X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=96747e4fba3a1c36dd4b227c7fe67eeb25a7b83b;hb=ff450fad8709ae81919af7a15ea382af7292794c;hp=5886ae0eaebcb6392078e094b6c9dbf50c20c70e;hpb=6c43dd36929855a7907380ffb36b4df249d4a557;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 5886ae0..96747e4 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -22,17 +22,24 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.DBRefEntryI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.StringUtils;
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.List;
+import java.util.ListIterator;
 import java.util.Vector;
 
+import com.stevesoft.pat.Regex;
+
 import fr.orsay.lri.varna.models.rna.RNA;
 
 /**
@@ -44,6 +51,11 @@ import fr.orsay.lri.varna.models.rna.RNA;
  */
 public class Sequence extends ASequence implements SequenceI
 {
+  private static final Regex limitrx = new Regex(
+          "[/][0-9]{1,}[-][0-9]{1,}$");
+
+  private static final Regex endrx = new Regex("[0-9]{1,}$");
+
   SequenceI datasetSequence;
 
   String name;
@@ -77,8 +89,22 @@ public class Sequence extends ASequence implements SequenceI
    */
   int index = -1;
 
-  /** array of sequence features - may not be null for a valid sequence object */
-  public SequenceFeature[] sequenceFeatures;
+  private SequenceFeatures sequenceFeatureStore;
+
+  /*
+   * A cursor holding the approximate current view position to the sequence,
+   * as determined by findIndex or findPosition or findPositions.
+   * Using a cursor as a hint allows these methods to be more performant for
+   * large sequences.
+   */
+  private SequenceCursor cursor;
+
+  /*
+   * A number that should be incremented whenever the sequence is edited.
+   * If the value matches the cursor token, then we can trust the cursor,
+   * if not then it should be recomputed. 
+   */
+  private int changeCount;
 
   /**
    * Creates a new Sequence object.
@@ -95,11 +121,13 @@ public class Sequence extends ASequence implements SequenceI
    */
   public Sequence(String name, String sequence, int start, int end)
   {
+    this();
     initSeqAndName(name, sequence.toCharArray(), start, end);
   }
 
   public Sequence(String name, char[] sequence, int start, int end)
   {
+    this();
     initSeqAndName(name, sequence, start, end);
   }
 
@@ -123,11 +151,6 @@ public class Sequence extends ASequence implements SequenceI
     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)
@@ -174,6 +197,14 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
+   * default constructor
+   */
+  private Sequence()
+  {
+    sequenceFeatureStore = new SequenceFeatures();
+  }
+
+  /**
    * Creates a new Sequence object.
    * 
    * @param name
@@ -212,8 +243,8 @@ public class Sequence extends ASequence implements SequenceI
    */
   public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
   {
+    this();
     initSeqFrom(seq, alAnnotation);
-
   }
 
   /**
@@ -229,34 +260,38 @@ public class Sequence extends ASequence implements SequenceI
   protected void initSeqFrom(SequenceI seq,
           AlignmentAnnotation[] alAnnotation)
   {
-    {
-      char[] oseq = seq.getSequence();
-      initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
-              seq.getStart(),
-            seq.getEnd());
-    }
+    char[] oseq = seq.getSequence(); // returns a copy of the array
+    initSeqAndName(seq.getName(), oseq, seq.getStart(), seq.getEnd());
+
     description = seq.getDescription();
     if (seq != datasetSequence)
     {
       setDatasetSequence(seq.getDatasetSequence());
     }
-    if (datasetSequence == null && seq.getDBRefs() != null)
+    
+    /*
+     * only copy DBRefs and seqfeatures if we really are a dataset sequence
+     */
+    if (datasetSequence == null)
     {
-      // only copy DBRefs and seqfeatures if we really are a dataset sequence
-      DBRefEntry[] dbr = seq.getDBRefs();
-      for (int i = 0; i < dbr.length; i++)
+      if (seq.getDBRefs() != null)
       {
-        addDBRef(new DBRefEntry(dbr[i]));
-      }
-      if (seq.getSequenceFeatures() != null)
-      {
-        SequenceFeature[] sf = seq.getSequenceFeatures();
-        for (int i = 0; i < sf.length; i++)
+        DBRefEntry[] dbr = seq.getDBRefs();
+        for (int i = 0; i < dbr.length; i++)
         {
-          addSequenceFeature(new SequenceFeature(sf[i]));
+          addDBRef(new DBRefEntry(dbr[i]));
         }
       }
+
+      /*
+       * make copies of any sequence features
+       */
+      for (SequenceFeature sf : seq.getSequenceFeatures())
+      {
+        addSequenceFeature(new SequenceFeature(sf));
+      }
     }
+
     if (seq.getAnnotation() != null)
     {
       AlignmentAnnotation[] sqann = seq.getAnnotation();
@@ -292,148 +327,89 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
-
   @Override
-  public void setSequenceFeatures(SequenceFeature[] features)
+  public void setSequenceFeatures(List<SequenceFeature> features)
   {
-    if (datasetSequence == null)
-    {
-      sequenceFeatures = features;
-    }
-    else
+    if (datasetSequence != null)
     {
-      if (datasetSequence.getSequenceFeatures() != features
-              && datasetSequence.getSequenceFeatures() != null
-              && datasetSequence.getSequenceFeatures().length > 0)
-      {
-        new Exception(
-                "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment")
-                .printStackTrace();
-      }
       datasetSequence.setSequenceFeatures(features);
+      return;
     }
+    sequenceFeatureStore = new SequenceFeatures(features);
   }
 
   @Override
-  public synchronized void addSequenceFeature(SequenceFeature sf)
+  public synchronized boolean addSequenceFeature(SequenceFeature sf)
   {
-    if (sequenceFeatures==null && datasetSequence != null)
-    {
-      datasetSequence.addSequenceFeature(sf);
-      return;
-    }
-    if (sequenceFeatures == null)
+    if (sf.getType() == null)
     {
-      sequenceFeatures = new SequenceFeature[0];
+      System.err.println("SequenceFeature type may not be null: "
+              + sf.toString());
+      return false;
     }
 
-    for (int i = 0; i < sequenceFeatures.length; i++)
+    if (datasetSequence != null)
     {
-      if (sequenceFeatures[i].equals(sf))
-      {
-        return;
-      }
+      return datasetSequence.addSequenceFeature(sf);
     }
 
-    SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1];
-    System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
-    temp[sequenceFeatures.length] = sf;
-
-    sequenceFeatures = temp;
+    return sequenceFeatureStore.add(sf);
   }
 
   @Override
   public void deleteFeature(SequenceFeature sf)
   {
-    if (sequenceFeatures == null)
-    {
-      if (datasetSequence!=null) {
-    	  datasetSequence.deleteFeature(sf);
-      }
-      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)
+    if (datasetSequence != null)
     {
-      sequenceFeatures = null;
+      datasetSequence.deleteFeature(sf);
     }
     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;
+      sequenceFeatureStore.delete(sf);
     }
   }
 
   /**
-   * 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).
+   * {@inheritDoc}
    * 
    * @return
    */
   @Override
-  public SequenceFeature[] getSequenceFeatures()
+  public List<SequenceFeature> getSequenceFeatures()
   {
-    SequenceFeature[] features = sequenceFeatures;
-
-    SequenceI seq = this;
-    int count = 0; // failsafe against loop in sequence.datasetsequence...
-    while (features == null && seq.getDatasetSequence() != null
-            && count++ < 10)
+    if (datasetSequence != null)
     {
-      seq = seq.getDatasetSequence();
-      features = ((Sequence) seq).sequenceFeatures;
+      return datasetSequence.getSequenceFeatures();
     }
-    return features;
+    return sequenceFeatureStore.getAllFeatures();
   }
 
   @Override
-  public void addPDBId(PDBEntry entry)
+  public SequenceFeaturesI getFeatures()
+  {
+    return datasetSequence != null ? datasetSequence.getFeatures()
+            : sequenceFeatureStore;
+  }
+
+  @Override
+  public boolean addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
     {
       pdbIds = new Vector<PDBEntry>();
+      pdbIds.add(entry);
+      return true;
     }
-    if (pdbIds.contains(entry))
-    {
-      updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
-    }
-    else
-    {
-      pdbIds.addElement(entry);
-    }
-  }
 
-  private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
-  {
-    if (newEntry.getFile() != null)
+    for (PDBEntry pdbe : pdbIds)
     {
-      oldEntry.setFile(newEntry.getFile());
+      if (pdbe.updateFrom(entry))
+      {
+        return false;
+      }
     }
+    pdbIds.addElement(entry);
+    return true;
   }
 
   /**
@@ -568,6 +544,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     this.sequence = seq.toCharArray();
     checkValidRange();
+    sequenceChanged();
   }
 
   @Override
@@ -585,7 +562,9 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public char[] getSequence()
   {
-    return sequence;
+    // return sequence;
+    return sequence == null ? null : Arrays.copyOf(sequence,
+            sequence.length);
   }
 
   /*
@@ -688,58 +667,320 @@ public class Sequence extends ASequence implements SequenceI
     return this.description;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#findIndex(int)
+  /**
+   * {@inheritDoc}
    */
   @Override
   public int findIndex(int pos)
   {
-    // returns the alignment position for a residue
+    /*
+     * use a valid, hopefully nearby, cursor if available
+     */
+    if (isValidCursor(cursor))
+    {
+      return findIndex(pos, cursor);
+    }
+
     int j = start;
     int i = 0;
-    // Rely on end being at least as long as the length of the sequence.
+    int startColumn = 0;
+
+    /*
+     * traverse sequence from the start counting gaps; make a note of
+     * the column of the first residue to save in the cursor
+     */
     while ((i < sequence.length) && (j <= end) && (j <= pos))
     {
-      if (!jalview.util.Comparison.isGap(sequence[i]))
+      if (!Comparison.isGap(sequence[i]))
       {
+        if (j == start)
+        {
+          startColumn = i;
+        }
         j++;
       }
-
       i++;
     }
 
-    if ((j == end) && (j < pos))
+    if (j == end && j < pos)
     {
       return end + 1;
     }
-    else
+
+    updateCursor(pos, i, startColumn);
+    return i;
+  }
+
+  /**
+   * Updates the cursor to the latest found residue and column position
+   * 
+   * @param residuePos
+   *          (start..)
+   * @param column
+   *          (1..)
+   * @param startColumn
+   *          column position of the first sequence residue
+   */
+  protected void updateCursor(int residuePos, int column, int startColumn)
+  {
+    int endColumn = cursor == null ? 0 : cursor.lastColumnPosition;
+    if (residuePos == this.end)
+    {
+      endColumn = column;
+    }
+
+    cursor = new SequenceCursor(this, residuePos, column, startColumn,
+            endColumn, this.changeCount);
+  }
+
+  /**
+   * Answers the aligned column position (1..) for the given residue position
+   * (start..) given a 'hint' of a residue/column location in the neighbourhood.
+   * The hint may be left of, at, or to the right of the required position.
+   * 
+   * @param pos
+   * @param curs
+   * @return
+   */
+  protected int findIndex(int pos, SequenceCursor curs)
+  {
+    if (!isValidCursor(curs))
+    {
+      /*
+       * wrong or invalidated cursor, compute de novo
+       */
+      return findIndex(pos);
+    }
+
+    if (curs.residuePosition == pos)
+    {
+      return curs.columnPosition;
+    }
+
+    /*
+     * move left or right to find pos from hint.position
+     */
+    int col = curs.columnPosition - 1; // convert from base 1 to 0-based array
+                                       // index
+    int newPos = curs.residuePosition;
+    int delta = newPos > pos ? -1 : 1;
+
+    while (newPos != pos)
     {
-      return i;
+      col += delta; // shift one column left or right
+      if (col < 0 || col == sequence.length)
+      {
+        break;
+      }
+      if (!Comparison.isGap(sequence[col]))
+      {
+        newPos += delta;
+      }
     }
+
+    col++; // convert back to base 1
+    updateCursor(pos, col, curs.firstColumnPosition);
+
+    return col;
   }
 
+  /**
+   * {@inheritDoc}
+   */
   @Override
-  public int findPosition(int i)
+  public int findPosition(final int column)
   {
+    /*
+     * use a valid, hopefully nearby, cursor if available
+     */
+    if (isValidCursor(cursor))
+    {
+      return findPosition(column + 1, cursor);
+    }
+    
+    // TODO recode this more naturally i.e. count residues only
+    // as they are found, not 'in anticipation'
+
+    /*
+     * traverse the sequence counting gaps; note the column position
+     * of the first residue, to save in the cursor
+     */
+    int firstResidueColumn = 0;
+    int lastPosFound = 0;
+    int lastPosFoundColumn = 0;
+    int seqlen = sequence.length;
+
+    if (seqlen > 0 && !Comparison.isGap(sequence[0]))
+    {
+      lastPosFound = start;
+      lastPosFoundColumn = 0;
+    }
+
     int j = 0;
     int pos = start;
-    int seqlen = sequence.length;
-    while ((j < i) && (j < seqlen))
+
+    while (j < column && j < seqlen)
     {
-      if (!jalview.util.Comparison.isGap(sequence[j]))
+      if (!Comparison.isGap(sequence[j]))
       {
+        lastPosFound = pos;
+        lastPosFoundColumn = j;
+        if (pos == this.start)
+        {
+          firstResidueColumn = j;
+        }
         pos++;
       }
-
       j++;
     }
+    if (j < seqlen && !Comparison.isGap(sequence[j]))
+    {
+      lastPosFound = pos;
+      lastPosFoundColumn = j;
+      if (pos == this.start)
+      {
+        firstResidueColumn = j;
+      }
+    }
+
+    /*
+     * update the cursor to the last residue position found (if any)
+     * (converting column position to base 1)
+     */
+    if (lastPosFound != 0)
+    {
+      updateCursor(lastPosFound, lastPosFoundColumn + 1,
+              firstResidueColumn + 1);
+    }
 
     return pos;
   }
 
   /**
+   * Answers true if the given cursor is not null, is for this sequence object,
+   * and has a token value that matches this object's changeCount, else false.
+   * This allows us to ignore a cursor as 'stale' if the sequence has been
+   * modified since the cursor was created.
+   * 
+   * @param curs
+   * @return
+   */
+  protected boolean isValidCursor(SequenceCursor curs)
+  {
+    if (curs == null || curs.sequence != this || curs.token != changeCount)
+    {
+      return false;
+    }
+    /*
+     * sanity check against range
+     */
+    if (curs.columnPosition < 0 || curs.columnPosition > sequence.length)
+    {
+      return false;
+    }
+    if (curs.residuePosition < start || curs.residuePosition > end)
+    {
+      return false;
+    }
+    return true;
+  }
+
+  /**
+   * Answers the sequence position (start..) for the given aligned column
+   * position (1..), given a hint of a cursor in the neighbourhood. The cursor
+   * may lie left of, at, or to the right of the column position.
+   * 
+   * @param col
+   * @param curs
+   * @return
+   */
+  protected int findPosition(final int col, SequenceCursor curs)
+  {
+    if (!isValidCursor(curs))
+    {
+      /*
+       * wrong or invalidated cursor, compute de novo
+       */
+      return findPosition(col - 1);// ugh back to base 0
+    }
+
+    if (curs.columnPosition == col)
+    {
+      cursor = curs; // in case this method becomes public
+      return curs.residuePosition; // easy case :-)
+    }
+
+    if (curs.lastColumnPosition > 0 && curs.lastColumnPosition < col)
+    {
+      /*
+       * sequence lies entirely to the left of col
+       * - return last residue + 1
+       */
+      return end + 1;
+    }
+
+    if (curs.firstColumnPosition > 0 && curs.firstColumnPosition > col)
+    {
+      /*
+       * sequence lies entirely to the right of col
+       * - return first residue
+       */
+      return start;
+    }
+
+    // todo could choose closest to col out of column,
+    // firstColumnPosition, lastColumnPosition as a start point
+
+    /*
+     * move left or right to find pos from cursor position
+     */
+    int firstResidueColumn = curs.firstColumnPosition;
+    int column = curs.columnPosition - 1; // to base 0
+    int newPos = curs.residuePosition;
+    int delta = curs.columnPosition > col ? -1 : 1;
+    boolean gapped = false;
+    int lastFoundPosition = curs.residuePosition;
+    int lastFoundPositionColumn = curs.columnPosition;
+
+    while (column != col - 1)
+    {
+      column += delta; // shift one column left or right
+      if (column < 0 || column == sequence.length)
+      {
+        break;
+      }
+      gapped = Comparison.isGap(sequence[column]);
+      if (!gapped)
+      {
+        newPos += delta;
+        lastFoundPosition = newPos;
+        lastFoundPositionColumn = column + 1;
+        if (lastFoundPosition == this.start)
+        {
+          firstResidueColumn = column + 1;
+        }
+      }
+    }
+
+    if (cursor == null || lastFoundPosition != cursor.residuePosition)
+    {
+      updateCursor(lastFoundPosition, lastFoundPositionColumn,
+              firstResidueColumn);
+    }
+
+    /*
+     * hack to give position to the right if on a gap
+     * or beyond the length of the sequence (see JAL-2562)
+     */
+    if (delta > 0 && (gapped || column >= sequence.length))
+    {
+      newPos++;
+    }
+
+    return newPos;
+  }
+
+  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 
@@ -823,6 +1064,40 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
+  public BitSet getInsertionsAsBits()
+  {
+    BitSet map = new BitSet();
+    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.set(lastj, j);
+          lastj = -1;
+        }
+      }
+      j++;
+    }
+    if (lastj != -1)
+    {
+      map.set(lastj, j);
+      lastj = -1;
+    }
+    return map;
+  }
+
+  @Override
   public void deleteChars(int i, int j)
   {
     int newstart = start, newend = end;
@@ -895,6 +1170,7 @@ public class Sequence extends ASequence implements SequenceI
     start = newstart;
     end = newend;
     sequence = tmp;
+    sequenceChanged();
   }
 
   @Override
@@ -925,6 +1201,7 @@ public class Sequence extends ASequence implements SequenceI
     }
 
     sequence = tmp;
+    sequenceChanged();
   }
 
   @Override
@@ -948,7 +1225,17 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void setDBRefs(DBRefEntry[] dbref)
   {
+    if (dbrefs == null && datasetSequence != null
+            && this != datasetSequence)
+    {
+      datasetSequence.setDBRefs(dbref);
+      return;
+    }
     dbrefs = dbref;
+    if (dbrefs != null)
+    {
+      DBRefUtils.ensurePrimaries(this);
+    }
   }
 
   @Override
@@ -965,7 +1252,12 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void addDBRef(DBRefEntry entry)
   {
-    // TODO add to dataset sequence instead if there is one?
+    if (datasetSequence != null)
+    {
+      datasetSequence.addDBRef(entry);
+      return;
+    }
+
     if (dbrefs == null)
     {
       dbrefs = new DBRefEntry[0];
@@ -993,12 +1285,23 @@ public class Sequence extends ASequence implements SequenceI
     temp[temp.length - 1] = entry;
 
     dbrefs = temp;
+
+    DBRefUtils.ensurePrimaries(this);
   }
 
   @Override
   public void setDatasetSequence(SequenceI seq)
   {
-    // TODO check for circular reference before setting?
+    if (seq == this)
+    {
+      throw new IllegalArgumentException(
+              "Implementation Error: self reference passed to SequenceI.setDatasetSequence");
+    }
+    if (seq != null && seq.getDatasetSequence() != null)
+    {
+      throw new IllegalArgumentException(
+              "Implementation error: cascading dataset sequences are not allowed.");
+    }
     datasetSequence = seq;
   }
 
@@ -1071,7 +1374,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public SequenceI deriveSequence()
   {
-    Sequence seq=null;
+    Sequence seq = null;
     if (datasetSequence == null)
     {
       if (isValidDatasetSequence())
@@ -1085,7 +1388,7 @@ public class Sequence extends ASequence implements SequenceI
       else
       {
         // Create a new, valid dataset sequence
-    	createDatasetSequence();
+        createDatasetSequence();
       }
     }
     return new Sequence(this);
@@ -1093,8 +1396,12 @@ public class Sequence extends ASequence implements SequenceI
 
   private boolean _isNa;
 
-  private long _seqhash = 0;
+  private int _seqhash = 0;
 
+  /**
+   * Answers false if the sequence is more than 85% nucleotide (ACGTU), else
+   * true
+   */
   @Override
   public boolean isProtein()
   {
@@ -1105,7 +1412,7 @@ public class Sequence extends ASequence implements SequenceI
     if (_seqhash != sequence.hashCode())
     {
       _seqhash = sequence.hashCode();
-      _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this });
+      _isNa = Comparison.isNucleotide(this);
     }
     return !_isNa;
   };
@@ -1128,10 +1435,10 @@ public class Sequence extends ASequence implements SequenceI
 
       dsseq.setDescription(description);
       // move features and database references onto dataset sequence
-      dsseq.sequenceFeatures = sequenceFeatures;
-      sequenceFeatures=null;
+      dsseq.sequenceFeatureStore = sequenceFeatureStore;
+      sequenceFeatureStore = null;
       dsseq.dbrefs = dbrefs;
-      dbrefs=null;
+      dbrefs = null;
       // TODO: search and replace any references to this sequence with
       // references to the dataset sequence in Mappings on dbref
       dsseq.pdbIds = pdbIds;
@@ -1188,11 +1495,11 @@ public class Sequence extends ASequence implements SequenceI
       return null;
     }
 
-    Vector subset = new Vector();
-    Enumeration e = annotation.elements();
+    Vector<AlignmentAnnotation> subset = new Vector<AlignmentAnnotation>();
+    Enumeration<AlignmentAnnotation> e = annotation.elements();
     while (e.hasMoreElements())
     {
-      AlignmentAnnotation ann = (AlignmentAnnotation) e.nextElement();
+      AlignmentAnnotation ann = e.nextElement();
       if (ann.label != null && ann.label.equals(label))
       {
         subset.addElement(ann);
@@ -1207,7 +1514,7 @@ public class Sequence extends ASequence implements SequenceI
     e = subset.elements();
     while (e.hasMoreElements())
     {
-      anns[i++] = (AlignmentAnnotation) e.nextElement();
+      anns[i++] = e.nextElement();
     }
     subset.removeAllElements();
     return anns;
@@ -1225,46 +1532,22 @@ public class Sequence extends ASequence implements SequenceI
     {
       return false;
     }
-    Vector newpdb = new Vector();
-    for (int i = 0; i < dbrefs.length; i++)
+    boolean added = false;
+    for (DBRefEntry dbr : dbrefs)
     {
-      if (DBRefSource.PDB.equals(dbrefs[i].getSource()))
+      if (DBRefSource.PDB.equals(dbr.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());
+        /*
+         * 'Add' any PDB dbrefs as a PDBEntry - add is only performed if the
+         * PDB id is not already present in a 'matching' PDBEntry
+         * Constructor parses out a chain code if appended to the accession id
+         * (a fudge used to 'store' the chain code in the DBRef)
+         */
+        PDBEntry pdbe = new PDBEntry(dbr);
+        added |= addPDBId(pdbe);
       }
-      return true;
     }
-    return false;
+    return added;
   }
 
   @Override
@@ -1284,12 +1567,12 @@ public class Sequence extends ASequence implements SequenceI
     if (entry.getSequenceFeatures() != null)
     {
 
-      SequenceFeature[] sfs = entry.getSequenceFeatures();
-      for (int si = 0; si < sfs.length; si++)
+      List<SequenceFeature> sfs = entry.getSequenceFeatures();
+      for (SequenceFeature feature : sfs)
       {
-        SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
-                : new SequenceFeature[] { new SequenceFeature(sfs[si]) };
-        if (sf != null && sf.length > 0)
+        SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
+                : new SequenceFeature[] { new SequenceFeature(feature) };
+        if (sf != null)
         {
           for (int sfi = 0; sfi < sf.length; sfi++)
           {
@@ -1302,10 +1585,10 @@ public class Sequence extends ASequence implements SequenceI
     // transfer PDB entries
     if (entry.getAllPDBEntries() != null)
     {
-      Enumeration e = entry.getAllPDBEntries().elements();
+      Enumeration<PDBEntry> e = entry.getAllPDBEntries().elements();
       while (e.hasMoreElements())
       {
-        PDBEntry pdb = (PDBEntry) e.nextElement();
+        PDBEntry pdb = e.nextElement();
         addPDBId(pdb);
       }
     }
@@ -1413,15 +1696,14 @@ public class Sequence extends ASequence implements SequenceI
     return null;
   }
 
-
   @Override
   public List<DBRefEntry> getPrimaryDBRefs()
   {
-    if (datasetSequence!=null)
+    if (datasetSequence != null)
     {
       return datasetSequence.getPrimaryDBRefs();
     }
-    if (dbrefs==null || dbrefs.length==0)
+    if (dbrefs == null || dbrefs.length == 0)
     {
       return Collections.emptyList();
     }
@@ -1474,4 +1756,104 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> findFeatures(int fromColumn, int toColumn,
+          String... types)
+  {
+    int startPos = findPosition(fromColumn - 1); // convert base 1 to base 0
+    int endPos = findPosition(toColumn - 1);
+    // to trace / debug behaviour:
+    // System.out
+    // .println(String
+    // .format("%s.findFeatures columns [%d-%d] positions [%d-%d] leaves cursor %s",
+    // getName(), fromColumn, toColumn, startPos,
+    // endPos, cursor));
+    List<SequenceFeature> result = new ArrayList<>();
+    if (datasetSequence != null)
+    {
+      result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
+              types);
+    }
+    else
+    {
+      result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
+    }
+
+    /*
+     * if the start or end column is gapped, startPos or endPos may be to the 
+     * left or right, and we may have included adjacent or enclosing features;
+     * remove any that are not enclosing, non-contact features
+     */
+    if (endPos > this.end || Comparison.isGap(sequence[fromColumn - 1])
+            || Comparison.isGap(sequence[toColumn - 1]))
+    {
+      ListIterator<SequenceFeature> it = result.listIterator();
+      while (it.hasNext())
+      {
+        SequenceFeature sf = it.next();
+        int featureStartColumn = findIndex(sf.getBegin());
+        int featureEndColumn = findIndex(sf.getEnd());
+        boolean noOverlap = featureStartColumn > toColumn
+                        || featureEndColumn < fromColumn;
+
+        /*
+         * reject an 'enclosing' feature if it is actually a contact feature
+         */
+        if (sf.isContactFeature() && featureStartColumn < fromColumn
+                && featureEndColumn > toColumn)
+        {
+          noOverlap = true;
+        }
+        if (noOverlap)
+        {
+          it.remove();
+        }
+      }
+    }
+
+    return result;
+  }
+
+  /**
+   * Invalidates any stale cursors (forcing recalculation) by incrementing the
+   * token that has to match the one presented by the cursor
+   */
+  @Override
+  public void sequenceChanged()
+  {
+    changeCount++;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public int replace(char c1, char c2)
+  {
+    if (c1 == c2)
+    {
+      return 0;
+    }
+    int count = 0;
+    synchronized (sequence)
+    {
+      for (int c = 0; c < sequence.length; c++)
+      {
+        if (sequence[c] == c1)
+        {
+          sequence[c] = c2;
+          count++;
+        }
+      }
+    }
+    if (count > 0)
+    {
+      sequenceChanged();
+    }
+
+    return count;
+  }
 }