X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=24f904cf8f00bbe72c62c62a3ccad57e3ee66fb8;hb=70a93ebbabd80e25c60a0e6444013ed4260b09a5;hp=cc4a0dca39ce909e4b3eb97f7029f903fce14aa6;hpb=bf1f3d11a1915e63b11852a1eb63824f984a4342;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cc4a0dc..24f904c 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -664,19 +664,16 @@ 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)
   {
     /*
-     * use a valid nearby cursor if available
+     * use a valid, hopefully nearby, cursor if available
      */
-    if (cursor != null && cursor.sequence == this
-            && cursor.token == changeCount)
+    if (isValidCursor(cursor))
     {
       return findIndex(pos, cursor);
     }
@@ -693,20 +690,25 @@ public class Sequence extends ASequence implements SequenceI
       i++;
     }
 
-    if ((j == end) && (j < pos))
+    if (j == end && j < pos)
     {
       return end + 1;
     }
-    else
-    {
-      updateCursor(pos, i);
-      return i;
-    }
+
+    updateCursor(pos, i);
+    return i;
   }
 
+  /**
+   * Updates the cursor to the latest found residue and column position
+   * 
+   * @param residuePos
+   *          (start..)
+   * @param column
+   *          (1..)
+   */
   protected void updateCursor(int residuePos, int column)
   {
-    // TODO probably want to synchronize this on something
     cursor = new SequenceCursor(this, residuePos, column, this.changeCount);
   }
 
@@ -721,7 +723,7 @@ public class Sequence extends ASequence implements SequenceI
    */
   protected int findIndex(int pos, SequenceCursor curs)
   {
-    if (curs.sequence != this || curs.token != changeCount)
+    if (!isValidCursor(curs))
     {
       /*
        * wrong or invalidated cursor, compute de novo
@@ -761,40 +763,93 @@ public class Sequence extends ASequence implements SequenceI
     return col;
   }
 
+  /**
+   * {@inheritDoc}
+   */
   @Override
-  public int findPosition(final int i)
+  public int findPosition(final int column)
   {
     /*
-     * use a valid nearby cursor if available
+     * use a valid, hopefully nearby, cursor if available
      */
-    if (cursor != null && cursor.sequence == this
-            && cursor.token == changeCount)
+    if (isValidCursor(cursor))
     {
-      return findPosition(i + 1, cursor);
+      return findPosition(column + 1, cursor);
+    }
+
+    // TODO recode this more naturally i.e. count residues only
+    // as they are found, not 'in anticipation'
+
+    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 (!Comparison.isGap(sequence[j]))
       {
+        lastPosFound = pos;
+        lastPosFoundColumn = j;
         pos++;
       }
-
       j++;
     }
+    if (j < seqlen && !Comparison.isGap(sequence[j]))
+    {
+      lastPosFound = pos;
+      lastPosFoundColumn = j;
+    }
 
-    if (j == i && !Comparison.isGap(sequence[i]))
+    /*
+     * update the cursor to the last residue position found (if any)
+     * (converting column position to base 1)
+     */
+    if (lastPosFound != 0)
     {
-      updateCursor(pos, i + 1);
+      updateCursor(lastPosFound, lastPosFoundColumn + 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.
@@ -805,7 +860,7 @@ public class Sequence extends ASequence implements SequenceI
    */
   protected int findPosition(final int col, SequenceCursor curs)
   {
-    if (curs.sequence != this || curs.token != changeCount)
+    if (!isValidCursor(curs))
     {
       /*
        * wrong or invalidated cursor, compute de novo
@@ -815,6 +870,7 @@ public class Sequence extends ASequence implements SequenceI
 
     if (curs.columnPosition == col)
     {
+      cursor = curs; // in case this method becomes public
       return curs.residuePosition; // easy case :-)
     }
 
@@ -825,6 +881,8 @@ public class Sequence extends ASequence implements SequenceI
     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)
     {
@@ -837,14 +895,21 @@ public class Sequence extends ASequence implements SequenceI
       if (!gapped)
       {
         newPos += delta;
+        lastFoundPosition = newPos;
+        lastFoundPositionColumn = column + 1;
       }
     }
 
+    if (cursor == null || lastFoundPosition != cursor.residuePosition)
+    {
+      updateCursor(lastFoundPosition, lastFoundPositionColumn);
+    }
+
     /*
      * hack to give position to the right if on a gap
-     * pending resolution of JAL-2562
+     * or beyond the length of the sequence (see JAL-2562)
      */
-    if (delta > 0 && gapped)
+    if (delta > 0 && (gapped || column >= sequence.length))
     {
       newPos++;
     }
@@ -934,7 +999,7 @@ public class Sequence extends ASequence implements SequenceI
    */
   protected Range findPositions(int fromCol, int toCol, SequenceCursor curs)
   {
-    if (curs.sequence != this || curs.token != changeCount)
+    if (!isValidCursor(curs))
     {
       /*
        * wrong or invalidated cursor, compute de novo