X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=d0c5674e257ae8ff0acf41bc53e81faf0953f863;hb=caf13e6a9dc82023cd8648420201e5ad60ce0393;hp=f386bf323d75a45aef6eb924dc0d6ca7e7a58895;hpb=c16d6b192b294503d2bd16294454cfe136426e7d;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index f386bf3..d0c5674 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
- * 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.
+ * 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.
  * 
- * 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 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
@@ -49,6 +48,7 @@ import jalview.datamodel.*;
 import jalview.schemes.*;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
 
 /**
  * DOCUMENT ME!
@@ -56,7 +56,7 @@ import jalview.structure.StructureSelectionManager;
  * @author $author$
  * @version $Revision$
  */
-public class AlignViewport implements SelectionSource
+public class AlignViewport implements SelectionSource, VamsasSource
 {
   private static final int RIGHT_JUSTIFY = 1;
 
@@ -131,8 +131,8 @@ public class AlignViewport implements SelectionSource
   boolean cursorMode = false;
 
   /**
-   * Keys are the feature types which are
-   * currently visible. Note: Values are not used!
+   * Keys are the feature types which are currently visible. Note: Values are
+   * not used!
    */
   Hashtable featuresDisplayed = null;
 
@@ -144,9 +144,11 @@ public class AlignViewport implements SelectionSource
   AlignmentAnnotation conservation;
 
   AlignmentAnnotation quality;
+
   AlignmentAnnotation[] groupConsensus;
+
   AlignmentAnnotation[] groupConservation;
-  
+
   boolean autoCalculateConsensus = true;
 
   /** DOCUMENT ME!! */
@@ -193,29 +195,41 @@ public class AlignViewport implements SelectionSource
   /**
    * Creates a new AlignViewport object.
    * 
-   * @param al alignment to view
+   * @param al
+   *          alignment to view
    */
   public AlignViewport(AlignmentI al)
   {
     setAlignment(al);
     init();
   }
+
   /**
    * Create a new AlignViewport object with a specific sequence set ID
+   * 
    * @param al
-   * @param seqsetid (may be null - but potential for ambiguous constructor exception)
+   * @param seqsetid
+   *          (may be null - but potential for ambiguous constructor exception)
    */
   public AlignViewport(AlignmentI al, String seqsetid)
   {
-    this(al,seqsetid,null);
+    this(al, seqsetid, null);
   }
+
   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); }
+    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();
   }
@@ -224,9 +238,9 @@ public class AlignViewport implements SelectionSource
    * Create a new AlignViewport with hidden regions
    * 
    * @param al
-   *                AlignmentI
+   *          AlignmentI
    * @param hiddenColumns
-   *                ColumnSelection
+   *          ColumnSelection
    */
   public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
   {
@@ -234,47 +248,69 @@ public class AlignViewport implements SelectionSource
     if (hiddenColumns != null)
     {
       this.colSel = hiddenColumns;
-      if (hiddenColumns.getHiddenColumns() != null && hiddenColumns.getHiddenColumns().size()>0)
+      if (hiddenColumns.getHiddenColumns() != null
+              && hiddenColumns.getHiddenColumns().size() > 0)
       {
         hasHiddenColumns = true;
-      } else {
+      }
+      else
+      {
         hasHiddenColumns = false;
       }
     }
     init();
   }
+
   /**
    * New viewport with hidden columns and an existing sequence set id
+   * 
    * @param al
    * @param hiddenColumns
-   * @param seqsetid (may be null)
+   * @param seqsetid
+   *          (may be null)
    */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid)
+  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+          String seqsetid)
   {
-    this(al,hiddenColumns,seqsetid,null);
+    this(al, hiddenColumns, seqsetid, 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)
+   * @param seqsetid
+   *          (may be null)
+   * @param viewid
+   *          (may be null)
    */
-  public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid, String viewid)
+  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) { 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); }
+    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);
     if (hiddenColumns != null)
     {
       this.colSel = hiddenColumns;
-      if (hiddenColumns.getHiddenColumns() != null && hiddenColumns.getHiddenColumns().size()>0)
+      if (hiddenColumns.getHiddenColumns() != null
+              && hiddenColumns.getHiddenColumns().size() > 0)
       {
         hasHiddenColumns = true;
-      } else {
+      }
+      else
+      {
         hasHiddenColumns = false;
       }
     }
@@ -298,9 +334,9 @@ public class AlignViewport implements SelectionSource
     autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
     padGaps = Cache.getDefault("PAD_GAPS", true);
-    shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP",true);
-    showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP",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");
@@ -351,16 +387,20 @@ public class AlignViewport implements SelectionSource
 
           alignment.addAnnotation(quality);
         }
-        showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", false);
-        
+        showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
+                false);
+
         {
-          
+
         }
       }
-      showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true);
+      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
+      // 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;
@@ -391,15 +431,18 @@ public class AlignViewport implements SelectionSource
     }
 
     wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
-    showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", 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);
   }
 
   /**
    * set the flag
    * 
    * @param b
-   *             features are displayed if true
+   *          features are displayed if true
    */
   public void setShowSequenceFeatures(boolean b)
   {
@@ -436,17 +479,13 @@ public class AlignViewport implements SelectionSource
   private boolean shownpfeats;
 
   /**
-   * consensus annotation includes all percentage for all symbols in column
-   */
-  private boolean includeAllConsensusSymbols=true;
-
-  /**
    * trigger update of conservation annotation
    */
   public void updateConservation(final AlignmentPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (alignment.isNucleotide() || conservation == null || !autoCalculateConsensus)
+    if (alignment.isNucleotide() || conservation == null
+            || !autoCalculateConsensus)
     {
       return;
     }
@@ -501,12 +540,14 @@ public class AlignViewport implements SelectionSource
 
       try
       {
-        int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null
-                                                                      // pointer
-                                                                      // possibility
-                                                                      // here.
-        if (aWidth < 0)
+        int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
+        // pointer
+        // possibility
+        // here.
+        if (aWidth <= 0)
         {
+          updatingConsensus = false;
+          UPDATING_CONSENSUS = false;
           return;
         }
 
@@ -514,10 +555,10 @@ public class AlignViewport implements SelectionSource
         consensus.annotations = new Annotation[aWidth];
 
         hconsensus = new Hashtable[aWidth];
-        AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
-                .getWidth(), hconsensus, includeAllConsensusSymbols);
-        AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation, includeAllConsensusSymbols);
-        
+        AAFrequency.calculate(alignment.getSequencesArray(), 0,
+                alignment.getWidth(), hconsensus, true);
+        updateAnnotation(true);
+
         if (globalColourScheme != null)
         {
           globalColourScheme.setConsensus(hconsensus);
@@ -539,6 +580,28 @@ public class AlignViewport implements SelectionSource
         ap.paintAlignment(true);
       }
     }
+
+    /**
+     * update the consensus annotation from the sequence profile data using
+     * current visualization settings.
+     */
+    public void updateAnnotation()
+    {
+      updateAnnotation(false);
+    }
+
+    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);
+      }
+    }
   }
 
   /**
@@ -593,11 +656,11 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param sg
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setSelectionGroup(SequenceGroup sg)
   {
-    selectionGroup = sg;    
+    selectionGroup = sg;
   }
 
   /**
@@ -614,7 +677,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setConservationSelected(boolean b)
   {
@@ -635,7 +698,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setAbovePIDThreshold(boolean b)
   {
@@ -676,7 +739,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param cs
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setGlobalColourScheme(ColourSchemeI cs)
   {
@@ -697,7 +760,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param res
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setStartRes(int res)
   {
@@ -708,7 +771,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setStartSeq(int seq)
   {
@@ -719,7 +782,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param res
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setEndRes(int res)
   {
@@ -742,7 +805,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param seq
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setEndSeq(int seq)
   {
@@ -773,7 +836,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param f
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setFont(Font f)
   {
@@ -801,7 +864,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param w
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setCharWidth(int w)
   {
@@ -822,7 +885,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param h
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setCharHeight(int h)
   {
@@ -843,7 +906,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param w
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setWrappedWidth(int w)
   {
@@ -874,7 +937,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param align
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setAlignment(AlignmentI align)
   {
@@ -895,7 +958,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setWrapAlignment(boolean state)
   {
@@ -906,7 +969,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setShowText(boolean state)
   {
@@ -917,7 +980,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setRenderGaps(boolean state)
   {
@@ -938,7 +1001,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setColourText(boolean state)
   {
@@ -949,7 +1012,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setShowBoxes(boolean state)
   {
@@ -1000,7 +1063,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param gap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setGapCharacter(char gap)
   {
@@ -1014,7 +1077,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param thresh
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setThreshold(int thresh)
   {
@@ -1035,7 +1098,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param inc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setIncrement(int inc)
   {
@@ -1066,7 +1129,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param tree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setCurrentTree(NJTree tree)
   {
@@ -1087,7 +1150,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setColourAppliesToAllGroups(boolean b)
   {
@@ -1118,7 +1181,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setShowJVSuffix(boolean b)
   {
@@ -1139,7 +1202,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setShowAnnotation(boolean b)
   {
@@ -1180,7 +1243,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setScaleAboveWrapped(boolean b)
   {
@@ -1191,7 +1254,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setScaleLeftWrapped(boolean b)
   {
@@ -1202,7 +1265,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param b
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setScaleRightWrapped(boolean b)
   {
@@ -1213,7 +1276,7 @@ public class AlignViewport implements SelectionSource
    * Property change listener for changes in alignment
    * 
    * @param listener
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void addPropertyChangeListener(
           java.beans.PropertyChangeListener listener)
@@ -1225,7 +1288,7 @@ public class AlignViewport implements SelectionSource
    * DOCUMENT ME!
    * 
    * @param listener
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void removePropertyChangeListener(
           java.beans.PropertyChangeListener listener)
@@ -1237,11 +1300,11 @@ public class AlignViewport implements SelectionSource
    * Property change listener for changes in alignment
    * 
    * @param prop
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param oldvalue
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param newvalue
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void firePropertyChange(String prop, Object oldvalue,
           Object newvalue)
@@ -1459,9 +1522,9 @@ public class AlignViewport implements SelectionSource
       for (int i = 0; i < sequences.length; i++)
       {
         sequences[i] = new Sequence(sequences[i], annots); // construct new
-                                                            // sequence with
-                                                            // subset of visible
-                                                            // annotation
+        // sequence with
+        // subset of visible
+        // annotation
       }
     }
     else
@@ -1480,8 +1543,8 @@ public class AlignViewport implements SelectionSource
    */
   public SequenceI[] getSequenceSelection()
   {
-    SequenceI[] sequences=null;
-    if (selectionGroup!=null)
+    SequenceI[] sequences = null;
+    if (selectionGroup != null)
     {
       sequences = selectionGroup.getSequencesInOrder(alignment);
     }
@@ -1503,90 +1566,7 @@ public class AlignViewport implements SelectionSource
   public jalview.datamodel.CigarArray getViewAsCigars(
           boolean selectedRegionOnly)
   {
-    CigarArray selection = null;
-    SequenceI[] seqs = null;
-    int i, iSize;
-    int start = 0, end = 0;
-    if (selectedRegionOnly && selectionGroup != null)
-    {
-      iSize = selectionGroup.getSize();
-      seqs = selectionGroup.getSequencesInOrder(alignment);
-      start = selectionGroup.getStartRes();
-      end = selectionGroup.getEndRes(); // inclusive for start and end in
-                                        // SeqCigar constructor
-    }
-    else
-    {
-      iSize = alignment.getHeight();
-      seqs = alignment.getSequencesArray();
-      end = alignment.getWidth() - 1;
-    }
-    SeqCigar[] selseqs = new SeqCigar[iSize];
-    for (i = 0; i < iSize; i++)
-    {
-      selseqs[i] = new SeqCigar(seqs[i], start, end);
-    }
-    selection = new CigarArray(selseqs);
-    // now construct the CigarArray operations
-    if (hasHiddenColumns)
-    {
-      Vector regions = colSel.getHiddenColumns();
-      int[] region;
-      int hideStart, hideEnd;
-      int last = start;
-      for (int j = 0; last < end & j < regions.size(); j++)
-      {
-        region = (int[]) regions.elementAt(j);
-        hideStart = region[0];
-        hideEnd = region[1];
-        // edit hidden regions to selection range
-        if (hideStart < last)
-        {
-          if (hideEnd > last)
-          {
-            hideStart = last;
-          }
-          else
-          {
-            continue;
-          }
-        }
-
-        if (hideStart > end)
-        {
-          break;
-        }
-
-        if (hideEnd > end)
-        {
-          hideEnd = end;
-        }
-
-        if (hideStart > hideEnd)
-        {
-          break;
-        }
-        /**
-         * form operations...
-         */
-        if (last < hideStart)
-        {
-          selection.addOperation(CigarArray.M, hideStart - last);
-        }
-        selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);
-        last = hideEnd + 1;
-      }
-      // Final match if necessary.
-      if (last < end)
-      {
-        selection.addOperation(CigarArray.M, end - last + 1);
-      }
-    }
-    else
-    {
-      selection.addOperation(CigarArray.M, end - start + 1);
-    }
-    return selection;
+    return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null));
   }
 
   /**
@@ -1594,24 +1574,27 @@ public class AlignViewport implements SelectionSource
    * to an analysis function
    * 
    * @param selectedOnly
-   *                boolean true to just return the selected view
+   *          boolean true to just return the selected view
    * @return AlignmentView
    */
-  jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+  public 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 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);
   }
 
   /**
@@ -1721,22 +1704,22 @@ public class AlignViewport implements SelectionSource
 
     return sequenceSetID;
   }
+
   /**
-   * unique viewId for synchronizing state with stored Jalview Project 
+   * unique viewId for synchronizing state with stored Jalview Project
    * 
    */
-  private String viewId=null;
+  private String viewId = null;
 
-  
   public String getViewId()
   {
-    if (viewId==null)
+    if (viewId == null)
     {
-      viewId = this.getSequenceSetId()+"."+this.hashCode()+"";
+      viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
     }
     return viewId;
   }
-  
+
   public void alignmentChanged(AlignmentPanel ap)
   {
     if (padGaps)
@@ -1793,8 +1776,8 @@ public class AlignViewport implements SelectionSource
       {
         Alignment al = (Alignment) alignment;
         Conservation c = new Conservation("All",
-                ResidueProperties.propHash, 3, al.getSequences(), 0, al
-                        .getWidth() - 1);
+                ResidueProperties.propHash, 3, al.getSequences(), 0,
+                al.getWidth() - 1);
         c.calculate();
         c.verdict(false, ConsPercGaps);
 
@@ -1808,8 +1791,8 @@ public class AlignViewport implements SelectionSource
       SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
       if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme) sg.cs).resetClustalX(sg
-                .getSequences(hiddenRepSequences), sg.getWidth());
+        ((ClustalxColourScheme) sg.cs).resetClustalX(
+                sg.getSequences(hiddenRepSequences), sg.getWidth());
       }
       sg.recalcConservation();
     }
@@ -1848,8 +1831,8 @@ public class AlignViewport implements SelectionSource
    * returns the visible column regions of the alignment
    * 
    * @param selectedRegionOnly
-   *                true to just return the contigs intersecting with the
-   *                selected area
+   *          true to just return the contigs intersecting with the selected
+   *          area
    * @return
    */
   public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
@@ -1888,7 +1871,7 @@ public class AlignViewport implements SelectionSource
    * the undo and redo list.
    * 
    * @param undoredo
-   *                the stored set of hashcodes as returned by getUndoRedoHash
+   *          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
    */
@@ -1946,11 +1929,12 @@ public class AlignViewport implements SelectionSource
   }
 
   /**
-   *  enable or disable the display of Database Cross References in the sequence ID tooltip
-   */ 
+   * enable or disable the display of Database Cross References in the sequence
+   * ID tooltip
+   */
   public void setShowDbRefs(boolean show)
   {
-    showdbrefs=show;
+    showdbrefs = show;
   }
 
   /**
@@ -1970,14 +1954,18 @@ public class AlignViewport implements SelectionSource
   {
     return shownpfeats;
   }
+
   /**
-   * enable or disable the display of Non-Positional sequence features in the sequence ID tooltip 
-   * @param show 
+   * enable or disable the display of Non-Positional sequence features in the
+   * sequence ID tooltip
+   * 
+   * @param show
    */
   public void setShowNpFeats(boolean show)
   {
-    shownpfeats=show;
+    shownpfeats = show;
   }
+
   /**
    * 
    * @return true if view has hidden rows
@@ -1986,6 +1974,7 @@ public class AlignViewport implements SelectionSource
   {
     return hasHiddenRows;
   }
+
   /**
    * 
    * @return true if view has hidden columns
@@ -1994,85 +1983,115 @@ public class AlignViewport implements SelectionSource
   {
     return hasHiddenColumns;
   }
+
   /**
    * when set, view will scroll to show the highlighted position
    */
-  public boolean followHighlight=true;
+  public boolean followHighlight = true;
+
   /**
-   * @return true if view should scroll to show the highlighted region of a sequence
+   * @return true if view should scroll to show the highlighted region of a
+   *         sequence
    * @return
    */
-  public boolean getFollowHighlight() {
+  public boolean getFollowHighlight()
+  {
     return followHighlight;
   }
-  public boolean followSelection=true;
+
+  public boolean followSelection = true;
+
   /**
-   * @return true if view selection should always follow the selections broadcast by other selection sources
+   * @return true if view selection should always follow the selections
+   *         broadcast by other selection sources
    */
-  public boolean getFollowSelection() {
+  public boolean getFollowSelection()
+  {
     return followSelection;
   }
-  private long sgrouphash=-1,colselhash=-1;
+
+  private long sgrouphash = -1, colselhash = -1;
 
   boolean showSeqFeaturesHeight;
+
   /**
-   * checks current SelectionGroup against record of last hash value, and updates record.
+   * 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)
+  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.
+   * 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)
+  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().sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this);
+    jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager().sendSelection(
+                    new SequenceGroup(getSelectionGroup()),
+                    new ColumnSelection(getColumnSelection()), this);
   }
+
   public void setShowSequenceFeaturesHeight(boolean selected)
   {
-    showSeqFeaturesHeight = selected; 
+    showSeqFeaturesHeight = selected;
   }
+
   public boolean getShowSequenceFeaturesHeight()
   {
-    return showSeqFeaturesHeight; 
+    return showSeqFeaturesHeight;
   }
-  boolean showUnconserved=false;
+
+  boolean showUnconserved = false;
+
   public boolean getShowUnconserved()
   {
     return showUnconserved;
   }
+
   public void setShowUnconserved(boolean showunconserved)
   {
-    showUnconserved=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
+   * @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++)
+    AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
+            .getSequenceSetId());
+    AlignmentPanel ap = null;
+    for (int p = 0; aps != null && p < aps.length; p++)
     {
       if (aps[p].av == this)
       {
@@ -2081,29 +2100,37 @@ public class AlignViewport implements SelectionSource
     }
     return null;
   }
+
   public boolean getSortByTree()
   {
     return sortByTree;
   }
-  public void setSortByTree(boolean sort) {
+
+  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
    */
@@ -2111,21 +2138,35 @@ public class AlignViewport implements SelectionSource
   {
     return showSequenceLogo;
   }
+
   /**
-   * @param showSequenceLogo the new value
+   * @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
+   * @param showConsensusHistogram
+   *          the showConsensusHistogram to set
    */
   public void setShowConsensusHistogram(boolean showConsensusHistogram)
   {
     this.showConsensusHistogram = showConsensusHistogram;
   }
-  
+
   /**
    * @return the showGroupConservation
    */
@@ -2133,13 +2174,16 @@ public class AlignViewport implements SelectionSource
   {
     return showGroupConservation;
   }
+
   /**
-   * @param showGroupConservation the showGroupConservation to set
+   * @param showGroupConservation
+   *          the showGroupConservation to set
    */
   public void setShowGroupConservation(boolean showGroupConservation)
   {
     this.showGroupConservation = showGroupConservation;
   }
+
   /**
    * @return the showGroupConsensus
    */
@@ -2147,59 +2191,56 @@ public class AlignViewport implements SelectionSource
   {
     return showGroupConsensus;
   }
+
   /**
-   * @param showGroupConsensus the showGroupConsensus to set
+   * @param showGroupConsensus
+   *          the showGroupConsensus to set
    */
   public void setShowGroupConsensus(boolean showGroupConsensus)
   {
     this.showGroupConsensus = showGroupConsensus;
   }
-  /**
-   * @return the includeAllConsensusSymbols
-   */
-  public boolean isIncludeAllConsensusSymbols()
-  {
-    return includeAllConsensusSymbols;
-  }
-  /**
-   * @param includeAllConsensusSymbols the includeAllConsensusSymbols to set
-   */
-  public void setIncludeAllConsensusSymbols(boolean includeAllConsensusSymbols)
-  {
-    this.includeAllConsensusSymbols = includeAllConsensusSymbols;
-  }
-  
+
   /**
    * 
-   * @return flag to indicate if the consensus histogram should be rendered by default
+   * @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.
+   * 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 
+   * @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))
+    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))
+      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
       {
-        // do nothing 
+        // do nothing
         return;
       }
-      if (colSel==null)
+      if (colSel == null)
       {
         colSel = new ColumnSelection();
       }
-      for (int cspos = sg.getStartRes(); cspos<=sg.getEndRes(); cspos++) {
+      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+      {
         colSel.addElement(cspos);
       }
-    }    
+    }
   }
 }