X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=693291f114d5881668773bc25d595bb9d7da9d98;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=18fb53b7d3cd51d786f2911e81442fd29d9aab1b;hpb=eb2477856cdeb2ec0e1f96457612d4fa972ad3c2;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 18fb53b..693291f 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,24 +1,24 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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, J Engelhardt, LM Lui, 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.datamodel;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 
@@ -26,33 +26,87 @@ import jalview.analysis.*;
 import jalview.schemes.*;
 
 /**
- * DOCUMENT ME!
- *
+ * Collects a set contiguous ranges on a set of sequences
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class SequenceGroup
+public class SequenceGroup implements AnnotatedCollectionI
 {
   String groupName;
+
   String description;
+
   Conservation conserve;
+
   Vector aaFrequency;
+
   boolean displayBoxes = true;
+
   boolean displayText = true;
+
   boolean colourText = false;
-  private Vector sequences = new Vector();
+
+  /**
+   * after Olivier's non-conserved only character display
+   */
+  boolean showNonconserved = false;
+
+  /**
+   * group members
+   */
+  private Vector<SequenceI> sequences = new Vector<SequenceI>();
+
+  /**
+   * representative sequence for this group (if any)
+   */
+  private SequenceI seqrep = null;
+
   int width = -1;
 
-  /** DOCUMENT ME!! */
+  /**
+   * Colourscheme applied to group if any
+   */
   public ColourSchemeI cs;
+
   int startRes = 0;
+
   int endRes = 0;
-  Color outlineColour = Color.black;
+
+  public Color outlineColour = Color.black;
+
+  public Color idColour = null;
+
   public int thresholdTextColour = 0;
+
   public Color textColour = Color.black;
+
   public Color textColour2 = Color.white;
 
   /**
+   * consensus calculation property
+   */
+  private boolean ignoreGapsInConsensus = true;
+
+  /**
+   * consensus calculation property
+   */
+  private boolean showSequenceLogo = false;
+
+  /**
+   * flag indicating if logo should be rendered normalised
+   */
+  private boolean normaliseSequenceLogo;
+
+  /**
+   * @return the includeAllConsSymbols
+   */
+  public boolean isShowSequenceLogo()
+  {
+    return showSequenceLogo;
+  }
+
+  /**
    * Creates a new SequenceGroup object.
    */
   public SequenceGroup()
@@ -62,20 +116,21 @@ public class SequenceGroup
 
   /**
    * Creates a new SequenceGroup object.
-   *
-   * @param sequences DOCUMENT ME!
-   * @param groupName DOCUMENT ME!
-   * @param scheme DOCUMENT ME!
-   * @param displayBoxes DOCUMENT ME!
-   * @param displayText DOCUMENT ME!
-   * @param colourText DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
+   * 
+   * @param sequences
+   * @param groupName
+   * @param scheme
+   * @param displayBoxes
+   * @param displayText
+   * @param colourText
+   * @param start
+   *          first column of group
+   * @param end
+   *          last column of group
    */
   public SequenceGroup(Vector sequences, String groupName,
-                       ColourSchemeI scheme, boolean displayBoxes,
-                       boolean displayText,
-                       boolean colourText, int start, int end)
+          ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
+          boolean colourText, int start, int end)
   {
     this.sequences = sequences;
     this.groupName = groupName;
@@ -88,18 +143,64 @@ public class SequenceGroup
     recalcConservation();
   }
 
+  /**
+   * copy constructor
+   * 
+   * @param seqsel
+   */
+  public SequenceGroup(SequenceGroup seqsel)
+  {
+    if (seqsel != null)
+    {
+      sequences = new Vector();
+      Enumeration<SequenceI> sq = seqsel.sequences.elements();
+      while (sq.hasMoreElements())
+      {
+        sequences.addElement(sq.nextElement());
+      }
+      ;
+      if (seqsel.groupName != null)
+      {
+        groupName = new String(seqsel.groupName);
+      }
+      displayBoxes = seqsel.displayBoxes;
+      displayText = seqsel.displayText;
+      colourText = seqsel.colourText;
+      startRes = seqsel.startRes;
+      endRes = seqsel.endRes;
+      cs = seqsel.cs;
+      if (seqsel.description != null)
+        description = new String(seqsel.description);
+      hidecols = seqsel.hidecols;
+      hidereps = seqsel.hidereps;
+      idColour = seqsel.idColour;
+      outlineColour = seqsel.outlineColour;
+      seqrep = seqsel.seqrep;
+      textColour = seqsel.textColour;
+      textColour2 = seqsel.textColour2;
+      thresholdTextColour = seqsel.thresholdTextColour;
+      width = seqsel.width;
+      ignoreGapsInConsensus = seqsel.ignoreGapsInConsensus;
+      if (seqsel.conserve != null)
+      {
+        recalcConservation(); // safer than
+        // aaFrequency = (Vector) seqsel.aaFrequency.clone(); // ??
+      }
+    }
+  }
+
   public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
   {
     int iSize = sequences.size();
     SequenceI[] seqs = new SequenceI[iSize];
     SequenceI[] inorder = getSequencesInOrder(align);
-    
-    for (int i = 0,ipos=0; i < inorder.length; i++)
+
+    for (int i = 0, ipos = 0; i < inorder.length; i++)
     {
       SequenceI seq = inorder[i];
 
-      seqs[ipos] = seq.getSubSequence(startRes, endRes+1);
-      if (seqs[ipos]!=null)
+      seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
+      if (seqs[ipos] != null)
       {
         seqs[ipos].setDescription(seq.getDescription());
         seqs[ipos].setDBRef(seq.getDBRef());
@@ -111,10 +212,28 @@ public class SequenceGroup
 
         if (seq.getAnnotation() != null)
         {
+          AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
+          // Only copy annotation that is either a score or referenced by the
+          // alignment's annotation vector
           for (int a = 0; a < seq.getAnnotation().length; a++)
           {
-            AlignmentAnnotation newannot = new AlignmentAnnotation(seq
-                    .getAnnotation()[a]);
+            AlignmentAnnotation tocopy = seq.getAnnotation()[a];
+            if (alann != null)
+            {
+              boolean found = false;
+              for (int pos = 0; pos < alann.length; pos++)
+              {
+                if (alann[pos] == tocopy)
+                {
+                  found = true;
+                  break;
+                }
+              }
+              if (!found)
+                continue;
+            }
+            AlignmentAnnotation newannot = new AlignmentAnnotation(
+                    seq.getAnnotation()[a]);
             newannot.restrict(startRes, endRes);
             newannot.setSequenceRef(seqs[ipos]);
             newannot.adjustForAlignment();
@@ -122,11 +241,13 @@ public class SequenceGroup
           }
         }
         ipos++;
-      } else {
+      }
+      else
+      {
         iSize--;
       }
     }
-    if (iSize!=inorder.length)
+    if (iSize != inorder.length)
     {
       SequenceI[] nseqs = new SequenceI[iSize];
       System.arraycopy(seqs, 0, nseqs, 0, iSize);
@@ -137,9 +258,10 @@ public class SequenceGroup
   }
 
   /**
-   * If sequence ends in gaps, the end residue can
-   * be correctly calculated here
-   * @param seq SequenceI
+   * If sequence ends in gaps, the end residue can be correctly calculated here
+   * 
+   * @param seq
+   *          SequenceI
    * @return int
    */
   public int findEndRes(SequenceI seq)
@@ -150,7 +272,7 @@ public class SequenceGroup
     for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
     {
       ch = seq.getCharAt(j);
-      if (!jalview.util.Comparison.isGap( (ch)))
+      if (!jalview.util.Comparison.isGap((ch)))
       {
         eres++;
       }
@@ -164,7 +286,13 @@ public class SequenceGroup
     return eres;
   }
 
-  public Vector getSequences(Hashtable hiddenReps)
+  public List<SequenceI> getSequences()
+  {
+    return sequences;
+  }
+
+  public List<SequenceI> getSequences(
+          Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
     if (hiddenReps == null)
     {
@@ -173,19 +301,17 @@ public class SequenceGroup
     else
     {
       Vector allSequences = new Vector();
-      SequenceI seq, seq2;
+      SequenceI seq;
       for (int i = 0; i < sequences.size(); i++)
       {
         seq = (SequenceI) sequences.elementAt(i);
         allSequences.addElement(seq);
         if (hiddenReps.containsKey(seq))
         {
-          SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
-          for (int h = 0; h < hsg.getSize(); h++)
+          SequenceCollectionI hsg = hiddenReps.get(seq);
+          for (SequenceI seq2 : hsg.getSequences())
           {
-            seq2 = hsg.getSequenceAt(h);
-            if (seq2 != seq
-                && !allSequences.contains(seq2))
+            if (seq2 != seq && !allSequences.contains(seq2))
             {
               allSequences.addElement(seq2);
             }
@@ -197,27 +323,23 @@ public class SequenceGroup
     }
   }
 
-  public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
+  public SequenceI[] getSequencesAsArray(
+          Map<SequenceI, SequenceCollectionI> map)
   {
-    Vector tmp = getSequences(hiddenReps);
+    List<SequenceI> tmp = getSequences(map);
     if (tmp == null)
     {
       return null;
     }
-    SequenceI[] result = new SequenceI[tmp.size()];
-    for (int i = 0; i < result.length; i++)
-    {
-      result[i] = (SequenceI) tmp.elementAt(i);
-    }
-
-    return result;
+    return tmp.toArray(new SequenceI[tmp.size()]);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param col DOCUMENT ME!
-   *
+   * 
+   * @param col
+   *          DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public boolean adjustForRemoveLeft(int col)
@@ -248,9 +370,10 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param col DOCUMENT ME!
-   *
+   * 
+   * @param col
+   *          DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public boolean adjustForRemoveRight(int col)
@@ -271,7 +394,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getName()
@@ -286,12 +409,14 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param name DOCUMENT ME!
+   * 
+   * @param name
+   *          DOCUMENT ME!
    */
   public void setName(String name)
   {
     groupName = name;
+    // TODO: URGENT: update dependent objects (annotation row)
   }
 
   public void setDescription(String desc)
@@ -301,7 +426,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Conservation getConservation()
@@ -311,8 +436,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
+   * 
+   * @param c
+   *          DOCUMENT ME!
    */
   public void setConservation(Conservation c)
   {
@@ -320,10 +446,14 @@ public class SequenceGroup
   }
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param recalc DOCUMENT ME!
+   * 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
+   * @param recalc
+   *          true means Group's conservation should be recalculated
    */
   public void addSequence(SequenceI s, boolean recalc)
   {
@@ -339,54 +469,117 @@ public class SequenceGroup
   }
 
   /**
-   * DOCUMENT ME!
+   * 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()
   {
-    if (cs == null)
+    if (cs == null && consensus == null && conservation == null)
     {
       return;
     }
-
+    if (cs != null)
+    {
+      cs.alignmentChanged(this, null);
+    }
     try
     {
-      cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));
-
-      if (cs instanceof ClustalxColourScheme)
+      Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+              endRes + 1, showSequenceLogo);
+      if (consensus != null)
+      {
+        _updateConsensusRow(cnsns);
+      }
+      if (cs != null)
       {
-        ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+        cs.setConsensus(cnsns);
+        cs.alignmentChanged(this, null);
       }
 
-      if (cs.conservationApplied())
+      if ((conservation != null)
+              || (cs != null && cs.conservationApplied()))
       {
         Conservation c = new Conservation(groupName,
-                                          ResidueProperties.propHash, 3,
-                                          sequences,
-                                          startRes, endRes + 1);
+                ResidueProperties.propHash, 3, sequences, startRes,
+                endRes + 1);
         c.calculate();
-        c.verdict(false, 25);
-
-        cs.setConservation(c);
-
-        if (cs instanceof ClustalxColourScheme)
+        c.verdict(false, consPercGaps);
+        if (conservation != null)
+        {
+          _updateConservationRow(c);
+        }
+        if (cs != null)
         {
-          ( (ClustalxColourScheme) cs).resetClustalX(sequences,
-              getWidth());
+          if (cs.conservationApplied())
+          {
+            cs.setConservation(c);
+            cs.alignmentChanged(this, null);
+          }
         }
       }
-    }
-    catch (java.lang.OutOfMemoryError err)
+    } catch (java.lang.OutOfMemoryError err)
     {
+      // TODO: catch OOM
       System.out.println("Out of memory loading groups: " + err);
     }
 
   }
 
+  private void _updateConservationRow(Conservation c)
+  {
+    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;
+    conservation.annotations = null;
+    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)
+    {
+      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;
+    consensus.annotations = null;
+    consensus.annotations = new Annotation[aWidth]; // should be alignment width
+
+    AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
+            ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
+                                                      // for
+                                                      // ignoreGapsInConsensusCalculation);
+  }
+
   /**
-   * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param recalc DOCUMENT ME!
+   * @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)
   {
@@ -402,9 +595,11 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param s DOCUMENT ME!
-   * @param recalc DOCUMENT ME!
+   * 
+   * @param s
+   *          DOCUMENT ME!
+   * @param recalc
+   *          DOCUMENT ME!
    */
   public void deleteSequence(SequenceI s, boolean recalc)
   {
@@ -418,7 +613,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getStartRes()
@@ -428,7 +623,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getEndRes()
@@ -437,9 +632,9 @@ public class SequenceGroup
   }
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
+   * Set the first column selected by this group. Runs from 0<=i<N_cols
+   * 
+   * @param i
    */
   public void setStartRes(int i)
   {
@@ -447,9 +642,9 @@ public class SequenceGroup
   }
 
   /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
+   * Set the groups last selected column. Runs from 0<=i<N_cols
+   * 
+   * @param i
    */
   public void setEndRes(int i)
   {
@@ -458,7 +653,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getSize()
@@ -468,9 +663,10 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   *
+   * 
+   * @param i
+   *          DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceI getSequenceAt(int i)
@@ -480,8 +676,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *          DOCUMENT ME!
    */
   public void setColourText(boolean state)
   {
@@ -490,7 +687,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public boolean getColourText()
@@ -500,8 +697,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *          DOCUMENT ME!
    */
   public void setDisplayText(boolean state)
   {
@@ -510,7 +708,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public boolean getDisplayText()
@@ -520,8 +718,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param state DOCUMENT ME!
+   * 
+   * @param state
+   *          DOCUMENT ME!
    */
   public void setDisplayBoxes(boolean state)
   {
@@ -530,7 +729,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public boolean getDisplayBoxes()
@@ -540,7 +739,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getWidth()
@@ -548,7 +747,7 @@ public class SequenceGroup
     // MC This needs to get reset when characters are inserted and deleted
     if (sequences.size() > 0)
     {
-      width = ( (SequenceI) sequences.elementAt(0)).getLength();
+      width = ((SequenceI) sequences.elementAt(0)).getLength();
     }
 
     for (int i = 1; i < sequences.size(); i++)
@@ -566,8 +765,9 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
-   * @param c DOCUMENT ME!
+   * 
+   * @param c
+   *          DOCUMENT ME!
    */
   public void setOutlineColour(Color c)
   {
@@ -576,7 +776,7 @@ public class SequenceGroup
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Color getOutlineColour()
@@ -585,28 +785,451 @@ public class SequenceGroup
   }
 
   /**
-   *
-   * returns the sequences in the group ordered by the ordering given by al
-   *
-   * @param al Alignment
-   * @return SequenceI[]
+   * 
+   * 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
+   * 
+   * @param 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)
+    {
+      return null;
+    }
+    if (!trim)
+    {
+      return seqs;
+    }
+    if (index < seqs.length)
+    {
+      SequenceI[] dummy = seqs;
+      seqs = new SequenceI[index];
+      while (--index >= 0)
+      {
+        seqs[index] = dummy[index];
+        dummy[index] = null;
       }
     }
-
     return seqs;
   }
+
+  /**
+   * @return the idColour
+   */
+  public Color getIdColour()
+  {
+    return idColour;
+  }
+
+  /**
+   * @param idColour
+   *          the idColour to set
+   */
+  public void setIdColour(Color idColour)
+  {
+    this.idColour = idColour;
+  }
+
+  /**
+   * @return the representative sequence for this group
+   */
+  public SequenceI getSeqrep()
+  {
+    return seqrep;
+  }
+
+  /**
+   * 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
+   */
+  public boolean hasSeqrep()
+  {
+    return seqrep != null;
+  }
+
+  /**
+   * visibility of rows or represented rows covered by group
+   */
+  private boolean hidereps = false;
+
+  /**
+   * 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
+   */
+  public boolean isHidereps()
+  {
+    return hidereps;
+  }
+
+  /**
+   * visibility of columns intersecting this group
+   */
+  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
+   */
+  public boolean isHideCols()
+  {
+    return hidecols;
+  }
+
+  /**
+   * 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 map
+   *          (may be null)
+   * @return new group containing sequences common to this group and alignment
+   */
+  public SequenceGroup intersect(AlignmentI alignment,
+          Map<SequenceI, SequenceCollectionI> map)
+  {
+    SequenceGroup sgroup = new SequenceGroup(this);
+    SequenceI[] insect = getSequencesInOrder(alignment);
+    sgroup.sequences = new Vector();
+    for (int s = 0; insect != null && s < insect.length; s++)
+    {
+      if (map == null || map.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 getShowNonconserved()
+  {
+    return showNonconserved;
+  }
+
+  /**
+   * @param showNonconserved
+   *          the showUnconserved to set
+   */
+  public void setShowNonconserved(boolean displayNonconserved)
+  {
+    this.showNonconserved = displayNonconserved;
+  }
+
+  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
+   */
+  public AlignmentAnnotation getConsensus()
+  {
+    // TODO get or calculate and get consensus annotation row for this group
+    int aWidth = this.getWidth();
+    // pointer
+    // possibility
+    // here.
+    if (aWidth < 0)
+    {
+      return null;
+    }
+    if (consensus == null)
+    {
+      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()
+  {
+    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;
+  }
+
+  /**
+   * 
+   * @return true if annotation rows have been instantiated for this group
+   */
+  public boolean hasAnnotationRows()
+  {
+    return consensus != null || conservation != null;
+  }
+
+  public SequenceI getConsensusSeq()
+  {
+    getConsensus();
+    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));
+        }
+        else
+        {
+          seqs.append(consensus.annotations[i].displayCharacter);
+        }
+      }
+    }
+
+    SequenceI sq = new Sequence("Group" + getName() + " Consensus",
+            seqs.toString());
+    sq.setDescription("Percentage Identity Consensus "
+            + ((ignoreGapsInConsensus) ? " without gaps" : ""));
+    return sq;
+  }
+
+  public void setIgnoreGapsConsensus(boolean state)
+  {
+    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 showConsHist
+   *          flag indicating if the consensus histogram for this group should
+   *          be rendered
+   */
+  public void setShowConsensusHistogram(boolean showConsHist)
+  {
+
+    if (showConsensusHistogram != showConsHist && consensus != null)
+    {
+      this.showConsensusHistogram = showConsHist;
+      recalcConservation();
+    }
+    this.showConsensusHistogram = showConsHist;
+  }
+
+  /**
+   * @return the showConsensusHistogram
+   */
+  public boolean isShowConsensusHistogram()
+  {
+    return showConsensusHistogram;
+  }
+
+  /**
+   * set flag indicating if logo should be normalised when rendered
+   * 
+   * @param norm
+   */
+  public void setNormaliseSequenceLogo(boolean norm)
+  {
+    normaliseSequenceLogo = norm;
+  }
+
+  public boolean isNormaliseSequenceLogo()
+  {
+    return normaliseSequenceLogo;
+  }
+
+  @Override
+  /**
+   * returns a new array with all annotation involving this group
+   */
+  public AlignmentAnnotation[] getAlignmentAnnotation()
+  {
+    // TODO add in other methods like 'getAlignmentAnnotation(String label),
+    // etc'
+    ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
+    for (SequenceI seq : (Vector<SequenceI>) sequences)
+    {
+      for (AlignmentAnnotation al : seq.getAnnotation())
+      {
+        if (al.groupRef == this)
+        {
+          annot.add(al);
+        }
+      }
+    }
+    if (consensus != null)
+    {
+      annot.add(consensus);
+    }
+    if (conservation != null)
+    {
+      annot.add(conservation);
+    }
+    return annot.toArray(new AlignmentAnnotation[0]);
+  }
+
+  @Override
+  public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
+  {
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    for (AlignmentAnnotation a : getAlignmentAnnotation())
+    {
+      if (a.getCalcId() == calcId)
+      {
+        aa.add(a);
+      }
+    }
+    return aa;
+  }
+
+  public void clear()
+  {
+    sequences.clear();
+  }
 }