X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=01bf677bf214512e098856bc1871a64a0492c07a;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=db52a60aa63bab9e7ee3bbff06a8dd32aff51da1;hpb=4e1cb9b8b058d9b633af223b1cdb7b220d5d2ccd;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index db52a60..01bf677 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.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 2.7)
+ * Copyright (C) 2011 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/>.
  */
 package jalview.datamodel;
 
@@ -46,23 +45,27 @@ public class SequenceGroup
   boolean displayText = true;
 
   boolean colourText = false;
+
   /**
    * after Olivier's non-conserved only character display
    */
-  boolean showUnconserved = false;
-  
+  boolean showNonconserved = false;
+
   /**
    * group members
    */
   private Vector sequences = new Vector();
+
   /**
    * representative sequence for this group (if any)
    */
   private SequenceI seqrep = null;
+
   int width = -1;
 
   /**
-   * Colourscheme applied to group if any */
+   * Colourscheme applied to group if any
+   */
   public ColourSchemeI cs;
 
   int startRes = 0;
@@ -82,21 +85,21 @@ public class SequenceGroup
   /**
    * consensus calculation property
    */
-  private boolean ignoreGapsInConsensus=true;
+  private boolean ignoreGapsInConsensus = true;
+
   /**
    * consensus calculation property
    */
-  private boolean includeAllConsSymbols=false;
+  private boolean showSequenceLogo = false;
 
   /**
    * @return the includeAllConsSymbols
    */
-  public boolean isIncludeAllConsSymbols()
+  public boolean isShowSequenceLogo()
   {
-    return includeAllConsSymbols;
+    return showSequenceLogo;
   }
 
-
   /**
    * Creates a new SequenceGroup object.
    */
@@ -115,9 +118,9 @@ public class SequenceGroup
    * @param displayText
    * @param colourText
    * @param start
-   *                first column of group
+   *          first column of group
    * @param end
-   *                last column of group
+   *          last column of group
    */
   public SequenceGroup(Vector sequences, String groupName,
           ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
@@ -133,20 +136,24 @@ public class SequenceGroup
     endRes = end;
     recalcConservation();
   }
+
   /**
    * copy constructor
+   * 
    * @param seqsel
    */
   public SequenceGroup(SequenceGroup seqsel)
   {
-    if (seqsel!=null)
+    if (seqsel != null)
     {
-      sequences=new Vector();
+      sequences = new Vector();
       Enumeration sq = seqsel.sequences.elements();
-      while (sq.hasMoreElements()) { 
-        sequences.addElement(sq.nextElement()); 
-      };
-      if (seqsel.groupName!=null)
+      while (sq.hasMoreElements())
+      {
+        sequences.addElement(sq.nextElement());
+      }
+      ;
+      if (seqsel.groupName != null)
       {
         groupName = new String(seqsel.groupName);
       }
@@ -155,8 +162,8 @@ public class SequenceGroup
       colourText = seqsel.colourText;
       startRes = seqsel.startRes;
       endRes = seqsel.endRes;
-      cs =seqsel.cs;
-      if (seqsel.description!=null)
+      cs = seqsel.cs;
+      if (seqsel.description != null)
         description = new String(seqsel.description);
       hidecols = seqsel.hidecols;
       hidereps = seqsel.hidereps;
@@ -168,9 +175,9 @@ public class SequenceGroup
       thresholdTextColour = seqsel.thresholdTextColour;
       width = seqsel.width;
       ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
-      if (seqsel.conserve!=null)
+      if (seqsel.conserve != null)
       {
-        recalcConservation(); // safer than 
+        recalcConservation(); // safer than
         // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
       }
     }
@@ -219,8 +226,8 @@ public class SequenceGroup
               if (!found)
                 continue;
             }
-            AlignmentAnnotation newannot = new AlignmentAnnotation(seq
-                    .getAnnotation()[a]);
+            AlignmentAnnotation newannot = new AlignmentAnnotation(
+                    seq.getAnnotation()[a]);
             newannot.restrict(startRes, endRes);
             newannot.setSequenceRef(seqs[ipos]);
             newannot.adjustForAlignment();
@@ -248,7 +255,7 @@ public class SequenceGroup
    * If sequence ends in gaps, the end residue can be correctly calculated here
    * 
    * @param seq
-   *                SequenceI
+   *          SequenceI
    * @return int
    */
   public int findEndRes(SequenceI seq)
@@ -325,7 +332,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param col
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -359,7 +366,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param col
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -398,7 +405,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setName(String name)
   {
@@ -425,7 +432,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setConservation(Conservation c)
   {
@@ -433,12 +440,14 @@ public class SequenceGroup
   }
 
   /**
-   * Add s to this sequence group
+   * Add s to this sequence group. If aligment sequence is already contained in
+   * group, it will not be added again, but recalculation may happen if the flag
+   * is set.
    * 
    * @param s
-   *                alignment sequence to be added
+   *          alignment sequence to be added
    * @param recalc
-   *                true means Group's conservation should be recalculated
+   *          true means Group's conservation should be recalculated
    */
   public void addSequence(SequenceI s, boolean recalc)
   {
@@ -454,7 +463,13 @@ public class SequenceGroup
   }
 
   /**
-   * calculate residue conservation for group
+   * Max Gaps Threshold for performing a conservation calculation TODO: make
+   * this a configurable property - or global to an alignment view
+   */
+  private int consPercGaps = 25;
+
+  /**
+   * calculate residue conservation for group - but only if necessary.
    */
   public void recalcConservation()
   {
@@ -462,43 +477,49 @@ public class SequenceGroup
     {
       return;
     }
-    
+
     try
     {
-      Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, endRes + 1, includeAllConsSymbols);
+      Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+              endRes + 1, showSequenceLogo);
       if (consensus != null)
       {
         _updateConsensusRow(cnsns);
       }
-      if (cs!=null)
+      if (cs != null)
       {
         cs.setConsensus(cnsns);
-      
-      if (cs instanceof ClustalxColourScheme)
-      {
-        ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
-      }
+
+        if (cs instanceof ClustalxColourScheme)
+        {
+          ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+        }
       }
 
-      if ((conservation!=null) || (cs!=null && cs.conservationApplied()))
+      if ((conservation != null)
+              || (cs != null && cs.conservationApplied()))
       {
         Conservation c = new Conservation(groupName,
                 ResidueProperties.propHash, 3, sequences, startRes,
                 endRes + 1);
         c.calculate();
-        c.verdict(false, 25);
-        if (conservation!=null)
+        c.verdict(false, consPercGaps);
+        if (conservation != null)
         {
           _updateConservationRow(c);
         }
-        if (cs!=null)
-        {
-          cs.setConservation(c);
-        
-        if (cs instanceof ClustalxColourScheme)
+        if (cs != null)
         {
-          ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
-        }
+          if (cs.conservationApplied())
+          {
+            cs.setConservation(c);
+
+            if (cs instanceof ClustalxColourScheme)
+            {
+              ((ClustalxColourScheme) cs).resetClustalX(sequences,
+                      getWidth());
+            }
+          }
         }
       }
     } catch (java.lang.OutOfMemoryError err)
@@ -511,35 +532,54 @@ public class SequenceGroup
 
   private void _updateConservationRow(Conservation c)
   {
-    if (conservation==null)
+    if (conservation == null)
     {
       getConservation();
     }
+    // update Labels
+    conservation.label = "Conservation for " + getName();
+    conservation.description = "Conservation for group " + getName()
+            + " less than " + consPercGaps + "% gaps";
     // preserve width if already set
-    int aWidth = (conservation.annotations!=null) ? (endRes<conservation.annotations.length ? conservation.annotations.length : endRes+1) : endRes+1;
+    int aWidth = (conservation.annotations != null) ? (endRes < conservation.annotations.length ? conservation.annotations.length
+            : endRes + 1)
+            : endRes + 1;
     conservation.annotations = null;
-    conservation.annotations = new Annotation[aWidth]; // should be alignment width
-    c.completeAnnotations(conservation,null, startRes, endRes+1);
+    conservation.annotations = new Annotation[aWidth]; // should be alignment
+                                                       // width
+    c.completeAnnotations(conservation, null, startRes, endRes + 1);
   }
+
   public Hashtable[] consensusData = null;
+
   private void _updateConsensusRow(Hashtable[] cnsns)
   {
-    if (consensus==null)
+    if (consensus == null)
     {
       getConsensus();
     }
+    consensus.label = "Consensus for " + getName();
+    consensus.description = "Percent Identity";
     consensusData = cnsns;
     // preserve width if already set
-    int aWidth = (consensus.annotations!=null) ? (endRes<consensus.annotations.length ? consensus.annotations.length : endRes+1) : endRes+1;
+    int aWidth = (consensus.annotations != null) ? (endRes < consensus.annotations.length ? consensus.annotations.length
+            : endRes + 1)
+            : endRes + 1;
     consensus.annotations = null;
     consensus.annotations = new Annotation[aWidth]; // should be alignment width
 
-    AAFrequency.completeConsensus(consensus,cnsns,startRes,endRes+1,ignoreGapsInConsensus, includeAllConsSymbols); // TODO: setting container for ignoreGapsInConsensusCalculation);
+    AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
+            ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
+                                                      // for
+                                                      // ignoreGapsInConsensusCalculation);
   }
 
   /**
-   * @param s sequence to either add or remove from group
-   * @param recalc flag passed to delete/addSequence to indicate if group properties should be recalculated
+   * @param s
+   *          sequence to either add or remove from group
+   * @param recalc
+   *          flag passed to delete/addSequence to indicate if group properties
+   *          should be recalculated
    */
   public void addOrRemove(SequenceI s, boolean recalc)
   {
@@ -557,9 +597,9 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param recalc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void deleteSequence(SequenceI s, boolean recalc)
   {
@@ -592,10 +632,9 @@ public class SequenceGroup
   }
 
   /**
-   * DOCUMENT ME!
+   * Set the first column selected by this group. Runs from 0<=i<N_cols
    * 
    * @param i
-   *                DOCUMENT ME!
    */
   public void setStartRes(int i)
   {
@@ -603,10 +642,9 @@ public class SequenceGroup
   }
 
   /**
-   * DOCUMENT ME!
+   * Set the groups last selected column. Runs from 0<=i<N_cols
    * 
    * @param i
-   *                DOCUMENT ME!
    */
   public void setEndRes(int i)
   {
@@ -627,7 +665,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -640,7 +678,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setColourText(boolean state)
   {
@@ -661,7 +699,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setDisplayText(boolean state)
   {
@@ -682,7 +720,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param state
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setDisplayBoxes(boolean state)
   {
@@ -729,7 +767,7 @@ public class SequenceGroup
    * DOCUMENT ME!
    * 
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setOutlineColour(Color c)
   {
@@ -749,36 +787,57 @@ public class SequenceGroup
   /**
    * 
    * returns the sequences in the group ordered by the ordering given by al.
-   * this used to return an array with null entries regardless, new behaviour is below.
-   * TODO: verify that this does not affect use in applet or application
+   * this used to return an array with null entries regardless, new behaviour is
+   * below. TODO: verify that this does not affect use in applet or application
+   * 
    * @param al
-   *                Alignment
-   * @return SequenceI[] intersection of sequences in group with al, ordered by al, or null if group does not intersect with al
+   *          Alignment
+   * @return SequenceI[] intersection of sequences in group with al, ordered by
+   *         al, or null if group does not intersect with al
    */
   public SequenceI[] getSequencesInOrder(AlignmentI al)
   {
+    return getSequencesInOrder(al, true);
+  }
+
+  /**
+   * return an array representing the intersection of the group with al,
+   * optionally returning an array the size of al.getHeight() where nulls mark
+   * the non-intersected sequences
+   * 
+   * @param al
+   * @param trim
+   * @return null or array
+   */
+  public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
+  {
     int sSize = sequences.size();
     int alHeight = al.getHeight();
 
-    SequenceI[] seqs = new SequenceI[sSize];
+    SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
 
     int index = 0;
     for (int i = 0; i < alHeight && index < sSize; i++)
     {
       if (sequences.contains(al.getSequenceAt(i)))
       {
-        seqs[index++] = al.getSequenceAt(i);
+        seqs[(trim) ? index : i] = al.getSequenceAt(i);
+        index++;
       }
     }
-    if (index==0)
+    if (index == 0)
     {
       return null;
     }
-    if (index<seqs.length)
+    if (!trim)
+    {
+      return seqs;
+    }
+    if (index < seqs.length)
     {
       SequenceI[] dummy = seqs;
       seqs = new SequenceI[index];
-      while (--index>=0)
+      while (--index >= 0)
       {
         seqs[index] = dummy[index];
         dummy[index] = null;
@@ -797,7 +856,7 @@ public class SequenceGroup
 
   /**
    * @param idColour
-   *                the idColour to set
+   *          the idColour to set
    */
   public void setIdColour(Color idColour)
   {
@@ -813,14 +872,17 @@ public class SequenceGroup
   }
 
   /**
-   * set the representative sequence for this group.
-   * Note - this affects the interpretation of the Hidereps attribute.
-   * @param seqrep the seqrep to set (null means no sequence representative)
+   * set the representative sequence for this group. Note - this affects the
+   * interpretation of the Hidereps attribute.
+   * 
+   * @param seqrep
+   *          the seqrep to set (null means no sequence representative)
    */
   public void setSeqrep(SequenceI seqrep)
   {
     this.seqrep = seqrep;
   }
+
   /**
    * 
    * @return true if group has a sequence representative
@@ -829,39 +891,48 @@ public class SequenceGroup
   {
     return seqrep != null;
   }
+
   /**
    * visibility of rows or represented rows covered by group
    */
-  private boolean hidereps=false;
+  private boolean hidereps = false;
+
   /**
-   * set visibility of sequences covered by (if no sequence representative is defined) 
-   * or represented by this group.
+   * set visibility of sequences covered by (if no sequence representative is
+   * defined) or represented by this group.
+   * 
    * @param visibility
    */
   public void setHidereps(boolean visibility)
   {
     hidereps = visibility;
   }
+
   /**
    * 
-   * @return true if sequences represented (or covered) by this group should be hidden
+   * @return true if sequences represented (or covered) by this group should be
+   *         hidden
    */
   public boolean isHidereps()
   {
     return hidereps;
   }
+
   /**
    * visibility of columns intersecting this group
    */
-  private boolean hidecols=false;
+  private boolean hidecols = false;
+
   /**
    * set intended visibility of columns covered by this group
+   * 
    * @param visibility
    */
   public void setHideCols(boolean visibility)
   {
     hidecols = visibility;
   }
+
   /**
    * 
    * @return true if columns covered by group should be hidden
@@ -870,52 +941,79 @@ public class SequenceGroup
   {
     return hidecols;
   }
+
   /**
-   * create a new sequence group from the intersection of this group
-   * with an alignment Hashtable of hidden representatives
+   * create a new sequence group from the intersection of this group with an
+   * alignment Hashtable of hidden representatives
    * 
-   * @param alignment (may not be null)
-   * @param hashtable (may be null)
+   * @param alignment
+   *          (may not be null)
+   * @param hashtable
+   *          (may be null)
    * @return new group containing sequences common to this group and alignment
    */
   public SequenceGroup intersect(AlignmentI alignment, Hashtable hashtable)
   {
     SequenceGroup sgroup = new SequenceGroup(this);
-    SequenceI[] insect=getSequencesInOrder(alignment);
+    SequenceI[] insect = getSequencesInOrder(alignment);
     sgroup.sequences = new Vector();
-    for (int s=0;insect!=null && s<insect.length;s++) { 
-      if (hashtable==null || hashtable.containsKey(insect[s]))
-              {
-      sgroup.sequences.addElement(insect[s]); }
-    }
-    //Enumeration en =getSequences(hashtable).elements();
-    //while (en.hasMoreElements())
-   // {
-   //   SequenceI elem = (SequenceI) en.nextElement();
-   //   if (alignment.getSequences().contains(elem))
-   //   {
-   //     sgroup.addSequence(elem, false);
-   //   }
-   // }
+    for (int s = 0; insect != null && s < insect.length; s++)
+    {
+      if (hashtable == null || hashtable.containsKey(insect[s]))
+      {
+        sgroup.sequences.addElement(insect[s]);
+      }
+    }
+    // Enumeration en =getSequences(hashtable).elements();
+    // while (en.hasMoreElements())
+    // {
+    // SequenceI elem = (SequenceI) en.nextElement();
+    // if (alignment.getSequences().contains(elem))
+    // {
+    // sgroup.addSequence(elem, false);
+    // }
+    // }
     return sgroup;
   }
 
   /**
    * @return the showUnconserved
    */
-  public boolean getShowunconserved()
+  public boolean getShowNonconserved()
   {
-    return showUnconserved;
+    return showNonconserved;
   }
 
   /**
-   * @param showUnconserved the showUnconserved to set
+   * @param showNonconserved
+   *          the showUnconserved to set
    */
-  public void setShowunconserved(boolean displayNonconserved)
+  public void setShowNonconserved(boolean displayNonconserved)
   {
-    this.showUnconserved = displayNonconserved;
+    this.showNonconserved = displayNonconserved;
   }
-  AlignmentAnnotation consensus=null,conservation=null;
+
+  AlignmentAnnotation consensus = null, conservation = null;
+
+  /**
+   * flag indicating if consensus histogram should be rendered
+   */
+  private boolean showConsensusHistogram;
+
+  /**
+   * set this alignmentAnnotation object as the one used to render consensus
+   * annotation
+   * 
+   * @param aan
+   */
+  public void setConsensus(AlignmentAnnotation aan)
+  {
+    if (consensus == null)
+    {
+      consensus = aan;
+    }
+  }
+
   /**
    * 
    * @return automatically calculated consensus row
@@ -931,32 +1029,52 @@ public class SequenceGroup
     {
       return null;
     }
-    if (consensus==null)
+    if (consensus == null)
     {
-       consensus = new AlignmentAnnotation("Consensus for "+getName(), "PID",
-              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
-      consensus.hasText = true;
-      consensus.autoCalculated = true;
-      consensus.groupRef = this;
+      consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+              100f, AlignmentAnnotation.BAR_GRAPH);
     }
+    consensus.hasText = true;
+    consensus.autoCalculated = true;
+    consensus.groupRef = this;
+    consensus.label = "Consensus for " + getName();
+    consensus.description = "Percent Identity";
     return consensus;
   }
-    /**
+
+  /**
+   * set this alignmentAnnotation object as the one used to render consensus
+   * annotation
+   * 
+   * @param aan
+   */
+  public void setConservationRow(AlignmentAnnotation aan)
+  {
+    if (conservation == null)
+    {
+      conservation = aan;
+    }
+  }
+
+  /**
    * get the conservation annotation row for this group
+   * 
    * @return autoCalculated annotation row
    */
-  public AlignmentAnnotation getConservationRow() {
-    int ConsPercGaps = 25;
-    if (conservation == null) {
-      conservation = new AlignmentAnnotation("Conservation for "+getName(),
-            "Conservation for group "+getName()+" less than " + ConsPercGaps
-                    + "% gaps", new Annotation[1], 0f, 11f,
-            AlignmentAnnotation.BAR_GRAPH);
+  public AlignmentAnnotation getConservationRow()
+  {
+    if (conservation == null)
+    {
+      conservation = new AlignmentAnnotation("", "", new Annotation[1], 0f,
+              11f, AlignmentAnnotation.BAR_GRAPH);
+    }
+
     conservation.hasText = true;
     conservation.autoCalculated = true;
     conservation.groupRef = this;
-      }
-    
+    conservation.label = "Conservation for " + getName();
+    conservation.description = "Conservation for group " + getName()
+            + " less than " + consPercGaps + "% gaps";
     return conservation;
   }
 
@@ -964,10 +1082,10 @@ public class SequenceGroup
    * 
    * @return true if annotation rows have been instantiated for this group
    */
-    public boolean hasAnnotationRows()
-    {
-      return consensus!=null || conservation!=null;
-    }
+  public boolean hasAnnotationRows()
+  {
+    return consensus != null || conservation != null;
+  }
 
   public SequenceI getConsensusSeq()
   {
@@ -988,34 +1106,65 @@ public class SequenceGroup
       }
     }
 
-    SequenceI sq = new Sequence("Group"+getName()+" Consensus", seqs.toString());
+    SequenceI sq = new Sequence("Group" + getName() + " Consensus",
+            seqs.toString());
     sq.setDescription("Percentage Identity Consensus "
             + ((ignoreGapsInConsensus) ? " without gaps" : ""));
-    return sq;    
+    return sq;
   }
 
   public void setIgnoreGapsConsensus(boolean state)
   {
-    if (this.ignoreGapsInConsensus!=state && consensus!=null)
+    if (this.ignoreGapsInConsensus != state && consensus != null)
     {
       ignoreGapsInConsensus = state;
       recalcConservation();
     }
     ignoreGapsInConsensus = state;
   }
+
   public boolean getIgnoreGapsConsensus()
   {
     return ignoreGapsInConsensus;
   }
+
+  /**
+   * @param showSequenceLogo
+   *          indicates if a sequence logo is shown for consensus annotation
+   */
+  public void setshowSequenceLogo(boolean showSequenceLogo)
+  {
+    // TODO: decouple calculation from settings update
+    if (this.showSequenceLogo != showSequenceLogo && consensus != null)
+    {
+      this.showSequenceLogo = showSequenceLogo;
+      recalcConservation();
+    }
+    this.showSequenceLogo = showSequenceLogo;
+  }
+
   /**
-   * @param includeAllConsSymbols the includeAllConsSymbols to set
+   * 
+   * @param showConsHist
+   *          flag indicating if the consensus histogram for this group should
+   *          be rendered
    */
-  public void setIncludeAllConsSymbols(boolean includeAllConsSymbols)
+  public void setShowConsensusHistogram(boolean showConsHist)
   {
-    if (this.includeAllConsSymbols!=includeAllConsSymbols && consensus!=null) {
-      this.includeAllConsSymbols = includeAllConsSymbols;
+
+    if (showConsensusHistogram != showConsHist && consensus != null)
+    {
+      this.showConsensusHistogram = showConsHist;
       recalcConservation();
     }
-    this.includeAllConsSymbols = includeAllConsSymbols;
+    this.showConsensusHistogram = showConsHist;
+  }
+
+  /**
+   * @return the showConsensusHistogram
+   */
+  public boolean isShowConsensusHistogram()
+  {
+    return showConsensusHistogram;
   }
 }