X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=5e33229f6c87dc19bd2ab5db8fd8b08bed84d587;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=d4069104c632bed90c27051a67c38c2cb8e2ab89;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index d406910..5e33229 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,30 +1,38 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * 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.
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import java.util.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.Conservation;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.ColourSchemeI;
+
+import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.schemes.*;
+import java.util.Map;
 
 /**
  * Collects a set contiguous ranges on a set of sequences
@@ -34,14 +42,32 @@ import jalview.schemes.*;
  */
 public class SequenceGroup implements AnnotatedCollectionI
 {
+  // TODO ideally this event notification functionality should be separated into
+  // a
+  // subclass of ViewportProperties similarly to ViewportRanges. Done here as
+  // quick fix for JAL-2665
+  public static final String SEQ_GROUP_CHANGED = "Sequence group changed";
+
+  protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+          this);
+
+  public void addPropertyChangeListener(PropertyChangeListener listener)
+  {
+    changeSupport.addPropertyChangeListener(listener);
+  }
+
+  public void removePropertyChangeListener(PropertyChangeListener listener)
+  {
+    changeSupport.removePropertyChangeListener(listener);
+  }
+  // end of event notification functionality initialisation
+
   String groupName;
 
   String description;
 
   Conservation conserve;
 
-  Vector aaFrequency;
-
   boolean displayBoxes = true;
 
   boolean displayText = true;
@@ -49,6 +75,12 @@ public class SequenceGroup implements AnnotatedCollectionI
   boolean colourText = false;
 
   /**
+   * True if the group is defined as a group on the alignment, false if it is
+   * just a selection.
+   */
+  boolean isDefined = false;
+
+  /**
    * after Olivier's non-conserved only character display
    */
   boolean showNonconserved = false;
@@ -56,7 +88,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * group members
    */
-  private Vector<SequenceI> sequences = new Vector<SequenceI>();
+  private List<SequenceI> sequences;
 
   /**
    * representative sequence for this group (if any)
@@ -68,11 +100,17 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * Colourscheme applied to group if any
    */
-  public ColourSchemeI cs;
+  public ResidueShaderI cs;
 
-  int startRes = 0;
+  /**
+   * start column (base 0)
+   */
+  private int startRes = 0;
 
-  int endRes = 0;
+  /**
+   * end column (base 0)
+   */
+  private int endRes = 0;
 
   public Color outlineColour = Color.black;
 
@@ -99,13 +137,23 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   private boolean normaliseSequenceLogo;
 
-  /**
-   * @return the includeAllConsSymbols
+  /*
+   * visibility of rows or represented rows covered by group
    */
-  public boolean isShowSequenceLogo()
-  {
-    return showSequenceLogo;
-  }
+  private boolean hidereps = false;
+
+  /*
+   * visibility of columns intersecting this group
+   */
+  private boolean hidecols = false;
+
+  AlignmentAnnotation consensus = null;
+
+  AlignmentAnnotation conservation = null;
+
+  private boolean showConsensusHistogram;
+
+  private AnnotatedCollectionI context;
 
   /**
    * Creates a new SequenceGroup object.
@@ -113,6 +161,8 @@ public class SequenceGroup implements AnnotatedCollectionI
   public SequenceGroup()
   {
     groupName = "JGroup:" + this.hashCode();
+    cs = new ResidueShader();
+    sequences = new ArrayList<>();
   }
 
   /**
@@ -129,16 +179,17 @@ public class SequenceGroup implements AnnotatedCollectionI
    * @param end
    *          last column of group
    */
-  public SequenceGroup(Vector sequences, String groupName,
+  public SequenceGroup(List<SequenceI> sequences, String groupName,
           ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
           boolean colourText, int start, int end)
   {
+    this();
     this.sequences = sequences;
     this.groupName = groupName;
     this.displayBoxes = displayBoxes;
     this.displayText = displayText;
     this.colourText = colourText;
-    this.cs = scheme;
+    this.cs = new ResidueShader(scheme);
     startRes = start;
     endRes = end;
     recalcConservation();
@@ -151,15 +202,11 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public SequenceGroup(SequenceGroup seqsel)
   {
+    this();
     if (seqsel != null)
     {
-      sequences = new Vector();
-      Enumeration<SequenceI> sq = seqsel.sequences.elements();
-      while (sq.hasMoreElements())
-      {
-        sequences.addElement(sq.nextElement());
-      }
-      ;
+      sequences = new ArrayList<>();
+      sequences.addAll(seqsel.sequences);
       if (seqsel.groupName != null)
       {
         groupName = new String(seqsel.groupName);
@@ -167,13 +214,20 @@ public class SequenceGroup implements AnnotatedCollectionI
       displayBoxes = seqsel.displayBoxes;
       displayText = seqsel.displayText;
       colourText = seqsel.colourText;
+
       startRes = seqsel.startRes;
       endRes = seqsel.endRes;
-      cs = seqsel.cs;
+      cs = new ResidueShader((ResidueShader) seqsel.cs);
       if (seqsel.description != null)
+      {
         description = new String(seqsel.description);
+      }
       hidecols = seqsel.hidecols;
       hidereps = seqsel.hidereps;
+      showNonconserved = seqsel.showNonconserved;
+      showSequenceLogo = seqsel.showSequenceLogo;
+      normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
+      showConsensusHistogram = seqsel.showConsensusHistogram;
       idColour = seqsel.idColour;
       outlineColour = seqsel.outlineColour;
       seqrep = seqsel.seqrep;
@@ -190,6 +244,22 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
+  /**
+   * Constructor that copies the given list of sequences
+   * 
+   * @param seqs
+   */
+  public SequenceGroup(List<SequenceI> seqs)
+  {
+    this();
+    this.sequences.addAll(seqs);
+  }
+
+  public boolean isShowSequenceLogo()
+  {
+    return showSequenceLogo;
+  }
+
   public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
   {
     int iSize = sequences.size();
@@ -199,16 +269,16 @@ public class SequenceGroup implements AnnotatedCollectionI
     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)
+      SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes,
+              endRes + 1);
+      if (seqipos != null)
       {
-        seqs[ipos].setDescription(seq.getDescription());
-        seqs[ipos].setDBRef(seq.getDBRef());
-        seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+        seqipos.setDescription(seq.getDescription());
+        seqipos.setDBRefs(seq.getDBRefs());
+        seqipos.setSequenceFeatures(seq.getSequenceFeatures());
         if (seq.getDatasetSequence() != null)
         {
-          seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
+          seqipos.setDatasetSequence(seq.getDatasetSequence());
         }
 
         if (seq.getAnnotation() != null)
@@ -222,7 +292,7 @@ public class SequenceGroup implements AnnotatedCollectionI
             if (alann != null)
             {
               boolean found = false;
-              for (int pos = 0; pos < alann.length; pos++)
+              for (int pos = 0, np = alann.length; pos < np; pos++)
               {
                 if (alann[pos] == tocopy)
                 {
@@ -231,14 +301,16 @@ public class SequenceGroup implements AnnotatedCollectionI
                 }
               }
               if (!found)
+              {
                 continue;
+              }
             }
             AlignmentAnnotation newannot = new AlignmentAnnotation(
                     seq.getAnnotation()[a]);
             newannot.restrict(startRes, endRes);
             newannot.setSequenceRef(seqs[ipos]);
             newannot.adjustForAlignment();
-            seqs[ipos].addAlignmentAnnotation(newannot);
+            seqipos.addAlignmentAnnotation(newannot);
           }
         }
         ipos++;
@@ -287,26 +359,27 @@ public class SequenceGroup implements AnnotatedCollectionI
     return eres;
   }
 
+  @Override
   public List<SequenceI> getSequences()
   {
     return sequences;
   }
 
+  @Override
   public List<SequenceI> getSequences(
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
     if (hiddenReps == null)
     {
+      // TODO: need a synchronizedCollection here ?
       return sequences;
     }
     else
     {
-      Vector allSequences = new Vector();
-      SequenceI seq;
-      for (int i = 0; i < sequences.size(); i++)
+      List<SequenceI> allSequences = new ArrayList<>();
+      for (SequenceI seq : sequences)
       {
-        seq = (SequenceI) sequences.elementAt(i);
-        allSequences.addElement(seq);
+        allSequences.add(seq);
         if (hiddenReps.containsKey(seq))
         {
           SequenceCollectionI hsg = hiddenReps.get(seq);
@@ -314,7 +387,7 @@ public class SequenceGroup implements AnnotatedCollectionI
           {
             if (seq2 != seq && !allSequences.contains(seq2))
             {
-              allSequences.addElement(seq2);
+              allSequences.add(seq2);
             }
           }
         }
@@ -458,55 +531,91 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public void addSequence(SequenceI s, boolean recalc)
   {
-    if (s != null && !sequences.contains(s))
+    synchronized (sequences)
     {
-      sequences.addElement(s);
-    }
+      if (s != null && !sequences.contains(s))
+      {
+        sequences.add(s);
+        changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+                sequences.size() - 1, sequences.size());
+      }
 
-    if (recalc)
-    {
-      recalcConservation();
+      if (recalc)
+      {
+        recalcConservation();
+      }
     }
   }
 
   /**
-   * Max Gaps Threshold for performing a conservation calculation TODO: make
-   * this a configurable property - or global to an alignment view
+   * Max Gaps Threshold (percent) for performing a conservation calculation
    */
   private int consPercGaps = 25;
 
   /**
-   * calculate residue conservation for group - but only if necessary.
+   * @return Max Gaps Threshold for performing a conservation calculation
    */
-  public void recalcConservation()
+  public int getConsPercGaps()
+  {
+    return consPercGaps;
+  }
+
+  /**
+   * set Max Gaps Threshold (percent) for performing a conservation calculation
+   * 
+   * @param consPercGaps
+   */
+  public void setConsPercGaps(int consPercGaps)
+  {
+    this.consPercGaps = consPercGaps;
+  }
+
+  /**
+   * calculate residue conservation and colourschemes for group - but only if
+   * necessary. returns true if the calculation resulted in a visible change to
+   * group
+   */
+  public boolean recalcConservation()
+  {
+    return recalcConservation(false);
+  }
+
+  /**
+   * calculate residue conservation for group - but only if necessary. returns
+   * true if the calculation resulted in a visible change to group
+   * 
+   * @param defer
+   *          when set, colourschemes for this group are not refreshed after
+   *          recalculation
+   */
+  public boolean recalcConservation(boolean defer)
   {
     if (cs == null && consensus == null && conservation == null)
     {
-      return;
-    }
-    if (cs != null)
-    {
-      cs.alignmentChanged(this, null);
+      return false;
     }
+    // TODO: try harder to detect changes in state in order to minimise
+    // recalculation effort
+    boolean upd = false;
     try
     {
-      Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes,
+      ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
               endRes + 1, showSequenceLogo);
       if (consensus != null)
       {
-        _updateConsensusRow(cnsns);
+        _updateConsensusRow(cnsns, sequences.size());
+        upd = true;
       }
       if (cs != null)
       {
         cs.setConsensus(cnsns);
-        cs.alignmentChanged(this, null);
+        upd = true;
       }
 
       if ((conservation != null)
               || (cs != null && cs.conservationApplied()))
       {
-        Conservation c = new Conservation(groupName,
-                ResidueProperties.propHash, 3, sequences, startRes,
+        Conservation c = new Conservation(groupName, sequences, startRes,
                 endRes + 1);
         c.calculate();
         c.verdict(false, consPercGaps);
@@ -519,16 +628,27 @@ public class SequenceGroup implements AnnotatedCollectionI
           if (cs.conservationApplied())
           {
             cs.setConservation(c);
-            cs.alignmentChanged(this, null);
           }
         }
+        // eager update - will cause a refresh of overview regardless
+        upd = true;
+      }
+      if (cs != null && !defer)
+      {
+        // TODO: JAL-2034 should cs.alignmentChanged modify return state
+        cs.alignmentChanged(context != null ? context : this, null);
+        return true;
+      }
+      else
+      {
+        return upd;
       }
     } catch (java.lang.OutOfMemoryError err)
     {
       // TODO: catch OOM
       System.out.println("Out of memory loading groups: " + err);
     }
-
+    return upd;
   }
 
   private void _updateConservationRow(Conservation c)
@@ -542,8 +662,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     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)
+    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
@@ -551,9 +673,9 @@ public class SequenceGroup implements AnnotatedCollectionI
     c.completeAnnotations(conservation, null, startRes, endRes + 1);
   }
 
-  public Hashtable[] consensusData = null;
+  public ProfilesI consensusData = null;
 
-  private void _updateConsensusRow(Hashtable[] cnsns)
+  private void _updateConsensusRow(ProfilesI cnsns, long nseq)
   {
     if (consensus == null)
     {
@@ -563,16 +685,19 @@ public class SequenceGroup implements AnnotatedCollectionI
     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)
+    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);
+            ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting
+                                                            // container
+    // for
+    // ignoreGapsInConsensusCalculation);
   }
 
   /**
@@ -584,31 +709,39 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public void addOrRemove(SequenceI s, boolean recalc)
   {
-    if (sequences.contains(s))
-    {
-      deleteSequence(s, recalc);
-    }
-    else
+    synchronized (sequences)
     {
-      addSequence(s, recalc);
+      if (sequences.contains(s))
+      {
+        deleteSequence(s, recalc);
+      }
+      else
+      {
+        addSequence(s, recalc);
+      }
     }
   }
 
   /**
-   * DOCUMENT ME!
+   * remove
    * 
    * @param s
-   *          DOCUMENT ME!
+   *          to be removed
    * @param recalc
-   *          DOCUMENT ME!
+   *          true means recalculate conservation
    */
   public void deleteSequence(SequenceI s, boolean recalc)
   {
-    sequences.removeElement(s);
-
-    if (recalc)
+    synchronized (sequences)
     {
-      recalcConservation();
+      sequences.remove(s);
+      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED,
+              sequences.size() + 1, sequences.size());
+
+      if (recalc)
+      {
+        recalcConservation();
+      }
     }
   }
 
@@ -617,6 +750,7 @@ public class SequenceGroup implements AnnotatedCollectionI
    * 
    * @return the first column selected by this group. Runs from 0<=i<N_cols
    */
+  @Override
   public int getStartRes()
   {
     return startRes;
@@ -626,6 +760,7 @@ public class SequenceGroup implements AnnotatedCollectionI
    * 
    * @return the groups last selected column. Runs from 0<=i<N_cols
    */
+  @Override
   public int getEndRes()
   {
     return endRes;
@@ -634,11 +769,15 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * Set the first column selected by this group. Runs from 0<=i<N_cols
    * 
-   * @param i
+   * @param newStart
    */
-  public void setStartRes(int i)
+  public void setStartRes(int newStart)
   {
-    startRes = i;
+    int before = startRes;
+    startRes = Math.max(0, newStart); // sanity check for negative start column
+                                      // positions
+    changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
+
   }
 
   /**
@@ -648,13 +787,13 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public void setEndRes(int i)
   {
+    int before = endRes;
     endRes = i;
+    changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes);
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * @return number of sequences in group
    */
   public int getSize()
   {
@@ -662,23 +801,17 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * DOCUMENT ME!
-   * 
    * @param i
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * @return the ith sequence
    */
   public SequenceI getSequenceAt(int i)
   {
-    return (SequenceI) sequences.elementAt(i);
+    return sequences.get(i);
   }
 
   /**
-   * DOCUMENT ME!
-   * 
    * @param state
-   *          DOCUMENT ME!
+   *          colourText
    */
   public void setColourText(boolean state)
   {
@@ -738,29 +871,27 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * DOCUMENT ME!
+   * computes the width of current set of sequences and returns it
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getWidth()
   {
-    // MC This needs to get reset when characters are inserted and deleted
-    if (sequences.size() > 0)
+    synchronized (sequences)
     {
-      width = ((SequenceI) sequences.elementAt(0)).getLength();
-    }
-
-    for (int i = 1; i < sequences.size(); i++)
-    {
-      SequenceI seq = (SequenceI) sequences.elementAt(i);
-
-      if (seq.getLength() > width)
+      // MC This needs to get reset when characters are inserted and deleted
+      boolean first = true;
+      for (SequenceI seq : sequences)
       {
-        width = seq.getLength();
+        if (first || seq.getLength() > width)
+        {
+          width = seq.getLength();
+          first = false;
+        }
       }
+      return width;
     }
-
-    return width;
   }
 
   /**
@@ -811,39 +942,42 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
   {
-    int sSize = sequences.size();
-    int alHeight = al.getHeight();
+    synchronized (sequences)
+    {
+      int sSize = sequences.size();
+      int alHeight = al.getHeight();
 
-    SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
+      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)))
+      int index = 0;
+      for (int i = 0; i < alHeight && index < sSize; i++)
       {
-        seqs[(trim) ? index : i] = al.getSequenceAt(i);
-        index++;
+        if (sequences.contains(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)
+      if (index == 0)
       {
-        seqs[index] = dummy[index];
-        dummy[index] = null;
+        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 seqs;
   }
 
   /**
@@ -866,6 +1000,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * @return the representative sequence for this group
    */
+  @Override
   public SequenceI getSeqrep()
   {
     return seqrep;
@@ -878,6 +1013,7 @@ public class SequenceGroup implements AnnotatedCollectionI
    * @param seqrep
    *          the seqrep to set (null means no sequence representative)
    */
+  @Override
   public void setSeqrep(SequenceI seqrep)
   {
     this.seqrep = seqrep;
@@ -887,17 +1023,13 @@ public class SequenceGroup implements AnnotatedCollectionI
    * 
    * @return true if group has a sequence representative
    */
+  @Override
   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.
    * 
@@ -919,11 +1051,6 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * visibility of columns intersecting this group
-   */
-  private boolean hidecols = false;
-
-  /**
    * set intended visibility of columns covered by this group
    * 
    * @param visibility
@@ -957,23 +1084,14 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     SequenceGroup sgroup = new SequenceGroup(this);
     SequenceI[] insect = getSequencesInOrder(alignment);
-    sgroup.sequences = new Vector();
+    sgroup.sequences = new ArrayList<>();
     for (int s = 0; insect != null && s < insect.length; s++)
     {
       if (map == null || map.containsKey(insect[s]))
       {
-        sgroup.sequences.addElement(insect[s]);
+        sgroup.sequences.add(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;
   }
 
@@ -994,13 +1112,6 @@ public class SequenceGroup implements AnnotatedCollectionI
     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
@@ -1017,7 +1128,8 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   /**
    * 
-   * @return automatically calculated consensus row
+   * @return automatically calculated consensus row note: the row is a stub if a
+   *         consensus calculation has not yet been performed on the group
    */
   public AlignmentAnnotation getConsensus()
   {
@@ -1096,9 +1208,10 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       if (consensus.annotations[i] != null)
       {
-        if (consensus.annotations[i].description.charAt(0) == '[')
+        String desc = consensus.annotations[i].description;
+        if (desc.length() > 1 && desc.charAt(0) == '[')
         {
-          seqs.append(consensus.annotations[i].description.charAt(1));
+          seqs.append(desc.charAt(1));
         }
         else
         {
@@ -1192,24 +1305,31 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     // TODO add in other methods like 'getAlignmentAnnotation(String label),
     // etc'
-    ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
-    for (SequenceI seq : (Vector<SequenceI>) sequences)
+    ArrayList<AlignmentAnnotation> annot = new ArrayList<>();
+    synchronized (sequences)
     {
-      for (AlignmentAnnotation al : seq.getAnnotation())
+      for (SequenceI seq : sequences)
       {
-        if (al.groupRef == this)
+        AlignmentAnnotation[] aa = seq.getAnnotation();
+        if (aa != null)
         {
-          annot.add(al);
+          for (AlignmentAnnotation al : aa)
+          {
+            if (al.groupRef == this)
+            {
+              annot.add(al);
+            }
+          }
         }
       }
-    }
-    if (consensus != null)
-    {
-      annot.add(consensus);
-    }
-    if (conservation != null)
-    {
-      annot.add(conservation);
+      if (consensus != null)
+      {
+        annot.add(consensus);
+      }
+      if (conservation != null)
+      {
+        annot.add(conservation);
+      }
     }
     return annot.toArray(new AlignmentAnnotation[0]);
   }
@@ -1217,19 +1337,152 @@ public class SequenceGroup implements AnnotatedCollectionI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation a : getAlignmentAnnotation())
+    return AlignmentAnnotation.findAnnotation(
+            Arrays.asList(getAlignmentAnnotation()), calcId);
+  }
+
+  @Override
+  public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+          String calcId, String label)
+  {
+    return AlignmentAnnotation.findAnnotations(
+            Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
+  }
+
+  /**
+   * Answer true if any annotation matches the calcId passed in (if not null).
+   * 
+   * @param calcId
+   * @return
+   */
+  public boolean hasAnnotation(String calcId)
+  {
+    return AlignmentAnnotation
+            .hasAnnotation(Arrays.asList(getAlignmentAnnotation()), calcId);
+  }
+
+  /**
+   * Remove all sequences from the group (leaving other properties unchanged).
+   */
+  public void clear()
+  {
+    synchronized (sequences)
     {
-      if (a.getCalcId() == calcId)
+      int before = sequences.size();
+      sequences.clear();
+      changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before,
+              sequences.size());
+    }
+  }
+
+  /**
+   * Sets the alignment or group context for this group, and whether it is
+   * defined as a group
+   * 
+   * @param ctx
+   *          the context for the group
+   * @param defined
+   *          whether the group is defined on the alignment or is just a
+   *          selection
+   * @throws IllegalArgumentException
+   *           if setting the context would result in a circular reference chain
+   */
+  public void setContext(AnnotatedCollectionI ctx, boolean defined)
+  {
+    setContext(ctx);
+    this.isDefined = defined;
+  }
+
+  /**
+   * Sets the alignment or group context for this group
+   * 
+   * @param ctx
+   *          the context for the group
+   * @throws IllegalArgumentException
+   *           if setting the context would result in a circular reference chain
+   */
+  public void setContext(AnnotatedCollectionI ctx)
+  {
+    AnnotatedCollectionI ref = ctx;
+    while (ref != null)
+    {
+      if (ref == this || ref.getContext() == ctx)
       {
-        aa.add(a);
+        throw new IllegalArgumentException(
+                "Circular reference in SequenceGroup.context");
       }
+      ref = ref.getContext();
     }
-    return aa;
+    this.context = ctx;
   }
 
-  public void clear()
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+   */
+  @Override
+  public AnnotatedCollectionI getContext()
+  {
+    return context;
+  }
+
+  public boolean isDefined()
+  {
+    return isDefined;
+  }
+
+  public void setColourScheme(ColourSchemeI scheme)
+  {
+    if (cs == null)
+    {
+      cs = new ResidueShader();
+    }
+    cs.setColourScheme(scheme);
+  }
+
+  public void setGroupColourScheme(ResidueShaderI scheme)
+  {
+    cs = scheme;
+  }
+
+  public ColourSchemeI getColourScheme()
+  {
+    return cs == null ? null : cs.getColourScheme();
+  }
+
+  public ResidueShaderI getGroupColourScheme()
+  {
+    return cs;
+  }
+
+  @Override
+  public boolean isNucleotide()
+  {
+    if (context != null)
+    {
+      return context.isNucleotide();
+    }
+    return false;
+  }
+
+  /**
+   * @param seq
+   * @return true if seq is a member of the group
+   */
+
+  public boolean contains(SequenceI seq1)
+  {
+    return sequences.contains(seq1);
+  }
+
+  /**
+   * @param seq
+   * @param apos
+   * @return true if startRes<=apos and endRes>=apos and seq is in the group
+   */
+  public boolean contains(SequenceI seq, int apos)
   {
-    sequences.clear();
+    return (startRes <= apos && endRes >= apos) && sequences.contains(seq);
   }
 }