X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceGroup.java;h=9236712b0b51d9d5c721fb269e68260bbd8093a6;hb=336e0c59bfd53d054da0bb332f858834f57e7bec;hp=679997e3c1a4847bc086eaeb2d26445bf6da757e;hpb=70d8cbb3e0f3e4986c09d9e5e42a7997d77cf9d5;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 679997e..9236712 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -1,599 +1,990 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-import jalview.analysis.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SequenceGroup
-{
-    String groupName;
-    Conservation conserve;
-    Vector aaFrequency;
-    boolean displayBoxes;
-    boolean displayText;
-    boolean colourText;
-    private Vector sequences = new Vector();
-    int width = -1;
-
-    /** DOCUMENT ME!! */
-    public ColourSchemeI cs;
-    int startRes = 0;
-    int endRes = 0;
-    Color outlineColour = Color.black;
-
-    /**
-     * Creates a new SequenceGroup object.
-     */
-    public SequenceGroup()
-    {
-        groupName = "Group";
-        this.displayBoxes = true;
-        this.displayText = true;
-        this.colourText = false;
-        cs = null;
-    }
-
-    /**
-     * 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!
-     */
-    public SequenceGroup(Vector sequences, String groupName,
-        ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
-        boolean colourText, int start, int end)
-    {
-        this.sequences = sequences;
-        this.groupName = groupName;
-        this.displayBoxes = displayBoxes;
-        this.displayText = displayText;
-        this.colourText = colourText;
-        this.cs = scheme;
-        startRes = start;
-        endRes = end;
-        recalcConservation();
-    }
-
-    /**
-     * Creates a new SequenceGroup object.
-     *
-     * @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!
-     */
-    public SequenceGroup(String groupName, ColourSchemeI scheme,
-        boolean displayBoxes, boolean displayText, boolean colourText,
-        int start, int end)
-    {
-        this.groupName = groupName;
-        this.displayBoxes = displayBoxes;
-        this.displayText = displayText;
-        this.colourText = colourText;
-        this.cs = scheme;
-        startRes = start;
-        endRes = end;
-    }
-
-    public SequenceI [] getSelectionAsNewSequences(AlignmentI align)
-    {
-      int iSize = sequences.size();
-      SequenceI [] seqs = new SequenceI[iSize];
-      SequenceI [] inorder = getSequencesInOrder(align);
-
-    for (int i = 0; i < iSize; i++)
-    {
-      SequenceI seq = inorder[i];
-
-      seqs[i] = new Sequence(seq.getName(),
-                             seq.getSequence(startRes, endRes + 1),
-                             seq.findPosition(startRes),
-                             findEndRes(seq));
-
-      seqs[i].setDescription(seq.getDescription());
-      seqs[i].setDBRef(seq.getDBRef());
-      seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
-      if (seq.getDatasetSequence() != null)
-        seqs[i].setDatasetSequence(seq.getDatasetSequence());
-
-      if(seq.getAnnotation()!=null)
-      {
-        for(int a=0; a<seq.getAnnotation().length; a++)
-          seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
-      }
-    }
-
-    return seqs;
-
-    }
-
-    /**
-     * If sequence ends in gaps, the end residue can
-     * be correctly calculated here
-     * @param seq SequenceI
-     * @return int
-     */
-    public int findEndRes(SequenceI seq)
-    {
-      int eres = 0;
-      char ch;
-
-      for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
-      {
-        ch = seq.getCharAt(j);
-        if (!jalview.util.Comparison.isGap( (ch)))
-        {
-          eres++;
-        }
-      }
-
-      if (eres > 0)
-      {
-        eres += seq.getStart() - 1;
-      }
-
-      return eres;
-    }
-
-    public Vector getSequences(boolean includeHidden)
-    {
-      if(!includeHidden)
-        return sequences;
-      else
-      {
-        Vector allSequences = new Vector();
-        SequenceI seq;
-        for (int i = 0; i < sequences.size(); i++)
-        {
-          seq = (SequenceI) sequences.elementAt(i);
-          allSequences.addElement(seq);
-          if (seq.getHiddenSequences() != null)
-          {
-            for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)
-            {
-              allSequences.addElement(
-                  seq.getHiddenSequences().getSequenceAt(h)
-                  );
-            }
-          }
-        }
-
-        return allSequences;
-      }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param col DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean adjustForRemoveLeft(int col)
-    {
-        // return value is true if the group still exists
-        if (startRes >= col)
-        {
-            startRes = startRes - col;
-        }
-
-        if (endRes >= col)
-        {
-            endRes = endRes - col;
-
-            if (startRes > endRes)
-            {
-                startRes = 0;
-            }
-        }
-        else
-        {
-            // must delete this group!!
-            return false;
-        }
-
-        return true;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param col DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean adjustForRemoveRight(int col)
-    {
-        if (startRes > col)
-        {
-            // delete this group
-            return false;
-        }
-
-        if (endRes >= col)
-        {
-            endRes = col;
-        }
-
-        return true;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getName()
-    {
-        return groupName;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param name DOCUMENT ME!
-     */
-    public void setName(String name)
-    {
-        groupName = name;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Conservation getConservation()
-    {
-        return conserve;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     */
-    public void setConservation(Conservation c)
-    {
-        conserve = c;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param recalc DOCUMENT ME!
-     */
-    public void addSequence(SequenceI s, boolean recalc)
-    {
-        if (!sequences.contains(s))
-        {
-            sequences.addElement(s);
-        }
-
-        if (recalc)
-        {
-            recalcConservation();
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void recalcConservation()
-    {
-        if(cs == null)
-          return;
-
-        try
-        {
-          cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
-
-          if (cs instanceof ClustalxColourScheme)
-          {
-            ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
-          }
-
-          if (cs.conservationApplied())
-          {
-            Conservation c = new Conservation(groupName,
-                                              ResidueProperties.propHash, 3, sequences,
-                                              0, getWidth());
-            c.calculate();
-            c.verdict(false, 25);
-
-            cs.setConservation(c);
-
-            if (cs instanceof ClustalxColourScheme)
-            {
-              ( (ClustalxColourScheme) cs).resetClustalX(sequences,
-                                                         getWidth());
-            }
-          }
-        }
-        catch (java.lang.OutOfMemoryError err)
-        {
-          System.out.println("Out of memory loading groups: " + err);
-        }
-
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param recalc DOCUMENT ME!
-     */
-    public void addOrRemove(SequenceI s, boolean recalc)
-    {
-        if (sequences.contains(s))
-        {
-            deleteSequence(s, recalc);
-        }
-        else
-        {
-            addSequence(s, recalc);
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     * @param recalc DOCUMENT ME!
-     */
-    public void deleteSequence(SequenceI s, boolean recalc)
-    {
-        sequences.removeElement(s);
-
-        if (recalc)
-        {
-            recalcConservation();
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStartRes()
-    {
-        return startRes;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEndRes()
-    {
-        return endRes;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void setStartRes(int i)
-    {
-        startRes = i;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void setEndRes(int i)
-    {
-        endRes = i;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getSize(boolean includeHidden)
-    {
-      if(!includeHidden)
-        return sequences.size();
-      else
-      {
-        int total = sequences.size();
-        SequenceI seq;
-        for (int i = 0; i < sequences.size(); i++)
-        {
-          seq = (SequenceI) sequences.elementAt(i);
-          if (seq.getHiddenSequences() != null)
-          {
-            total += seq.getHiddenSequences().getSize(false);
-          }
-        }
-        return total;
-      }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceI getSequenceAt(int i)
-    {
-        return (SequenceI) sequences.elementAt(i);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setColourText(boolean state)
-    {
-        colourText = state;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getColourText()
-    {
-        return colourText;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setDisplayText(boolean state)
-    {
-        displayText = state;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getDisplayText()
-    {
-        return displayText;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param state DOCUMENT ME!
-     */
-    public void setDisplayBoxes(boolean state)
-    {
-        displayBoxes = state;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean getDisplayBoxes()
-    {
-        return displayBoxes;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWidth()
-    {
-        // MC This needs to get reset when characters are inserted and deleted
-        if (sequences.size() > 0)
-        {
-            width = ((SequenceI) sequences.elementAt(0)).getLength();
-        }
-
-        for (int i = 1; i < sequences.size(); i++)
-        {
-            SequenceI seq = (SequenceI) sequences.elementAt(i);
-
-            if (seq.getLength() > width)
-            {
-                width = seq.getLength();
-            }
-        }
-
-        return width;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     */
-    public void setOutlineColour(Color c)
-    {
-        outlineColour = c;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color getOutlineColour()
-    {
-        return outlineColour;
-    }
-
-    /**
-     *
-     * returns the sequences in the group ordered by the ordering given by al
-     *
-     * @param al Alignment
-     * @return SequenceI[]
-     */
-    public SequenceI[] getSequencesInOrder(AlignmentI al)
-    {
-        int sSize = sequences.size();
-        int alHeight = al.getHeight();
-
-        SequenceI[] seqs = new SequenceI[sSize];
-
-        int index = 0;
-        for (int i = 0; i < alHeight && index<sSize; i++)
-        {
-          if(sequences.contains( al.getSequenceAt(i) ) )
-            seqs[index++] = al.getSequenceAt(i);
-        }
-
-        return seqs;
-    }
-}
+/*
+ * 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
+ * 
+ * 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
+ */
+package jalview.datamodel;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.schemes.*;
+
+/**
+ * Collects a set contiguous ranges on a set of sequences
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceGroup
+{
+  String groupName;
+
+  String description;
+
+  Conservation conserve;
+
+  Vector aaFrequency;
+
+  boolean displayBoxes = true;
+
+  boolean displayText = true;
+
+  boolean colourText = false;
+  /**
+   * after Olivier's non-conserved only character display
+   */
+  boolean showUnconserved = 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 */
+  public ColourSchemeI cs;
+
+  int startRes = 0;
+
+  int endRes = 0;
+
+  public Color outlineColour = Color.black;
+
+  public Color idColour = null;
+
+  public int thresholdTextColour = 0;
+
+  public Color textColour = Color.black;
+
+  public Color textColour2 = Color.white;
+
+  private boolean ignoreGapsInConsensusCalculation=true;
+
+  /**
+   * Creates a new SequenceGroup object.
+   */
+  public SequenceGroup()
+  {
+    groupName = "JGroup:" + this.hashCode();
+  }
+
+  /**
+   * Creates a new SequenceGroup object.
+   * 
+   * @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)
+  {
+    this.sequences = sequences;
+    this.groupName = groupName;
+    this.displayBoxes = displayBoxes;
+    this.displayText = displayText;
+    this.colourText = colourText;
+    this.cs = scheme;
+    startRes = start;
+    endRes = end;
+    recalcConservation();
+  }
+  /**
+   * copy constructor
+   * @param seqsel
+   */
+  public SequenceGroup(SequenceGroup seqsel)
+  {
+    if (seqsel!=null)
+    {
+      sequences=new Vector();
+      Enumeration 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;
+      ignoreGapsInConsensusCalculation = seqsel.ignoreGapsInConsensusCalculation;
+      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++)
+    {
+      SequenceI seq = inorder[i];
+
+      seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
+      if (seqs[ipos] != null)
+      {
+        seqs[ipos].setDescription(seq.getDescription());
+        seqs[ipos].setDBRef(seq.getDBRef());
+        seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
+        if (seq.getDatasetSequence() != null)
+        {
+          seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
+        }
+
+        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 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();
+            seqs[ipos].addAlignmentAnnotation(newannot);
+          }
+        }
+        ipos++;
+      }
+      else
+      {
+        iSize--;
+      }
+    }
+    if (iSize != inorder.length)
+    {
+      SequenceI[] nseqs = new SequenceI[iSize];
+      System.arraycopy(seqs, 0, nseqs, 0, iSize);
+      seqs = nseqs;
+    }
+    return seqs;
+
+  }
+
+  /**
+   * If sequence ends in gaps, the end residue can be correctly calculated here
+   * 
+   * @param seq
+   *                SequenceI
+   * @return int
+   */
+  public int findEndRes(SequenceI seq)
+  {
+    int eres = 0;
+    char ch;
+
+    for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
+    {
+      ch = seq.getCharAt(j);
+      if (!jalview.util.Comparison.isGap((ch)))
+      {
+        eres++;
+      }
+    }
+
+    if (eres > 0)
+    {
+      eres += seq.getStart() - 1;
+    }
+
+    return eres;
+  }
+
+  public Vector getSequences(Hashtable hiddenReps)
+  {
+    if (hiddenReps == null)
+    {
+      return sequences;
+    }
+    else
+    {
+      Vector allSequences = new Vector();
+      SequenceI seq, seq2;
+      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++)
+          {
+            seq2 = hsg.getSequenceAt(h);
+            if (seq2 != seq && !allSequences.contains(seq2))
+            {
+              allSequences.addElement(seq2);
+            }
+          }
+        }
+      }
+
+      return allSequences;
+    }
+  }
+
+  public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
+  {
+    Vector tmp = getSequences(hiddenReps);
+    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;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param col
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean adjustForRemoveLeft(int col)
+  {
+    // return value is true if the group still exists
+    if (startRes >= col)
+    {
+      startRes = startRes - col;
+    }
+
+    if (endRes >= col)
+    {
+      endRes = endRes - col;
+
+      if (startRes > endRes)
+      {
+        startRes = 0;
+      }
+    }
+    else
+    {
+      // must delete this group!!
+      return false;
+    }
+
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param col
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean adjustForRemoveRight(int col)
+  {
+    if (startRes > col)
+    {
+      // delete this group
+      return false;
+    }
+
+    if (endRes >= col)
+    {
+      endRes = col;
+    }
+
+    return true;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String getName()
+  {
+    return groupName;
+  }
+
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param name
+   *                DOCUMENT ME!
+   */
+  public void setName(String name)
+  {
+    groupName = name;
+  }
+
+  public void setDescription(String desc)
+  {
+    description = desc;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Conservation getConservation()
+  {
+    return conserve;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
+   */
+  public void setConservation(Conservation c)
+  {
+    conserve = c;
+  }
+
+  /**
+   * Add s to this sequence group
+   * 
+   * @param s
+   *                alignment sequence to be added
+   * @param recalc
+   *                true means Group's conservation should be recalculated
+   */
+  public void addSequence(SequenceI s, boolean recalc)
+  {
+    if (s != null && !sequences.contains(s))
+    {
+      sequences.addElement(s);
+    }
+
+    if (recalc)
+    {
+      recalcConservation();
+    }
+  }
+
+  /**
+   * calculate residue conservation for group
+   */
+  public void recalcConservation()
+  {
+    if (cs == null && consensus == null && conservation == null)
+    {
+      return;
+    }
+    
+    try
+    {
+      Hashtable cnsns[] = AAFrequency.calculate(sequences, startRes, endRes + 1);
+      if (consensus != null)
+      {
+        _updateConsensusRow(cnsns);
+      }
+      if (cs!=null)
+      {
+        cs.setConsensus(cnsns);
+      
+      if (cs instanceof ClustalxColourScheme)
+      {
+        ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+      }
+      }
+
+      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)
+        {
+          _updateConservationRow(c);
+        }
+        if (cs!=null)
+        {
+          cs.setConservation(c);
+        
+        if (cs instanceof ClustalxColourScheme)
+        {
+          ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+        }
+        }
+      }
+    } 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();
+    }
+    // preserve width if already set
+    int aWidth = (conservation.annotations!=null) ? (endRes<conservation.annotations.length ? conservation.annotations.length : endRes+1) : endRes+1;
+    c.completeAnnotations(conservation,null, aWidth);
+  }
+
+  private void _updateConsensusRow(Hashtable[] cnsns)
+  {
+    if (consensus==null)
+    {
+      getConsensus();
+    }
+    // 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,ignoreGapsInConsensusCalculation); // TODO: setting container for ignoreGapsInConsensusCalculation);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param recalc
+   *                DOCUMENT ME!
+   */
+  public void addOrRemove(SequenceI s, boolean recalc)
+  {
+    if (sequences.contains(s))
+    {
+      deleteSequence(s, recalc);
+    }
+    else
+    {
+      addSequence(s, recalc);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   * @param recalc
+   *                DOCUMENT ME!
+   */
+  public void deleteSequence(SequenceI s, boolean recalc)
+  {
+    sequences.removeElement(s);
+
+    if (recalc)
+    {
+      recalcConservation();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getStartRes()
+  {
+    return startRes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getEndRes()
+  {
+    return endRes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   */
+  public void setStartRes(int i)
+  {
+    startRes = i;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   */
+  public void setEndRes(int i)
+  {
+    endRes = i;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getSize()
+  {
+    return sequences.size();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public SequenceI getSequenceAt(int i)
+  {
+    return (SequenceI) sequences.elementAt(i);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
+   */
+  public void setColourText(boolean state)
+  {
+    colourText = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getColourText()
+  {
+    return colourText;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
+   */
+  public void setDisplayText(boolean state)
+  {
+    displayText = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getDisplayText()
+  {
+    return displayText;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param state
+   *                DOCUMENT ME!
+   */
+  public void setDisplayBoxes(boolean state)
+  {
+    displayBoxes = state;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean getDisplayBoxes()
+  {
+    return displayBoxes;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getWidth()
+  {
+    // MC This needs to get reset when characters are inserted and deleted
+    if (sequences.size() > 0)
+    {
+      width = ((SequenceI) sequences.elementAt(0)).getLength();
+    }
+
+    for (int i = 1; i < sequences.size(); i++)
+    {
+      SequenceI seq = (SequenceI) sequences.elementAt(i);
+
+      if (seq.getLength() > width)
+      {
+        width = seq.getLength();
+      }
+    }
+
+    return width;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param c
+   *                DOCUMENT ME!
+   */
+  public void setOutlineColour(Color c)
+  {
+    outlineColour = c;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Color getOutlineColour()
+  {
+    return outlineColour;
+  }
+
+  /**
+   * 
+   * 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)
+  {
+    int sSize = sequences.size();
+    int alHeight = al.getHeight();
+
+    SequenceI[] seqs = new SequenceI[sSize];
+
+    int index = 0;
+    for (int i = 0; i < alHeight && index < sSize; i++)
+    {
+      if (sequences.contains(al.getSequenceAt(i)))
+      {
+        seqs[index++] = al.getSequenceAt(i);
+      }
+    }
+    if (index==0)
+    {
+      return null;
+    }
+    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 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);
+    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);
+   //   }
+   // }
+    return sgroup;
+  }
+
+  /**
+   * @return the showUnconserved
+   */
+  public boolean getShowunconserved()
+  {
+    return showUnconserved;
+  }
+
+  /**
+   * @param showUnconserved the showUnconserved to set
+   */
+  public void setShowunconserved(boolean displayNonconserved)
+  {
+    this.showUnconserved = displayNonconserved;
+  }
+  AlignmentAnnotation consensus=null,conservation=null;
+  /**
+   * 
+   * @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("Consensus for "+getName(), "PID",
+              new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+      consensus.hasText = true;
+      consensus.autoCalculated = true;
+      consensus.groupRef = this;
+    }
+    return consensus;
+  }
+    /**
+   * 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",
+            "Conservation of total alignment less than " + ConsPercGaps
+                    + "% gaps", new Annotation[1], 0f, 11f,
+            AlignmentAnnotation.BAR_GRAPH);
+    conservation.hasText = true;
+    conservation.autoCalculated = true;
+    conservation.groupRef = this;
+      }
+    
+    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 "
+            + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+    return sq;    
+  }
+
+  public void setIgnoreGapsConsensus(boolean state)
+  {
+    if (this.ignoreGapsInConsensusCalculation!=state && consensus!=null)
+    {
+      ignoreGapsInConsensusCalculation = state;
+      recalcConservation();
+    }
+    ignoreGapsInConsensusCalculation = state;
+  }
+}