X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=a01d185c24267ea6368818907139a0ce9d5a6c86;hb=d065bc916cb63af83cdab7319f5177a855724aba;hp=8ea6ca324547d0ac06767cf3f13d6eab4f8d8273;hpb=a22ecca7f6262d7795d36629198e7531e2805daf;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 8ea6ca3..a01d185 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -260,9 +260,8 @@ 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)
@@ -563,7 +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);
   }
 
   /*
@@ -722,7 +723,10 @@ public class Sequence extends ASequence implements SequenceI
    */
   protected void updateCursor(int residuePos, int column, int startColumn)
   {
-    int endColumn = cursor == null ? 0 : cursor.lastColumnPosition;
+    /*
+     * preserve end residue column provided cursor was valid
+     */
+    int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0;
     if (residuePos == this.end)
     {
       endColumn = column;
@@ -909,7 +913,7 @@ public class Sequence extends ASequence implements SequenceI
       return curs.residuePosition; // easy case :-)
     }
 
-    if (curs.lastColumnPosition > 0 && curs.lastColumnPosition <= col)
+    if (curs.lastColumnPosition > 0 && curs.lastColumnPosition < col)
     {
       /*
        * sequence lies entirely to the left of col
@@ -918,7 +922,7 @@ public class Sequence extends ASequence implements SequenceI
       return end + 1;
     }
 
-    if (curs.firstColumnPosition > 0 && curs.firstColumnPosition >= col)
+    if (curs.firstColumnPosition > 0 && curs.firstColumnPosition > col)
     {
       /*
        * sequence lies entirely to the right of col
@@ -980,6 +984,53 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
+   * {@inheritDoc}
+   */
+  @Override
+  public Range findPositions(int fromColumn, int toColumn)
+  {
+    if (toColumn < fromColumn || fromColumn < 1)
+    {
+      return null;
+    }
+
+    /*
+     * find the first non-gapped position, if any
+     */
+    int firstPosition = 0;
+    int col = fromColumn - 1;
+    int length = sequence.length;
+    while (col < length && col < toColumn)
+    {
+      if (!Comparison.isGap(sequence[col]))
+      {
+        firstPosition = findPosition(col++);
+        break;
+      }
+      col++;
+    }
+
+    if (firstPosition == 0)
+    {
+      return null;
+    }
+
+    /*
+     * find the last non-gapped position
+     */
+    int lastPosition = firstPosition;
+    while (col < length && col < toColumn)
+    {
+      if (!Comparison.isGap(sequence[col++]))
+      {
+        lastPosition++;
+      }
+    }
+
+    return new Range(firstPosition, lastPosition);
+  }
+
+  /**
    * Returns an int array where indices correspond to each residue in the
    * sequence and the element value gives its position in the alignment
    * 
@@ -1395,7 +1446,7 @@ 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
@@ -1763,52 +1814,45 @@ public class Sequence extends ASequence implements SequenceI
           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);
-    }
+    int endPos = fromColumn == toColumn ? startPos
+            : findPosition(toColumn - 1);
+
+    List<SequenceFeature> result = getFeatures().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;
+     * if end column is gapped, endPos may be to the 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]))
+    if (endPos > this.end || 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)
+        int sfBegin = sf.getBegin();
+        int sfEnd = sf.getEnd();
+        int featureStartColumn = findIndex(sfBegin);
+        if (featureStartColumn > toColumn)
         {
-          noOverlap = true;
+          it.remove();
         }
-        if (noOverlap)
+        else if (featureStartColumn < fromColumn)
         {
-          it.remove();
+          int featureEndColumn = sfEnd == sfBegin ? featureStartColumn
+                  : findIndex(sfEnd);
+          if (featureEndColumn < fromColumn)
+          {
+            it.remove();
+          }
+          else if (featureEndColumn > toColumn && sf.isContactFeature())
+          {
+            /*
+             * remove an enclosing feature if it is a contact feature
+             */
+            it.remove();
+          }
         }
       }
     }
@@ -1825,4 +1869,34 @@ public class Sequence extends ASequence implements SequenceI
   {
     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;
+  }
 }