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);
}
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);
}
*/
protected int findIndex(int pos, SequenceCursor curs)
{
- if (curs.sequence != this || curs.token != changeCount)
+ if (!isValidCursor(curs))
{
/*
* wrong or invalidated cursor, compute de novo
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.
*/
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
if (curs.columnPosition == col)
{
+ cursor = curs; // in case this method becomes public
return curs.residuePosition; // easy case :-)
}
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)
{
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++;
}
*/
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