X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=ff8f7df33959c561cc8eefe9cdd119a15e87edab;hb=fd026dead85b733e64fdc7c2e6c88d1adc10626a;hp=eb832f2f68a8b3c2c58dd8c415176c10bec59906;hpb=d545553b53ac1bd1e29eb72250cdb29745f7292f;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
old mode 100755
new mode 100644
index eb832f2..ff8f7df
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -1,22 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
-
 package jalview.appletgui;
 
 import java.util.*;
@@ -27,82 +25,134 @@ import jalview.analysis.*;
 import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
 
-public class AlignViewport
+public class AlignViewport implements SelectionSource, VamsasSource
 {
   int startRes;
+
   int endRes;
 
   int startSeq;
-  int endSeq;
 
+  int endSeq;
 
   boolean cursorMode = false;
 
   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 showConservation = true;
+
   boolean showQuality = true;
+
   boolean showConsensus = true;
 
+  boolean upperCasebold = false;
+
   boolean colourAppliesToAllGroups = true;
+
   ColourSchemeI globalColourScheme = null;
+
   boolean conservationColourSelected = false;
+
   boolean abovePIDThreshold = false;
 
   SequenceGroup selectionGroup;
 
   int charHeight;
+
   int charWidth;
+
   int wrappedWidth;
 
   Font font = new Font("SansSerif", Font.PLAIN, 10);
+
   boolean validCharWidth = true;
+
   AlignmentI alignment;
 
   ColumnSelection colSel = new ColumnSelection();
 
   int threshold;
+
   int increment;
 
   NJTree currentTree = null;
 
   boolean scaleAboveWrapped = true;
+
   boolean scaleLeftWrapped = true;
+
   boolean scaleRightWrapped = true;
 
   // The following vector holds the features which are
- // currently visible, in the correct order or rendering
-  Hashtable featuresDisplayed;
+  // currently visible, in the correct order or rendering
+  public Hashtable featuresDisplayed;
 
   boolean hasHiddenColumns = false;
+
   boolean hasHiddenRows = false;
+
   boolean showHiddenMarkers = true;
 
+  public Hashtable[] hconsensus;
 
-  public Vector vconsensus;
   AlignmentAnnotation consensus;
+
   AlignmentAnnotation conservation;
+
   AlignmentAnnotation quality;
 
+  AlignmentAnnotation[] groupConsensus;
+
+  AlignmentAnnotation[] groupConservation;
+
   boolean autocalculateConsensus = true;
 
   public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+          this);
 
   boolean ignoreGapsInConsensusCalculation = false;
 
-  jalview.bin.JalviewLite applet;
+  public jalview.bin.JalviewLite applet;
+
+  Hashtable sequenceColours;
 
   boolean MAC = false;
 
+  Stack historyList = new Stack();
+
+  Stack redoList = new Stack();
+
+  String sequenceSetID;
+
+  Hashtable hiddenRepSequences;
+  
+  public void finalize() {
+    applet=null;
+    quality=null;
+    alignment=null;
+    colSel=null;
+  }
+
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     this.applet = applet;
@@ -111,77 +161,165 @@ public class AlignViewport
     this.endRes = al.getWidth() - 1;
     this.startSeq = 0;
     this.endSeq = al.getHeight() - 1;
-    setFont(font);
-
-    if(System.getProperty("os.name").startsWith("Mac"))
-      MAC = true;
-
     if (applet != null)
     {
-      String param = applet.getParameter("showFullId");
+      // get the width and height scaling factors if they were specified
+      String param = applet.getParameter("widthScale");
       if (param != null)
       {
-        showJVSuffix = Boolean.valueOf(param).booleanValue();
+        try
+        {
+          widthScale = new Float(param).floatValue();
+        } catch (Exception e)
+        {
+        }
+        if (widthScale <= 1.0)
+        {
+          System.err
+                  .println("Invalid alignment character width scaling factor ("
+                          + widthScale + "). Ignoring.");
+          widthScale = 1;
+        }
+        if (applet.debug)
+        {
+          System.err
+                  .println("Alignment character width scaling factor is now "
+                          + widthScale);
+        }
       }
-
-      param = applet.getParameter("showAnnotation");
+      param = applet.getParameter("heightScale");
       if (param != null)
       {
-        showAnnotation = Boolean.valueOf(param).booleanValue();
+        try
+        {
+          heightScale = new Float(param).floatValue();
+        } catch (Exception e)
+        {
+        }
+        if (heightScale <= 1.0)
+        {
+          System.err
+                  .println("Invalid alignment character height scaling factor ("
+                          + heightScale + "). Ignoring.");
+          heightScale = 1;
+        }
+        if (applet.debug)
+        {
+          System.err
+                  .println("Alignment character height scaling factor is now "
+                          + heightScale);
+        }
       }
+    }
+    setFont(font);
 
-      param = applet.getParameter("showConservation");
-      if (param != null)
-      {
-        showConservation = Boolean.valueOf(param).booleanValue();
-      }
+    MAC = new jalview.util.Platform().isAMac();
 
-      param = applet.getParameter("showQuality");
-      if (param != null)
-      {
-        showQuality = Boolean.valueOf(param).booleanValue();
-      }
+    if (applet != null)
+    {
+      showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
+
+      showAnnotation = applet.getDefaultParameter("showAnnotation", showAnnotation);
+      
+      showConservation = applet.getDefaultParameter("showConservation", showConservation);
+      
+      showQuality = applet.getDefaultParameter("showQuality", showQuality);
+
+      showConsensus = applet.getDefaultParameter("showConsensus", showConsensus);
+
+      showUnconserved = applet.getDefaultParameter("showUnconserved", showUnconserved);
 
-      param = applet.getParameter("showConsensus");
+      String param = applet.getParameter("upperCase");
       if (param != null)
       {
-        showConsensus = Boolean.valueOf(param).booleanValue();
+        if (param.equalsIgnoreCase("bold"))
+        {
+          upperCasebold = true;
+        }
       }
+      sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
+
+      followHighlight = applet.getDefaultParameter("automaticScrolling",followHighlight);
+      followSelection = followHighlight;
+
+      showSequenceLogo = applet.getDefaultParameter("showSequenceLogo", showSequenceLogo);
+      
+      showGroupConsensus = applet.getDefaultParameter("showGroupConsensus", showGroupConsensus);
+      
+      showGroupConservation = applet.getDefaultParameter("showGroupConservation", showGroupConservation);
+        
+      showConsensusHistogram = applet.getDefaultParameter("showConsensusHistogram", showConsensusHistogram);
+      
     }
-    // We must set conservation and consensus before setting colour,
-    // as Blosum and Clustal require this to be done
-    updateConservation();
-    updateConsensus();
-
 
     if (applet != null)
     {
       String colour = applet.getParameter("defaultColour");
 
-      if(colour == null)
+      if (colour == null)
       {
         colour = applet.getParameter("userDefinedColour");
-        if(colour !=null)
+        if (colour != null)
+        {
           colour = "User Defined";
+        }
       }
 
-      if(colour != null)
+      if (colour != null)
       {
-        globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
+        globalColourScheme = ColourSchemeProperty.getColour(alignment,
+                colour);
         if (globalColourScheme != null)
         {
-          globalColourScheme.setConsensus(vconsensus);
+          globalColourScheme.setConsensus(hconsensus);
         }
       }
 
-      if(applet.getParameter("userDefinedColour")!=null)
+      if (applet.getParameter("userDefinedColour") != null)
+      {
+        ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
+                .getParameter("userDefinedColour"));
+      }
+    }
+    if (hconsensus == null)
+    {
+      if (!alignment.isNucleotide())
       {
-        ((UserColourScheme)globalColourScheme).parseAppletParameter(
-            applet.getParameter("userDefinedColour"));
+        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 (showConservation)
+        {
+          alignment.addAnnotation(conservation);
+        }
+
+        if (showQuality)
+        {
+          quality = new AlignmentAnnotation("Quality",
+                  "Alignment Quality based on Blosum62 scores",
+                  new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+          quality.hasText = true;
+          quality.autoCalculated = true;
+
+          alignment.addAnnotation(quality);
+        }
       }
 
+      consensus = new AlignmentAnnotation("Consensus", "PID",
+              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+      consensus.hasText = true;
+      consensus.autoCalculated = true;
 
+      if (showConsensus)
+      {
+        alignment.addAnnotation(consensus);
+      }
     }
+
   }
 
   public void showSequenceFeatures(boolean b)
@@ -194,195 +332,320 @@ public class AlignViewport
     return showSequenceFeatures;
   }
 
-
-  public void updateConservation()
+  class ConservationThread extends Thread
   {
-    if(alignment.isNucleotide())
-          return;
+    AlignmentPanel ap;
 
-    Conservation cons = new jalview.analysis.Conservation("All",
-        jalview.schemes.ResidueProperties.propHash, 3,
-        alignment.getSequences(), 0,
-        alignment.getWidth() - 1);
-    cons.calculate();
-    cons.verdict(false, ConsPercGaps);
-    cons.findQuality();
-    int alWidth = alignment.getWidth();
-    Annotation[] annotations = new Annotation[alWidth];
-    Annotation[] qannotations = new Annotation[alWidth];
-    String sequence = cons.getConsSequence().getSequence();
-    float minR, minG, minB, maxR, maxG, 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 = cons.qualityRange[0].floatValue();
-    float qmax = cons.qualityRange[1].floatValue();
-
-    for (int i = 0; i < alWidth; i++)
+    public ConservationThread(AlignmentPanel ap)
+    {
+      this.ap = ap;
+    }
+
+    public void run()
     {
-      float value = 0;
       try
       {
-        value = Integer.parseInt(sequence.charAt(i) + "");
-      }
-      catch (Exception ex)
-      {
-        if (sequence.charAt(i) == '*')
+        updatingConservation = true;
+
+        while (UPDATING_CONSERVATION)
         {
-          value = 11;
+          try
+          {
+            if (ap != null)
+            {
+              ap.paintAlignment(false);
+            }
+            Thread.sleep(200);
+          } catch (Exception ex)
+          {
+            ex.printStackTrace();
+          }
         }
-        if (sequence.charAt(i) == '+')
+
+        UPDATING_CONSERVATION = true;
+
+        int alWidth = (alignment==null) ? -1 : alignment.getWidth();
+        if (alWidth < 0)
         {
-          value = 10;
+          updatingConservation = false;
+          UPDATING_CONSERVATION = false;
+          return;
         }
-      }
-      float vprop = value - min;
-      vprop /= max;
-
-      annotations[i] = new Annotation(sequence.charAt(i) + "",
-                                      "", ' ', value,
-                                      new Color(minR + maxR * vprop,
-                                                minG + maxG * vprop,
-                                                minB + maxB * vprop));
-      // Quality calc
-      value = ( (Double) cons.quality.elementAt(i)).floatValue();
-      vprop = value - qmin;
-      vprop /= qmax;
-      qannotations[i] = new Annotation(" ",
-                                       String.valueOf(value), ' ', value,
-                                       new
-                                       Color(minR + maxR * vprop,
-                                             minG + maxG * vprop,
-                                             minB + maxB * vprop));
-    }
 
-    if (conservation == null)
-    {
-      conservation = new AlignmentAnnotation("Conservation",
-                                             "Conservation of total alignment less than " +
-                                             ConsPercGaps + "% gaps",
-                                             annotations,
-                                             0f, // cons.qualityRange[0].floatValue(),
-                                             11f, // cons.qualityRange[1].floatValue()
-                                             AlignmentAnnotation.BAR_GRAPH);
-      if (showConservation)
+        Conservation cons = new jalview.analysis.Conservation("All",
+                jalview.schemes.ResidueProperties.propHash, 3,
+                alignment.getSequences(), 0, alWidth - 1);
+
+        cons.calculate();
+        cons.verdict(false, ConsPercGaps);
+
+        if (quality != null)
+        {
+          cons.findQuality();
+        }
+
+        char[] sequence = cons.getConsSequence().getSequence();
+        float minR;
+        float minG;
+        float minB;
+        float maxR;
+        float maxG;
+        float maxB;
+        minR = 0.3f;
+        minG = 0.0f;
+        minB = 0f;
+        maxR = 1.0f - minR;
+        maxG = 0.9f - minG;
+        maxB = 0f - minB; // scalable range for colouring both Conservation and
+        // Quality
+
+        float min = 0f;
+        float max = 11f;
+        float qmin = 0f;
+        float qmax = 0f;
+
+        char c;
+
+        conservation.annotations = new Annotation[alWidth];
+
+        if (quality != null)
+        {
+          quality.graphMax = cons.qualityRange[1].floatValue();
+          quality.annotations = new Annotation[alWidth];
+          qmin = cons.qualityRange[0].floatValue();
+          qmax = cons.qualityRange[1].floatValue();
+        }
+
+        for (int i = 0; i < alWidth; i++)
+        {
+          float value = 0;
+
+          c = sequence[i];
+
+          if (Character.isDigit(c))
+          {
+            value = (int) (c - '0');
+          }
+          else if (c == '*')
+          {
+            value = 11;
+          }
+          else if (c == '+')
+          {
+            value = 10;
+          }
+          // TODO - refactor to use a graduatedColorScheme to calculate the
+          // histogram colors.
+          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.elementAt(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)
       {
-        alignment.addAnnotation(conservation);
+        System.out.println("Out of memory calculating conservation!!");
+        conservation = null;
+        quality = null;
+        System.gc();
       }
-      quality = new AlignmentAnnotation("Quality",
-                                        "Alignment Quality based on Blosum62 scores",
-                                        qannotations,
-                                        cons.qualityRange[0].floatValue(),
-                                        cons.qualityRange[1].floatValue(),
-                                        AlignmentAnnotation.BAR_GRAPH);
-      if (showQuality)
+
+      UPDATING_CONSERVATION = false;
+      updatingConservation = false;
+
+      if (ap != null)
       {
-        alignment.addAnnotation(quality);
+        ap.paintAlignment(true);
       }
+
     }
-    else
+  }
+
+  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)
     {
-      conservation.annotations = annotations;
-      quality.annotations = qannotations;
-      quality.graphMax = cons.qualityRange[1].floatValue();
+      return;
     }
 
+    conservationThread = new ConservationThread(ap);
+    conservationThread.start();
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void updateConsensus(final AlignmentPanel ap)
+  {
+    consensusThread = new ConsensusThread(ap);
+    consensusThread.start();
   }
 
-  public void updateConsensus()
+  class ConsensusThread extends Thread
   {
-    Annotation[] annotations = new Annotation[alignment.getWidth()];
+    AlignmentPanel ap;
 
-    // this routine prevents vconsensus becoming a new object each time
-    // consenus is calculated. Important for speed of Blosum62
-    // and PID colouring of alignment
-    if (vconsensus == null)
+    public ConsensusThread(AlignmentPanel ap)
     {
-      vconsensus = alignment.getAAFrequency();
+      this.ap = ap;
     }
-    else
+
+    public void run()
     {
-      Vector temp = alignment.getAAFrequency();
-      vconsensus.removeAllElements();
-      Enumeration e = temp.elements();
-      while (e.hasMoreElements())
+      updatingConsensus = true;
+      while (UPDATING_CONSENSUS)
       {
-        vconsensus.addElement(e.nextElement());
+        try
+        {
+          if (ap != null)
+          {
+            ap.paintAlignment(false);
+          }
+
+          Thread.sleep(200);
+        } catch (Exception ex)
+        {
+          ex.printStackTrace();
+        }
       }
-    }
-    Hashtable hash = null;
-    for (int i = 0; i < alignment.getWidth(); i++)
-    {
-      hash = (Hashtable) vconsensus.elementAt(i);
-      float value = 0;
-      if(ignoreGapsInConsensusCalculation)
-        value = ((Float)hash.get("pid_nogaps")).floatValue();
-      else
-        value = ((Float)hash.get("pid_gaps")).floatValue();
 
-      String maxRes = hash.get("maxResidue").toString();
-      String mouseOver = hash.get("maxResidue") + " ";
-      if (maxRes.length() > 1)
+      UPDATING_CONSENSUS = true;
+
+      try
       {
-        mouseOver = "[" + maxRes + "] ";
-        maxRes = "+";
-      }
+        int aWidth = alignment==null ? -1 : alignment.getWidth();
+        if (aWidth < 0)
+        {
+          UPDATING_CONSENSUS = false;
+          updatingConsensus = false;
+          return;
+        }
 
+        consensus.annotations = null;
+        consensus.annotations = new Annotation[aWidth];
+
+        hconsensus = new Hashtable[aWidth];
+        AAFrequency.calculate(alignment.getSequencesArray(), 0,
+                alignment.getWidth(), hconsensus, true); // always calculate the
+                                                         // full profile
+        updateAnnotation(true);
+        //AAFrequency.completeConsensus(consensus, hconsensus, 0, aWidth,
+        //        ignoreGapsInConsensusCalculation,
+        //        true);
+        
+        if (globalColourScheme != null)
+        {
+          globalColourScheme.setConsensus(hconsensus);
+        }
 
-      mouseOver += (int) value + "%";
-      annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+      } catch (OutOfMemoryError error)
+      {
+        alignment.deleteAnnotation(consensus);
 
-    }
+        consensus = null;
+        hconsensus = null;
+        System.out.println("Out of memory calculating consensus!!");
+        System.gc();
+      }
+      UPDATING_CONSENSUS = false;
+      updatingConsensus = false;
 
-    if (consensus == null)
-    {
-      consensus = new AlignmentAnnotation("Consensus",
-                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      if (showConsensus)
+      if (ap != null)
       {
-        alignment.addAnnotation(consensus);
+        ap.paintAlignment(true);
       }
     }
-    else
+
+    /**
+     * update the consensus annotation from the sequence profile data using
+     * current visualization settings.
+     */
+    public void updateAnnotation()
     {
-      consensus.annotations = annotations;
+      updateAnnotation(false);
     }
 
-    if(globalColourScheme!=null)
-          globalColourScheme.setConsensus(vconsensus);
-
+    protected void updateAnnotation(boolean immediate)
+    {
+      // 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);
+      }
+    }
   }
+
   /**
-   * get the consensus sequence as displayed under the PID consensus annotation row.
-   * @return consensus sequence as a new sequence object
-   */
-  /**
-   * get the consensus sequence as displayed under the PID consensus annotation row.
+   * 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();
-    if (consensus==null)
+  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) {
+    }
+    StringBuffer seqs = new StringBuffer();
+    for (int i = 0; i < consensus.annotations.length; i++)
+    {
+      if (consensus.annotations[i] != null)
+      {
         if (consensus.annotations[i].description.charAt(0) == '[')
-          seqs.append(consensus.annotations[i].description.charAt(1));          
+        {
+          seqs.append(consensus.annotations[i].description.charAt(1));
+        }
         else
-          seqs.append(consensus.annotations[i].displayCharacter);          
+        {
+          seqs.append(consensus.annotations[i].displayCharacter);
+        }
       }
     }
     SequenceI sq = new Sequence("Consensus", seqs.toString());
-    sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    sq.setDescription("Percentage Identity Consensus "
+            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
     return sq;
   }
+
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -452,7 +715,8 @@ public class AlignViewport
   {
     if (res > alignment.getWidth() - 1)
     {
-      // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
+      // log.System.out.println(" Corrected res from " + res + " to maximum " +
+      // (alignment.getWidth()-1));
       res = alignment.getWidth() - 1;
     }
     if (res < 0)
@@ -481,18 +745,30 @@ public class AlignViewport
   }
 
   java.awt.Frame nullFrame;
+
+  protected FeatureSettings featureSettings = null;
+
+  private float heightScale = 1, widthScale = 1;
+
   public void setFont(Font f)
   {
     font = f;
-    if(nullFrame == null)
+    if (nullFrame == null)
     {
       nullFrame = new java.awt.Frame();
       nullFrame.addNotify();
     }
 
     java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
-    setCharHeight(fm.getHeight());
-    charWidth = fm.charWidth('M');
+    setCharHeight((int) (heightScale * fm.getHeight()));
+    charWidth = (int) (widthScale * fm.charWidth('M'));
+
+    if (upperCasebold)
+    {
+      Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
+      fm = nullFrame.getGraphics().getFontMetrics(f2);
+      charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10));
+    }
   }
 
   public Font getFont()
@@ -616,8 +892,10 @@ public class AlignViewport
   public void setHiddenColumns(ColumnSelection colsel)
   {
     this.colSel = colsel;
-    if(colSel.getHiddenColumns()!=null)
+    if (colSel.getHiddenColumns() != null)
+    {
       hasHiddenColumns = true;
+    }
   }
 
   public ColumnSelection getColumnSelection()
@@ -703,59 +981,66 @@ public class AlignViewport
   public void setIgnoreGapsConsensus(boolean b)
   {
     ignoreGapsInConsensusCalculation = b;
-    updateConsensus();
-    if (globalColourScheme!=null)
+    updateConsensus(null);
+    if (globalColourScheme != null)
     {
       globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
-          ignoreGapsInConsensusCalculation);
+              ignoreGapsInConsensusCalculation);
 
     }
   }
 
   /**
    * Property change listener for changes in alignment
-   *
-   * @param listener DOCUMENT ME!
+   * 
+   * @param listener
+   *          DOCUMENT ME!
    */
   public void addPropertyChangeListener(
-      java.beans.PropertyChangeListener listener)
+          java.beans.PropertyChangeListener listener)
   {
-      changeSupport.addPropertyChangeListener(listener);
+    changeSupport.addPropertyChangeListener(listener);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param listener DOCUMENT ME!
+   * 
+   * @param listener
+   *          DOCUMENT ME!
    */
   public void removePropertyChangeListener(
-      java.beans.PropertyChangeListener listener)
+          java.beans.PropertyChangeListener listener)
   {
-      changeSupport.removePropertyChangeListener(listener);
+    changeSupport.removePropertyChangeListener(listener);
   }
 
   /**
    * Property change listener for changes in alignment
-   *
-   * @param prop DOCUMENT ME!
-   * @param oldvalue DOCUMENT ME!
-   * @param newvalue DOCUMENT ME!
+   * 
+   * @param prop
+   *          DOCUMENT ME!
+   * @param oldvalue
+   *          DOCUMENT ME!
+   * @param newvalue
+   *          DOCUMENT ME!
    */
-  public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+  public void firePropertyChange(String prop, Object oldvalue,
+          Object newvalue)
   {
-      changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+    changeSupport.firePropertyChange(prop, oldvalue, newvalue);
   }
 
-
-
   public boolean getIgnoreGapsConsensus()
   {
     return ignoreGapsInConsensusCalculation;
   }
+
   public void hideSelectedColumns()
   {
     if (colSel.size() < 1)
+    {
       return;
+    }
 
     colSel.hideSelectedColumns();
     setSelectionGroup(null);
@@ -765,61 +1050,130 @@ public class AlignViewport
 
   public void invertColumnSelection()
   {
-    int column;
     for (int i = 0; i < alignment.getWidth(); i++)
     {
-      column = i;
-
-      if (colSel.contains(column))
-        colSel.removeElement(column);
+      if (colSel.contains(i))
+      {
+        colSel.removeElement(i);
+      }
       else
-        colSel.addElement(column);
-
+      {
+        if (!hasHiddenColumns || colSel.isVisible(i))
+        {
+          colSel.addElement(i);
+        }
+      }
     }
   }
 
-
   public void hideColumns(int start, int end)
   {
-    if(start==end)
+    if (start == end)
+    {
       colSel.hideColumns(start);
+    }
     else
+    {
       colSel.hideColumns(start, end);
+    }
 
     hasHiddenColumns = true;
   }
 
-  public void hideSequence(SequenceI seq)
+  public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
   {
-    if(seq!=null)
+    int sSize = sg.getSize();
+    if (sSize < 2)
     {
-      alignment.getHiddenSequences().hideSequence(seq);
-      hasHiddenRows = true;
-      firePropertyChange("alignment", null, alignment.getSequences());
+      return;
     }
+
+    if (hiddenRepSequences == null)
+    {
+      hiddenRepSequences = new Hashtable();
+    }
+
+    hiddenRepSequences.put(repSequence, sg);
+
+    // Hide all sequences except the repSequence
+    SequenceI[] seqs = new SequenceI[sSize - 1];
+    int index = 0;
+    for (int i = 0; i < sSize; i++)
+    {
+      if (sg.getSequenceAt(i) != repSequence)
+      {
+        if (index == sSize - 1)
+        {
+          return;
+        }
+
+        seqs[index++] = sg.getSequenceAt(i);
+      }
+    }
+
+    hideSequence(seqs);
+
   }
 
   public void hideAllSelectedSeqs()
   {
-    if (selectionGroup == null)
+    if (selectionGroup == null || selectionGroup.getSize() < 1)
+    {
       return;
+    }
 
     SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
 
-    for (int i = 0; i < seqs.length; i++)
+    hideSequence(seqs);
+
+    setSelectionGroup(null);
+  }
+
+  public void hideSequence(SequenceI[] seq)
+  {
+    if (seq != null)
     {
-      alignment.getHiddenSequences().hideSequence(seqs[i]);
+      for (int i = 0; i < seq.length; i++)
+      {
+        alignment.getHiddenSequences().hideSequence(seq[i]);
+      }
+
+      hasHiddenRows = true;
+      firePropertyChange("alignment", null, alignment.getSequences());
     }
-    firePropertyChange("alignment", null, alignment.getSequences());
-    hasHiddenRows = true;
-    setSelectionGroup(null);
   }
+  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);
+      }
+
+      for (int t = 0; t < tmp.size(); t++)
+      {
+        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+      }
+      firePropertyChange("alignment", null, alignment.getSequences());
+      sendSelection();
+    }
 
+    if (alignment.getHiddenSequences().getSize() < 1)
+    {
+      hasHiddenRows = false;
+    }
+  }
   public void showColumn(int col)
   {
     colSel.revealHiddenColumns(col);
-    if(colSel.getHiddenColumns()==null)
+    if (colSel.getHiddenColumns() == null)
+    {
       hasHiddenColumns = false;
+    }
   }
 
   public void showAllHiddenColumns()
@@ -830,33 +1184,36 @@ public class AlignViewport
 
   public void showAllHiddenSeqs()
   {
-    if(alignment.getHiddenSequences().getSize()>0)
+    if (alignment.getHiddenSequences().getSize() > 0)
     {
-      if(selectionGroup==null)
+      if (selectionGroup == null)
       {
         selectionGroup = new SequenceGroup();
-        selectionGroup.setEndRes(alignment.getWidth()-1);
+        selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
-      Vector tmp = alignment.getHiddenSequences().showAll();
-      for(int t=0; t<tmp.size(); t++)
+      Vector tmp = alignment.getHiddenSequences().showAll(
+              hiddenRepSequences);
+      for (int t = 0; t < tmp.size(); t++)
       {
-        selectionGroup.addSequence(
-            (SequenceI)tmp.elementAt(t), false
-            );
+        selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
       }
       firePropertyChange("alignment", null, alignment.getSequences());
       hasHiddenRows = false;
+      hiddenRepSequences = null;
+      sendSelection();
     }
   }
 
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
-    return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+    return alignment.getHiddenSequences().adjustForHiddenSeqs(
+            alignmentIndex);
   }
 
   /**
-   * This method returns the a new SequenceI [] with
-   * the selection sequence and start and end points adjusted
+   * This method returns the a new SequenceI [] with the selection sequence and
+   * start and end points adjusted
+   * 
    * @return String[]
    */
   public SequenceI[] getSelectionAsNewSequence()
@@ -864,126 +1221,98 @@ public class AlignViewport
     SequenceI[] sequences;
 
     if (selectionGroup == null)
+    {
       sequences = alignment.getSequencesArray();
+    }
     else
+    {
       sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+    }
 
     return sequences;
   }
 
   /**
-   * This method returns the visible alignment as text, as
-   * seen on the GUI, ie if columns are hidden they will not
-   * be returned in the result.
-   * Use this for calculating trees, PCA, redundancy etc on views
-   * which contain hidden columns.
-   * @return String[]
+   * get the currently selected sequence objects or all the sequences in the
+   * alignment.
+   * 
+   * @return array of references to sequence objects
    */
-  public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
+  public SequenceI[] getSequenceSelection()
   {
-    CigarArray selection=null;
-    SequenceI [] seqs= null;
-    int i, iSize;
-    int start = 0, end = 0;
-    if(selectedRegionOnly && selectionGroup!=null)
-    {
-      iSize = selectionGroup.getSize(false);
-      seqs = selectionGroup.getSequencesInOrder(alignment);
-      start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
-    }
-    else
+    SequenceI[] sequences = null;
+    if (selectionGroup != null)
     {
-      iSize = alignment.getHeight();
-      seqs = alignment.getSequencesArray();
-      end = alignment.getWidth()-1;
+      sequences = selectionGroup.getSequencesInOrder(alignment);
     }
-    SeqCigar[] selseqs = new SeqCigar[iSize];
-    for(i=0; i<iSize; i++)
+    if (sequences == null)
     {
-      selseqs[i] = new SeqCigar(seqs[i], start, end);
+      sequences = alignment.getSequencesArray();
     }
-    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;
-        }
+    return sequences;
+  }
 
-        if (hideStart>end)
-          break;
-
-        if (hideEnd>end)
-          hideEnd=end;
-
-        if (hideStart>hideEnd)
-          break;
-        /**
-         * form operations...
-         */
-        if (last<hideStart)
-          selection.addOperation(CigarArray.M, hideStart-last);
-        selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
-        last = hideEnd+1;
-      }
-      // Final match if necessary.
-      if (last<end)
-        selection.addOperation(CigarArray.M, end-last);
-    } else {
-      selection.addOperation(CigarArray.M, end-start);
-    }
-    return selection;
+  /**
+   * 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 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);
-    return null;
+  jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+  {    
+    return getAlignmentView(selectedOnly, false);
   }
+  
   /**
-   * 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 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)
+  public String[] getViewAsString(boolean selectedRegionOnly)
   {
-    String [] selection = null;
-    SequenceI [] seqs= null;
+    String[] selection = null;
+    SequenceI[] seqs = null;
     int i, iSize;
     int start = 0, end = 0;
-    if(selectedRegionOnly && selectionGroup!=null)
+    if (selectedRegionOnly && selectionGroup != null)
     {
-      iSize = selectionGroup.getSize(false);
+      iSize = selectionGroup.getSize();
       seqs = selectionGroup.getSequencesInOrder(alignment);
       start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes()+1;
+      end = selectionGroup.getEndRes() + 1;
     }
     else
     {
@@ -994,52 +1323,52 @@ public class AlignViewport
 
     selection = new String[iSize];
 
-
-    for(i=0; i<iSize; i++)
+    for (i = 0; i < iSize; i++)
     {
       if (hasHiddenColumns)
       {
-           StringBuffer visibleSeq = new StringBuffer();
-           Vector regions = colSel.getHiddenColumns();
-
-           int blockStart = start, blockEnd=end;
-           int [] region;
-           int hideStart, hideEnd;
+        StringBuffer visibleSeq = new StringBuffer();
+        Vector regions = colSel.getHiddenColumns();
 
-           for (int j = 0; j < regions.size(); j++)
-           {
-             region = (int[]) regions.elementAt(j);
-             hideStart = region[0];
-             hideEnd = region[1];
+        int blockStart = start, blockEnd = end;
+        int[] region;
+        int hideStart, hideEnd;
 
-             if(hideStart < start)
-             {
-               continue;
-             }
+        for (int j = 0; j < regions.size(); j++)
+        {
+          region = (int[]) regions.elementAt(j);
+          hideStart = region[0];
+          hideEnd = region[1];
 
-             blockStart = Math.min(blockStart, hideEnd+1);
-             blockEnd = Math.min(blockEnd, hideStart);
+          if (hideStart < start)
+          {
+            continue;
+          }
 
-             if(blockStart>blockEnd)
-             {
-                break;
-             }
+          blockStart = Math.min(blockStart, hideEnd + 1);
+          blockEnd = Math.min(blockEnd, hideStart);
 
+          if (blockStart > blockEnd)
+          {
+            break;
+          }
 
-             visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+          visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
 
-             blockStart = hideEnd+1;
-             blockEnd = end;
-           }
+          blockStart = hideEnd + 1;
+          blockEnd = end;
+        }
 
-           if(end>blockStart)
-             visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        if (end > blockStart)
+        {
+          visibleSeq.append(seqs[i].getSequence(blockStart, end));
+        }
 
-           selection[i] = visibleSeq.toString();
+        selection[i] = visibleSeq.toString();
       }
       else
       {
-        selection[i] = seqs[i].getSequence(start, end);
+        selection[i] = seqs[i].getSequenceAsString(start, end);
       }
     }
 
@@ -1056,5 +1385,377 @@ public class AlignViewport
     showHiddenMarkers = show;
   }
 
+  public Color getSequenceColour(SequenceI seq)
+  {
+    if (sequenceColours == null || !sequenceColours.containsKey(seq))
+    {
+      return Color.white;
+    }
+    else
+    {
+      return (Color) sequenceColours.get(seq);
+    }
+  }
+
+  public void setSequenceColour(SequenceI seq, Color col)
+  {
+    if (sequenceColours == null)
+    {
+      sequenceColours = new Hashtable();
+    }
+
+    if (col == null)
+    {
+      sequenceColours.remove(seq);
+    }
+    else
+    {
+      sequenceColours.put(seq, col);
+    }
+  }
+
+  public String getSequenceSetId()
+  {
+    if (sequenceSetID == null)
+    {
+      sequenceSetID = alignment.hashCode() + "";
+    }
+
+    return sequenceSetID;
+  }
+  /**
+   * unique viewId for synchronizing state (e.g. with stored Jalview Project)
+   * 
+   */
+  private String viewId = null;
+
+  public String getViewId()
+  {
+    if (viewId == null)
+    {
+      viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
+    }
+    return viewId;
+  }
+
+  public void alignmentChanged(AlignmentPanel ap)
+  {
+    alignment.padGaps();
+
+    if (hconsensus != null && autocalculateConsensus)
+    {
+      updateConsensus(ap);
+      updateConservation(ap);
+    }
+
+    // Reset endRes of groups if beyond alignment width
+    int alWidth = alignment.getWidth();
+    Vector groups = alignment.getGroups();
+    if (groups != null)
+    {
+      for (int i = 0; i < groups.size(); i++)
+      {
+        SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+        if (sg.getEndRes() > alWidth)
+        {
+          sg.setEndRes(alWidth - 1);
+        }
+      }
+    }
+
+    if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
+    {
+      selectionGroup.setEndRes(alWidth - 1);
+    }
+
+    resetAllColourSchemes();
+
+    // AW alignment.adjustSequenceAnnotations();
+  }
+
+  void resetAllColourSchemes()
+  {
+    ColourSchemeI cs = globalColourScheme;
+    if (cs != null)
+    {
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
+                alignment.getWidth());
+      }
+
+      cs.setConsensus(hconsensus);
+      if (cs.conservationApplied())
+      {
+        Alignment al = (Alignment) alignment;
+        Conservation c = new Conservation("All",
+                ResidueProperties.propHash, 3, al.getSequences(), 0,
+                al.getWidth() - 1);
+        c.calculate();
+        c.verdict(false, ConsPercGaps);
+
+        cs.setConservation(c);
+      }
+    }
+
+    int s, sSize = alignment.getGroups().size();
+    for (s = 0; s < sSize; s++)
+    {
+      SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
+      if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
+      {
+        ((ClustalxColourScheme) sg.cs).resetClustalX(
+                sg.getSequences(hiddenRepSequences), sg.getWidth());
+      }
+      sg.recalcConservation();
+    }
+  }
+
+  boolean centreColumnLabels;
+
+  public boolean getCentreColumnLabels()
+  {
+    return centreColumnLabels;
+  }
+
+  public void updateSequenceIdColours()
+  {
+    Vector groups = alignment.getGroups();
+    for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
+    {
+      SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
+      if (sg.idColour != null)
+      {
+        Vector sqs = sg.getSequences(hiddenRepSequences);
+        for (int s = 0, sSize = sqs.size(); s < sSize; s++)
+        {
+          this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour);
+        }
+      }
+    }
+  }
+
+  public boolean followHighlight = true;
+
+  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;
+
+  /**
+   * checks current SelectionGroup against record of last hash value, and
+   * updates record.
+   * 
+   * @return true if SelectionGroup changed since last call
+   */
+  boolean isSelectionGroupChanged()
+  {
+    int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode();
+    if (hc != sgrouphash)
+    {
+      sgrouphash = hc;
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * checks current colsel against record of last hash value, and updates
+   * record.
+   * 
+   * @return true if colsel changed since last call
+   */
+  boolean isColSelChanged()
+  {
+    int hc = (colSel == null) ? -1 : colSel.hashCode();
+    if (hc != colselhash)
+    {
+      colselhash = hc;
+      return true;
+    }
+    return false;
+  }
+  public void sendSelection()
+  {
+    jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager(applet).sendSelection(
+                    new SequenceGroup(getSelectionGroup()),
+                    new ColumnSelection(getColumnSelection()), this);
+  }
+
+
+
+
+  /**
+   * show non-conserved residues only
+   */
+  public boolean showUnconserved = false;
+
+  /**
+   * when set, alignment should be reordered according to a newly opened tree
+   */
+  public boolean sortByTree = false;
+
+  /**
+   * @return the showUnconserved
+   */
+  public boolean getShowunconserved()
+  {
+    return showUnconserved;
+  }
+
+  /**
+   * @param showNonconserved
+   *          the showUnconserved to set
+   */
+  public void setShowunconserved(boolean displayNonconserved)
+  {
+    this.showUnconserved = displayNonconserved;
+  }
+
+  /**
+   * 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)
+    {
+      // TODO: decouple settings setting from calculation when refactoring
+      // annotation update method from alignframe to viewport
+      this.showSequenceLogo = showSequenceLogo;
+      if (consensusThread != null)
+      {
+        consensusThread.updateAnnotation();
+      }
+    }
+    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))
+      {
+        // do nothing
+        return;
+      }
+      if (colSel == null)
+      {
+        colSel = new ColumnSelection();
+      }
+      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+      {
+        colSel.addElement(cspos);
+      }
+    }
+  }
 }