X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=b0b04cae8739551cd24ee5b045d62d5391d81b01;hb=1ed150e97b6a7df6ebe5cf92ead96cd147a58b7e;hp=dd02bc12626f3b396b3109ee24a6a0aa92747c9d;hpb=2cf0e6316cf8b4e545bad1648966b02fad49017f;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index dd02bc1..b0b04ca 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,481 +1,857 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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.util.*;
+
 import java.util.*;
 
 /** Data structure to hold and manipulate a multiple sequence alignment
  */
 public class Alignment implements AlignmentI
 {
+    protected Alignment dataset;
+    protected Vector sequences;
+    protected Vector groups = new Vector();
+    protected Vector superGroup = new Vector();
+    protected char gapCharacter = '-';
+    protected int type = NUCLEOTIDE;
+    public static final int PROTEIN = 0;
+    public static final int NUCLEOTIDE = 1;
+
+    /** DOCUMENT ME!! */
+    public AlignmentAnnotation[] annotations;
+
+    HiddenSequences hiddenSequences = new HiddenSequences(this);
+
+
+    /** Make an alignment from an array of Sequences.
+     *
+     * @param sequences
+     */
+    public Alignment(SequenceI[] seqs)
+    {
+        int i=0;
 
-  protected Vector      sequences;
-  protected Vector      groups = new Vector();
-  protected char      gapCharacter = '-';
+        if( jalview.util.Comparison.isNucleotide(seqs))
+          type = NUCLEOTIDE;
+        else
+          type = PROTEIN;
 
-  /** Make an alignment from an array of Sequences.
-  *
-  * @param sequences
-  */
-  public Alignment(SequenceI[] seqs) {
-    sequences = new Vector();
+        sequences = new Vector();
 
-    for (int i=0; i < seqs.length; i++)
-      sequences.addElement(seqs[i]);
+        for (i = 0; i < seqs.length; i++)
+        {
+            sequences.addElement(seqs[i]);
 
-    getWidth();
-  }
+            if(seqs[i].getDatasetSequence()!=null
+            && seqs[i].getDatasetSequence().getAnnotation()!=null)
+            {
 
-  public Vector      getSequences() {
-    return sequences;
-  }
+              for(int a=0; a<seqs[i].getDatasetSequence().getAnnotation().length; a++)
+              {
+                       this.addAnnotation(seqs[i].getDatasetSequence().getAnnotation()[a], seqs[i]);
+              }
+            }
+        }
 
-  public SequenceI getSequenceAt(int i) {
-    if (i < sequences.size()) {
-      return (SequenceI)sequences.elementAt(i);
+        getWidth();
     }
 
-    return null;
-  }
-
-  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   * Should put the new sequence in a sequence group!!!
-   *
-   * @param snew
-   */
-  public void addSequence(SequenceI snew) {
-    sequences.addElement(snew);
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getSequences()
+    {
+        return sequences;
+    }
 
-    ((SequenceGroup)groups.lastElement()).addSequence(snew);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceI getSequenceAt(int i)
+    {
+        if (i < sequences.size())
+        {
+            return (SequenceI) sequences.elementAt(i);
+        }
 
-  public void addSequence(SequenceI[] seq) {
-    for (int i=0; i < seq.length; i++) {
-      addSequence(seq[i]);
+        return null;
     }
-  }
 
-  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-   * Should put the new sequence in a sequence group!!!
-   *
-   * @param snew
-   */
-  public void setSequenceAt(int i,SequenceI snew) {
-    SequenceI oldseq = getSequenceAt(i);
-    deleteSequence(oldseq);
-
-    sequences.setElementAt(snew,i);
+    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
+     *
+     * @param snew
+     */
+    public void addSequence(SequenceI snew)
+    {
+        sequences.addElement(snew);
+    }
 
-    ((SequenceGroup)groups.lastElement()).addSequence(snew);
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq DOCUMENT ME!
+     */
+    public void addSequence(SequenceI[] seq)
+    {
+        for (int i = 0; i < seq.length; i++)
+        {
+            addSequence(seq[i]);
+        }
+    }
 
-  public Vector getGroups() {
-    return groups;
-  }
+    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
+     *
+     * @param snew
+     */
+    public void setSequenceAt(int i, SequenceI snew)
+    {
+        SequenceI oldseq = getSequenceAt(i);
+        deleteSequence(oldseq);
 
-  /** Sorts the sequences by sequence group size - largest to smallest.
-   * Uses QuickSort.
-   */
-  public void sortGroups() {
-    float[]  arr = new float [groups.size()];
-    Object[] s   = new Object[groups.size()];
+        sequences.setElementAt(snew, i);
+    }
 
-    for (int i=0; i < groups.size(); i++) {
-      arr[i] = ((SequenceGroup)groups.elementAt(i)).sequences.size();
-      s[i]   = groups.elementAt(i);
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getGroups()
+    {
+        return groups;
     }
 
-    QuickSort.sort(arr,s);
+    /** Takes out columns consisting entirely of gaps (-,.," ")
+     */
+    public void removeGaps()
+    {
+        SequenceI current;
+        int iSize = getWidth();
 
-    Vector newg = new Vector(groups.size());
+        for (int i = 0; i < iSize; i++)
+        {
+            boolean delete = true;
+
+            for (int j = 0; j < getHeight(); j++)
+            {
+                current = getSequenceAt(j);
+
+                if (current.getLength() > i)
+                {
+                    /* MC Should move this to a method somewhere */
+                    if (!jalview.util.Comparison.isGap(current.getCharAt(i)))
+                    {
+                        delete = false;
+                    }
+                }
+            }
+
+            if (delete)
+            {
+                deleteColumns(i, i);
+                iSize--;
+                i--;
+            }
+        }
+    }
 
-    for (int i=groups.size()-1; i >= 0; i--) {
-      newg.addElement(s[i]);
+    /** Removes a range of columns (start to end inclusive).
+     *
+     * @param start Start column in the alignment
+     * @param end End column in the alignment
+     */
+    public void deleteColumns(int start, int end)
+    {
+        deleteColumns(0, getHeight() - 1, start, end);
     }
 
-    groups = newg;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param seq1 DOCUMENT ME!
+     * @param seq2 DOCUMENT ME!
+     * @param start DOCUMENT ME!
+     * @param end DOCUMENT ME!
+     */
+    public void deleteColumns(int seq1, int seq2, int start, int end)
+    {
+        for (int i = 0; i <= (end - start); i++)
+        {
+            for (int j = seq1; j <= seq2; j++)
+            {
+                getSequenceAt(j).deleteCharAt(start);
+            }
+        }
+    }
 
-  /** Takes out columns consisting entirely of gaps (-,.," ")
-   */
-  public void removeGaps()
-  {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void trimLeft(int i)
+    {
+        int j, jSize = getHeight();
+        for (j = 0; j < jSize; j++)
+        {
+            SequenceI s = getSequenceAt(j);
+            int newstart = s.findPosition(i);
+
+            if(i>s.getLength())
+            {
+              sequences.removeElement(s);
+              j--;
+              jSize--;
+            }
+            else
+            {
+              s.setStart(newstart);
+              s.setSequence(s.getSequence().substring(i));
+            }
+        }
+    }
 
-    SequenceI current;
-    int iSize = getWidth();
-    for (int i=0; i < iSize; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void trimRight(int i)
     {
-      boolean delete = true;
-      for (int j=0; j < getHeight(); j++)
-      {
-        current = getSequenceAt(j);
-        if (current.getLength() > i)
+        for (int j = 0; j < getHeight(); j++)
         {
-	    /* MC Should move this to a method somewhere */
-          if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))
-            delete = false;
+            SequenceI s = getSequenceAt(j);
+            int newend = s.findPosition(i);
 
+            s.setEnd(newend);
+            if(s.getLength()>i)
+              s.setSequence(s.getSequence().substring(0, i + 1));
         }
-      }
+    }
 
-      if ( delete )
-      {
-        deleteColumns(i,i);
-        iSize--;
-        i--;
-      }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     */
+    public void deleteSequence(SequenceI s)
+    {
+        for (int i = 0; i < getHeight(); i++)
+        {
+            if (getSequenceAt(i) == s)
+            {
+                deleteSequence(i);
+            }
+        }
     }
 
+    /**
+     * DOCUMENT ME!
+     *
+     * @param i DOCUMENT ME!
+     */
+    public void deleteSequence(int i)
+    {
+        sequences.removeElementAt(i);
+    }
 
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param threshold DOCUMENT ME!
+     * @param sel DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector removeRedundancy(float threshold, Vector sel)
+    {
+        Vector del = new Vector();
 
-  /** Returns an array of Sequences containing columns
-   * start to end (inclusive) only.
-   *
-   * @param start start column to fetch
-   * @param end end column to fetch
-   * @return Array of Sequences, ready to put into a new Alignment
-   */
-  public SequenceI[] getColumns(int start, int end) {
-    return getColumns(0,getHeight()-1,start,end);
-  }
+        for (int i = 1; i < sel.size(); i++)
+        {
+            for (int j = 0; j < i; j++)
+            {
+                // Only do the comparison if either have not been deleted
+                if (!del.contains((SequenceI) sel.elementAt(i)) ||
+                        !del.contains((SequenceI) sel.elementAt(j)))
+                {
+                    // use PID instead of Comparison (which is really not pleasant)
+                    float pid = Comparison.PID((SequenceI) sel.elementAt(j),
+                            (SequenceI) sel.elementAt(i));
+
+                    if (pid >= threshold)
+                    {
+                        // Delete the shortest one
+                        if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel
+                                                                                         .elementAt(
+                                    i)).getSequence().length())
+                        {
+                            del.addElement(sel.elementAt(i));
+                        }
+                        else
+                        {
+                            del.addElement(sel.elementAt(i));
+                        }
+                    }
+                }
+            }
+        }
 
-  /** Removes a range of columns (start to end inclusive).
-   *
-   * @param start Start column in the alignment
-   * @param end End column in the alignment
-   */
-  public void deleteColumns(int start, int end) {
-    deleteColumns(0,getHeight()-1,start,end);
-  }
+        // Now delete the sequences
+        for (int i = 0; i < del.size(); i++)
+        {
+            deleteSequence((SequenceI) del.elementAt(i));
+        }
 
-  public void deleteColumns(int seq1, int seq2, int start, int end) {
+        return del;
+    }
 
-    for (int i=0; i <= (end-start); i++) {
-      for (int j=seq1; j <= seq2; j++) {
-        getSequenceAt(j).deleteCharAt(start);
-      }
+    /**    */
+    public SequenceGroup findGroup(int i)
+    {
+        return findGroup(getSequenceAt(i));
     }
-  }
 
-  public void insertColumns(SequenceI[] seqs, int pos) {
-    if (seqs.length == getHeight()) {
-      for (int i=0; i < getHeight();i++) {
-        String tmp = new String(getSequenceAt(i).getSequence());
-        getSequenceAt(i).setSequence(tmp.substring(0,pos) + seqs[i].getSequence() + tmp.substring(pos));
-      }
+    /**    */
+    public SequenceGroup findGroup(SequenceI s)
+    {
+        for (int i = 0; i < this.groups.size(); i++)
+        {
+            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-    }
-  }
+            if (sg.sequences.contains(s))
+            {
+                return sg;
+            }
+        }
 
-  public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {
-    SequenceI[] seqs = new Sequence[(seq2-seq1)+1];
-    for (int i=seq1; i<= seq2; i++ ) {
-      seqs[i] = new Sequence(getSequenceAt(i).getName(),
-                             getSequenceAt(i).getSequence().substring(start,end),
-                             getSequenceAt(i).findPosition(start),
-                             getSequenceAt(i).findPosition(end));
+        return null;
     }
-    return seqs;
-  }
 
-  public void trimLeft(int i) {
-    for (int j = 0;j< getHeight();j++) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceGroup[] findAllGroups(SequenceI s)
+    {
+        Vector temp = new Vector();
+
+        int gSize = groups.size();
+        for (int i = 0; i < gSize; i++)
+        {
+            SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+            if(sg==null || sg.sequences==null)
+            {
+              this.deleteGroup(sg);
+              gSize--;
+              continue;
+            }
+
+            if (sg.sequences.contains(s))
+            {
+                temp.addElement(sg);
+            }
+        }
 
-      SequenceI s        = getSequenceAt(j);
-      int       newstart = s.findPosition(i);
+        SequenceGroup[] ret = new SequenceGroup[temp.size()];
 
-      s.setStart(newstart);
-      s.setSequence(s.getSequence().substring(i));
+        for (int i = 0; i < temp.size(); i++)
+        {
+            ret[i] = (SequenceGroup) temp.elementAt(i);
+        }
 
+        return ret;
     }
-  }
 
-  public void  trimRight(int i) {
-    for (int j = 0;j< getHeight();j++) {
-      SequenceI s      = getSequenceAt(j);
-      int       newend = s.findPosition(i);
 
-      s.setEnd(newend);
-      s.setSequence(s.getSequence().substring(0,i+1));
-    }
-  }
 
-  public void deleteSequence(SequenceI s)
-  {
-    for (int i=0; i < getHeight(); i++)
-      if (getSequenceAt(i) == s)
-        deleteSequence(i);
-  }
+    /**    */
+    public void addGroup(SequenceGroup sg)
+    {
+        if (!groups.contains(sg))
+        {
+            groups.addElement(sg);
+        }
+    }
 
-  public void  deleteSequence(int i)
-  {
-    sequences.removeElementAt(i);
-  }
+    /**
+     * DOCUMENT ME!
+     */
+    public void deleteAllGroups()
+    {
+        groups.removeAllElements();
+        superGroup.removeAllElements();
 
+        int i = 0;
 
-  public Vector removeRedundancy(float threshold, Vector sel) {
-    Vector del = new Vector();
+        while (i < sequences.size())
+        {
+            SequenceI s = getSequenceAt(i);
+            s.setColor(java.awt.Color.white);
+            i++;
+        }
+    }
 
-    for (int i = 1; i < sel.size(); i++)
+    /**    */
+    public void deleteGroup(SequenceGroup g)
     {
-      for (int j = 0; j < i; j++)
-      {
-        // Only do the comparison if either have not been deleted
-        if (!del.contains( (SequenceI) sel.elementAt(i)) ||
-            !del.contains( (SequenceI) sel.elementAt(j)))
+        if (groups.contains(g))
         {
+            groups.removeElement(g);
+        }
+    }
 
-          float pid = Comparison.compare( (SequenceI) sel.elementAt(j),
-                                         (SequenceI) sel.elementAt(i));
+    /**    */
+    public SequenceI findName(String name)
+    {
+        int i = 0;
 
-          if (pid >= threshold)
-          {
-            // Delete the shortest one
-            if ( ( (SequenceI) sel.elementAt(j)).getSequence().length() >
-                ( (SequenceI) sel.elementAt(i)).getSequence().length())
-              del.addElement(sel.elementAt(i));
-            else
-              del.addElement(sel.elementAt(i));
-          }
+        while (i < sequences.size())
+        {
+            if (getSequenceAt(i).getName().equals(name))
+            {
+                return getSequenceAt(i);
+            }
+
+            i++;
         }
-      }
+
+        return null;
     }
 
-    // Now delete the sequences
-    for (int i=0; i < del.size(); i++)
-      deleteSequence((SequenceI)del.elementAt(i));
 
-    return del;
-  }
+    /**    */
+    public int findIndex(SequenceI s)
+    {
+        int i = 0;
 
-  public void sortByPID(SequenceI s) {
+        while (i < sequences.size())
+        {
+            if (s == getSequenceAt(i))
+            {
+                return i;
+            }
 
-    float     scores[] = new float[getHeight()];
-    SequenceI seqs[]   = new SequenceI[getHeight()];
+            i++;
+        }
 
-    for (int i = 0; i < getHeight(); i++) {
-      scores[i] = Comparison.compare(getSequenceAt(i),s);
-      seqs[i]   = getSequenceAt(i);
+        return -1;
     }
 
-    QuickSort.sort(scores,0,scores.length-1,seqs);
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getHeight()
+    {
+        return sequences.size();
+    }
 
-    int len = 0;
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getWidth()
+    {
+        int maxLength = -1;
 
-    if (getHeight()%2 == 0) {
-      len = getHeight()/2;
-    } else {
-      len = (getHeight()+1)/2;
-    }
+        for (int i = 0; i < sequences.size(); i++)
+        {
+            if (getSequenceAt(i).getLength() > maxLength)
+            {
+                maxLength = getSequenceAt(i).getLength();
+            }
+        }
 
-    for (int i = 0; i < len; i++) {
-      SequenceI tmp = seqs[i];
-      sequences.setElementAt(seqs[getHeight()-i-1],i);
-      sequences.setElementAt(tmp,getHeight()-i-1);
+        return maxLength;
     }
-  }
 
-  public void sortByID() {
-    String    ids[]   = new String[getHeight()];
-    SequenceI seqs[]  = new SequenceI[getHeight()];
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public int getMaxIdLength()
+    {
+        int max = 0;
+        int i = 0;
 
-    for (int i = 0; i < getHeight(); i++) {
-      ids[i]  = getSequenceAt(i).getName();
-      seqs[i] = getSequenceAt(i);
-    }
+        while (i < sequences.size())
+        {
+            SequenceI seq = getSequenceAt(i);
+            String tmp = seq.getName() + "/" + seq.getStart() + "-" +
+                seq.getEnd();
 
-    QuickSort.sort(ids,seqs);
+            if (tmp.length() > max)
+            {
+                max = tmp.length();
+            }
 
-    int len = 0;
+            i++;
+        }
 
-    if (getHeight()%2 == 0) {
-      len = getHeight()/2;
-    } else {
-      len = (getHeight()+1)/2;
-      System.out.println("Sort len is odd = " + len);
-    }
-    for (int i = 0; i < len; i++) {
-      System.out.println("Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName());
-      SequenceI tmp = seqs[i];
-      sequences.setElementAt(seqs[getHeight()-i-1],i);
-      sequences.setElementAt(tmp,getHeight()-i-1);
+        return max;
     }
-  }
 
-  /**    */
-  public SequenceGroup findGroup(int i) {
-    return findGroup(getSequenceAt(i));
-  }
-
-  /**    */
-  public SequenceGroup findGroup(SequenceI s) {
-    for (int i = 0; i < this.groups.size();i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param gc DOCUMENT ME!
+     */
+    public void setGapCharacter(char gc)
     {
-      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-      if (sg.sequences.contains(s))
-        return sg;
+        gapCharacter = gc;
 
+        for (int i = 0; i < sequences.size(); i++)
+        {
+            Sequence seq = (Sequence) sequences.elementAt(i);
+            seq.sequence = seq.sequence.replace('.', gc);
+            seq.sequence = seq.sequence.replace('-', gc);
+            seq.sequence = seq.sequence.replace(' ', gc);
+        }
     }
-    return null;
-  }
 
-  public SequenceGroup [] findAllGroups(SequenceI s)
-  {
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public char getGapCharacter()
+    {
+        return gapCharacter;
+    }
 
-    ArrayList temp = new ArrayList();
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getAAFrequency()
+    {
+        return AAFrequency.calculate(sequences, 0, getWidth());
+    }
 
-    for (int i = 0; i < this.groups.size();i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean isAligned()
     {
-      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
-      if (sg.sequences.contains(s))
-       temp.add(sg);
+        int width = getWidth();
+
+        for (int i = 0; i < sequences.size(); i++)
+        {
+            if (getSequenceAt(i).getLength() != width)
+            {
+                return false;
+            }
+        }
+
+        return true;
     }
 
-    SequenceGroup [] ret = new SequenceGroup[temp.size()];
-    temp.toArray( ret );
+    /**
+     * DOCUMENT ME!
+     *
+     * @param aa DOCUMENT ME!
+     */
+    public void deleteAnnotation(AlignmentAnnotation aa)
+    {
+        int aSize = 1;
+
+        if (annotations != null)
+        {
+            aSize = annotations.length;
+        }
+
+        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+
+        int tIndex = 0;
 
-    return ret;
+        for (int i = 0; i < aSize; i++)
+        {
+            if (annotations[i] == aa)
+            {
+                continue;
+            }
 
-  }
-  /**    */
-  public void addToGroup(SequenceGroup g, SequenceI s) {
-    if (!(g.sequences.contains(s))) {
-      g.sequences.addElement(s);
+            temp[tIndex] = annotations[i];
+            tIndex++;
+        }
+
+        annotations = temp;
     }
-  }
-  /**    */
-  public void removeFromGroup(SequenceGroup g,SequenceI s) {
-    if (g != null && g.sequences != null) {
-      if (g.sequences.contains(s)) {
-        g.sequences.removeElement(s);
-        if (g.sequences.size() == 0) {
-          groups.removeElement(g);
+
+    /**
+     *
+     * @param aa AlignmentAnnotation
+     * @param seqRef The sequence to associate this annotation with
+     * @return The adjusted AlignmentAnnotation, with dataset sequence and annotation added
+     */
+    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef)
+    {
+      if(seqRef!=null)
+      {
+          //We can only add Annotations to the dataset sequences
+           if(seqRef.getDatasetSequence()==null)
+           {
+                  setDataset(null);
+            }
+
+        AlignmentAnnotation []  old = seqRef.getDatasetSequence().getAnnotation();
+
+        //First check if this is a new annotation or not. If it is new,
+        //we must add the annotation to the dataset
+        boolean newAnnotation = true;
+        if(seqRef.getDatasetSequence().getAnnotation()!=null)
+        {
+          for(int a=0; a<old.length; a++)
+          {
+            if(old[a] == aa)
+            {
+
+              newAnnotation = false;
+              break;
+            }
+          }
         }
+
+        if(newAnnotation)
+         {
+           seqRef.getDatasetSequence().addAlignmentAnnotation(aa);
+         }
+
+          AlignmentAnnotation copy = null;
+          if (aa.graph > 0)
+            copy = new AlignmentAnnotation(
+                aa.label, aa.description, aa.annotations, aa.graphMin,
+                aa.graphMax, aa.graph
+                );
+          else
+            copy = new AlignmentAnnotation(
+                aa.label, aa.description, aa.annotations
+                );
+
+         copy.datasetAnnotation = aa;
+
+         addAnnotation(copy);
+
+         copy.sequenceRef = seqRef;
+
+         return copy;
+      }
+      else
+      {
+        addAnnotation(aa);
+        return aa;
       }
     }
-  }
 
-  /**    */
-  public void addGroup(SequenceGroup sg) {
-    if(!groups.contains(sg))
-      groups.addElement(sg);
-  }
+    public void adjustSequenceAnnotations()
+    {
+      if(annotations!=null)
+      {
+        for (int a = 0; a < annotations.length; a++)
+        {
+          if (annotations[a].sequenceRef != null)
+          {
+            annotations[a].adjustForAlignment();
+          }
+        }
+      }
+    }
 
-  /**    */
-  public SequenceGroup addGroup() {
-    SequenceGroup sg = new SequenceGroup();
-    groups.addElement(sg);
-    return sg;
-  }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param aa DOCUMENT ME!
+     */
+    public void addAnnotation(AlignmentAnnotation aa)
+    {
+        int aSize = 1;
+        if (annotations != null)
+        {
+            aSize = annotations.length + 1;
+        }
 
-  /**    */
-  public void deleteGroup(SequenceGroup g) {
-    if (groups.contains(g)) {
-      groups.removeElement(g);
-    }
-  }
+        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
 
-  /**    */
-  public SequenceI findName(String name) {
-    int i = 0;
-    while (i < sequences.size()) {
-      SequenceI s = getSequenceAt(i);
-      if (s.getName().equals(name))
-        return s;
+        temp[aSize-1] = aa;
 
-      i++;
-    }
-    return null;
-  }
+        int i = 0;
 
-  /**    */
-  public SequenceI findbyDisplayId(String name) {
-    int i = 0;
-    while (i < sequences.size()) {
-      SequenceI s = getSequenceAt(i);
-      if (s.getDisplayId().equals(name))
-        return s;
+        if (aSize > 1)
+        {
+            for (i = 0; i < (aSize-1); i++)
+            {
+                temp[i] = annotations[i];
+            }
+        }
 
-      i++;
+        annotations = temp;
     }
-    return null;
-  }
 
-  /**    */
-  public int findIndex(SequenceI s)
-  {
-    int i=0;
-    while (i < sequences.size())
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index)
     {
-      if (s == getSequenceAt(i))
-        return i;
+      if(aa==null || annotations==null || annotations.length-1<index)
+        return;
 
-      i++;
-    }
-    return -1;
-  }
+      int aSize = annotations.length;
+      AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
 
-  public int getHeight() {
-    return sequences.size();
-  }
+      temp[index] = aa;
 
+      for (int i = 0; i < aSize; i++)
+      {
+        if(i==index)
+          continue;
 
-  public int getWidth()
-  {
-    int maxLength = -1;
-    for (int i = 0; i < sequences.size(); i++)
+        if(i<index)
+          temp[i] = annotations[i];
+        else
+          temp[i] = annotations[i-1];
+      }
+
+        annotations = temp;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public AlignmentAnnotation[] getAlignmentAnnotation()
     {
-      if (getSequenceAt(i).getLength() > maxLength)
-        maxLength = getSequenceAt(i).getLength();
+        return annotations;
     }
 
-    return maxLength;
-  }
+    public void setNucleotide(boolean b)
+    {
+      if(b)
+        type = NUCLEOTIDE;
+      else
+        type = PROTEIN;
+    }
 
+    public boolean isNucleotide()
+    {
+      if(type==NUCLEOTIDE)
+        return true;
+      else
+        return false;
+    }
+
+    public void setDataset(Alignment data)
+    {
+      if(dataset==null && data==null)
+      {
+        // Create a new dataset for this alignment.
+        // Can only be done once, if dataset is not null
+        // This will not be performed
+        Sequence[] seqs = new Sequence[getHeight()];
+        for (int i = 0; i < getHeight(); i++)
+        {
 
-  public int getMaxIdLength() {
-    int max = 0;
-    int i   = 0;
+          seqs[i] = new Sequence(getSequenceAt(i).getName(),
+                                 AlignSeq.extractGaps(
+                                     jalview.util.Comparison.GapChars,
+                                     getSequenceAt(i).getSequence()
+                                 ),
+                                 getSequenceAt(i).getStart(),
+                                 getSequenceAt(i).getEnd());
 
-    while (i < sequences.size()) {
-      SequenceI seq = getSequenceAt(i);
-      String    tmp = seq.getName() + "/" + seq.getStart() + "-" + seq.getEnd();
+          getSequenceAt(i).setDatasetSequence(seqs[i]);
+        }
 
-      if (tmp.length() > max) {
-        max = tmp.length();
+        dataset = new Alignment(seqs);
+      }
+      else if(dataset==null && data!=null)
+      {
+        dataset = data;
       }
+    }
 
-      i++;
-    }
-    return max;
-  }
-
-  public void setGapCharacter(char gc)
-  {
-    char old = getGapCharacter();
-    gapCharacter = gc;
-    for (int i=0; i < sequences.size(); i++)
-     {
-       Sequence seq = (Sequence)sequences.elementAt(i);
-       seq.sequence = seq.sequence.replace(old, gc);
-     }
-  }
-
-  public char getGapCharacter() {
-    return gapCharacter;
-  }
-
-  public Vector getAAFrequency()
-  {
-    return AAFrequency.calculate(sequences, 0, getWidth());
-  }
-}
+    public Alignment getDataset()
+    {
+      return dataset;
+    }
 
+    public boolean padGaps() {
+      boolean modified=false;
 
+      //Remove excess gaps from the end of alignment
+      int maxLength = -1;
 
+      SequenceI current;
+      for (int i = 0; i < sequences.size(); i++)
+      {
+        current = getSequenceAt(i);
+        for (int j = current.getLength(); j > maxLength; j--)
+        {
+          if (j > maxLength && !jalview.util.Comparison.isGap(
+              current.getCharAt(j)))
+          {
+            maxLength = j;
+            break;
+          }
+        }
+      }
 
+      maxLength++;
 
+      for (int i = 0; i < sequences.size();
+           i++)
+      {
+        current = getSequenceAt(i);
 
+        if (current.getLength() < maxLength)
+        {
+          current.insertCharAt(maxLength - 1, gapCharacter);
+          modified=true;
+        }
+        else if(current.getLength() > maxLength)
+        {
+          current.deleteChars(maxLength, current.getLength());
+        }
+      }
+      return modified;
+    }
 
+    public HiddenSequences getHiddenSequences()
+    {
+      return hiddenSequences;
+    }
 
+}