X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=e2fc057ed5947fefd2574623d9479554a55d33f3;hb=582d39cb05dfbb5f956f74d4a97a17d9f63b0786;hp=f593226bb64dd4c74215bbcaa207b8cd9817e6e8;hpb=35a881a8aec76741fc7f2826c0056b315bfdccac;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index f593226..e2fc057 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,641 +1,686 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.datamodel;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Sequence implements SequenceI
-{
-    SequenceI datasetSequence;
-    String name;
-    String sequence;
-    String description;
-    int start;
-    int end;
-    Color color = Color.white;
-    Vector pdbIds;
-    String vamsasId;
-    Vector 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;
-        }
-
-        this.end = endRes;
-      }
-
-    }
-
-    /**
-     * 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.
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public Sequence(SequenceI seq)
-    {
-        this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param v DOCUMENT ME!
-     */
-    public void setSequenceFeatures(SequenceFeature [] features)
-    {
-        sequenceFeatures = features;
-    }
-
-    public void addSequenceFeature(SequenceFeature sf)
-    {
-      if(sequenceFeatures==null)
-      {
-        sequenceFeatures = new SequenceFeature[0];
-      }
-
-      for(int i=0; i<sequenceFeatures.length; i++)
-      {
-        if(sequenceFeatures[i].equals(sf))
-        {
-          return;
-        }
-      }
-
-      SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];
-      System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
-      temp[sequenceFeatures.length] = sf;
-
-
-      sequenceFeatures = temp;
-    }
-
-    SequenceFeature [] sfarray;
-
-        public SequenceFeature[] getsfarray()
-        {
-          return sfarray;
-        }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SequenceFeature [] getSequenceFeatures()
-    {
-        return sequenceFeatures;
-    }
-
-    public void addPDBId(PDBEntry entry)
-    {
-      if(pdbIds == null)
-        pdbIds = new Vector();
-
-      pdbIds.addElement(entry);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param id DOCUMENT ME!
-     */
-    public void setPDBId(Vector id)
-    {
-        pdbIds = id;
-    }
-
-    /**
-     * 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)
-      {
-        result.append("/" + start + "-" + 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;
-        checkValidRange();
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getSequence()
-    {
-        return this.sequence;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getSequence(int start, int end)
-    {
-        // 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);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public char getCharAt(int i)
-    {
-        if (i < sequence.length())
-        {
-            return sequence.charAt(i);
-        }
-        else
-        {
-            return ' ';
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param desc DOCUMENT ME!
-     */
-    public void setDescription(String desc)
-    {
-        this.description = desc;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public String getDescription()
-    {
-        return this.description;
-    }
-
-    /**
-     * 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;
-
-        while ((i < sequence.length()) && (j <= end) && (j <= pos))
-        {
-            if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
-            {
-                j++;
-            }
-
-            i++;
-        }
-
-        if ((j == end) && (j < pos))
-        {
-            return end + 1;
-        }
-        else
-        {
-            return i;
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int findPosition(int i)
-    {
-        // Returns the sequence position for an alignment position
-        int j = 0;
-        int pos = start;
-
-        while ((j < i) && (j < sequence.length()))
-        {
-            if (!jalview.util.Comparison.isGap((sequence.charAt(j))))
-            {
-                pos++;
-            }
-
-            j++;
-        }
-
-        return pos;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public int[] gapMap()
-    {
-        // Returns an int array giving the position of each residue in the sequence in the alignment
-        String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);
-        int[] map = new int[seq.length()];
-        int j = 0;
-        int p = 0;
-
-        while (j < sequence.length())
-        {
-            if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
-            {
-                map[p++] = j;
-            }
-
-            j++;
-        }
-
-        return map;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     */
-    public void deleteCharAt(int i)
-    {
-        if (i >= sequence.length())
-        {
-            return;
-        }
-
-        sequence = sequence.substring(0, i) + sequence.substring(i + 1);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     */
-    public void deleteChars(int i, int j)
-    {
-        if (i >= sequence.length())
-        {
-            return;
-        }
-
-        if (j >= sequence.length())
-        {
-            sequence = sequence.substring(0, i);
-        }
-        else
-        {
-            sequence = sequence.substring(0, i) + sequence.substring(j);
-        }
-    }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param c DOCUMENT ME!
-     * @param chop DOCUMENT ME!
-     */
-    public void insertCharAt(int i, char c)
-    {
-        String tmp = new String(sequence);
-
-        if (i < sequence.length())
-        {
-            sequence = tmp.substring(0, i) + String.valueOf(c) +
-                tmp.substring(i);
-        }
-        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);
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param c DOCUMENT ME!
-     */
-    public void setColor(Color c)
-    {
-        this.color = c;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color getColor()
-    {
-        return color;
-    }
-
-    public String getVamsasId()
-    {
-      return vamsasId;
-    }
-
-    public void setVamsasId(String id)
-    {
-      vamsasId = id;
-    }
-
-    public void setDBRef(Vector dbref)
-    {
-      dbrefs = dbref;
-    }
-    public Vector getDBRef()
-    {
-      return dbrefs;
-    }
-
-    public void addDBRef(DBRefEntry entry)
-    {
-      if(dbrefs == null)
-        dbrefs = new Vector();
-
-      dbrefs.addElement(entry);
-    }
-
-    public void setDatasetSequence(SequenceI seq)
-    {
-      datasetSequence = seq;
-    }
-
-    public SequenceI getDatasetSequence()
-    {
-      return datasetSequence;
-    }
-
-    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;
-    }
-
-    public void addAlignmentAnnotation(AlignmentAnnotation annotation)
-    {
-      if(this.annotation==null)
-        this.annotation = new Vector();
-
-      this.annotation.addElement( annotation );
-    }
-
-    public SequenceGroup getHiddenSequences()
-    {
-      return hiddenSequences;
-    }
-
-    public void addHiddenSequence(SequenceI seq)
-    {
-      if(hiddenSequences==null)
-      {
-        hiddenSequences = new SequenceGroup();
-      }
-      hiddenSequences.addSequence(seq, false);
-    }
-
-    public void showHiddenSequence(SequenceI seq)
-    {
-      hiddenSequences.deleteSequence(seq, false);
-      if (hiddenSequences.getSize() < 1)
-      {
-        hiddenSequences = null;
-      }
-
-    }
-}
+/*
+* 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
+*/
+package jalview.datamodel;
+
+import java.awt.*;
+
+import java.util.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Sequence implements SequenceI
+{
+  SequenceI datasetSequence;
+  String name;
+  private String 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 */
+  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;
+      }
+
+      this.end = endRes;
+    }
+
+  }
+
+  /**
+   * 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.
+   *
+   * @param seq DOCUMENT ME!
+   */
+  public Sequence(SequenceI seq)
+  {
+    this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param v DOCUMENT ME!
+   */
+  public void setSequenceFeatures(SequenceFeature[] features)
+  {
+    sequenceFeatures = features;
+  }
+
+  public synchronized void addSequenceFeature(SequenceFeature sf)
+  {
+    if (sequenceFeatures == null)
+    {
+      sequenceFeatures = new SequenceFeature[0];
+    }
+
+    for (int i = 0; i < sequenceFeatures.length; i++)
+    {
+      if (sequenceFeatures[i].equals(sf))
+      {
+        return;
+      }
+    }
+
+    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;
+
+    int index=0;
+    for (index = 0; index < sequenceFeatures.length; index++)
+    {
+      if (sequenceFeatures[index].equals(sf))
+      {
+        break;
+      }
+    }
+
+
+    if(index==sequenceFeatures.length)
+      return;
+
+    int sfLength = sequenceFeatures.length;
+    if(sfLength<2)
+    {
+      sequenceFeatures = null;
+    }
+    else
+    {
+      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);
+
+      sequenceFeatures = temp;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public SequenceFeature[] getSequenceFeatures()
+  {
+    return sequenceFeatures;
+  }
+
+  public void addPDBId(PDBEntry entry)
+  {
+    if (pdbIds == null)
+      pdbIds = new Vector();
+
+    pdbIds.addElement(entry);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param id DOCUMENT ME!
+   */
+  public void setPDBId(Vector id)
+  {
+    pdbIds = id;
+  }
+
+  /**
+   * 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)
+    {
+      result.append("/" + start + "-" + 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;
+    checkValidRange();
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getSequence()
+  {
+    return this.sequence;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getSequence(int start, int end)
+  {
+    // 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.setDescription(description);
+    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 ' ';
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param desc DOCUMENT ME!
+   */
+  public void setDescription(String desc)
+  {
+    this.description = desc;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public String getDescription()
+  {
+    return this.description;
+  }
+
+  /**
+   * 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;
+
+    while ( (i < sequence.length()) && (j <= end) && (j <= pos))
+    {
+      if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
+      {
+        j++;
+      }
+
+      i++;
+    }
+
+    if ( (j == end) && (j < pos))
+    {
+      return end + 1;
+    }
+    else
+    {
+      return 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)
+  {
+    int j = 0;
+    int pos = start;
+    int seqlen = sequence.length();
+    while ( (j < i) && (j < seqlen))
+    {
+      if (!jalview.util.Comparison.isGap( (sequence.charAt(j))))
+      {
+        pos++;
+      }
+
+      j++;
+    }
+
+    return pos;
+  }
+
+  /**
+   * 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;
+
+    while (j < sequence.length())
+    {
+      if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
+      {
+        map[p++] = j;
+      }
+
+      j++;
+    }
+
+    return map;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   */
+  public void deleteCharAt(int i)
+  {
+    if (i >= sequence.length())
+    {
+      return;
+    }
+
+    sequence = sequence.substring(0, i) + sequence.substring(i + 1);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   */
+  public void deleteChars(int i, int j)
+  {
+    if (i >= sequence.length())
+    {
+      return;
+    }
+
+    if (j >= sequence.length())
+    {
+      sequence = sequence.substring(0, i);
+    }
+    else
+    {
+      sequence = sequence.substring(0, i) + sequence.substring(j);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param c DOCUMENT ME!
+   * @param chop DOCUMENT ME!
+   */
+  public void insertCharAt(int i, int length, char c)
+  {
+    StringBuffer tmp;
+
+    if (i >= sequence.length())
+    {
+      tmp = new StringBuffer(sequence);
+    }
+    else
+      tmp = new StringBuffer(sequence.substring(0, i));
+
+    while (length > 0)
+    {
+      tmp.append(c);
+      length--;
+    }
+
+    if (i < sequence.length())
+    {
+      tmp.append(sequence.substring(i));
+    }
+
+    sequence = tmp.toString();
+  }
+
+  public void insertCharAt(int i, char c)
+  {
+    insertCharAt(i, 1, c);
+  }
+
+  public String getVamsasId()
+  {
+    return vamsasId;
+  }
+
+  public void setVamsasId(String id)
+  {
+    vamsasId = id;
+  }
+
+  public void setDBRef(DBRefEntry[] dbref)
+  {
+    dbrefs = dbref;
+  }
+
+  public DBRefEntry[] getDBRef()
+  {
+    return dbrefs;
+  }
+
+  public void addDBRef(DBRefEntry entry)
+  {
+    if (dbrefs == null)
+      dbrefs = new DBRefEntry[0];
+
+    DBRefEntry[] temp = new DBRefEntry[dbrefs.length + 1];
+    System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);
+
+    temp[temp.length - 1] = entry;
+
+    dbrefs = temp;
+  }
+
+  public void setDatasetSequence(SequenceI seq)
+  {
+    datasetSequence = seq;
+  }
+
+  public SequenceI getDatasetSequence()
+  {
+    return datasetSequence;
+  }
+
+  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;
+  }
+
+  public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+  {
+    if (this.annotation == null)
+      this.annotation = new Vector();
+
+    this.annotation.addElement(annotation);
+  }
+
+  public SequenceGroup getHiddenSequences()
+  {
+    return hiddenSequences;
+  }
+
+  public void addHiddenSequence(SequenceI seq)
+  {
+    if (hiddenSequences == null)
+    {
+      hiddenSequences = new SequenceGroup();
+    }
+    hiddenSequences.addSequence(seq, false);
+  }
+
+  public void showHiddenSequence(SequenceI seq)
+  {
+    hiddenSequences.deleteSequence(seq, false);
+    if (hiddenSequences.getSize(false) < 1)
+    {
+      hiddenSequences = null;
+    }
+  }
+}
+
+