorMode = false;
+  int startRes;
 
-    // The following vector holds the features which are
-    // currently visible, in the correct order or rendering
-    Hashtable featuresDisplayed = null;
+  int endRes;
 
+  int startSeq;
 
-    /** DOCUMENT ME!! */
-    public Hashtable [] hconsensus;
-    AlignmentAnnotation consensus;
-    AlignmentAnnotation conservation;
-    AlignmentAnnotation quality;
-    boolean autoCalculateConsensus = true;
+  int endSeq;
 
-    /** DOCUMENT ME!! */
-    public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+  boolean showJVSuffix = true;
 
-    // JBPNote Prolly only need this in the applet version.
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.
-      PropertyChangeSupport(this);
+  boolean showText = true;
 
-    boolean ignoreGapsInConsensusCalculation = false;
+  boolean showColourText = false;
 
-    boolean isDataset = false;
+  boolean showBoxes = true;
 
-    boolean antiAlias = false;
+  boolean wrapAlignment = false;
 
-    boolean padGaps = false;
+  boolean renderGaps = true;
 
-    Rectangle explodedPosition;
+  boolean showSequenceFeatures = false;
 
-    String viewName;
+  boolean showAnnotation = true;
 
-    String sequenceSetID;
+  boolean colourAppliesToAllGroups = true;
 
-    boolean gatherViewsHere = false;
+  ColourSchemeI globalColourScheme = null;
 
-    Stack historyList = new Stack();
-    Stack redoList = new Stack();
+  boolean conservationColourSelected = false;
 
-    Hashtable sequenceColours;
+  boolean abovePIDThreshold = false;
 
-    int thresholdTextColour = 0;
-    Color textColour = Color.black;
-    Color textColour2 = Color.white;
+  SequenceGroup selectionGroup;
 
-    boolean rightAlignIds = false;
+  int charHeight;
 
-    Hashtable hiddenRepSequences;
+  int charWidth;
 
+  boolean validCharWidth;
 
-    /**
-     * 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();
-    }
+  int wrappedWidth;
 
-    void init()
-    {
-        this.startRes = 0;
-        this.endRes = alignment.getWidth() - 1;
-        this.startSeq = 0;
-        this.endSeq = alignment.getHeight() - 1;
+  Font font;
 
-      antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+  boolean seqNameItalics;
 
-      showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
-      showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+  AlignmentI alignment;
 
-      rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+  ColumnSelection colSel = new ColumnSelection();
 
-      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+  int threshold;
 
-      padGaps = Cache.getDefault("PAD_GAPS", true);
+  int increment;
 
-       String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
-       String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
-       String fontSize = Cache.getDefault("FONT_SIZE", "10");
+  NJTree currentTree = null;
 
-       seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+  boolean scaleAboveWrapped = false;
 
-       int style = 0;
+  boolean scaleLeftWrapped = true;
 
-       if (fontStyle.equals("bold"))
-       {
-         style = 1;
-       }
-       else if (fontStyle.equals("italic"))
-       {
-         style = 2;
-       }
+  boolean scaleRightWrapped = true;
 
-       setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+  boolean hasHiddenColumns = false;
 
-       alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );
+  boolean hasHiddenRows = false;
 
+  boolean showHiddenMarkers = 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;
-
-
-            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);
-            }
-          }
+  boolean cursorMode = false;
 
-          consensus = new AlignmentAnnotation("Consensus", "PID",
-                                               new Annotation[1], 0f, 100f,
-                                               AlignmentAnnotation.BAR_GRAPH);
-          consensus.hasText = true;
-          consensus.autoCalculated=true;
+  /**
+   * Keys are the feature types which are currently visible. Note: Values are
+   * not used!
+   */
+  Hashtable featuresDisplayed = null;
 
-           if (Cache.getDefault("SHOW_IDENTITY", true))
-           {
-             alignment.addAnnotation(consensus);
-           }
-        }
+  /** DOCUMENT ME!! */
+  public Hashtable[] hconsensus;
 
-        if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
-        {
-          globalColourScheme = ColourSchemeProperty.getColour(alignment,
-              jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+  AlignmentAnnotation consensus;
 
-            if (globalColourScheme instanceof UserColourScheme)
-            {
-                globalColourScheme = UserDefinedColours.loadDefaultColours();
-        ( (UserColourScheme) globalColourScheme).setThreshold(0,
-            getIgnoreGapsConsensus());
-            }
-
-            if (globalColourScheme != null)
-            {
-                globalColourScheme.setConsensus(hconsensus);
-            }
-        }
+  AlignmentAnnotation conservation;
 
-        wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
-    }
+  AlignmentAnnotation quality;
 
+  AlignmentAnnotation[] groupConsensus;
 
+  AlignmentAnnotation[] groupConservation;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowSequenceFeatures(boolean b)
-    {
-        showSequenceFeatures = b;
-    }
+  boolean autoCalculateConsensus = true;
 
-    public boolean getShowSequenceFeatures()
-    {
-      return showSequenceFeatures;
-    }
+  /** DOCUMENT ME!! */
+  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
-  class ConservationThread
-      extends Thread
-    {
-      AlignmentPanel ap;
-      public ConservationThread(AlignmentPanel ap)
-      {
-        this.ap = ap;
-      }
+  // JBPNote Prolly only need this in the applet version.
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+          this);
 
-      public void run()
-      {
-        try
-        {
-          updatingConservation = true;
+  boolean ignoreGapsInConsensusCalculation = false;
 
-          while (UPDATING_CONSERVATION)
-          {
-            try
-            {
-              if (ap != null)
-              {
-              ap.paintAlignment(true);
-              }
-              Thread.sleep(200);
-            }
-            catch (Exception ex)
-            {
-              ex.printStackTrace();
-            }
-          }
+  boolean isDataset = false;
 
-          UPDATING_CONSERVATION = true;
+  boolean antiAlias = false;
 
+  boolean padGaps = false;
 
-          int alWidth = alignment.getWidth();
-          if(alWidth<0)
-        {
-            return;
-        }
+  Rectangle explodedPosition;
 
-          Conservation cons = new jalview.analysis.Conservation("All",
-              jalview.schemes.ResidueProperties.propHash, 3,
-              alignment.getSequences(), 0, alWidth -1);
+  String viewName;
 
-          cons.calculate();
-          cons.verdict(false, ConsPercGaps);
+  String sequenceSetID;
 
-          if (quality!=null)
-          {
-            cons.findQuality();
-          }
+  boolean gatherViewsHere = false;
 
-          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();
-          }
+  Stack historyList = new Stack();
 
-          for (int i = 0; i < alWidth; i++)
-          {
-            float value = 0;
+  Stack redoList = new Stack();
 
-            c = sequence[i];
+  Hashtable sequenceColours;
 
-            if (Character.isDigit(c))
-          {
-              value = (int) (c - '0');
-          }
-            else if (c == '*')
-          {
-              value = 11;
-          }
-            else if (c == '+')
-          {
-              value = 10;
-          }
+  int thresholdTextColour = 0;
 
-            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)
-        {
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
+  Color textColour = Color.black;
 
+  Color textColour2 = Color.white;
 
-            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);
-            }
-          });
+  boolean rightAlignIds = false;
 
-          conservation = null;
-          quality = null;
+  Hashtable hiddenRepSequences;
 
-          System.out.println("Conservation calculation: " + error);
-          System.gc();
+  boolean sortByTree;
 
-        }
+  /**
+   * Creates a new AlignViewport object.
+   * 
+   * @param al
+   *          alignment to view
+   */
+  public AlignViewport(AlignmentI al)
+  {
+    setAlignment(al);
+    init();
+  }
 
-        UPDATING_CONSERVATION = false;
-        updatingConservation = false;
+  /**
+   * Create a new AlignViewport object with a specific sequence set ID
+   * 
+   * @param al
+   * @param seqsetid
+   *          (may be null - but potential for ambiguous constructor exception)
+   */
+  public AlignViewport(AlignmentI al, String seqsetid)
+  {
+    this(al, seqsetid, null);
+  }
 
-        if(ap!=null)
-        {
-        ap.paintAlignment(true);
-        }
+  public AlignViewport(AlignmentI al, String seqsetid, String viewid)
+  {
+    sequenceSetID = seqsetid;
+    viewId = viewid;
+    // TODO remove these once 2.4.VAMSAS release finished
+    if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+    {
+      Cache.log.debug("Setting viewport's sequence set id : "
+              + sequenceSetID);
+    }
+    if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+    {
+      Cache.log.debug("Setting viewport's view id : " + viewId);
+    }
+    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
+              && hiddenColumns.getHiddenColumns().size() > 0)
+      {
+        hasHiddenColumns = true;
+      }
+      else
+      {
+        hasHiddenColumns = false;
       }
     }
+    init();
+  }
 
+  /**
+   * New viewport with hidden columns and an existing sequence set id
+   * 
+   * @param al
+   * @param hiddenColumns
+   * @param seqsetid
+   *          (may be null)
+   */
+  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+          String seqsetid)
+  {
+    this(al, hiddenColumns, seqsetid, null);
+  }
 
-    ConservationThread conservationThread;
-
-    ConsensusThread consensusThread;
-
-    boolean consUpdateNeeded = false;
-
-    static boolean UPDATING_CONSENSUS = false;
-
-    static boolean UPDATING_CONSERVATION = false;
-
-    boolean updatingConsensus = false;
-
-    boolean updatingConservation = false;
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateConservation(final AlignmentPanel ap)
-    {
-      if (alignment.isNucleotide() || conservation==null)
+  /**
+   * New viewport with hidden columns and an existing sequence set id and viewid
+   * 
+   * @param al
+   * @param hiddenColumns
+   * @param seqsetid
+   *          (may be null)
+   * @param viewid
+   *          (may be null)
+   */
+  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+          String seqsetid, String viewid)
+  {
+    sequenceSetID = seqsetid;
+    viewId = viewid;
+    // TODO remove these once 2.4.VAMSAS release finished
+    if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
     {
-        return;
-    }
-
-      conservationThread = new ConservationThread(ap);
-      conservationThread.start();
+      Cache.log.debug("Setting viewport's sequence set id : "
+              + sequenceSetID);
     }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void updateConsensus(final AlignmentPanel ap)
+    if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
     {
-      consensusThread = new ConsensusThread(ap);
-      consensusThread.start();
+      Cache.log.debug("Setting viewport's view id : " + viewId);
     }
-
-  class ConsensusThread
-      extends Thread
+    setAlignment(al);
+    if (hiddenColumns != null)
     {
-      AlignmentPanel ap;
-      public ConsensusThread(AlignmentPanel ap)
+      this.colSel = hiddenColumns;
+      if (hiddenColumns.getHiddenColumns() != null
+              && hiddenColumns.getHiddenColumns().size() > 0)
       {
-        this.ap = ap;
+        hasHiddenColumns = true;
       }
-      public void run()
+      else
       {
-        updatingConsensus = true;
-        while (UPDATING_CONSENSUS)
-        {
-          try
-          {
-            if (ap != null)
-            {
-            ap.paintAlignment(true);
-            }
+        hasHiddenColumns = false;
+      }
+    }
+    init();
+  }
 
-            Thread.sleep(200);
-          }
-          catch (Exception ex)
-          {
-            ex.printStackTrace();
-          }
-        }
+  void init()
+  {
+    this.startRes = 0;
+    this.endRes = alignment.getWidth() - 1;
+    this.startSeq = 0;
+    this.endSeq = alignment.getHeight() - 1;
 
+    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
 
-        UPDATING_CONSENSUS = true;
+    showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+    showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
 
-        try
-        {
-          int aWidth = alignment.getWidth();
-          if(aWidth<0)
-        {
-            return;
-        }
+    rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+    centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
+    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
-          consensus.annotations = null;
-          consensus.annotations = new Annotation[aWidth];
+    padGaps = Cache.getDefault("PAD_GAPS", true);
+    shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
+    showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
 
+    String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+    String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
+    String fontSize = Cache.getDefault("FONT_SIZE", "10");
 
-          hconsensus = new Hashtable[aWidth];
-          AAFrequency.calculate(alignment.getSequencesArray(),
-                                0,
-                                alignment.getWidth(),
-                                hconsensus);
+    seqNameItalics = Cache.getDefault("ID_ITALICS", true);
 
-          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();
-          }
+    int style = 0;
 
-            String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
-            String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
+    if (fontStyle.equals("bold"))
+    {
+      style = 1;
+    }
+    else if (fontStyle.equals("italic"))
+    {
+      style = 2;
+    }
 
-            if (maxRes.length() > 1)
-            {
-              mouseOver = "[" + maxRes + "] ";
-              maxRes = "+";
-            }
+    setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
 
-            mouseOver += ( (int) value + "%");
-          consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
-              value);
-          }
+    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 (globalColourScheme != null)
+        if (Cache.getDefault("SHOW_CONSERVATION", true))
         {
-            globalColourScheme.setConsensus(hconsensus);
+          alignment.addAnnotation(conservation);
         }
 
-        }
-        catch (OutOfMemoryError error)
+        if (Cache.getDefault("SHOW_QUALITY", true))
         {
-          alignment.deleteAnnotation(consensus);
+          quality = new AlignmentAnnotation("Quality",
+                  "Alignment Quality based on Blosum62 scores",
+                  new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+          quality.hasText = true;
+          quality.autoCalculated = true;
 
-          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);
-            }
-          });
-
-          System.out.println("Consensus calculation: " + error);
-          System.gc();
+          alignment.addAnnotation(quality);
         }
-        UPDATING_CONSENSUS = false;
-        updatingConsensus = false;
+        showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
+                false);
 
-        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
-     */
-  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)
+      showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
+              true);
+      showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+      showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
+      // TODO: add menu option action that nulls or creates consensus object
+      // depending on if the user wants to see the annotation or not in a
+      // specific alignment
+      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))
       {
-          if (consensus.annotations[i].description.charAt(0) == '[')
-        {
-            seqs.append(consensus.annotations[i].description.charAt(1));
-        }
-          else
-        {
-            seqs.append(consensus.annotations[i].displayCharacter);
-        }
+        alignment.addAnnotation(consensus);
       }
     }
 
-      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()
+    if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
     {
-        return selectionGroup;
-    }
+      globalColourScheme = ColourSchemeProperty.getColour(alignment,
+              jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void setSelectionGroup(SequenceGroup sg)
-    {
-        selectionGroup = sg;
-    }
+      if (globalColourScheme instanceof UserColourScheme)
+      {
+        globalColourScheme = UserDefinedColours.loadDefaultColours();
+        ((UserColourScheme) globalColourScheme).setThreshold(0,
+                getIgnoreGapsConsensus());
+      }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getConservationSelected()
-    {
-        return conservationColourSelected;
+      if (globalColourScheme != null)
+      {
+        globalColourScheme.setConsensus(hconsensus);
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setConservationSelected(boolean b)
-    {
-        conservationColourSelected = b;
-    }
+    wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
+    showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
+            false);
+    sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
+    followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
+            true);
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getAbovePIDThreshold()
-    {
-        return abovePIDThreshold;
-    }
+  /**
+   * set the flag
+   * 
+   * @param b
+   *          features are displayed if true
+   */
+  public void setShowSequenceFeatures(boolean b)
+  {
+    showSequenceFeatures = b;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setAbovePIDThreshold(boolean b)
-    {
-        abovePIDThreshold = b;
-    }
+  public boolean getShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartRes()
-    {
-        return startRes;
-    }
+  ConservationThread conservationThread;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndRes()
-    {
-        return endRes;
-    }
+  ConsensusThread consensusThread;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartSeq()
-    {
-        return startSeq;
-    }
+  boolean consUpdateNeeded = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     */
-    public void setGlobalColourScheme(ColourSchemeI cs)
-    {
-        globalColourScheme = cs;
-    }
+  static boolean UPDATING_CONSENSUS = false;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public ColourSchemeI getGlobalColourScheme()
+  static boolean UPDATING_CONSERVATION = false;
+
+  boolean updatingConsensus = false;
+
+  boolean updatingConservation = false;
+
+  /**
+   * centre columnar annotation labels in displayed alignment annotation TODO:
+   * add to jalviewXML and annotation display settings
+   */
+  boolean centreColumnLabels = false;
+
+  private boolean showdbrefs;
+
+  private boolean shownpfeats;
+
+  /**
+   * trigger update of conservation annotation
+   */
+  public void updateConservation(final AlignmentPanel ap)
+  {
+    // see note in mantis : issue number 8585
+    if (alignment.isNucleotide() || conservation == null
+            || !autoCalculateConsensus)
     {
-        return globalColourScheme;
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param res DOCUMENT ME!
-     */
-    public void setStartRes(int res)
+    conservationThread = new ConservationThread(this, ap);
+    conservationThread.start();
+  }
+
+  /**
+   * trigger update of consensus annotation
+   */
+  public void updateConsensus(final AlignmentPanel ap)
+  {
+    // see note in mantis : issue number 8585
+    if (consensus == null || !autoCalculateConsensus)
     {
-        this.startRes = res;
+      return;
     }
+    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.paintAlignment(false);
+          }
 
-        if (res < 0)
+          Thread.sleep(200);
+        } catch (Exception ex)
         {
-            res = 0;
+          ex.printStackTrace();
         }
+      }
 
-        this.endRes = res;
-    }
+      UPDATING_CONSENSUS = true;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setEndSeq(int seq)
-    {
-        if (seq > alignment.getHeight())
+      try
+      {
+        int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
+        // pointer
+        // possibility
+        // here.
+        if (aWidth <= 0)
         {
-            seq = alignment.getHeight();
+          updatingConsensus = false;
+          UPDATING_CONSENSUS = false;
+          return;
         }
 
-        if (seq < 0)
+        consensus.annotations = null;
+        consensus.annotations = new Annotation[aWidth];
+
+        hconsensus = new Hashtable[aWidth];
+        AAFrequency.calculate(alignment.getSequencesArray(), 0,
+                alignment.getWidth(), hconsensus, true);
+        updateAnnotation(true);
+
+        if (globalColourScheme != null)
         {
-            seq = 0;
+          globalColourScheme.setConsensus(hconsensus);
         }
 
-        this.endSeq = seq;
+      } catch (OutOfMemoryError error)
+      {
+        alignment.deleteAnnotation(consensus);
+
+        consensus = null;
+        hconsensus = null;
+        new OOMWarning("calculating consensus", error);
+      }
+      UPDATING_CONSENSUS = false;
+      updatingConsensus = false;
+
+      if (ap != null)
+      {
+        ap.paintAlignment(true);
+      }
     }
 
     /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
+     * update the consensus annotation from the sequence profile data using
+     * current visualization settings.
      */
-    public int getEndSeq()
+    public void updateAnnotation()
     {
-        return endSeq;
+      updateAnnotation(false);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param f DOCUMENT ME!
-     */
-    public void setFont(Font f)
+    protected void updateAnnotation(boolean immediate)
     {
-        font = f;
-
-        Container c = new Container();
-
-        java.awt.FontMetrics fm = c.getFontMetrics(font);
-        setCharHeight(fm.getHeight());
-        setCharWidth(fm.charWidth('M'));
-        validCharWidth = true;
+      // TODO: make calls thread-safe, so if another thread calls this method,
+      // it will either return or wait until one calculation is finished.
+      if (immediate
+              || (!updatingConsensus && consensus != null && hconsensus != null))
+      {
+        AAFrequency.completeConsensus(consensus, hconsensus, 0,
+                hconsensus.length, ignoreGapsInConsensusCalculation,
+                showSequenceLogo);
+      }
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Font getFont()
+  /**
+   * 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 font;
+      updateConsensus(null);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param w DOCUMENT ME!
-     */
-    public void setCharWidth(int w)
+    if (consensus == null)
     {
-        this.charWidth = w;
+      return null;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getCharWidth()
+    StringBuffer seqs = new StringBuffer();
+    for (int i = 0; i < consensus.annotations.length; i++)
     {
-        return charWidth;
+      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!
-     *
-     * @param h DOCUMENT ME!
-     */
-    public void setCharHeight(int h)
-    {
-        this.charHeight = h;
-    }
+    SequenceI sq = new Sequence("Consensus", seqs.toString());
+    sq.setDescription("Percentage Identity Consensus "
+            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    return sq;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getCharHeight()
-    {
-        return charHeight;
-    }
+  /**
+   * 
+   * 
+   * @return null or the currently selected sequence region
+   */
+  public SequenceGroup getSelectionGroup()
+  {
+    return selectionGroup;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param w DOCUMENT ME!
-     */
-    public void setWrappedWidth(int w)
-    {
-        this.wrappedWidth = w;
-    }
+  /**
+   * Set the selection group for this window.
+   * 
+   * @param sg - group holding references to sequences in this alignment view
+   *          
+   */
+  public void setSelectionGroup(SequenceGroup sg)
+  {
+    selectionGroup = sg;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWrappedWidth()
-    {
-        return wrappedWidth;
-    }
+  /**
+   * GUI state
+   * @return true if conservation based shading is enabled
+   */
+  public boolean getConservationSelected()
+  {
+    return conservationColourSelected;
+  }
 
+  /**
+   * GUI state
+   * @param b
+   *          enable conservation based shading
+   */
+  public void setConservationSelected(boolean b)
+  {
+    conservationColourSelected = b;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public AlignmentI getAlignment()
-    {
-        return alignment;
-    }
+  /**
+   * GUI state
+   * @return true if percent identity threshold is applied to shading
+   */
+  public boolean getAbovePIDThreshold()
+  {
+    return abovePIDThreshold;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param align DOCUMENT ME!
-     */
-    public void setAlignment(AlignmentI align)
-    {
-        this.alignment = align;
-    }
+  /**
+   * GUI state
+   * 
+   * 
+   * @param b indicate if percent identity threshold is applied to shading
+   */
+  public void setAbovePIDThreshold(boolean b)
+  {
+    abovePIDThreshold = b;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setWrapAlignment(boolean state)
-    {
-        wrapAlignment = state;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getStartRes()
+  {
+    return startRes;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowText(boolean state)
-    {
-        showText = state;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getEndRes()
+  {
+    return endRes;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setRenderGaps(boolean state)
-    {
-        renderGaps = state;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getStartSeq()
+  {
+    return startSeq;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourText()
-    {
-        return showColourText;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param cs
+   *          DOCUMENT ME!
+   */
+  public void setGlobalColourScheme(ColourSchemeI cs)
+  {
+    globalColourScheme = cs;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setColourText(boolean state)
-    {
-        showColourText = state;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public ColourSchemeI getGlobalColourScheme()
+  {
+    return globalColourScheme;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setShowBoxes(boolean state)
-    {
-        showBoxes = state;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param res
+   *          DOCUMENT ME!
+   */
+  public void setStartRes(int res)
+  {
+    this.startRes = res;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getWrapAlignment()
-    {
-        return wrapAlignment;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *          DOCUMENT ME!
+   */
+  public void setStartSeq(int seq)
+  {
+    this.startSeq = seq;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowText()
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param res
+   *          DOCUMENT ME!
+   */
+  public void setEndRes(int res)
+  {
+    if (res > (alignment.getWidth() - 1))
     {
-        return showText;
+      // log.System.out.println(" Corrected res from " + res + " to maximum " +
+      // (alignment.getWidth()-1));
+      res = alignment.getWidth() - 1;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowBoxes()
+    if (res < 0)
     {
-        return showBoxes;
+      res = 0;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getGapCharacter()
-    {
-        return getAlignment().getGapCharacter();
-    }
+    this.endRes = res;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gap DOCUMENT ME!
-     */
-    public void setGapCharacter(char gap)
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *          DOCUMENT ME!
+   */
+  public void setEndSeq(int seq)
+  {
+    if (seq > alignment.getHeight())
     {
-        if (getAlignment() != null)
-        {
-            getAlignment().setGapCharacter(gap);
-        }
+      seq = alignment.getHeight();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param thresh DOCUMENT ME!
-     */
-    public void setThreshold(int thresh)
+    if (seq < 0)
     {
-        threshold = thresh;
+      seq = 0;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getThreshold()
-    {
-        return threshold;
-    }
+    this.endSeq = seq;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param inc DOCUMENT ME!
-     */
-    public void setIncrement(int inc)
-    {
-        increment = inc;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getEndSeq()
+  {
+    return endSeq;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getIncrement()
-    {
-        return increment;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param f
+   *          DOCUMENT ME!
+   */
+  public void setFont(Font f)
+  {
+    font = f;
 
+    Container c = new Container();
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public ColumnSelection getColumnSelection()
-    {
-        return colSel;
-    }
+    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 tree DOCUMENT ME!
-     */
-    public void setCurrentTree(NJTree tree)
-    {
-        currentTree = tree;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param w
+   *          DOCUMENT ME!
+   */
+  public void setCharWidth(int w)
+  {
+    this.charWidth = w;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public NJTree getCurrentTree()
-    {
-        return currentTree;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getCharWidth()
+  {
+    return charWidth;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setColourAppliesToAllGroups(boolean b)
-    {
-        colourAppliesToAllGroups = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param h
+   *          DOCUMENT ME!
+   */
+  public void setCharHeight(int h)
+  {
+    this.charHeight = h;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourAppliesToAllGroups()
-    {
-        return colourAppliesToAllGroups;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getCharHeight()
+  {
+    return charHeight;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getShowJVSuffix()
-    {
-        return showJVSuffix;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param w
+   *          DOCUMENT ME!
+   */
+  public void setWrappedWidth(int w)
+  {
+    this.wrappedWidth = w;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowJVSuffix(boolean b)
-    {
-        showJVSuffix = b;
-    }
+  /**
+   * 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 boolean getShowAnnotation()
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param align
+   *          DOCUMENT ME!
+   */
+  public void setAlignment(AlignmentI align)
+  {
+    if (alignment != null && alignment.getCodonFrames() != null)
     {
-        return showAnnotation;
+      StructureSelectionManager.getStructureSelectionManager(Desktop.instance)
+              .removeMappings(alignment.getCodonFrames());
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setShowAnnotation(boolean b)
+    this.alignment = align;
+    if (alignment.getCodonFrames() != null)
     {
-        showAnnotation = b;
+      StructureSelectionManager.getStructureSelectionManager(Desktop.instance).addMappings(
+              alignment.getCodonFrames());
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleAboveWrapped()
-    {
-        return scaleAboveWrapped;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *          DOCUMENT ME!
+   */
+  public void setWrapAlignment(boolean state)
+  {
+    wrapAlignment = state;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleLeftWrapped()
-    {
-        return scaleLeftWrapped;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *          DOCUMENT ME!
+   */
+  public void setShowText(boolean state)
+  {
+    showText = state;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getScaleRightWrapped()
-    {
-        return scaleRightWrapped;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *          DOCUMENT ME!
+   */
+  public void setRenderGaps(boolean state)
+  {
+    renderGaps = state;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleAboveWrapped(boolean b)
-    {
-        scaleAboveWrapped = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getColourText()
+  {
+    return showColourText;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleLeftWrapped(boolean b)
-    {
-        scaleLeftWrapped = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *          DOCUMENT ME!
+   */
+  public void setColourText(boolean state)
+  {
+    showColourText = state;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param b DOCUMENT ME!
-     */
-    public void setScaleRightWrapped(boolean b)
-    {
-        scaleRightWrapped = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *          DOCUMENT ME!
+   */
+  public void setShowBoxes(boolean state)
+  {
+    showBoxes = state;
+  }
 
-    /**
-     * Property change listener for changes in alignment
-     *
-     * @param listener DOCUMENT ME!
-     */
-    public void addPropertyChangeListener(
-        java.beans.PropertyChangeListener listener)
-    {
-        changeSupport.addPropertyChangeListener(listener);
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getWrapAlignment()
+  {
+    return wrapAlignment;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param listener DOCUMENT ME!
-     */
-    public void removePropertyChangeListener(
-        java.beans.PropertyChangeListener listener)
-    {
-        changeSupport.removePropertyChangeListener(listener);
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowText()
+  {
+    return showText;
+  }
 
-    /**
-     * 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);
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowBoxes()
+  {
+    return showBoxes;
+  }
 
-    public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
-    {
-      ignoreGapsInConsensusCalculation = b;
-      updateConsensus(ap);
-      if(globalColourScheme!=null)
-      {
-      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-                                      ignoreGapsInConsensusCalculation);
-      }
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public char getGapCharacter()
+  {
+    return getAlignment().getGapCharacter();
+  }
 
-    public boolean getIgnoreGapsConsensus()
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param gap
+   *          DOCUMENT ME!
+   */
+  public void setGapCharacter(char gap)
+  {
+    if (getAlignment() != null)
     {
-     return ignoreGapsInConsensusCalculation;
+      getAlignment().setGapCharacter(gap);
     }
+  }
 
-    public void setDataset(boolean b)
-    {
-      isDataset = b;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param thresh
+   *          DOCUMENT ME!
+   */
+  public void setThreshold(int thresh)
+  {
+    threshold = thresh;
+  }
 
-    public boolean isDataset()
-    {
-      return isDataset;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getThreshold()
+  {
+    return threshold;
+  }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param inc
+   *          DOCUMENT ME!
+   */
+  public void setIncrement(int inc)
+  {
+    increment = inc;
+  }
 
-    public void hideSelectedColumns()
-    {
-      if (colSel.size() < 1)
-    {
-        return;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getIncrement()
+  {
+    return increment;
+  }
 
-      colSel.hideSelectedColumns();
-      setSelectionGroup(null);
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public ColumnSelection getColumnSelection()
+  {
+    return colSel;
+  }
 
-      hasHiddenColumns = true;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param tree
+   *          DOCUMENT ME!
+   */
+  public void setCurrentTree(NJTree tree)
+  {
+    currentTree = tree;
+  }
 
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public NJTree getCurrentTree()
+  {
+    return currentTree;
+  }
 
-    public void hideColumns(int start, int end)
-    {
-      if(start==end)
-    {
-        colSel.hideColumns(start);
-    }
-      else
-    {
-        colSel.hideColumns(start, end);
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *          DOCUMENT ME!
+   */
+  public void setColourAppliesToAllGroups(boolean b)
+  {
+    colourAppliesToAllGroups = b;
+  }
 
-      hasHiddenColumns = true;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getColourAppliesToAllGroups()
+  {
+    return colourAppliesToAllGroups;
+  }
 
-    public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
-    {
-      int sSize = sg.getSize();
-      if(sSize < 2)
-    {
-        return;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowJVSuffix()
+  {
+    return showJVSuffix;
+  }
 
-      if(hiddenRepSequences==null)
-    {
-        hiddenRepSequences = new Hashtable();
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *          DOCUMENT ME!
+   */
+  public void setShowJVSuffix(boolean b)
+  {
+    showJVSuffix = b;
+  }
 
-       hiddenRepSequences.put(repSequence, sg);
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getShowAnnotation()
+  {
+    return showAnnotation;
+  }
 
-      //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)
-        {
-            return;
-        }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *          DOCUMENT ME!
+   */
+  public void setShowAnnotation(boolean b)
+  {
+    showAnnotation = b;
+  }
 
-          seqs[index++] = sg.getSequenceAt(i);
-        }
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getScaleAboveWrapped()
+  {
+    return scaleAboveWrapped;
+  }
 
-      hideSequence(seqs);
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getScaleLeftWrapped()
+  {
+    return scaleLeftWrapped;
+  }
 
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getScaleRightWrapped()
+  {
+    return scaleRightWrapped;
+  }
 
-    public void hideAllSelectedSeqs()
-    {
-    if (selectionGroup == null || selectionGroup.getSize()<1)
-    {
-        return;
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *          DOCUMENT ME!
+   */
+  public void setScaleAboveWrapped(boolean b)
+  {
+    scaleAboveWrapped = b;
+  }
 
-      SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *          DOCUMENT ME!
+   */
+  public void setScaleLeftWrapped(boolean b)
+  {
+    scaleLeftWrapped = b;
+  }
 
-      hideSequence(seqs);
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param b
+   *          DOCUMENT ME!
+   */
+  public void setScaleRightWrapped(boolean b)
+  {
+    scaleRightWrapped = b;
+  }
 
-      setSelectionGroup(null);
-    }
+  /**
+   * 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);
+  }
 
-    public void hideSequence(SequenceI [] seq)
+  /**
+   * 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)
     {
-      if(seq!=null)
-      {
-        for (int i = 0; i < seq.length; i++)
-        {
-          alignment.getHiddenSequences().hideSequence(seq[i]);
-        }
-        hasHiddenRows = true;
-        firePropertyChange("alignment", null, alignment.getSequences());
-      }
+      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+              ignoreGapsInConsensusCalculation);
     }
+  }
 
-    public void showSequence(int index)
-    {
-      Vector tmp = alignment.getHiddenSequences().showSequence(index
-          , hiddenRepSequences);
-      if(tmp.size()>0)
-      {
-        if(selectionGroup==null)
-        {
-          selectionGroup = new SequenceGroup();
-          selectionGroup.setEndRes(alignment.getWidth()-1);
-        }
+  public boolean getIgnoreGapsConsensus()
+  {
+    return ignoreGapsInConsensusCalculation;
+  }
 
-        for (int t = 0; t < tmp.size(); t++)
-        {
-          selectionGroup.addSequence(
-              (SequenceI) tmp.elementAt(t), false
-              );
-        }
-        firePropertyChange("alignment", null, alignment.getSequences());
-      }
+  public void setDataset(boolean b)
+  {
+    isDataset = b;
+  }
 
-      if(alignment.getHiddenSequences().getSize()<1)
+  public boolean isDataset()
+  {
+    return isDataset;
+  }
+
+  public void hideSelectedColumns()
+  {
+    if (colSel.size() < 1)
     {
-        hasHiddenRows = false;
+      return;
     }
+
+    colSel.hideSelectedColumns();
+    setSelectionGroup(null);
+
+    hasHiddenColumns = true;
   }
 
-    public void showColumn(int col)
+  public void hideColumns(int start, int end)
+  {
+    if (start == end)
     {
-      colSel.revealHiddenColumns(col);
-      if(colSel.getHiddenColumns()==null)
+      colSel.hideColumns(start);
+    }
+    else
     {
-        hasHiddenColumns = false;
+      colSel.hideColumns(start, end);
     }
+
+    hasHiddenColumns = true;
   }
 
-    public void showAllHiddenColumns()
+  public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+  {
+    int sSize = sg.getSize();
+    if (sSize < 2)
     {
-      colSel.revealAllHiddenColumns();
-      hasHiddenColumns = false;
+      return;
     }
 
-    public void showAllHiddenSeqs()
+    if (hiddenRepSequences == null)
     {
-      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;
-      }
+      hiddenRepSequences = new Hashtable();
     }
 
+    hiddenRepSequences.put(repSequence, sg);
 
-
-    public void invertColumnSelection()
+    // Hide all sequences except the repSequence
+    SequenceI[] seqs = new SequenceI[sSize - 1];
+    int index = 0;
+    for (int i = 0; i < sSize; i++)
     {
-      for(int i=0; i<alignment.getWidth(); i++)
-      {
-        if(colSel.contains(i))
+      if (sg.getSequenceAt(i) != repSequence)
       {
-          colSel.removeElement(i);
-      }
-        else
+        if (index == sSize - 1)
         {
-          if (!hasHiddenColumns || colSel.isVisible(i))
-          {
-            colSel.addElement(i);
-          }
+          return;
         }
+
+        seqs[index++] = sg.getSequenceAt(i);
       }
     }
+    sg.setSeqrep(repSequence);
+    sg.setHidereps(true);
+    hideSequence(seqs);
 
-    public int adjustForHiddenSeqs(int alignmentIndex)
+  }
+
+  public void hideAllSelectedSeqs()
+  {
+    if (selectionGroup == null || selectionGroup.getSize() < 1)
     {
-      return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+      return;
     }
 
-    /**
-     * This method returns an array of new SequenceI objects 
-     * derived from the whole alignment or just the current
-     * selection with start and end points adjusted
-     * @note if you need references to the actual SequenceI objects in the alignment or currently selected then use getSequenceSelection()
-     * @return String[]
-     */
-    public SequenceI[] getSelectionAsNewSequence()
-    {
-      SequenceI[] sequences;
+    SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
 
-      if (selectionGroup == null)
-    {
-        sequences = alignment.getSequencesArray();
-        for (int i=0; i<sequences.length; i++)
-        {
-          sequences[i] = new Sequence(sequences[i]); // construct new sequence
-        }
-    }
-      else
+    hideSequence(seqs);
+
+    setSelectionGroup(null);
+  }
+
+  public void hideSequence(SequenceI[] seq)
+  {
+    if (seq != null)
     {
-        sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+      for (int i = 0; i < seq.length; i++)
+      {
+        alignment.getHiddenSequences().hideSequence(seq[i]);
+      }
+      hasHiddenRows = true;
+      firePropertyChange("alignment", null, alignment.getSequences());
     }
+  }
 
-      return sequences;
-    }
-    /**
-     * get the currently selected sequence objects or all the sequences in the alignment.
-     * @return array of references to sequence objects
-     */
-    public SequenceI[] getSequenceSelection()
+  public void showSequence(int index)
+  {
+    Vector tmp = alignment.getHiddenSequences().showSequence(index,
+            hiddenRepSequences);
+    if (tmp.size() > 0)
     {
-      SequenceI[] sequences;
-      if (selectionGroup==null)
+      if (selectionGroup == null)
       {
-        sequences = alignment.getSequencesArray();
+        selectionGroup = new SequenceGroup();
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
-      else
+
+      for (int t = 0; t < tmp.size(); t++)
       {
-        sequences = selectionGroup.getSequencesInOrder(alignment);
+        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
       }
-      return sequences;
+      firePropertyChange("alignment", null, alignment.getSequences());
+      sendSelection();
     }
-    /**
-     * 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
+
+    if (alignment.getHiddenSequences().getSize() < 1)
+    {
+      hasHiddenRows = false;
+    }
+  }
+
+  public void showColumn(int col)
+  {
+    colSel.revealHiddenColumns(col);
+    if (colSel.getHiddenColumns() == null)
+    {
+      hasHiddenColumns = false;
+    }
+  }
+
+  public void showAllHiddenColumns()
+  {
+    colSel.revealAllHiddenColumns();
+    hasHiddenColumns = false;
+  }
+
+  public void showAllHiddenSeqs()
+  {
+    if (alignment.getHiddenSequences().getSize() > 0)
+    {
+      if (selectionGroup == null)
       {
-        iSize = alignment.getHeight();
-        seqs = alignment.getSequencesArray();
-        end = alignment.getWidth()-1;
+        selectionGroup = new SequenceGroup();
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
-      SeqCigar[] selseqs = new SeqCigar[iSize];
-      for(i=0; i<iSize; i++)
+      Vector tmp = alignment.getHiddenSequences().showAll(
+              hiddenRepSequences);
+      for (int t = 0; t < tmp.size(); t++)
       {
-        selseqs[i] = new SeqCigar(seqs[i], start, end);
+        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
       }
-      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;
-          }
-        }
+      firePropertyChange("alignment", null, alignment.getSequences());
+      sendSelection();
+      hasHiddenRows = false;
+      hiddenRepSequences = null;
+    }
+  }
 
-          if (hideStart>end)
-        {
-            break;
-        }
+  public void invertColumnSelection()
+  {
+    colSel.invertColumnSelection(0, alignment.getWidth());
+  }
 
-          if (hideEnd>end)
-        {
-            hideEnd=end;
-        }
+  public int adjustForHiddenSeqs(int alignmentIndex)
+  {
+    return alignment.getHiddenSequences().adjustForHiddenSeqs(
+            alignmentIndex);
+  }
 
-          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)
+  /**
+   * This method returns an array of new SequenceI objects derived from the
+   * whole alignment or just the current selection with start and end points
+   * adjusted
+   * 
+   * @note if you need references to the actual SequenceI objects in the
+   *       alignment or currently selected then use getSequenceSelection()
+   * @return selection as new sequenceI objects
+   */
+  public SequenceI[] getSelectionAsNewSequence()
+  {
+    SequenceI[] sequences;
+
+    if (selectionGroup == null)
+    {
+      sequences = alignment.getSequencesArray();
+      AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
+      for (int i = 0; i < sequences.length; i++)
       {
-          selection.addOperation(CigarArray.M, end-last+1);
+        sequences[i] = new Sequence(sequences[i], annots); // construct new
+        // sequence with
+        // subset of visible
+        // annotation
       }
     }
     else
     {
-        selection.addOperation(CigarArray.M, end-start+1);
-      }
-      return selection;
+      sequences = selectionGroup.getSelectionAsNewSequences(alignment);
     }
-    /**
-     * 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;
+
+    return sequences;
+  }
+
+  /**
+   * get the currently selected sequence objects or all the sequences in the
+   * alignment.
+   * 
+   * @return array of references to sequence objects
+   */
+  public SequenceI[] getSequenceSelection()
+  {
+    SequenceI[] sequences = null;
+    if (selectionGroup != null)
+    {
+      sequences = selectionGroup.getSequencesInOrder(alignment);
     }
-    /**
-     * 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)
+    if (sequences == null)
     {
-      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();
-      }
+      sequences = alignment.getSequencesArray();
+    }
+    return sequences;
+  }
 
-      selection = new String[iSize];
-    if (hasHiddenColumns)
+  /**
+   * 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)
+  {
+    return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null));
+  }
+
+  /**
+   * 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
+   */
+  public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+  {
+    return getAlignmentView(selectedOnly, false);
+  }
+  
+  /**
+   * 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
+   * @param markGroups
+   *          boolean true to annotate the alignment view with groups on the alignment (and intersecting with selected region if selectedOnly is true) 
+   * @return AlignmentView
+   */
+  public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups)
+  {
+    return new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups);
+  }
+
+  /**
+   * 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)
     {
-        selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+      iSize = selectionGroup.getSize();
+      seqs = selectionGroup.getSequencesInOrder(alignment);
+      start = selectionGroup.getStartRes();
+      end = selectionGroup.getEndRes() + 1;
     }
     else
     {
-        for(i=0; i<iSize; i++)
-        {
-          selection[i] = seqs[i].getSequenceAsString(start, end);
-        }
+      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);
       }
-      return selection;
+
     }
+    return selection;
+  }
 
-  public int [][] getVisibleRegionBoundaries(int min, int max)
+  public int[][] getVisibleRegionBoundaries(int min, int max)
   {
     Vector regions = new Vector();
     int start = min;
@@ -1695,15 +1666,14 @@ public class AlignViewport
       }
 
       regions.addElement(new int[]
-                         {start, end});
+      { start, end });
 
       if (hasHiddenColumns)
       {
         start = colSel.adjustForHiddenColumns(end);
         start = colSel.getHiddenBoundaryLeft(start) + 1;
       }
-    }
-    while (end < max);
+    } while (end < max);
 
     int[][] startEnd = new int[regions.size()][2];
 
@@ -1713,154 +1683,603 @@ public class AlignViewport
 
   }
 
-    public boolean getShowHiddenMarkers()
+  public boolean getShowHiddenMarkers()
+  {
+    return showHiddenMarkers;
+  }
+
+  public void setShowHiddenMarkers(boolean show)
+  {
+    showHiddenMarkers = show;
+  }
+
+  public String getSequenceSetId()
+  {
+    if (sequenceSetID == null)
     {
-      return showHiddenMarkers;
+      sequenceSetID = alignment.hashCode() + "";
     }
 
-    public void setShowHiddenMarkers(boolean show)
+    return sequenceSetID;
+  }
+
+  /**
+   * unique viewId for synchronizing state with stored Jalview Project
+   * 
+   */
+  private String viewId = null;
+
+  public String getViewId()
+  {
+    if (viewId == null)
     {
-      showHiddenMarkers = show;
+      viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
     }
+    return viewId;
+  }
 
-    public String getSequenceSetId()
+  public void alignmentChanged(AlignmentPanel ap)
+  {
+    if (padGaps)
+    {
+      alignment.padGaps();
+    }
+    if (hconsensus != null && autoCalculateConsensus)
     {
-      if(sequenceSetID==null)
+      updateConservation(ap);
+    }
+    if (autoCalculateConsensus)
     {
-        sequenceSetID =  alignment.hashCode()+"";
+      updateConsensus(ap);
     }
 
-      return sequenceSetID;
+    // 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);
+        }
+      }
     }
 
-    public void alignmentChanged(AlignmentPanel ap)
+    if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
     {
-        if (padGaps)
+      selectionGroup.setEndRes(alWidth - 1);
+    }
+
+    resetAllColourSchemes();
+
+    // alignment.adjustSequenceAnnotations();
+  }
+
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = globalColourScheme;
+    if (cs != null)
     {
-          alignment.padGaps();
+      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);
+      }
     }
 
-        if (hconsensus != null && autoCalculateConsensus)
-        {
-          updateConsensus(ap);
-          updateConservation(ap);
-        }
+    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();
+    }
+  }
 
-        //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);
-          }
-        }
+  public Color getSequenceColour(SequenceI seq)
+  {
+    if (sequenceColours == null || !sequenceColours.containsKey(seq))
+    {
+      return Color.white;
     }
+    else
+    {
+      return (Color) sequenceColours.get(seq);
+    }
+  }
 
-        if(selectionGroup!=null && selectionGroup.getEndRes()>alWidth)
+  public void setSequenceColour(SequenceI seq, Color col)
+  {
+    if (sequenceColours == null)
     {
-          selectionGroup.setEndRes(alWidth-1);
+      sequenceColours = new Hashtable();
     }
 
-        resetAllColourSchemes();
+    if (col == null)
+    {
+      sequenceColours.remove(seq);
+    }
+    else
+    {
+      sequenceColours.put(seq, col);
+    }
+  }
 
-       // alignment.adjustSequenceAnnotations();
+  /**
+   * 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;
+  }
 
+  /**
+   * get hash of undo and redo list for the alignment
+   * 
+   * @return long[] { historyList.hashCode, redoList.hashCode };
+   */
+  public long[] getUndoRedoHash()
+  {
+    if (historyList == null || redoList == null)
+      return new long[]
+      { -1, -1 };
+    return new long[]
+    { historyList.hashCode(), this.redoList.hashCode() };
+  }
 
-    void resetAllColourSchemes()
+  /**
+   * test if a particular set of hashcodes are different to the hashcodes for
+   * the undo and redo list.
+   * 
+   * @param undoredo
+   *          the stored set of hashcodes as returned by getUndoRedoHash
+   * @return true if the hashcodes differ (ie the alignment has been edited) or
+   *         the stored hashcode array differs in size
+   */
+  public boolean isUndoRedoHashModified(long[] undoredo)
+  {
+    if (undoredo == null)
     {
-      ColourSchemeI cs = globalColourScheme;
-      if(cs!=null)
-      {
-        if (cs instanceof ClustalxColourScheme)
-        {
-          ( (ClustalxColourScheme) cs).
-              resetClustalX(alignment.getSequences(),
-                            alignment.getWidth());
-        }
+      return true;
+    }
+    long[] cstate = getUndoRedoHash();
+    if (cstate.length != undoredo.length)
+    {
+      return true;
+    }
 
-        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);
-        }
+    for (int i = 0; i < cstate.length; i++)
+    {
+      if (cstate[i] != undoredo[i])
+      {
+        return true;
       }
+    }
+    return false;
+  }
 
-      int s, sSize = alignment.getGroups().size();
-      for(s=0; s<sSize; s++)
+  public boolean getCentreColumnLabels()
+  {
+    return centreColumnLabels;
+  }
+
+  public void setCentreColumnLabels(boolean centrecolumnlabels)
+  {
+    centreColumnLabels = centrecolumnlabels;
+  }
+
+  public void updateSequenceIdColours()
+  {
+    Vector groups = alignment.getGroups();
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+    for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
+    {
+      SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
+      if (sg.idColour != null)
       {
-        SequenceGroup sg = (SequenceGroup)alignment.getGroups().elementAt(s);
-        if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)
+        Vector sqs = sg.getSequences(hiddenRepSequences);
+        for (int s = 0, sSize = sqs.size(); s < sSize; s++)
         {
-          ((ClustalxColourScheme)sg.cs).resetClustalX(
-              sg.getSequences(hiddenRepSequences), sg.getWidth());
+          sequenceColours.put(sqs.elementAt(s), sg.idColour);
         }
-        sg.recalcConservation();
       }
     }
+  }
 
+  /**
+   * enable or disable the display of Database Cross References in the sequence
+   * ID tooltip
+   */
+  public void setShowDbRefs(boolean show)
+  {
+    showdbrefs = show;
+  }
 
-    public Color getSequenceColour(SequenceI seq)
-    {
-      if(sequenceColours==null || !sequenceColours.containsKey(seq))
-    {
-        return Color.white;
-    }
-      else
+  /**
+   * 
+   * @return true if Database References are to be displayed on tooltips.
+   */
+  public boolean isShowDbRefs()
+  {
+    return showdbrefs;
+  }
+
+  /**
+   * 
+   * @return true if Non-positional features are to be displayed on tooltips.
+   */
+  public boolean isShowNpFeats()
+  {
+    return shownpfeats;
+  }
+
+  /**
+   * enable or disable the display of Non-Positional sequence features in the
+   * sequence ID tooltip
+   * 
+   * @param show
+   */
+  public void setShowNpFeats(boolean show)
+  {
+    shownpfeats = show;
+  }
+
+  /**
+   * 
+   * @return true if view has hidden rows
+   */
+  public boolean hasHiddenRows()
+  {
+    return hasHiddenRows;
+  }
+
+  /**
+   * 
+   * @return true if view has hidden columns
+   */
+  public boolean hasHiddenColumns()
+  {
+    return hasHiddenColumns;
+  }
+
+  /**
+   * when set, view will scroll to show the highlighted position
+   */
+  public boolean followHighlight = true;
+
+  /**
+   * @return true if view should scroll to show the highlighted region of a
+   *         sequence
+   * @return
+   */
+  public boolean getFollowHighlight()
+  {
+    return followHighlight;
+  }
+
+  public boolean followSelection = true;
+
+  /**
+   * @return true if view selection should always follow the selections
+   *         broadcast by other selection sources
+   */
+  public boolean getFollowSelection()
+  {
+    return followSelection;
+  }
+
+  private long sgrouphash = -1, colselhash = -1;
+
+  boolean showSeqFeaturesHeight;
+
+  /**
+   * checks current SelectionGroup against record of last hash value, and
+   * updates record.
+   * @param b update the record of last hash value
+   * 
+   * @return true if SelectionGroup changed since last call (when b is true)
+   */
+  boolean isSelectionGroupChanged(boolean b)
+  {
+    int hc = (selectionGroup == null || selectionGroup.getSize()==0) ? -1 : selectionGroup.hashCode();
+    if (hc!=-1 && hc != sgrouphash)
     {
-        return (Color)sequenceColours.get(seq);
+      if (b) {sgrouphash = hc;}
+      return true;
     }
+    return false;
   }
 
-    public void setSequenceColour(SequenceI seq, Color col)
-    {
-      if(sequenceColours==null)
+  /**
+   * checks current colsel against record of last hash value, and optionally updates
+   * record.
+
+   * @param b update the record of last hash value
+   * @return true if colsel changed since last call (when b is true)
+   */
+  boolean isColSelChanged(boolean b)
+  {
+    int hc = (colSel == null || colSel.size()==0) ? -1 : colSel.hashCode();
+    if (hc!=-1 && hc != colselhash)
     {
-        sequenceColours = new Hashtable();
+      if (b) {colselhash = hc;}
+      return true;
     }
+    return false;
+  }
+
+  public void sendSelection()
+  {
+    jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance).sendSelection(
+                    new SequenceGroup(getSelectionGroup()),
+                    new ColumnSelection(getColumnSelection()), this);
+  }
+
+  public void setShowSequenceFeaturesHeight(boolean selected)
+  {
+    showSeqFeaturesHeight = selected;
+  }
+
+  public boolean getShowSequenceFeaturesHeight()
+  {
+    return showSeqFeaturesHeight;
+  }
+
+  boolean showUnconserved = false;
 
-      if(col == null)
+  public boolean getShowUnconserved()
+  {
+    return showUnconserved;
+  }
+
+  public void setShowUnconserved(boolean showunconserved)
+  {
+    showUnconserved = showunconserved;
+  }
+
+  /**
+   * return the alignPanel containing the given viewport. Use this to get the
+   * components currently handling the given viewport.
+   * 
+   * @param av
+   * @return null or an alignPanel guaranteed to have non-null alignFrame
+   *         reference
+   */
+  public AlignmentPanel getAlignPanel()
+  {
+    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
+            .getSequenceSetId());
+    AlignmentPanel ap = null;
+    for (int p = 0; aps != null && p < aps.length; p++)
     {
-        sequenceColours.remove(seq);
+      if (aps[p].av == this)
+      {
+        return aps[p];
+      }
     }
-      else
+    return null;
+  }
+
+  public boolean getSortByTree()
+  {
+    return sortByTree;
+  }
+
+  public void setSortByTree(boolean sort)
+  {
+    sortByTree = sort;
+  }
+
+  /**
+   * should conservation rows be shown for groups
+   */
+  boolean showGroupConservation = false;
+
+  /**
+   * should consensus rows be shown for groups
+   */
+  boolean showGroupConsensus = false;
+
+  /**
+   * should consensus profile be rendered by default
+   */
+  public boolean showSequenceLogo = false;
+
+  /**
+   * should consensus histograms be rendered by default
+   */
+  public boolean showConsensusHistogram = true;
+
+  /**
+   * @return the showConsensusProfile
+   */
+  public boolean isShowSequenceLogo()
+  {
+    return showSequenceLogo;
+  }
+
+  /**
+   * @param showSequenceLogo
+   *          the new value
+   */
+  public void setShowSequenceLogo(boolean showSequenceLogo)
+  {
+    if (showSequenceLogo != this.showSequenceLogo)
     {
-        sequenceColours.put(seq, col);
-    }
+      // TODO: decouple settings setting from calculation when refactoring
+      // annotation update method from alignframe to viewport
+      this.showSequenceLogo = showSequenceLogo;
+      if (consensusThread != null)
+      {
+        consensusThread.updateAnnotation();
+      }
     }
-    /**
-     * 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)
+    this.showSequenceLogo = showSequenceLogo;
+  }
+
+  /**
+   * @param showConsensusHistogram
+   *          the showConsensusHistogram to set
+   */
+  public void setShowConsensusHistogram(boolean showConsensusHistogram)
+  {
+    this.showConsensusHistogram = showConsensusHistogram;
+  }
+
+  /**
+   * @return the showGroupConservation
+   */
+  public boolean isShowGroupConservation()
+  {
+    return showGroupConservation;
+  }
+
+  /**
+   * @param showGroupConservation
+   *          the showGroupConservation to set
+   */
+  public void setShowGroupConservation(boolean showGroupConservation)
+  {
+    this.showGroupConservation = showGroupConservation;
+  }
+
+  /**
+   * @return the showGroupConsensus
+   */
+  public boolean isShowGroupConsensus()
+  {
+    return showGroupConsensus;
+  }
+
+  /**
+   * @param showGroupConsensus
+   *          the showGroupConsensus to set
+   */
+  public void setShowGroupConsensus(boolean showGroupConsensus)
+  {
+    this.showGroupConsensus = showGroupConsensus;
+  }
+
+  /**
+   * 
+   * @return flag to indicate if the consensus histogram should be rendered by
+   *         default
+   */
+  public boolean isShowConsensusHistogram()
+  {
+    return this.showConsensusHistogram;
+  }
+
+  /**
+   * synthesize a column selection if none exists so it covers the given
+   * selection group. if wholewidth is false, no column selection is made if the
+   * selection group covers the whole alignment width.
+   * 
+   * @param sg
+   * @param wholewidth
+   */
+  public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+  {
+    int sgs, sge;
+    if (sg != null
+            && (sgs = sg.getStartRes()) >= 0
+            && sg.getStartRes() <= (sge = sg.getEndRes())
+            && (colSel == null || colSel.getSelected() == null || colSel
+                    .getSelected().size() == 0))
+    {
+      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
       {
-        start = selectionGroup.getStartRes();
-        end = selectionGroup.getEndRes()+1;
+        // do nothing
+        return;
       }
-      else
+      if (colSel == null)
+      {
+        colSel = new ColumnSelection();
+      }
+      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
       {
-        end = alignment.getWidth();
+        colSel.addElement(cspos);
       }
-      viscontigs = colSel.getVisibleContigs(start, end);
-      return viscontigs;
     }
+  }
+
+  public StructureSelectionManager getStructureSelectionManager()
+  {
+    return StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+  }
 
+  /**
+   * 
+   * @param pdbEntries
+   * @return a series of SequenceI arrays, one for each PDBEntry, listing which sequence in the alignment holds a reference to it
+   */
+  public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
+  {
+    ArrayList<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+    for (PDBEntry pdb: pdbEntries) {
+    ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+    for (int i = 0; i < alignment.getHeight(); i++)
+    {
+      Vector pdbs = alignment.getSequenceAt(i)
+              .getDatasetSequence().getPDBId();
+      if (pdbs == null)
+        continue;
+      SequenceI sq;
+      for (int p = 0; p < pdbs.size(); p++)
+      {
+        PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+        if (p1.getId().equals(pdb.getId()))
+        {
+          if (!seqs.contains(sq=alignment.getSequenceAt(i)))
+            seqs.add(sq);
 
+          continue;
+        }
+      }
+    }
+    seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+    }
+    return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+  }
 }