X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=52d9a720235bf2cd1dc8c760106cc169e1d43e43;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=fc52190ce6021cbc31db3cfd38d8e13fa381d23a;hpb=06118a7ac64edb37e3d741f9a768dba9ebb949fc;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index fc52190..52d9a72 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,777 +1,1175 @@
 /*
-* 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
 package jalview.datamodel;
 
-import java.awt.*;
-
 import java.util.*;
 
+import jalview.analysis.*;
 
 /**
- * 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 String sequence;
-    String description;
-    int start;
-    int end;
-    Color color = Color.white;
-    Vector 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;
-
-    /** DOCUMENT ME!! */
-    public SequenceFeature [] sequenceFeatures;
-
-    /** This array holds hidden sequences
-     * of which this sequence is the representitive member of a group
-     */
-    SequenceGroup hiddenSequences;
-
-    /**
-     * Creates a new Sequence object.
-     *
-     * @param name DOCUMENT ME!
-     * @param sequence DOCUMENT ME!
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     */
-    public Sequence(String name, String sequence, int start, int end)
-    {
-      this.name = name;
-      this.sequence = sequence;
-      this.start = start;
-      this.end = end;
-
-      parseId();
-
-      checkValidRange();
-    }
-
-    com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
-                        "[/][0-9]{1,}[-][0-9]{1,}$");
-    com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
-                        "[0-9]{1,}$");
-
-    void parseId()
-    {
-        // 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 )));
-            setEnd(   Integer.parseInt( endrx.stringMatched() ));
-         }
-    }
-
-    void checkValidRange()
-    {
-      if (end < 1)
-      {
-        int endRes = 0;
-        char ch;
-        for (int j = 0; j < sequence.length(); j++)
-        {
-          ch = sequence.charAt(j);
-          if (!jalview.util.Comparison.isGap( (ch)))
-          {
-            endRes++;
-          }
-        }
-        if (endRes > 0)
-        {
-          endRes += start - 1;
-        }
+  SequenceI datasetSequence;
 
-        this.end = endRes;
-      }
+  String name;
 
-    }
+  private char[] sequence;
+
+  String description;
 
-    /**
-     * Creates a new Sequence object.
-     *
-     * @param name DOCUMENT ME!
-     * @param sequence DOCUMENT ME!
-     */
-    public Sequence(String name, String sequence)
+  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
+   */
+  Vector annotation;
+
+  /** array of seuqence 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)
+   */
+  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();
+  }
+
+  public Sequence(String name, char[] sequence, int start, int end)
+  {
+    this.name = name;
+    this.sequence = sequence;
+    this.start = start;
+    this.end = end;
+    parseId();
+    checkValidRange();
+  }
+
+  com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
+          "[/][0-9]{1,}[-][0-9]{1,}$");
+
+  com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$");
+
+  void parseId()
+  {
+    if (name == null)
     {
-        this(name, sequence, 1, -1);
+      System.err
+              .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+      name = "";
     }
-
-    /**
-     * Creates a new Sequence object.
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public Sequence(SequenceI seq)
+    // Does sequence have the /start-end signiature?
+    if (limitrx.search(name))
     {
-        this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+      name = limitrx.left();
+      endrx.search(limitrx.stringMatched());
+      setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
+              endrx.matchedFrom() - 1)));
+      setEnd(Integer.parseInt(endrx.stringMatched()));
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param v DOCUMENT ME!
-     */
-    public void setSequenceFeatures(SequenceFeature [] features)
+  void checkValidRange()
+  {
+    // Note: JAL-774 : http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239
     {
-        sequenceFeatures = features;
+      int endRes = 0;
+      for (int j = 0; j < sequence.length; j++)
+      {
+        if (!jalview.util.Comparison.isGap(sequence[j]))
+        {
+          endRes++;
+        }
+      }
+      if (endRes > 0)
+      {
+        endRes += start - 1;
+      }
+
+      if (end<endRes) { 
+        end = endRes;
+      }
     }
 
-    public synchronized void addSequenceFeature(SequenceFeature sf)
+  }
+
+  /**
+   * Creates a new Sequence object.
+   * 
+   * @param name
+   *          DOCUMENT ME!
+   * @param sequence
+   *          DOCUMENT ME!
+   */
+  public Sequence(String name, String sequence)
+  {
+    this(name, sequence, 1, -1);
+  }
+
+  /**
+   * 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
+   */
+  public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
+  {
+    this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+    description = seq.getDescription();
+    if (seq.getSequenceFeatures() != null)
     {
-      if(sequenceFeatures==null)
+      SequenceFeature[] sf = seq.getSequenceFeatures();
+      for (int i = 0; i < sf.length; i++)
       {
-        sequenceFeatures = new SequenceFeature[0];
+        addSequenceFeature(new SequenceFeature(sf[i]));
       }
-
-      for(int i=0; i<sequenceFeatures.length; 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(sequenceFeatures[i].equals(sf))
+        if (sqann[i] == null)
+        {
+          continue;
+        }
+        boolean found = (alAnnotation == null);
+        if (!found)
         {
-          return;
+          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);
         }
       }
-
-      SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];
-      System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
-      temp[sequenceFeatures.length] = sf;
-
-      sequenceFeatures = temp;
     }
+    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!
+   */
+  public void setSequenceFeatures(SequenceFeature[] features)
+  {
+    sequenceFeatures = features;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceFeature [] getSequenceFeatures()
+  public synchronized void addSequenceFeature(SequenceFeature sf)
+  {
+    if (sequenceFeatures == null)
     {
-        return sequenceFeatures;
+      sequenceFeatures = new SequenceFeature[0];
     }
 
-    public void addPDBId(PDBEntry entry)
+    for (int i = 0; i < sequenceFeatures.length; i++)
     {
-      if(pdbIds == null)
-        pdbIds = new Vector();
+      if (sequenceFeatures[i].equals(sf))
+      {
+        return;
+      }
+    }
 
-      pdbIds.addElement(entry);
+    SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1];
+    System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
+    temp[sequenceFeatures.length] = sf;
+
+    sequenceFeatures = temp;
+  }
+
+  public void deleteFeature(SequenceFeature sf)
+  {
+    if (sequenceFeatures == null)
+    {
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param id DOCUMENT ME!
-     */
-    public void setPDBId(Vector id)
+    int index = 0;
+    for (index = 0; index < sequenceFeatures.length; index++)
     {
-        pdbIds = id;
+      if (sequenceFeatures[index].equals(sf))
+      {
+        break;
+      }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Vector getPDBId()
+    if (index == sequenceFeatures.length)
     {
-        return pdbIds;
+      return;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getDisplayId(boolean jvsuffix)
+    int sfLength = sequenceFeatures.length;
+    if (sfLength < 2)
+    {
+      sequenceFeatures = null;
+    }
+    else
     {
-      StringBuffer result = new StringBuffer(name);
-      if (jvsuffix)
+      SequenceFeature[] temp = new SequenceFeature[sfLength - 1];
+      System.arraycopy(sequenceFeatures, 0, temp, 0, index);
+
+      if (index < sfLength)
       {
-        result.append("/" + start + "-" + end);
+        System.arraycopy(sequenceFeatures, index + 1, temp, index,
+                sequenceFeatures.length - index - 1);
       }
 
-      return result.toString();
+      sequenceFeatures = temp;
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param name DOCUMENT ME!
-     */
-    public void setName(String name)
-    {
-      this.name = name;
-      this.parseId();
-    }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public SequenceFeature[] getSequenceFeatures()
+  {
+    return sequenceFeatures;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getName()
+  public void addPDBId(PDBEntry entry)
+  {
+    if (pdbIds == null)
     {
-       return this.name;
+      pdbIds = new Vector();
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param start DOCUMENT ME!
-     */
-    public void setStart(int start)
+    if (!pdbIds.contains(entry))
     {
-        this.start = start;
+      pdbIds.addElement(entry);
     }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param id
+   *          DOCUMENT ME!
+   */
+  public void setPDBId(Vector id)
+  {
+    pdbIds = id;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getStart()
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public Vector getPDBId()
+  {
+    return pdbIds;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String getDisplayId(boolean jvsuffix)
+  {
+    StringBuffer result = new StringBuffer(name);
+    if (jvsuffix)
     {
-        return this.start;
+      result.append("/" + start + "-" + end);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param end DOCUMENT ME!
-     */
-    public void setEnd(int end)
+    return result.toString();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param name
+   *          DOCUMENT ME!
+   */
+  public void setName(String name)
+  {
+    this.name = name;
+    this.parseId();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String getName()
+  {
+    return this.name;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param start
+   *          DOCUMENT ME!
+   */
+  public void setStart(int start)
+  {
+    this.start = start;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getStart()
+  {
+    return this.start;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param end
+   *          DOCUMENT ME!
+   */
+  public void setEnd(int end)
+  {
+    this.end = end;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getEnd()
+  {
+    return this.end;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public int getLength()
+  {
+    return this.sequence.length;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *          DOCUMENT ME!
+   */
+  public void setSequence(String seq)
+  {
+    this.sequence = seq.toCharArray();
+    checkValidRange();
+  }
+
+  public String getSequenceAsString()
+  {
+    return new String(sequence);
+  }
+
+  public String getSequenceAsString(int start, int end)
+  {
+    return new String(getSequence(start, end));
+  }
+
+  public char[] getSequence()
+  {
+    return sequence;
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.SequenceI#getSequence(int, int)
+   */
+  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 >= sequence.length)
     {
-        this.end = end;
+      return new char[0];
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getEnd()
+    if (end >= sequence.length)
     {
-        return this.end;
+      end = sequence.length;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int getLength()
+    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
+   */
+  public SequenceI getSubSequence(int start, int end)
+  {
+    if (start < 0)
     {
-        return this.sequence.length();
+      start = 0;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void setSequence(String seq)
+    char[] seq = getSequence(start, end);
+    if (seq.length == 0)
     {
-        this.sequence = seq;
-        checkValidRange();
+      return null;
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getSequence()
+    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)
     {
-        return this.sequence;
+      nseq.setDatasetSequence(datasetSequence);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getSequence(int start, int end)
+    else
     {
-        // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
-        if (start >= sequence.length())
-        {
-            return "";
-        }
-
-        if (end >= sequence.length())
-        {
-            end = sequence.length();
-        }
-
-        return this.sequence.substring(start, end);
-    }
-    /**
-     * 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;
-      String seq = getSequence(start, end);
-      if (seq=="")
-        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.setDatasetSequence(getDatasetSequence());
-      return nseq;
-    }
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getCharAt(int i)
-    {
-        if (i < sequence.length())
-        {
-            return sequence.charAt(i);
-        }
-        else
-        {
-            return ' ';
-        }
+      nseq.setDatasetSequence(this);
     }
+    return nseq;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param desc DOCUMENT ME!
-     */
-    public void setDescription(String desc)
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param i
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public char getCharAt(int i)
+  {
+    if (i < sequence.length)
     {
-        this.description = desc;
+      return sequence[i];
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getDescription()
+    else
     {
-        return this.description;
+      return ' ';
     }
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param pos DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int findIndex(int pos)
-    {
-        // returns the alignment position for a residue
-        int j = start;
-        int i = 0;
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param desc
+   *          DOCUMENT ME!
+   */
+  public void setDescription(String desc)
+  {
+    this.description = desc;
+  }
 
-        while ((i < sequence.length()) && (j <= end) && (j <= pos))
-        {
-            if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
-            {
-                j++;
-            }
+  /**
+   * DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  public String getDescription()
+  {
+    return this.description;
+  }
 
-            i++;
-        }
+  /**
+   * Return the alignment position for a sequence position
+   * 
+   * @param pos
+   *          lying from start to end
+   * 
+   * @return aligned position of residue pos
+   */
+  public int findIndex(int pos)
+  {
+    // returns the alignment position for a residue
+    int j = start;
+    int i = 0;
+    // 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]))
+      {
+        j++;
+      }
 
-        if ((j == end) && (j < pos))
-        {
-            return end + 1;
-        }
-        else
-        {
-            return i;
-        }
+      i++;
     }
 
-    /**
-     * 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
-     */
-    public int findPosition(int i)
+    if ((j == end) && (j < pos))
     {
-        int j = 0;
-        int pos = start;
-        int seqlen=sequence.length();
-        while ((j < i) && (j < seqlen))
-        {
-            if (!jalview.util.Comparison.isGap((sequence.charAt(j))))
-            {
-                pos++;
-            }
+      return end + 1;
+    }
+    else
+    {
+      return i;
+    }
+  }
 
-            j++;
-        }
+  /**
+   * 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
+   */
+  public int findPosition(int i)
+  {
+    int j = 0;
+    int pos = start;
+    int seqlen = sequence.length;
+    while ((j < i) && (j < seqlen))
+    {
+      if (!jalview.util.Comparison.isGap(sequence[j]))
+      {
+        pos++;
+      }
 
-        return pos;
+      j++;
     }
 
-    /**
-     * 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, sequence);
-        int[] map = new int[seq.length()];
-        int j = 0;
-        int p = 0;
+    return pos;
+  }
 
-        while (j < sequence.length())
-        {
-            if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
-            {
-                map[p++] = j;
-            }
+  /**
+   * 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));
+    int[] map = new int[seq.length()];
+    int j = 0;
+    int p = 0;
 
-            j++;
-        }
+    while (j < sequence.length)
+    {
+      if (!jalview.util.Comparison.isGap(sequence[j]))
+      {
+        map[p++] = j;
+      }
 
-        return map;
+      j++;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void deleteCharAt(int i)
+    return map;
+  }
+
+  /*
+   * (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))
     {
-        if (i >= sequence.length())
-        {
-            return;
-        }
+      map[j] = pos;
+      if (!jalview.util.Comparison.isGap(sequence[j]))
+      {
+        pos++;
+      }
 
-        sequence = sequence.substring(0, i) + sequence.substring(i + 1);
+      j++;
     }
+    return map;
+  }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     */
-    public void deleteChars(int i, int j)
+  /*
+   * (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)
     {
-        if (i >= sequence.length())
-        {
-            return;
-        }
-
-        if (j >= sequence.length())
-        {
-            sequence = sequence.substring(0, i);
-        }
-        else
-        {
-            sequence = sequence.substring(0, i) + sequence.substring(j);
-        }
+      return;
     }
 
+    char[] tmp;
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param c DOCUMENT ME!
-     * @param chop DOCUMENT ME!
-     */
-    public void insertCharAt(int i, char c)
+    if (j >= sequence.length)
     {
-        String tmp = new String(sequence);
-
-        if (i < sequence.length())
+      tmp = new char[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);
+    }
+    boolean createNewDs = false;
+    for (int s = i; s < j; s++)
+    {
+      if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+      {
+        if (createNewDs)
         {
-            sequence = tmp.substring(0, i) + String.valueOf(c) +
-                tmp.substring(i);
+          newend--;
         }
         else
         {
-            // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet!
-            char[] ch = new char[(1 + i) - sequence.length()];
-
-            for (int j = 0, k = ch.length; j < k; j++)
-                ch[j] = c;
-
-            sequence = tmp + String.valueOf(ch);
+          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
+            }
+          }
         }
+      }
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     */
-    public void setColor(Color c)
+    // deletion occured in the middle of the sequence
+    if (createNewDs && this.datasetSequence != null)
     {
-        this.color = c;
+      // 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!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color getColor()
-    {
-        return color;
-    }
+  /**
+   * 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];
 
-    public String getVamsasId()
+    if (i >= sequence.length)
     {
-      return vamsasId;
+      System.arraycopy(sequence, 0, tmp, 0, sequence.length);
+      i = sequence.length;
     }
-
-    public void setVamsasId(String id)
+    else
     {
-      vamsasId = id;
+      System.arraycopy(sequence, 0, tmp, 0, i);
     }
 
-    public void setDBRef(DBRefEntry [] dbref)
+    int index = i;
+    while (length > 0)
     {
-      dbrefs = dbref;
+      tmp[index++] = c;
+      length--;
     }
 
-    public DBRefEntry [] getDBRef()
+    if (i < sequence.length)
     {
-      return dbrefs;
+      System.arraycopy(sequence, i, tmp, index, sequence.length - i);
     }
 
-    public void addDBRef(DBRefEntry entry)
-    {
-      if(dbrefs == null)
-        dbrefs = new DBRefEntry[0];
+    sequence = tmp;
+  }
 
-      DBRefEntry [] temp = new DBRefEntry[dbrefs.length+1];
-      System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
+  public void insertCharAt(int i, char c)
+  {
+    insertCharAt(i, 1, c);
+  }
 
-      temp[temp.length-1] = entry;
+  public String getVamsasId()
+  {
+    return vamsasId;
+  }
 
-      dbrefs = temp;
-    }
+  public void setVamsasId(String id)
+  {
+    vamsasId = id;
+  }
 
-    public void setDatasetSequence(SequenceI seq)
+  public void setDBRef(DBRefEntry[] dbref)
+  {
+    dbrefs = dbref;
+  }
+
+  public DBRefEntry[] getDBRef()
+  {
+    if (dbrefs == null && datasetSequence != null
+            && this != datasetSequence)
     {
-      datasetSequence = seq;
+      return datasetSequence.getDBRef();
     }
+    return dbrefs;
+  }
 
-    public SequenceI getDatasetSequence()
+  public void addDBRef(DBRefEntry entry)
+  {
+    if (dbrefs == null)
     {
-      return datasetSequence;
+      dbrefs = new DBRefEntry[0];
     }
 
-    public AlignmentAnnotation [] getAnnotation()
+    int i, iSize = dbrefs.length;
+
+    for (i = 0; i < iSize; i++)
     {
-      if(annotation==null)
-        return null;
+      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);
+    temp[temp.length - 1] = entry;
 
-      AlignmentAnnotation [] ret = new AlignmentAnnotation[annotation.size()];
-      for(int r = 0; r<ret.length; r++)
-        ret[r] = (AlignmentAnnotation)annotation.elementAt(r);
+    dbrefs = temp;
+  }
 
-      return ret;
+  public void setDatasetSequence(SequenceI seq)
+  {
+    datasetSequence = seq;
+  }
+
+  public SequenceI getDatasetSequence()
+  {
+    return datasetSequence;
+  }
+
+  public AlignmentAnnotation[] getAnnotation()
+  {
+    if (annotation == null)
+    {
+      return null;
     }
 
-    public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+    AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
+    for (int r = 0; r < ret.length; r++)
     {
-      if(this.annotation==null)
-        this.annotation = new Vector();
+      ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
+    }
+
+    return ret;
+  }
 
-      this.annotation.addElement( annotation );
+  public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+  {
+    if (this.annotation == null)
+    {
+      this.annotation = new Vector();
     }
 
-    public SequenceGroup getHiddenSequences()
+    this.annotation.addElement(annotation);
+    annotation.setSequenceRef(this);
+  }
+
+  public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
+  {
+    if (this.annotation != null)
     {
-      return hiddenSequences;
+      this.annotation.removeElement(annotation);
+      if (this.annotation.size() == 0)
+        this.annotation = null;
     }
+  }
 
-    public void addHiddenSequence(SequenceI seq)
+  /**
+   * 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(hiddenSequences==null)
+      if (jalview.util.Comparison.isGap(sequence[i]))
       {
-        hiddenSequences = new SequenceGroup();
+        return false;
       }
-      hiddenSequences.addSequence(seq, false);
     }
+    return true;
+  }
 
-    public void showHiddenSequence(SequenceI seq)
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.SequenceI#deriveSequence()
+   */
+  public SequenceI deriveSequence()
+  {
+    SequenceI seq = new Sequence(this);
+    if (datasetSequence != null)
     {
-      hiddenSequences.deleteSequence(seq, false);
-      if (hiddenSequences.getSize(false) < 1)
+      // duplicate current sequence with same dataset
+      seq.setDatasetSequence(datasetSequence);
+    }
+    else
+    {
+      if (isValidDatasetSequence())
+      {
+        // Use this as dataset sequence
+        seq.setDatasetSequence(this);
+      }
+      else
       {
-        hiddenSequences = null;
+        // 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;
+  }
 
-    public void changeCase(boolean toUpper, int start, int end)
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.SequenceI#createDatasetSequence()
+   */
+  public SequenceI createDatasetSequence()
+  {
+    if (datasetSequence == null)
     {
-      StringBuffer newSeq = new StringBuffer();
-
-      if(end>sequence.length())
-        end = sequence.length();
+      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;
+  }
 
-      if (start > 0)
+  /*
+   * (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++)
       {
-        newSeq.append(sequence.substring(0, start));
+        if (annotations[i] != null)
+          addAlignmentAnnotation(annotations[i]);
       }
-
-      if (toUpper)
-        newSeq.append(sequence.substring(start, end).toUpperCase());
-      else
-        newSeq.append(sequence.substring(start, end).toLowerCase());
-
-      if (end < sequence.length())
-        newSeq.append(sequence.substring(end));
-
-      sequence = newSeq.toString();
     }
+  }
 
-    public void toggleCase(int start, int end)
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
+   */
+  public AlignmentAnnotation[] getAnnotation(String label)
+  {
+    if (annotation == null || annotation.size() == 0)
     {
-      StringBuffer newSeq = new StringBuffer();
-
-     if(end>sequence.length())
-       end = sequence.length();
-
-     if (start > 0)
-     {
-       newSeq.append(sequence.substring(0, start));
-     }
-
-     char nextChar;
-     for(int c=start; c<end; c++)
-     {
-       nextChar = sequence.charAt(c);
-       if(Character.isLetter(nextChar))
-       {
-         if(Character.isUpperCase(nextChar))
-           nextChar = Character.toLowerCase(nextChar);
-         else
-           nextChar = Character.toUpperCase(nextChar);
-       }
-
-
-       newSeq.append(nextChar);
-     }
-
-     if (end < sequence.length())
-       newSeq.append(sequence.substring(end));
-
-     sequence = newSeq.toString();
+      return null;
     }
 
-  public SequenceI getSubSequence(int start)
-  {
-    int e=getLength();
-    if (start>=e)
+    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;
-    return getSubSequence(start, getLength());
+    }
+    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 int removeGaps() {
-    if (sequence!=null)
-      return removeGaps(0, getLength());
-    return 0;
+  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;
   }
 
-  public int removeGaps(int start, int end) {
-    int jSize = getLength();
-    int oSize=jSize;
-    if (jSize<=start)
-      return 0;
-    if (end>jSize)
-      end = jSize;
+  /*
+   * (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)
+    {
 
-    // Removing a range is much quicker than removing gaps
-    // one by one for long sequences
-    int j = start;
-    int rangeStart=-1, rangeEnd=-1;
+      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]);
+          }
+        }
+      }
+    }
 
-    do
+    // transfer PDB entries
+    if (entry.getPDBId() != null)
     {
-      if (jalview.util.Comparison.isGap(getCharAt(j)))
+      Enumeration e = entry.getPDBId().elements();
+      while (e.hasMoreElements())
       {
-        if(rangeStart==-1)
-         {
-           rangeStart = j;
-           rangeEnd = j+1;
-         }
-         else
-         {
-           rangeEnd++;
-         }
-         j++;
+        PDBEntry pdb = (PDBEntry) e.nextElement();
+        addPDBId(pdb);
       }
-      else
+    }
+    // transfer database references
+    DBRefEntry[] entryRefs = entry.getDBRef();
+    if (entryRefs != null)
+    {
+      for (int r = 0; r < entryRefs.length; r++)
       {
-        if(rangeStart>-1)
+        DBRefEntry newref = new DBRefEntry(entryRefs[r]);
+        if (newref.getMap() != null && mp != null)
         {
-          deleteChars(rangeStart, rangeEnd);
-          j-=rangeEnd-rangeStart;
-          jSize-=rangeEnd-rangeStart;
-          rangeStart = -1;
-          rangeEnd = -1;
+          // remap ref using our local mapping
         }
-        else
-          j++;
+        // we also assume all version string setting is done by dbSourceProxy
+        /*
+         * if (!newref.getSource().equalsIgnoreCase(dbSource)) {
+         * newref.setSource(dbSource); }
+         */
+        addDBRef(newref);
       }
     }
-    while (j < end && j < jSize);
-    if(rangeStart>-1)
-    {
-     deleteChars(rangeStart, rangeEnd);
-     jSize-=rangeEnd-rangeStart;
-    }
-    return oSize-jSize; // number of deleted characters.
   }
 
 }