X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=64b79b7416d1381b1cb921bcef718354f36f41c7;hb=482e093c4670a813c9eec254990178b209e32dbc;hp=00d1be8ce452ddae2132c82a52afcc684a5efadb;hpb=f14d234620501b7b5024a9f98e94c520641e7a09;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 00d1be8..64b79b7 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,834 +1,1129 @@
-/*
- * 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;
-
-        if( jalview.util.Comparison.isNucleotide(seqs))
-          type = NUCLEOTIDE;
-        else
-          type = PROTEIN;
-
-        sequences = new Vector();
-
-        for (i = 0; i < seqs.length; i++)
-        {
-            sequences.addElement(seqs[i]);
-
-            if(seqs[i].getDatasetSequence()!=null
-            && seqs[i].getDatasetSequence().getAnnotation()!=null)
-            {
-
-              for(int a=0; a<seqs[i].getDatasetSequence().getAnnotation().length; a++)
-              {
-                       this.addAnnotation(seqs[i].getDatasetSequence().getAnnotation()[a], seqs[i]);
-              }
-            }
-        }
-
-        getWidth();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getSequences()
-    {
-        return sequences;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceI getSequenceAt(int i)
-    {
-        if (i < sequences.size())
-        {
-            return (SequenceI) sequences.elementAt(i);
-        }
-
-        return null;
-    }
-
-    /** Adds a sequence to the alignment.  Recalculates maxLength and size.
-     *
-     * @param snew
-     */
-    public void addSequence(SequenceI snew)
-    {
-        sequences.addElement(snew);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void addSequence(SequenceI[] seq)
-    {
-        for (int i = 0; i < seq.length; i++)
-        {
-            addSequence(seq[i]);
-        }
-    }
-
-    /** 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);
-
-        sequences.setElementAt(snew, i);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getGroups()
-    {
-        return groups;
-    }
-
-    /** Takes out columns consisting entirely of gaps (-,.," ")
-     */
-    public void removeGaps()
-    {
-        SequenceI current;
-        int iSize = getWidth();
-
-        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--;
-            }
-        }
-    }
-
-    /** 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);
-    }
-
-    /**
-     * 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);
-            }
-        }
-    }
-
-    /**
-     * 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));
-            }
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void trimRight(int i)
-    {
-        for (int j = 0; j < getHeight(); j++)
-        {
-            SequenceI s = getSequenceAt(j);
-            int newend = s.findPosition(i);
-
-            s.setEnd(newend);
-            if(s.getLength()>i)
-              s.setSequence(s.getSequence().substring(0, i + 1));
-        }
-    }
-
-    /**
-     * 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();
-
-        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));
-                        }
-                    }
-                }
-            }
-        }
-
-        // Now delete the sequences
-        for (int i = 0; i < del.size(); i++)
-        {
-            deleteSequence((SequenceI) del.elementAt(i));
-        }
-
-        return del;
-    }
-
-    /**    */
-    public SequenceGroup findGroup(int i)
-    {
-        return findGroup(getSequenceAt(i));
-    }
-
-    /**    */
-    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;
-            }
-        }
-
-        return null;
-    }
-
-    /**
-     * 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);
-            }
-        }
-
-        SequenceGroup[] ret = new SequenceGroup[temp.size()];
-
-        for (int i = 0; i < temp.size(); i++)
-        {
-            ret[i] = (SequenceGroup) temp.elementAt(i);
-        }
-
-        return ret;
-    }
-
-
-
-    /**    */
-    public void addGroup(SequenceGroup sg)
-    {
-        if (!groups.contains(sg))
-        {
-            groups.addElement(sg);
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void deleteAllGroups()
-    {
-        groups.removeAllElements();
-        superGroup.removeAllElements();
-
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            SequenceI s = getSequenceAt(i);
-            s.setColor(java.awt.Color.white);
-            i++;
-        }
-    }
-
-    /**    */
-    public void deleteGroup(SequenceGroup g)
-    {
-        if (groups.contains(g))
-        {
-            groups.removeElement(g);
-        }
-    }
-
-    /**    */
-    public SequenceI findName(String name)
-    {
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            if (getSequenceAt(i).getName().equals(name))
-            {
-                return getSequenceAt(i);
-            }
-
-            i++;
-        }
-
-        return null;
-    }
-
-
-    /**    */
-    public int findIndex(SequenceI s)
-    {
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            if (s == getSequenceAt(i))
-            {
-                return i;
-            }
-
-            i++;
-        }
-
-        return -1;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getHeight()
-    {
-        return sequences.size();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getWidth()
-    {
-        int maxLength = -1;
-
-        for (int i = 0; i < sequences.size(); i++)
-        {
-            if (getSequenceAt(i).getLength() > maxLength)
-            {
-                maxLength = getSequenceAt(i).getLength();
-            }
-        }
-
-        return maxLength;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getMaxIdLength()
-    {
-        int max = 0;
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            SequenceI seq = getSequenceAt(i);
-            String tmp = seq.getName() + "/" + seq.getStart() + "-" +
-                seq.getEnd();
-
-            if (tmp.length() > max)
-            {
-                max = tmp.length();
-            }
-
-            i++;
-        }
-
-        return max;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param gc DOCUMENT ME!
-     */
-    public void setGapCharacter(char gc)
-    {
-        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);
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getGapCharacter()
-    {
-        return gapCharacter;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getAAFrequency()
-    {
-        return AAFrequency.calculate(sequences, 0, getWidth());
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean isAligned()
-    {
-        int width = getWidth();
-
-        for (int i = 0; i < sequences.size(); i++)
-        {
-            if (getSequenceAt(i).getLength() != width)
-            {
-                return false;
-            }
-        }
-
-        return true;
-    }
-
-    /**
-     * 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;
-
-        for (int i = 0; i < aSize; i++)
-        {
-            if (annotations[i] == aa)
-            {
-                continue;
-            }
-
-            temp[tIndex] = annotations[i];
-            tIndex++;
-        }
-
-        annotations = temp;
-    }
-
-    /**
-     *
-     * @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 adjustSequenceAnnotations()
-    {
-      if(annotations!=null)
-      {
-        for (int a = 0; a < annotations.length; a++)
-        {
-          if (annotations[a].sequenceRef != null)
-          {
-            annotations[a].adjustForAlignment();
-          }
-        }
-      }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param aa DOCUMENT ME!
-     */
-    public void addAnnotation(AlignmentAnnotation aa)
-    {
-        int aSize = 1;
-        if (annotations != null)
-        {
-            aSize = annotations.length + 1;
-        }
-
-        AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-
-        temp[aSize-1] = aa;
-
-        int i = 0;
-
-        if (aSize > 1)
-        {
-            for (i = 0; i < (aSize-1); i++)
-            {
-                temp[i] = annotations[i];
-            }
-        }
-
-        annotations = temp;
-    }
-
-    public void setAnnotationIndex(AlignmentAnnotation aa, int index)
-    {
-      if(aa==null || annotations==null || annotations.length-1<index)
-        return;
-
-      int aSize = annotations.length;
-      AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-
-      temp[index] = aa;
-
-      for (int i = 0; i < aSize; i++)
-      {
-        if(i==index)
-          continue;
-
-        if(i<index)
-          temp[i] = annotations[i];
-        else
-          temp[i] = annotations[i-1];
-      }
-
-        annotations = temp;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public AlignmentAnnotation[] getAlignmentAnnotation()
-    {
-        return annotations;
-    }
-
-    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++)
-        {
-
-          seqs[i] = new Sequence(getSequenceAt(i).getName(),
-                                 AlignSeq.extractGaps(
-                                     jalview.util.Comparison.GapChars,
-                                     getSequenceAt(i).getSequence()
-                                 ),
-                                 getSequenceAt(i).getStart(),
-                                 getSequenceAt(i).getEnd());
-
-          getSequenceAt(i).setDatasetSequence(seqs[i]);
-        }
-
-        dataset = new Alignment(seqs);
-      }
-      else if(dataset==null && data!=null)
-      {
-        dataset = data;
-      }
-    }
-
-    public Alignment getDataset()
-    {
-      return dataset;
-    }
-
-    public boolean padGaps() {
-      boolean modified=false;
-      int Width = getWidth();
-      SequenceI current;
-      for (int i = 0; i < sequences.size();
-           i++)
-      {
-        current = getSequenceAt(i);
-
-        if (current.getLength() < Width)
-        {
-          current.insertCharAt(Width - 1, gapCharacter);
-          modified=true;
-        }
-      }
-      return modified;
-    }
-
-    public HiddenSequences getHiddenSequences()
-    {
-      return hiddenSequences;
-    }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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 jalview.analysis.*;
+
+/**
+ * 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 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);
+
+  public Hashtable alignmentProperties;
+
+  private void initAlignment(SequenceI[] seqs)
+  {
+    int i = 0;
+
+    if (jalview.util.Comparison.isNucleotide(seqs))
+    {
+      type = NUCLEOTIDE;
+    }
+    else
+    {
+      type = PROTEIN;
+    }
+
+    sequences = new Vector();
+
+    for (i = 0; i < seqs.length; i++)
+    {
+      sequences.addElement(seqs[i]);
+    }
+
+  }
+
+  /**
+   * Make an alignment from an array of Sequences.
+   * 
+   * @param sequences
+   */
+  public Alignment(SequenceI[] seqs)
+  {
+    initAlignment(seqs);
+  }
+
+  /**
+   * Make a new alignment from an array of SeqCigars
+   * 
+   * @param seqs
+   *                SeqCigar[]
+   */
+  public Alignment(SeqCigar[] alseqs)
+  {
+    SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
+            gapCharacter, new ColumnSelection(), null);
+    initAlignment(seqs);
+  }
+
+  /**
+   * Make a new alignment from an CigarArray JBPNote - can only do this when
+   * compactAlignment does not contain hidden regions. JBPNote - must also check
+   * that compactAlignment resolves to a set of SeqCigars - or construct them
+   * appropriately.
+   * 
+   * @param compactAlignment
+   *                CigarArray
+   */
+  public static AlignmentI createAlignment(CigarArray compactAlignment)
+  {
+    throw new Error("Alignment(CigarArray) not yet implemented");
+    // this(compactAlignment.refCigars);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Vector getSequences()
+  {
+    return sequences;
+  }
+
+  public SequenceI[] getSequencesArray()
+  {
+    if (sequences == null)
+      return null;
+    SequenceI[] reply = new SequenceI[sequences.size()];
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      reply[i] = (SequenceI) sequences.elementAt(i);
+    }
+    return reply;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public SequenceI getSequenceAt(int i)
+  {
+    if (i < sequences.size())
+    {
+      return (SequenceI) sequences.elementAt(i);
+    }
+
+    return null;
+  }
+
+  /**
+   * Adds a sequence to the alignment. Recalculates maxLength and size.
+   * 
+   * @param snew
+   */
+  public void addSequence(SequenceI snew)
+  {
+    if (dataset != null)
+    {
+      // maintain dataset integrity
+      if (snew.getDatasetSequence() != null)
+      {
+        getDataset().addSequence(snew.getDatasetSequence());
+      }
+      else
+      {
+        // derive new sequence
+        SequenceI adding = snew.deriveSequence();
+        getDataset().addSequence(adding.getDatasetSequence());
+        snew = adding;
+      }
+    }
+    if (sequences == null)
+    {
+      initAlignment(new SequenceI[]
+      { snew });
+    }
+    else
+    {
+      sequences.addElement(snew);
+    }
+    if (hiddenSequences != null)
+      hiddenSequences.adjustHeightSequenceAdded();
+  }
+
+  /**
+   * 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);
+
+    sequences.setElementAt(snew, i);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Vector getGroups()
+  {
+    return groups;
+  }
+
+  public void finalize()
+  {
+    if (getDataset() != null)
+      getDataset().removeAlignmentRef();
+
+    dataset = null;
+    sequences = null;
+    groups = null;
+    annotations = null;
+    hiddenSequences = null;
+  }
+
+  /**
+   * decrement the alignmentRefs counter by one and call finalize if it goes to
+   * zero.
+   */
+  private void removeAlignmentRef()
+  {
+    if (--alignmentRefs == 0)
+    {
+      finalize();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param s
+   *                DOCUMENT ME!
+   */
+  public void deleteSequence(SequenceI s)
+  {
+    deleteSequence(findIndex(s));
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param i
+   *                DOCUMENT ME!
+   */
+  public void deleteSequence(int i)
+  {
+    if (i > -1 && i < getHeight())
+    {
+      sequences.removeElementAt(i);
+      hiddenSequences.adjustHeightSequenceDeleted(i);
+    }
+  }
+
+  /**    */
+  public SequenceGroup findGroup(SequenceI s)
+  {
+    for (int i = 0; i < this.groups.size(); i++)
+    {
+      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+      if (sg.getSequences(null).contains(s))
+      {
+        return sg;
+      }
+    }
+
+    return null;
+  }
+
+  /**
+   * 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.getSequences(null) == null)
+      {
+        this.deleteGroup(sg);
+        gSize--;
+        continue;
+      }
+
+      if (sg.getSequences(null).contains(s))
+      {
+        temp.addElement(sg);
+      }
+    }
+
+    SequenceGroup[] ret = new SequenceGroup[temp.size()];
+
+    for (int i = 0; i < temp.size(); i++)
+    {
+      ret[i] = (SequenceGroup) temp.elementAt(i);
+    }
+
+    return ret;
+  }
+
+  /**    */
+  public void addGroup(SequenceGroup sg)
+  {
+    if (!groups.contains(sg))
+    {
+      if (hiddenSequences.getSize() > 0)
+      {
+        int i, iSize = sg.getSize();
+        for (i = 0; i < iSize; i++)
+        {
+          if (!sequences.contains(sg.getSequenceAt(i)))
+          {
+            sg.deleteSequence(sg.getSequenceAt(i), false);
+            iSize--;
+            i--;
+          }
+        }
+
+        if (sg.getSize() < 1)
+        {
+          return;
+        }
+      }
+
+      groups.addElement(sg);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   */
+  public void deleteAllGroups()
+  {
+    groups.removeAllElements();
+  }
+
+  /**    */
+  public void deleteGroup(SequenceGroup g)
+  {
+    if (groups.contains(g))
+    {
+      groups.removeElement(g);
+    }
+  }
+
+  /**    */
+  public SequenceI findName(String name)
+  {
+    return findName(name, false);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+   */
+  public SequenceI findName(String token, boolean b)
+  {
+    return findName(null, token, b);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+   *      boolean)
+   */
+  public SequenceI findName(SequenceI startAfter, String token, boolean b)
+  {
+
+    int i = 0;
+    SequenceI sq = null;
+    String sqname = null;
+    if (startAfter != null)
+    {
+      // try to find the sequence in the alignment
+      boolean matched = false;
+      while (i < sequences.size())
+      {
+        if (getSequenceAt(i++) == startAfter)
+        {
+          matched = true;
+          break;
+        }
+      }
+      if (!matched)
+      {
+        i = 0;
+      }
+    }
+    while (i < sequences.size())
+    {
+      sq = getSequenceAt(i);
+      sqname = sq.getName();
+      if (sqname.equals(token) // exact match
+              || (b && // allow imperfect matches - case varies
+              (sqname.equalsIgnoreCase(token))))
+      {
+        return getSequenceAt(i);
+      }
+
+      i++;
+    }
+
+    return null;
+  }
+
+  public SequenceI[] findSequenceMatch(String name)
+  {
+    Vector matches = new Vector();
+    int i = 0;
+
+    while (i < sequences.size())
+    {
+      if (getSequenceAt(i).getName().equals(name))
+      {
+        matches.addElement(getSequenceAt(i));
+      }
+      i++;
+    }
+
+    SequenceI[] result = new SequenceI[matches.size()];
+    for (i = 0; i < result.length; i++)
+    {
+      result[i] = (SequenceI) matches.elementAt(i);
+    }
+
+    return result;
+
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+   */
+  public int findIndex(SequenceI s)
+  {
+    int i = 0;
+
+    while (i < sequences.size())
+    {
+      if (s == getSequenceAt(i))
+      {
+        return i;
+      }
+
+      i++;
+    }
+
+    return -1;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+   */
+  public int findIndex(SearchResults results)
+  {
+    int i = 0;
+
+    while (i < sequences.size())
+    {
+      if (results.involvesSequence(getSequenceAt(i)))
+      {
+        return i;
+      }
+      i++;
+    }
+    return -1;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getHeight()
+  {
+    return sequences.size();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getWidth()
+  {
+    int maxLength = -1;
+
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      if (getSequenceAt(i).getLength() > maxLength)
+      {
+        maxLength = getSequenceAt(i).getLength();
+      }
+    }
+
+    return maxLength;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param gc
+   *                DOCUMENT ME!
+   */
+  public void setGapCharacter(char gc)
+  {
+    gapCharacter = gc;
+
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      Sequence seq = (Sequence) sequences.elementAt(i);
+      seq.setSequence(seq.getSequenceAsString().replace('.', gc).replace(
+              '-', gc).replace(' ', gc));
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public char getGapCharacter()
+  {
+    return gapCharacter;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public boolean isAligned()
+  {
+    int width = getWidth();
+
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      if (getSequenceAt(i).getLength() != width)
+      {
+        return false;
+      }
+    }
+
+    return true;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
+   */
+  public boolean deleteAnnotation(AlignmentAnnotation aa)
+  {
+    int aSize = 1;
+
+    if (annotations != null)
+    {
+      aSize = annotations.length;
+    }
+
+    if (aSize < 1)
+    {
+      return false;
+    }
+
+    AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+
+    boolean swap = false;
+    int tIndex = 0;
+
+    for (int i = 0; i < aSize; i++)
+    {
+      if (annotations[i] == aa)
+      {
+        swap = true;
+        continue;
+      }
+      if (tIndex < temp.length)
+        temp[tIndex++] = annotations[i];
+    }
+
+    if (swap)
+    {
+      annotations = temp;
+      if (aa.sequenceRef != null)
+        aa.sequenceRef.removeAlignmentAnnotation(aa);
+    }
+    return swap;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param aa
+   *                DOCUMENT ME!
+   */
+  public void addAnnotation(AlignmentAnnotation aa)
+  {
+    int aSize = 1;
+    if (annotations != null)
+    {
+      aSize = annotations.length + 1;
+    }
+
+    AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+    temp[aSize - 1] = aa;
+
+    int i = 0;
+
+    if (aSize > 1)
+    {
+      for (i = 0; i < (aSize - 1); i++)
+      {
+        temp[i] = annotations[i];
+      }
+    }
+
+    annotations = temp;
+  }
+
+  public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+  {
+    if (aa == null || annotations == null || annotations.length - 1 < index)
+    {
+      return;
+    }
+
+    int aSize = annotations.length;
+    AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+    temp[index] = aa;
+
+    for (int i = 0; i < aSize; i++)
+    {
+      if (i == index)
+      {
+        continue;
+      }
+
+      if (i < index)
+      {
+        temp[i] = annotations[i];
+      }
+      else
+      {
+        temp[i] = annotations[i - 1];
+      }
+    }
+
+    annotations = temp;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public AlignmentAnnotation[] getAlignmentAnnotation()
+  {
+    return annotations;
+  }
+
+  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
+      SequenceI[] seqs = new SequenceI[getHeight()];
+      SequenceI currentSeq;
+      for (int i = 0; i < getHeight(); i++)
+      {
+        currentSeq = getSequenceAt(i);
+        if (currentSeq.getDatasetSequence() != null)
+        {
+          seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+        }
+        else
+        {
+          seqs[i] = currentSeq.createDatasetSequence();
+        }
+      }
+
+      dataset = new Alignment(seqs);
+    }
+    else if (dataset == null && data != null)
+    {
+      dataset = data;
+    }
+    dataset.addAlignmentRef();
+  }
+
+  /**
+   * reference count for number of alignments referencing this one.
+   */
+  int alignmentRefs = 0;
+
+  /**
+   * increase reference count to this alignment.
+   */
+  private void addAlignmentRef()
+  {
+    alignmentRefs++;
+  }
+
+  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++;
+
+    int cLength;
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      current = getSequenceAt(i);
+      cLength = current.getLength();
+
+      if (cLength < maxLength)
+      {
+        current.insertCharAt(cLength, maxLength - cLength, gapCharacter);
+        modified = true;
+      }
+      else if (current.getLength() > maxLength)
+      {
+        current.deleteChars(maxLength, current.getLength());
+      }
+    }
+    return modified;
+  }
+  /**
+   * Justify the sequences to the left or right by deleting and inserting gaps before the initial residue or after the terminal residue
+   * @param right true if alignment padded to right, false to justify to left
+   * @return true if alignment was changed
+   */
+  public boolean justify(boolean right)
+  {
+    boolean modified = false;
+
+    // Remove excess gaps from the end of alignment
+    int maxLength = -1;
+    int ends[] = new int[sequences.size()*2];
+    SequenceI current;
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      current = getSequenceAt(i);
+      // This should really be a sequence method
+      ends[i*2] = current.findIndex(current.getStart());
+      ends[i*2+1] = current.findIndex(current.getStart()+current.getLength());
+      boolean hitres=false;
+      for (int j = 0,rs=0,ssiz=current.getLength(); j<ssiz; j++)
+      {
+        if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+        {
+          if (!hitres)
+          {
+            ends[i*2] = j;
+            hitres=true;
+          } else {
+            ends[i*2+1] = j;
+            if (j-ends[i*2]>maxLength)
+            {
+              maxLength = j-ends[i*2];
+            }
+          }
+        }
+      }
+    }
+
+    maxLength++;
+    // now edit the flanking gaps to justify to either left or right
+    int cLength,extent,diff;
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      current = getSequenceAt(i);
+      
+      cLength = 1+ends[i*2+1]-ends[i*2];
+      diff = maxLength-cLength; // number of gaps to indent
+      extent = current.getLength();
+      if (right)
+      {
+        // right justify
+        if (extent>ends[i*2+1])
+        {
+          current.deleteChars(ends[i*2+1]+1, extent);
+          modified = true;
+        }
+        if (ends[i*2]>diff)
+        {
+          current.deleteChars(0, ends[i*2]-diff);
+          modified = true;
+        } else {
+          if (ends[i*2]<diff)
+          {
+            current.insertCharAt(0, diff-ends[i*2],gapCharacter);
+            modified = true;
+          }
+        }
+      } else {
+        // left justify
+        if (ends[i*2]>0)
+        {
+          current.deleteChars(0, ends[i*2]);
+          modified = true;
+          ends[i*2+1]-=ends[i*2];
+          extent-=ends[i*2];
+        }
+        if (extent>maxLength)
+        {
+          current.deleteChars(maxLength+1, extent);
+          modified = true;
+        } else {
+          if (extent<maxLength)
+          {
+            current.insertCharAt(extent, maxLength-extent,gapCharacter);
+            modified = true;
+          }
+        }
+      }
+    }
+    return modified;
+  }
+
+  public HiddenSequences getHiddenSequences()
+  {
+    return hiddenSequences;
+  }
+
+  public CigarArray getCompactAlignment()
+  {
+    SeqCigar alseqs[] = new SeqCigar[sequences.size()];
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
+    }
+    CigarArray cal = new CigarArray(alseqs);
+    cal.addOperation(CigarArray.M, getWidth());
+    return cal;
+  }
+
+  public void setProperty(Object key, Object value)
+  {
+    if (alignmentProperties == null)
+      alignmentProperties = new Hashtable();
+
+    alignmentProperties.put(key, value);
+  }
+
+  public Object getProperty(Object key)
+  {
+    if (alignmentProperties != null)
+      return alignmentProperties.get(key);
+    else
+      return null;
+  }
+
+  public Hashtable getProperties()
+  {
+    return alignmentProperties;
+  }
+
+  AlignedCodonFrame[] codonFrameList = null;
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+   */
+  public void addCodonFrame(AlignedCodonFrame codons)
+  {
+    if (codons == null)
+      return;
+    if (codonFrameList == null)
+    {
+      codonFrameList = new AlignedCodonFrame[]
+      { codons };
+      return;
+    }
+    AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
+    System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
+    t[codonFrameList.length] = codons;
+    codonFrameList = t;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
+   */
+  public AlignedCodonFrame getCodonFrame(int index)
+  {
+    return codonFrameList[index];
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+   */
+  public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+  {
+    if (seq == null || codonFrameList == null)
+      return null;
+    Vector cframes = new Vector();
+    for (int f = 0; f < codonFrameList.length; f++)
+    {
+      if (codonFrameList[f].involvesSequence(seq))
+        cframes.addElement(codonFrameList[f]);
+    }
+    if (cframes.size() == 0)
+      return null;
+    AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
+    cframes.copyInto(cfr);
+    return cfr;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#getCodonFrames()
+   */
+  public AlignedCodonFrame[] getCodonFrames()
+  {
+    return codonFrameList;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+   */
+  public boolean removeCodonFrame(AlignedCodonFrame codons)
+  {
+    if (codons == null || codonFrameList == null)
+      return false;
+    boolean removed = false;
+    int i = 0, iSize = codonFrameList.length;
+    while (i < iSize)
+    {
+      if (codonFrameList[i] == codons)
+      {
+        removed = true;
+        if (i + 1 < iSize)
+        {
+          System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
+                  - i - 1);
+        }
+        iSize--;
+      }
+      else
+      {
+        i++;
+      }
+    }
+    return removed;
+  }
+
+  public void append(AlignmentI toappend)
+  {
+    // TODO test this method for a future 2.5 release
+    // currently tested for use in jalview.gui.SequenceFetcher
+    boolean samegap = toappend.getGapCharacter()==getGapCharacter();
+    char oldc = toappend.getGapCharacter();
+    boolean hashidden = toappend.getHiddenSequences()!=null && toappend.getHiddenSequences().hiddenSequences!=null;
+    // get all sequences including any hidden ones
+    Vector sqs = (hashidden) ? toappend.getHiddenSequences().getFullAlignment().getSequences() : toappend.getSequences();
+    if (sqs != null)
+    {
+      Enumeration sq = sqs.elements();
+      while (sq.hasMoreElements())
+      {
+        SequenceI addedsq=(SequenceI) sq.nextElement();
+        if (!samegap)
+        {
+          char[] oldseq = addedsq.getSequence();
+          for (int c=0;c<oldseq.length;c++)
+          {
+            if (oldseq[c]==oldc)
+            {
+              oldseq[c] = gapCharacter;
+            }
+          }
+        }
+        addSequence(addedsq);
+      }
+    }
+    AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
+    for (int a = 0; alan != null && a < alan.length; a++)
+    {
+      addAnnotation(alan[a]);
+    }
+    AlignedCodonFrame[] acod = toappend.getCodonFrames();
+    for (int a = 0; acod != null && a < acod.length; a++)
+    {
+      this.addCodonFrame(acod[a]);
+    }
+    Vector sg = toappend.getGroups();
+    if (sg != null)
+    {
+      Enumeration el = sg.elements();
+      while (el.hasMoreElements())
+      {
+        addGroup((SequenceGroup) el.nextElement());
+      }
+    }
+    if (toappend.getHiddenSequences()!=null)
+    {
+      HiddenSequences hs = toappend.getHiddenSequences();
+      if (hiddenSequences==null)
+      {
+        hiddenSequences = new HiddenSequences(this);
+      }
+      if (hs.hiddenSequences!=null)
+      {
+        for (int s=0;s<hs.hiddenSequences.length; s++)
+        {
+          // hide the newly appended sequence in the alignment
+          if (hs.hiddenSequences[s]!=null)
+          {
+            hiddenSequences.hideSequence(hs.hiddenSequences[s]);
+          }
+        }
+      }
+    }
+    if (toappend.getProperties()!=null)
+    {
+      // we really can't do very much here - just try to concatenate strings where property collisions occur.
+      Enumeration key = toappend.getProperties().keys();
+      while (key.hasMoreElements())
+      {
+        Object k = key.nextElement();
+        Object ourval = this.getProperty(k);
+        Object toapprop = toappend.getProperty(k);
+        if (ourval!=null)
+        {
+          if (ourval.getClass().equals(toapprop.getClass()) && !ourval.equals(toapprop))
+          {
+            if (ourval instanceof String)
+            {
+              // append strings
+              this.setProperty(k, ((String) ourval)+"; "+((String) toapprop));
+            } else {
+              if (ourval instanceof Vector)
+              {
+                // append vectors
+                Enumeration theirv = ((Vector) toapprop).elements();
+                while (theirv.hasMoreElements())
+                {
+                  ((Vector)ourval).addElement(theirv);
+                }
+              }
+            }
+          }
+        } else {
+          // just add new property directly
+          setProperty(k, toapprop);
+        }
+       
+      }
+    }
+  }
+
+}