X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=4506742051dd57e0ac0d00462713bd13783dcfef;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=0e72690aa69e439df38b52b505a04662a500b007;hpb=649c3dff0ddf4047b11e83950642501897c60d5c;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 0e72690..4506742 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,110 +1,156 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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 2.9.0b1)
+ * Copyright (C) 2015 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 jalview.util.StringUtils;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
 
-import jalview.analysis.*;
+import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
  * 
  * Implements the SequenceI interface for a char[] based sequence object.
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class Sequence
-    implements SequenceI
+public class Sequence extends ASequence implements SequenceI
 {
   SequenceI datasetSequence;
+
   String name;
-  private char [] sequence;
+
+  private char[] sequence;
+
   String description;
+
   int start;
+
   int end;
-  Vector pdbIds;
+
+  Vector<PDBEntry> pdbIds;
+
   String vamsasId;
+
   DBRefEntry[] dbrefs;
 
-  /** This annotation is displayed below the alignment but the
-   * positions are tied to the residues of this sequence */
-  Vector annotation;
+  RNA rna;
 
-  /** array of seuqence features - may not be null for a valid sequence object */
-  public SequenceFeature[] sequenceFeatures;
+  /**
+   * This annotation is displayed below the alignment but the positions are tied
+   * to the residues of this sequence
+   *
+   * TODO: change to List<>
+   */
+  Vector<AlignmentAnnotation> annotation;
+
+  /**
+   * The index of the sequence in a MSA
+   */
+  int index = -1;
 
+  /** array of sequence features - may not be null for a valid sequence object */
+  public SequenceFeature[] sequenceFeatures;
 
   /**
    * Creates a new Sequence object.
-   *
-   * @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)
+   * 
+   * @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)
   {
-    this.name = name;
-    this.sequence = sequence.toCharArray();
-    this.start = start;
-    this.end = end;
-    parseId();
-    checkValidRange();
+    initSeqAndName(name, sequence.toCharArray(), start, end);
   }
 
-  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;
-    this.start = start;
-    this.end = end;
+    initSeqAndName(name, sequence, start, end);
+  }
+
+  /**
+   * Stage 1 constructor - assign name, sequence, and set start and end fields.
+   * start and end are updated values from name2 if it ends with /start-end
+   * 
+   * @param name2
+   * @param sequence2
+   * @param start2
+   * @param end2
+   */
+  protected void initSeqAndName(String name2, char[] sequence2, int start2,
+          int end2)
+  {
+    this.name = name2;
+    this.sequence = sequence2;
+    this.start = start2;
+    this.end = end2;
     parseId();
     checkValidRange();
   }
 
   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()
   {
-    // Does sequence have the /start-end signiature?
+    if (name == null)
+    {
+      System.err
+              .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+      name = "";
+    }
+    // Does sequence have the /start-end signature?
     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++;
         }
@@ -114,16 +160,21 @@ public class Sequence
         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)
   {
@@ -131,53 +182,71 @@ public class Sequence
   }
 
   /**
-   * Creates a new Sequence object with new features, DBRefEntries, AlignmentAnnotations, and PDBIds
-   * but inherits any existing dataset sequence reference.
-   * @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, 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 
+   * 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(),
+    initSeqFrom(seq, alAnnotation);
+
+  }
+
+  protected void initSeqFrom(SequenceI seq,
+          AlignmentAnnotation[] alAnnotation)
+  {
+    initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
             seq.getEnd());
     description = seq.getDescription();
-    if (seq.getSequenceFeatures()!=null) {
+    if (seq.getSequenceFeatures() != null)
+    {
       SequenceFeature[] sf = seq.getSequenceFeatures();
-      for (int i=0; i<sf.length; i++) {
+      for (int i = 0; i < sf.length; i++)
+      {
         addSequenceFeature(new SequenceFeature(sf[i]));
       }
     }
-    if (seq.getDBRef()!=null) {
+    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++) {
+      for (int i = 0; i < dbr.length; i++)
+      {
         addDBRef(new DBRefEntry(dbr[i]));
       }
     }
-    setDatasetSequence(seq.getDatasetSequence());
-    if (seq.getAnnotation()!=null) {
+    if (seq.getAnnotation() != null)
+    {
       AlignmentAnnotation[] sqann = seq.getAnnotation();
-      for (int i=0;i<sqann.length; i++)
+      for (int i = 0; i < sqann.length; i++)
       {
-        if (sqann[i]==null)
+        if (sqann[i] == null)
         {
           continue;
         }
-        boolean found = (alAnnotation==null);
+        boolean found = (alAnnotation == null);
         if (!found)
         {
-          for (int apos = 0; !found && apos<alAnnotation.length; apos++)
+          for (int apos = 0; !found && apos < alAnnotation.length; apos++)
           {
             found = (alAnnotation[apos] == sqann[i]);
           }
@@ -190,10 +259,12 @@ public class Sequence
         }
       }
     }
-    if (seq.getPDBId()!=null) {
-      Vector ids = seq.getPDBId();
+    if (seq.getAllPDBEntries() != null)
+    {
+      Vector ids = seq.getAllPDBEntries();
       Enumeration e = ids.elements();
-      while (e.hasMoreElements()) {
+      while (e.hasMoreElements())
+      {
         this.addPDBId(new PDBEntry((PDBEntry) e.nextElement()));
       }
     }
@@ -201,8 +272,9 @@ public class Sequence
 
   /**
    * DOCUMENT ME!
-   *
-   * @param v DOCUMENT ME!
+   * 
+   * @param v
+   *          DOCUMENT ME!
    */
   public void setSequenceFeatures(SequenceFeature[] features)
   {
@@ -233,12 +305,12 @@ public class Sequence
 
   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))
@@ -247,28 +319,25 @@ public class Sequence
       }
     }
 
-
-    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)
+      if (index < sfLength)
       {
-        System.arraycopy(sequenceFeatures,
-                         index + 1,
-                         temp,
-                         index, sequenceFeatures.length - index -1);
+        System.arraycopy(sequenceFeatures, index + 1, temp, index,
+                sequenceFeatures.length - index - 1);
       }
 
       sequenceFeatures = temp;
@@ -276,48 +345,78 @@ public class Sequence
   }
 
   /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
+   * Returns the sequence features (if any), looking first on the sequence, then
+   * on its dataset sequence, and so on until a non-null value is found (or
+   * none). This supports retrieval of sequence features stored on the sequence
+   * (as in the applet) or on the dataset sequence (as in the Desktop version).
+   * 
+   * @return
    */
   public SequenceFeature[] getSequenceFeatures()
   {
-    return sequenceFeatures;
+    SequenceFeature[] features = sequenceFeatures;
+
+    SequenceI seq = this;
+    int count = 0; // failsafe against loop in sequence.datasetsequence...
+    while (features == null && seq.getDatasetSequence() != null
+            && count++ < 10)
+    {
+      seq = seq.getDatasetSequence();
+      features = ((Sequence) seq).sequenceFeatures;
+    }
+    return features;
   }
 
   public void addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
     {
-      pdbIds = new Vector();
+      pdbIds = new Vector<PDBEntry>();
     }
+    if (pdbIds.contains(entry))
+    {
+      updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
+    }
+    else
+    {
+      pdbIds.addElement(entry);
+    }
+  }
 
-    pdbIds.addElement(entry);
+  private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
+  {
+    if (newEntry.getFile() != null)
+    {
+      oldEntry.setFile(newEntry.getFile());
+    }
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param id DOCUMENT ME!
+   * 
+   * @param id
+   *          DOCUMENT ME!
    */
-  public void setPDBId(Vector id)
+  @Override
+  public void setPDBId(Vector<PDBEntry> id)
   {
     pdbIds = id;
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
-  public Vector getPDBId()
+  @Override
+  public Vector<PDBEntry> getAllPDBEntries()
   {
     return pdbIds;
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getDisplayId(boolean jvsuffix)
@@ -333,8 +432,9 @@ public class Sequence
 
   /**
    * DOCUMENT ME!
-   *
-   * @param name DOCUMENT ME!
+   * 
+   * @param name
+   *          DOCUMENT ME!
    */
   public void setName(String name)
   {
@@ -344,7 +444,7 @@ public class Sequence
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getName()
@@ -354,8 +454,9 @@ public class Sequence
 
   /**
    * DOCUMENT ME!
-   *
-   * @param start DOCUMENT ME!
+   * 
+   * @param start
+   *          DOCUMENT ME!
    */
   public void setStart(int start)
   {
@@ -364,7 +465,7 @@ public class Sequence
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getStart()
@@ -374,8 +475,9 @@ public class Sequence
 
   /**
    * DOCUMENT ME!
-   *
-   * @param end DOCUMENT ME!
+   * 
+   * @param end
+   *          DOCUMENT ME!
    */
   public void setEnd(int end)
   {
@@ -384,7 +486,7 @@ public class Sequence
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getEnd()
@@ -394,7 +496,7 @@ public class Sequence
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public int getLength()
@@ -404,8 +506,9 @@ public class Sequence
 
   /**
    * DOCUMENT ME!
-   *
-   * @param seq DOCUMENT ME!
+   * 
+   * @param seq
+   *          DOCUMENT ME!
    */
   public void setSequence(String seq)
   {
@@ -413,7 +516,6 @@ public class Sequence
     checkValidRange();
   }
 
-
   public String getSequenceAsString()
   {
     return new String(sequence);
@@ -424,25 +526,24 @@ public class Sequence
     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)
   {
-    if (start<0)
-      start=0;
-    // 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];
@@ -453,26 +554,20 @@ public class Sequence
       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
-   * @return SequenceI
-   */
+  @Override
   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;
@@ -482,22 +577,23 @@ public class Sequence
     // JBPNote - this is an incomplete copy.
     SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend);
     nseq.setDescription(description);
-    if (datasetSequence!=null)
+    if (datasetSequence != null)
     {
-        nseq.setDatasetSequence(datasetSequence);
+      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)
@@ -514,8 +610,9 @@ public class Sequence
 
   /**
    * DOCUMENT ME!
-   *
-   * @param desc DOCUMENT ME!
+   * 
+   * @param desc
+   *          DOCUMENT ME!
    */
   public void setDescription(String desc)
   {
@@ -524,7 +621,7 @@ public class Sequence
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   public String getDescription()
@@ -532,20 +629,18 @@ public class Sequence
     return this.description;
   }
 
-  /**
-   * Return the alignment position for a sequence position
-   *
-   * @param pos lying from start to end
-   *
-   * @return aligned position of residue pos
+  /*
+   * (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]))
       {
@@ -555,7 +650,7 @@ public class Sequence
       i++;
     }
 
-    if ( (j == end) && (j < pos))
+    if ((j == end) && (j < pos))
     {
       return end + 1;
     }
@@ -565,21 +660,15 @@ public class Sequence
     }
   }
 
-  /**
-   * Returns the sequence position for an alignment position
-   *
-   * @param i column index in alignment (from 1)
-   *
-   * @return residue number for residue (left of and) nearest ith column
-   */
+  @Override
   public int findPosition(int i)
   {
     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++;
       }
@@ -591,14 +680,16 @@ public class Sequence
   }
 
   /**
-   * 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;
@@ -616,31 +707,75 @@ public class Sequence
     return map;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SequenceI#deleteChars(int, int)
-   */
-  public void deleteChars(int i, int j)
+  @Override
+  public int[] findPositionMap()
   {
-    int newstart=start,newend=end;
-    if (i >= sequence.length)
+    int map[] = new int[sequence.length];
+    int j = 0;
+    int pos = start;
+    int seqlen = sequence.length;
+    while ((j < seqlen))
     {
-      return;
-    }
+      map[j] = pos;
+      if (!jalview.util.Comparison.isGap(sequence[j]))
+      {
+        pos++;
+      }
 
-    char [] tmp;
+      j++;
+    }
+    return map;
+  }
 
-    if (j >= sequence.length)
+  @Override
+  public List<int[]> getInsertions()
+  {
+    ArrayList<int[]> map = new ArrayList<int[]>();
+    int lastj = -1, j = 0;
+    int pos = start;
+    int seqlen = sequence.length;
+    while ((j < seqlen))
+    {
+      if (jalview.util.Comparison.isGap(sequence[j]))
+      {
+        if (lastj == -1)
+        {
+          lastj = j;
+        }
+      }
+      else
+      {
+        if (lastj != -1)
+        {
+          map.add(new int[] { lastj, j - 1 });
+          lastj = -1;
+        }
+      }
+      j++;
+    }
+    if (lastj != -1)
     {
-      tmp = new char[i];
-      System.arraycopy(sequence,0,tmp,0,i);
+      map.add(new int[] { lastj, j - 1 });
+      lastj = -1;
     }
-    else
+    return map;
+  }
+
+  @Override
+  public void deleteChars(int i, int j)
+  {
+    int newstart = start, newend = end;
+    if (i >= sequence.length || i < 0)
     {
-      tmp = new char[sequence.length-j+i];
-      System.arraycopy(sequence,0,tmp,0,i);
-      System.arraycopy(sequence,j,tmp,i,sequence.length-j);
+      return;
     }
-    boolean createNewDs=false;
+
+    char[] tmp = StringUtils.deleteChars(sequence, i, j);
+    boolean createNewDs = false;
+    // TODO: take a (second look) at the dataset creation validation method for
+    // the very large sequence case
+    int eindex = -1, sindex = -1;
+    boolean ecalc = false, scalc = false;
     for (int s = i; s < j; s++)
     {
       if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
@@ -648,26 +783,41 @@ public class Sequence
         if (createNewDs)
         {
           newend--;
-        } else {
-          int sindex = findIndex(start)-1;
-          if (sindex==s)
+        }
+        else
         {
-          // 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)
+          if (!scalc)
           {
-            // delete characters at end of sequence
-            newend = findPosition(i-1);
+            sindex = findIndex(start) - 1;
+            scalc = true;
+          }
+          if (sindex == s)
+          {
+            // delete characters including start of sequence
+            newstart = findPosition(j);
             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
           }
-        }
+          else
+          {
+            // delete characters after start.
+            if (!ecalc)
+            {
+              eindex = findIndex(end) - 1;
+              ecalc = true;
+            }
+            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
+            }
+          }
         }
       }
     }
@@ -686,17 +836,10 @@ public class Sequence
     sequence = tmp;
   }
 
-
-  /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param c DOCUMENT ME!
-   * @param chop DOCUMENT ME!
-   */
+  @Override
   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)
     {
@@ -704,51 +847,61 @@ public class Sequence
       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;
   }
 
+  @Override
   public void insertCharAt(int i, char c)
   {
     insertCharAt(i, 1, c);
   }
 
+  @Override
   public String getVamsasId()
   {
     return vamsasId;
   }
 
+  @Override
   public void setVamsasId(String id)
   {
     vamsasId = id;
   }
 
+  @Override
   public void setDBRef(DBRefEntry[] dbref)
   {
     dbrefs = dbref;
   }
 
+  @Override
   public DBRefEntry[] getDBRef()
   {
+    if (dbrefs == null && datasetSequence != null
+            && this != datasetSequence)
+    {
+      return datasetSequence.getDBRef();
+    }
     return dbrefs;
   }
 
+  @Override
   public void addDBRef(DBRefEntry entry)
   {
     if (dbrefs == null)
@@ -758,10 +911,18 @@ public class Sequence
 
     int i, iSize = dbrefs.length;
 
-    for(i=0; i<iSize; i++)
+    for (i = 0; i < iSize; i++)
     {
-      if(dbrefs[i].equals(entry))
+      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;
       }
     }
@@ -773,80 +934,81 @@ public class Sequence
     dbrefs = temp;
   }
 
+  @Override
   public void setDatasetSequence(SequenceI seq)
   {
     datasetSequence = seq;
   }
 
+  @Override
   public SequenceI getDatasetSequence()
   {
     return datasetSequence;
   }
 
+  @Override
   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 annotation == null ? null : annotation
+            .toArray(new AlignmentAnnotation[annotation.size()]);
+  }
 
-    return ret;
+  @Override
+  public boolean hasAnnotation(AlignmentAnnotation ann)
+  {
+    return annotation == null ? false : annotation.contains(ann);
   }
 
+  @Override
   public void addAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation == null)
     {
-      this.annotation = new Vector();
+      this.annotation = new Vector<AlignmentAnnotation>();
+    }
+    if (!this.annotation.contains(annotation))
+    {
+      this.annotation.addElement(annotation);
     }
-
-    this.annotation.addElement(annotation);
     annotation.setSequenceRef(this);
   }
 
   public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
   {
-    if(this.annotation!=null)
+    if (this.annotation != null)
     {
       this.annotation.removeElement(annotation);
-      if(this.annotation.size()==0)
+      if (this.annotation.size() == 0)
+      {
         this.annotation = null;
+      }
     }
   }
 
-
   /**
-   * test if this is a valid candidate for another
-   * sequence's dataset sequence.
-   *
+   * test if this is a valid candidate for another sequence's dataset sequence.
+   * 
    */
   private boolean isValidDatasetSequence()
   {
-    if (datasetSequence!=null)
+    if (datasetSequence != null)
     {
-          return false;
+      return false;
     }
-      for (int i=0;i<sequence.length; i++)
+    for (int i = 0; i < sequence.length; i++)
     {
-          if (jalview.util.Comparison.isGap(sequence[i]))
+      if (jalview.util.Comparison.isGap(sequence[i]))
       {
-              return false;
+        return false;
       }
     }
-      return true;
+    return true;
   }
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SequenceI#deriveSequence()
-   */
+
+  @Override
   public SequenceI deriveSequence()
   {
-    SequenceI seq=new Sequence(this);
+    SequenceI seq = new Sequence(this);
     if (datasetSequence != null)
     {
       // duplicate current sequence with same dataset
@@ -858,10 +1020,13 @@ public class Sequence
       {
         // Use this as dataset sequence
         seq.setDatasetSequence(this);
-      } else {
+      }
+      else
+      {
         // Create a new, valid dataset sequence
         SequenceI ds = seq;
-        ds.setSequence(AlignSeq.extractGaps(jalview.util.Comparison.GapChars, new String(sequence)));
+        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.
@@ -869,49 +1034,92 @@ public class Sequence
     }
     return seq;
   }
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] annotations)
+
+  /*
+   * (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(getAllPDBEntries());
+      setPDBId(null);
+      datasetSequence.updatePDBIds();
+      if (annotation != null)
+      {
+        for (AlignmentAnnotation aa : annotation)
+        {
+          AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+          _aa.sequenceRef = datasetSequence;
+          _aa.adjustForAlignment(); // uses annotation's own record of
+                                    // sequence-column mapping
+          datasetSequence.addAlignmentAnnotation(_aa);
+        }
+      }
+    }
+    return datasetSequence;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
+   * annotations)
    */
   public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
   {
-    if (annotation!=null) {
+    if (annotation != null)
+    {
       annotation.removeAllElements();
     }
-    if (annotations!=null) {
-      for (int i=0; i<annotations.length; i++)
+    if (annotations != null)
+    {
+      for (int i = 0; i < annotations.length; i++)
       {
-        if (annotations[i]!=null)
+        if (annotations[i] != null)
+        {
           addAlignmentAnnotation(annotations[i]);
+        }
       }
     }
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
-   */
+  @Override
   public AlignmentAnnotation[] getAnnotation(String label)
   {
-    if (annotation==null || annotation.size()==0)
+    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))
+      if (ann.label != null && ann.label.equals(label))
       {
         subset.addElement(ann);
       }
     }
-    if (subset.size()==0)
+    if (subset.size() == 0)
     {
       return null;
     }
     AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()];
-    int i=0;
+    int i = 0;
     e = subset.elements();
     while (e.hasMoreElements())
     {
@@ -921,6 +1129,196 @@ public class Sequence
     return anns;
   }
 
-}
+  @Override
+  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;
+  }
+
+  @Override
+  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.getAllPDBEntries() != null)
+    {
+      Enumeration e = entry.getAllPDBEntries().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;
+  }
+
+  public void setRNA(RNA r)
+  {
+    rna = r;
+  }
+
+  public RNA getRNA()
+  {
+    return rna;
+  }
+
+  @Override
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label)
+  {
+    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+    if (this.annotation != null)
+    {
+      for (AlignmentAnnotation ann : annotation)
+      {
+        if (ann.calcId != null && ann.calcId.equals(calcId)
+                && ann.label != null && ann.label.equals(label))
+        {
+          result.add(ann);
+        }
+      }
+    }
+    return result;
+  }
 
+  public String toString()
+  {
+    return getDisplayId(false);
+  }
+
+  @Override
+  public PDBEntry getPDBEntry(String pdbIdStr)
+  {
+    if (getDatasetSequence() == null
+            || getDatasetSequence().getAllPDBEntries() == null)
+    {
+      return null;
+    }
+    List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+    for (PDBEntry entry : entries)
+    {
+      if (entry.getId().equalsIgnoreCase(pdbIdStr))
+      {
+        return entry;
+      }
+    }
+    return null;
+  }
+
+}