X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=23c3de72baa784ccc1c6399f39087865b9b70cdb;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=02fc54345bf53e3c4473ca36b45b38fe01943120;hpb=0452450533728e478ef8c893ea2cb3483c740fb3;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 02fc543..23c3de7 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,60 +1,81 @@
 /*
-* 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
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel;
 
+import jalview.analysis.AlignSeq;
 
-import java.util.*;
-
+import java.util.Enumeration;
+import java.util.Vector;
 
 /**
- * DOCUMENT ME!
- *
+ * 
+ * Implements the SequenceI interface for a char[] based sequence object.
+ * 
  * @author $author$
  * @version $Revision$
  */
 public class Sequence implements SequenceI
 {
   SequenceI datasetSequence;
+
   String name;
-  private char [] sequence;
+
+  private char[] sequence;
+
   String description;
+
   int start;
+
   int end;
+
   Vector pdbIds;
+
   String vamsasId;
+
   DBRefEntry[] dbrefs;
 
-  /** This annotation is displayed below the alignment but the
-   * positions are tied to the residues of this sequence */
+  /**
+   * This annotation is displayed below the alignment but the positions are tied
+   * to the residues of this sequence
+   */
   Vector annotation;
 
-  /** DOCUMENT ME!! */
-  public SequenceFeature[] sequenceFeatures;
+  /**
+   * The index of the sequence in a MSA
+   */
+  int index = -1;
 
+  /** array of seuqence features - may not be null for a valid sequence object */
+  public SequenceFeature[] sequenceFeatures;
 
   /**
    * Creates a new Sequence object.
-   *
-   * @param name DOCUMENT ME!
-   * @param sequence DOCUMENT ME!
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
+   * 
+   * @param name
+   *          display name string
+   * @param sequence
+   *          string to form a possibly gapped sequence out of
+   * @param start
+   *          first position of non-gap residue in the sequence
+   * @param end
+   *          last position of ungapped residues (nearly always only used for
+   *          display purposes)
    */
   public Sequence(String name, String sequence, int start, int end)
   {
@@ -66,7 +87,7 @@ public class Sequence implements SequenceI
     checkValidRange();
   }
 
-  public Sequence(String name, char [] sequence, int start, int end)
+  public Sequence(String name, char[] sequence, int start, int end)
   {
     this.name = name;
     this.sequence = sequence;
@@ -77,31 +98,38 @@ public class Sequence implements SequenceI
   }
 
   com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
-      "[/][0-9]{1,}[-][0-9]{1,}$");
-  com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
-      "[0-9]{1,}$");
+          "[/][0-9]{1,}[-][0-9]{1,}$");
+
+  com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
 
   void parseId()
   {
+    if (name == null)
+    {
+      System.err
+              .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+      name = "";
+    }
     // Does sequence have the /start-end signiature?
     if (limitrx.search(name))
     {
       name = limitrx.left();
       endrx.search(limitrx.stringMatched());
       setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
-          endrx.matchedFrom() - 1)));
+              endrx.matchedFrom() - 1)));
       setEnd(Integer.parseInt(endrx.stringMatched()));
     }
   }
 
   void checkValidRange()
   {
-    if (end < 1)
+    // Note: JAL-774 :
+    // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
     {
       int endRes = 0;
       for (int j = 0; j < sequence.length; j++)
       {
-        if (!jalview.util.Comparison.isGap( sequence[j] ))
+        if (!jalview.util.Comparison.isGap(sequence[j]))
         {
           endRes++;
         }
@@ -111,16 +139,21 @@ public class Sequence implements SequenceI
         endRes += start - 1;
       }
 
-      this.end = endRes;
+      if (end < endRes)
+      {
+        end = endRes;
+      }
     }
 
   }
 
   /**
    * Creates a new Sequence object.
-   *
-   * @param name DOCUMENT ME!
-   * @param sequence DOCUMENT ME!
+   * 
+   * @param name
+   *          DOCUMENT ME!
+   * @param sequence
+   *          DOCUMENT ME!
    */
   public Sequence(String name, String sequence)
   {
@@ -128,24 +161,91 @@ public class Sequence implements SequenceI
   }
 
   /**
-   * Creates a new Sequence object.
-   *
-   * @param seq DOCUMENT ME!
+   * Creates a new Sequence object with new features, DBRefEntries,
+   * AlignmentAnnotations, and PDBIds but inherits any existing dataset sequence
+   * reference.
+   * 
+   * @param seq
+   *          DOCUMENT ME!
    */
   public Sequence(SequenceI seq)
   {
-    this(seq.getName(),
-         seq.getSequence(),
-         seq.getStart(),
-         seq.getEnd());
-    description = seq.getDescription();
+    this(seq, seq.getAnnotation());
   }
 
+  /**
+   * Create a new sequence object with new features, DBRefEntries, and PDBIds
+   * but inherits any existing dataset sequence reference, and duplicate of any
+   * annotation that is present in the given annotation array.
+   * 
+   * @param seq
+   *          the sequence to be copied
+   * @param alAnnotation
+   *          an array of annotation including some associated with seq
+   */
+  public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
+  {
+    this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+    description = seq.getDescription();
+    if (seq.getSequenceFeatures() != null)
+    {
+      SequenceFeature[] sf = seq.getSequenceFeatures();
+      for (int i = 0; i < sf.length; i++)
+      {
+        addSequenceFeature(new SequenceFeature(sf[i]));
+      }
+    }
+    setDatasetSequence(seq.getDatasetSequence());
+    if (datasetSequence == null && seq.getDBRef() != null)
+    {
+      // only copy DBRefs if we really are a dataset sequence
+      DBRefEntry[] dbr = seq.getDBRef();
+      for (int i = 0; i < dbr.length; i++)
+      {
+        addDBRef(new DBRefEntry(dbr[i]));
+      }
+    }
+    if (seq.getAnnotation() != null)
+    {
+      AlignmentAnnotation[] sqann = seq.getAnnotation();
+      for (int i = 0; i < sqann.length; i++)
+      {
+        if (sqann[i] == null)
+        {
+          continue;
+        }
+        boolean found = (alAnnotation == null);
+        if (!found)
+        {
+          for (int apos = 0; !found && apos < alAnnotation.length; apos++)
+          {
+            found = (alAnnotation[apos] == sqann[i]);
+          }
+        }
+        if (found)
+        {
+          // only copy the given annotation
+          AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]);
+          addAlignmentAnnotation(newann);
+        }
+      }
+    }
+    if (seq.getPDBId() != null)
+    {
+      Vector ids = seq.getPDBId();
+      Enumeration e = ids.elements();
+      while (e.hasMoreElements())
+      {
+        this.addPDBId(new PDBEntry((PDBEntry) e.nextElement()));
+      }
+    }
+  }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param v DOCUMENT ME!
+   * 
+   * @param v
+   *          DOCUMENT ME!
    */
   public void setSequenceFeatures(SequenceFeature[] features)
   {
@@ -176,10 +276,12 @@ public class Sequence implements SequenceI
 
   public void deleteFeature(SequenceFeature sf)
   {
-    if(sequenceFeatures==null)
+    if (sequenceFeatures == null)
+    {
       return;
+    }
 
-    int index=0;
+    int index = 0;
     for (index = 0; index < sequenceFeatures.length; index++)
     {
       if (sequenceFeatures[index].equals(sf))
@@ -188,25 +290,26 @@ public class Sequence implements SequenceI
       }
     }
 
-
-    if(index==sequenceFeatures.length)
+    if (index == sequenceFeatures.length)
+    {
       return;
+    }
 
     int sfLength = sequenceFeatures.length;
-    if(sfLength<2)
+    if (sfLength < 2)
     {
       sequenceFeatures = null;
     }
     else
     {
-      SequenceFeature[] temp = new SequenceFeature[sfLength-1];
+      SequenceFeature[] temp = new SequenceFeature[sfLength - 1];
       System.arraycopy(sequenceFeatures, 0, temp, 0, index);
 
-      if(index<sfLength)
-        System.arraycopy(sequenceFeatures,
-                         index + 1,
-                         temp,
-                         index, sequenceFeatures.length - index -1);
+      if (index < sfLength)
+      {
+        System.arraycopy(sequenceFeatures, index + 1, temp, index,
+                sequenceFeatures.length - index - 1);
+      }
 
       sequenceFeatures = temp;
     }
@@ -214,7 +317,7 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public SequenceFeature[] getSequenceFeatures()
@@ -225,15 +328,20 @@ public class Sequence implements SequenceI
   public void addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
+    {
       pdbIds = new Vector();
-
-    pdbIds.addElement(entry);
+    }
+    if (!pdbIds.contains(entry))
+    {
+      pdbIds.addElement(entry);
+    }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param id DOCUMENT ME!
+   * 
+   * @param id
+   *          DOCUMENT ME!
    */
   public void setPDBId(Vector id)
   {
@@ -242,7 +350,7 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public Vector getPDBId()
@@ -252,7 +360,7 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getDisplayId(boolean jvsuffix)
@@ -268,8 +376,9 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
-   * @param name DOCUMENT ME!
+   * 
+   * @param name
+   *          DOCUMENT ME!
    */
   public void setName(String name)
   {
@@ -279,7 +388,7 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getName()
@@ -289,8 +398,9 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
-   * @param start DOCUMENT ME!
+   * 
+   * @param start
+   *          DOCUMENT ME!
    */
   public void setStart(int start)
   {
@@ -299,7 +409,7 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getStart()
@@ -309,8 +419,9 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
-   * @param end DOCUMENT ME!
+   * 
+   * @param end
+   *          DOCUMENT ME!
    */
   public void setEnd(int end)
   {
@@ -319,7 +430,7 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getEnd()
@@ -329,7 +440,7 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getLength()
@@ -339,8 +450,9 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
+   * 
+   * @param seq
+   *          DOCUMENT ME!
    */
   public void setSequence(String seq)
   {
@@ -348,7 +460,6 @@ public class Sequence implements SequenceI
     checkValidRange();
   }
 
-
   public String getSequenceAsString()
   {
     return new String(sequence);
@@ -359,23 +470,22 @@ public class Sequence implements SequenceI
     return new String(getSequence(start, end));
   }
 
-
-  public char [] getSequence()
+  public char[] getSequence()
   {
     return sequence;
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.SequenceI#getSequence(int, int)
    */
-  public char [] getSequence(int start, int end)
+  public char[] getSequence(int start, int end)
   {
-    // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
+    if (start < 0)
+      start = 0;
+    // JBPNote - left to user to pad the result here (TODO:Decide on this
+    // policy)
     if (start >= sequence.length)
     {
       return new char[0];
@@ -386,43 +496,55 @@ public class Sequence implements SequenceI
       end = sequence.length;
     }
 
-    char [] reply = new char[end-start];
-    System.arraycopy(sequence, start, reply, 0, end-start);
+    char[] reply = new char[end - start];
+    System.arraycopy(sequence, start, reply, 0, end - start);
 
     return reply;
   }
 
-
   /**
-   * make a new Sequence object from start to end (including gaps) over this seqeunce
-   * @param start int
-   * @param end int
+   * make a new Sequence object from start to end (including gaps) over this
+   * seqeunce
+   * 
+   * @param start
+   *          int
+   * @param end
+   *          int
    * @return SequenceI
    */
   public SequenceI getSubSequence(int start, int end)
   {
     if (start < 0)
+    {
       start = 0;
-    char [] seq = getSequence(start, end);
+    }
+    char[] seq = getSequence(start, end);
     if (seq.length == 0)
+    {
       return null;
+    }
     int nstart = findPosition(start);
     int nend = findPosition(end) - 1;
     // JBPNote - this is an incomplete copy.
     SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
     nseq.setDescription(description);
-    if (datasetSequence!=null)
-        nseq.setDatasetSequence(datasetSequence);
+    if (datasetSequence != null)
+    {
+      nseq.setDatasetSequence(datasetSequence);
+    }
     else
-        nseq.setDatasetSequence(this);
+    {
+      nseq.setDatasetSequence(this);
+    }
     return nseq;
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   *
+   * 
+   * @param i
+   *          DOCUMENT ME!
+   * 
    * @return DOCUMENT ME!
    */
   public char getCharAt(int i)
@@ -439,8 +561,9 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
-   * @param desc DOCUMENT ME!
+   * 
+   * @param desc
+   *          DOCUMENT ME!
    */
   public void setDescription(String desc)
   {
@@ -449,7 +572,7 @@ public class Sequence implements SequenceI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getDescription()
@@ -457,20 +580,18 @@ public class Sequence implements SequenceI
     return this.description;
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param pos DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.SequenceI#findIndex(int)
    */
   public int findIndex(int pos)
   {
     // returns the alignment position for a residue
     int j = start;
     int i = 0;
-
-    while ( (i < sequence.length) && (j <= end) && (j <= pos))
+    // Rely on end being at least as long as the length of the sequence.
+    while ((i < sequence.length) && (j <= end) && (j <= pos))
     {
       if (!jalview.util.Comparison.isGap(sequence[i]))
       {
@@ -480,7 +601,7 @@ public class Sequence implements SequenceI
       i++;
     }
 
-    if ( (j == end) && (j < pos))
+    if ((j == end) && (j < pos))
     {
       return end + 1;
     }
@@ -492,9 +613,10 @@ public class Sequence implements SequenceI
 
   /**
    * Returns the sequence position for an alignment position
-   *
-   * @param i column index in alignment (from 1)
-   *
+   * 
+   * @param i
+   *          column index in alignment (from 1)
+   * 
    * @return residue number for residue (left of and) nearest ith column
    */
   public int findPosition(int i)
@@ -502,9 +624,9 @@ public class Sequence implements SequenceI
     int j = 0;
     int pos = start;
     int seqlen = sequence.length;
-    while ( (j < i) && (j < seqlen))
+    while ((j < i) && (j < seqlen))
     {
-      if (!jalview.util.Comparison.isGap( sequence[j] ))
+      if (!jalview.util.Comparison.isGap(sequence[j]))
       {
         pos++;
       }
@@ -516,14 +638,16 @@ public class Sequence implements SequenceI
   }
 
   /**
-   * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment
-   *
-   * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object
+   * Returns an int array where indices correspond to each residue in the
+   * sequence and the element value gives its position in the alignment
+   * 
+   * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
+   *         residues in SequenceI object
    */
   public int[] gapMap()
   {
-    String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.
-        GapChars, new String(sequence));
+    String seq = jalview.analysis.AlignSeq.extractGaps(
+            jalview.util.Comparison.GapChars, new String(sequence));
     int[] map = new int[seq.length()];
     int j = 0;
     int p = 0;
@@ -541,46 +665,122 @@ public class Sequence implements SequenceI
     return map;
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.SequenceI#findPositionMap()
+   */
+  public int[] findPositionMap()
+  {
+    int map[] = new int[sequence.length];
+    int j = 0;
+    int pos = start;
+    int seqlen = sequence.length;
+    while ((j < seqlen))
+    {
+      map[j] = pos;
+      if (!jalview.util.Comparison.isGap(sequence[j]))
+      {
+        pos++;
+      }
+
+      j++;
+    }
+    return map;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.SequenceI#deleteChars(int, int)
    */
   public void deleteChars(int i, int j)
   {
+    int newstart = start, newend = end;
     if (i >= sequence.length)
     {
       return;
     }
 
-    char [] tmp;
+    char[] tmp;
 
     if (j >= sequence.length)
     {
       tmp = new char[i];
-      System.arraycopy(sequence,0,tmp,0,i);
+      System.arraycopy(sequence, 0, tmp, 0, i);
     }
     else
     {
-      tmp = new char[sequence.length-j+i];
-      System.arraycopy(sequence,0,tmp,0,i);
-      System.arraycopy(sequence,j,tmp,i,sequence.length-j);
+      tmp = new char[sequence.length - j + i];
+      System.arraycopy(sequence, 0, tmp, 0, i);
+      System.arraycopy(sequence, j, tmp, i, sequence.length - j);
     }
-
+    boolean createNewDs = false;
+    for (int s = i; s < j; s++)
+    {
+      if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+      {
+        if (createNewDs)
+        {
+          newend--;
+        }
+        else
+        {
+          int sindex = findIndex(start) - 1;
+          if (sindex == s)
+          {
+            // delete characters including start of sequence
+            newstart = findPosition(j);
+            break; // don't need to search for any more residue characters.
+          }
+          else
+          {
+            // delete characters after start.
+            int eindex = findIndex(end) - 1;
+            if (eindex < j)
+            {
+              // delete characters at end of sequence
+              newend = findPosition(i - 1);
+              break; // don't need to search for any more residue characters.
+            }
+            else
+            {
+              createNewDs = true;
+              newend--; // decrease end position by one for the deleted residue
+              // and search further
+            }
+          }
+        }
+      }
+    }
+    // deletion occured in the middle of the sequence
+    if (createNewDs && this.datasetSequence != null)
+    {
+      // construct a new sequence
+      Sequence ds = new Sequence(datasetSequence);
+      // TODO: remove any non-inheritable properties ?
+      // TODO: create a sequence mapping (since there is a relation here ?)
+      ds.deleteChars(i, j);
+      datasetSequence = ds;
+    }
+    start = newstart;
+    end = newend;
     sequence = tmp;
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param c DOCUMENT ME!
-   * @param chop DOCUMENT ME!
+   * 
+   * @param i
+   *          DOCUMENT ME!
+   * @param c
+   *          DOCUMENT ME!
+   * @param chop
+   *          DOCUMENT ME!
    */
   public void insertCharAt(int i, int length, char c)
   {
-    char [] tmp = new char[sequence.length+length];
+    char[] tmp = new char[sequence.length + length];
 
     if (i >= sequence.length)
     {
@@ -588,21 +788,20 @@ public class Sequence implements SequenceI
       i = sequence.length;
     }
     else
-   {
+    {
       System.arraycopy(sequence, 0, tmp, 0, i);
-   }
-
+    }
 
     int index = i;
     while (length > 0)
     {
-      tmp[ index++ ] = c;
+      tmp[index++] = c;
       length--;
     }
 
     if (i < sequence.length)
     {
-      System.arraycopy(sequence, i, tmp, index, sequence.length-i );
+      System.arraycopy(sequence, i, tmp, index, sequence.length - i);
     }
 
     sequence = tmp;
@@ -630,23 +829,38 @@ public class Sequence implements SequenceI
 
   public DBRefEntry[] getDBRef()
   {
+    if (dbrefs == null && datasetSequence != null
+            && this != datasetSequence)
+    {
+      return datasetSequence.getDBRef();
+    }
     return dbrefs;
   }
 
   public void addDBRef(DBRefEntry entry)
   {
     if (dbrefs == null)
+    {
       dbrefs = new DBRefEntry[0];
+    }
 
     int i, iSize = dbrefs.length;
 
-    for(i=0; i<iSize; i++)
-      if(dbrefs[i].getAccessionId().equals(entry.getAccessionId())
-      && dbrefs[i].getSource().equals(entry.getSource())
-      && dbrefs[i].getVersion().equals(entry.getVersion()))
+    for (i = 0; i < iSize; i++)
+    {
+      if (dbrefs[i].equalRef(entry))
       {
+        if (entry.getMap() != null)
+        {
+          if (dbrefs[i].getMap() == null)
+          {
+            // overwrite with 'superior' entry that contains a mapping.
+            dbrefs[i] = entry;
+          }
+        }
         return;
       }
+    }
 
     DBRefEntry[] temp = new DBRefEntry[iSize + 1];
     System.arraycopy(dbrefs, 0, temp, 0, iSize);
@@ -668,11 +882,15 @@ public class Sequence implements SequenceI
   public AlignmentAnnotation[] getAnnotation()
   {
     if (annotation == null)
+    {
       return null;
+    }
 
     AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
     for (int r = 0; r < ret.length; r++)
+    {
       ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
+    }
 
     return ret;
   }
@@ -680,40 +898,307 @@ public class Sequence implements SequenceI
   public void addAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation == null)
+    {
       this.annotation = new Vector();
-
-    this.annotation.addElement(annotation);
+    }
+    if (!this.annotation.contains(annotation))
+    {
+      this.annotation.addElement(annotation);
+    }
+    annotation.setSequenceRef(this);
   }
 
+  public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
+  {
+    if (this.annotation != null)
+    {
+      this.annotation.removeElement(annotation);
+      if (this.annotation.size() == 0)
+        this.annotation = null;
+    }
+  }
 
   /**
-   * test if this is a valid candidate for another
-   * sequence's dataset sequence.
-   *
-   */
-  private boolean isValidDatasetSequence() {
-      if (datasetSequence!=null)
-          return false;
-      for (int i=0;i<sequence.length; i++)
-          if (jalview.util.Comparison.isGap(sequence[i]))
-              return false;
-      return true;
+   * test if this is a valid candidate for another sequence's dataset sequence.
+   * 
+   */
+  private boolean isValidDatasetSequence()
+  {
+    if (datasetSequence != null)
+    {
+      return false;
+    }
+    for (int i = 0; i < sequence.length; i++)
+    {
+      if (jalview.util.Comparison.isGap(sequence[i]))
+      {
+        return false;
+      }
+    }
+    return true;
   }
-  /* (non-Javadoc)
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.datamodel.SequenceI#deriveSequence()
    */
-  public SequenceI deriveSequence() {
-      SequenceI seq = new Sequence(name, sequence, start, end);
-      seq.setDescription(description);
-      if (datasetSequence!=null) {
-          seq.setDatasetSequence(datasetSequence);
-      } else {
-          if (isValidDatasetSequence())
-              seq.setDatasetSequence(this);
+  public SequenceI deriveSequence()
+  {
+    SequenceI seq = new Sequence(this);
+    if (datasetSequence != null)
+    {
+      // duplicate current sequence with same dataset
+      seq.setDatasetSequence(datasetSequence);
+    }
+    else
+    {
+      if (isValidDatasetSequence())
+      {
+        // Use this as dataset sequence
+        seq.setDatasetSequence(this);
+      }
+      else
+      {
+        // Create a new, valid dataset sequence
+        SequenceI ds = seq;
+        ds.setSequence(AlignSeq.extractGaps(
+                jalview.util.Comparison.GapChars, new String(sequence)));
+        setDatasetSequence(ds);
+        ds.setSequenceFeatures(getSequenceFeatures());
+        seq = this; // and return this sequence as the derived sequence.
       }
-      return seq;
+    }
+    return seq;
   }
 
-}
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.SequenceI#createDatasetSequence()
+   */
+  public SequenceI createDatasetSequence()
+  {
+    if (datasetSequence == null)
+    {
+      datasetSequence = new Sequence(getName(), AlignSeq.extractGaps(
+              jalview.util.Comparison.GapChars, getSequenceAsString()),
+              getStart(), getEnd());
+      datasetSequence.setSequenceFeatures(getSequenceFeatures());
+      datasetSequence.setDescription(getDescription());
+      setSequenceFeatures(null);
+      // move database references onto dataset sequence
+      datasetSequence.setDBRef(getDBRef());
+      setDBRef(null);
+      datasetSequence.setPDBId(getPDBId());
+      setPDBId(null);
+      datasetSequence.updatePDBIds();
+    }
+    return datasetSequence;
+  }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
+   * annotations)
+   */
+  public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
+  {
+    if (annotation != null)
+    {
+      annotation.removeAllElements();
+    }
+    if (annotations != null)
+    {
+      for (int i = 0; i < annotations.length; i++)
+      {
+        if (annotations[i] != null)
+          addAlignmentAnnotation(annotations[i]);
+      }
+    }
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
+   */
+  public AlignmentAnnotation[] getAnnotation(String label)
+  {
+    if (annotation == null || annotation.size() == 0)
+    {
+      return null;
+    }
 
+    Vector subset = new Vector();
+    Enumeration e = annotation.elements();
+    while (e.hasMoreElements())
+    {
+      AlignmentAnnotation ann = (AlignmentAnnotation) e.nextElement();
+      if (ann.label != null && ann.label.equals(label))
+      {
+        subset.addElement(ann);
+      }
+    }
+    if (subset.size() == 0)
+    {
+      return null;
+    }
+    AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()];
+    int i = 0;
+    e = subset.elements();
+    while (e.hasMoreElements())
+    {
+      anns[i++] = (AlignmentAnnotation) e.nextElement();
+    }
+    subset.removeAllElements();
+    return anns;
+  }
+
+  public boolean updatePDBIds()
+  {
+    if (datasetSequence != null)
+    {
+      // TODO: could merge DBRefs
+      return datasetSequence.updatePDBIds();
+    }
+    if (dbrefs == null || dbrefs.length == 0)
+    {
+      return false;
+    }
+    Vector newpdb = new Vector();
+    for (int i = 0; i < dbrefs.length; i++)
+    {
+      if (DBRefSource.PDB.equals(dbrefs[i].getSource()))
+      {
+        PDBEntry pdbe = new PDBEntry();
+        pdbe.setId(dbrefs[i].getAccessionId());
+        if (pdbIds == null || pdbIds.size() == 0)
+        {
+          newpdb.addElement(pdbe);
+        }
+        else
+        {
+          Enumeration en = pdbIds.elements();
+          boolean matched = false;
+          while (!matched && en.hasMoreElements())
+          {
+            PDBEntry anentry = (PDBEntry) en.nextElement();
+            if (anentry.getId().equals(pdbe.getId()))
+            {
+              matched = true;
+            }
+          }
+          if (!matched)
+          {
+            newpdb.addElement(pdbe);
+          }
+        }
+      }
+    }
+    if (newpdb.size() > 0)
+    {
+      Enumeration en = newpdb.elements();
+      while (en.hasMoreElements())
+      {
+        addPDBId((PDBEntry) en.nextElement());
+      }
+      return true;
+    }
+    return false;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
+   * jalview.datamodel.Mapping)
+   */
+  public void transferAnnotation(SequenceI entry, Mapping mp)
+  {
+    if (datasetSequence != null)
+    {
+      datasetSequence.transferAnnotation(entry, mp);
+      return;
+    }
+    if (entry.getDatasetSequence() != null)
+    {
+      transferAnnotation(entry.getDatasetSequence(), mp);
+      return;
+    }
+    // transfer any new features from entry onto sequence
+    if (entry.getSequenceFeatures() != null)
+    {
+
+      SequenceFeature[] sfs = entry.getSequenceFeatures();
+      for (int si = 0; si < sfs.length; si++)
+      {
+        SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
+                : new SequenceFeature[]
+                { new SequenceFeature(sfs[si]) };
+        if (sf != null && sf.length > 0)
+        {
+          for (int sfi = 0; sfi < sf.length; sfi++)
+          {
+            addSequenceFeature(sf[sfi]);
+          }
+        }
+      }
+    }
+
+    // transfer PDB entries
+    if (entry.getPDBId() != null)
+    {
+      Enumeration e = entry.getPDBId().elements();
+      while (e.hasMoreElements())
+      {
+        PDBEntry pdb = (PDBEntry) e.nextElement();
+        addPDBId(pdb);
+      }
+    }
+    // transfer database references
+    DBRefEntry[] entryRefs = entry.getDBRef();
+    if (entryRefs != null)
+    {
+      for (int r = 0; r < entryRefs.length; r++)
+      {
+        DBRefEntry newref = new DBRefEntry(entryRefs[r]);
+        if (newref.getMap() != null && mp != null)
+        {
+          // remap ref using our local mapping
+        }
+        // we also assume all version string setting is done by dbSourceProxy
+        /*
+         * if (!newref.getSource().equalsIgnoreCase(dbSource)) {
+         * newref.setSource(dbSource); }
+         */
+        addDBRef(newref);
+      }
+    }
+  }
+
+  /**
+   * @return The index (zero-based) on this sequence in the MSA. It returns
+   *         {@code -1} if this information is not available.
+   */
+  public int getIndex()
+  {
+    return index;
+  }
+
+  /**
+   * Defines the position of this sequence in the MSA. Use the value {@code -1}
+   * if this information is undefined.
+   * 
+   * @param The
+   *          position for this sequence. This value is zero-based (zero for
+   *          this first sequence)
+   */
+  public void setIndex(int value)
+  {
+    index = value;
+  }
+}