+ * 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 (curs.sequence != this || curs.token != changeCount)
+ {
+ /*
+ * wrong or invalidated cursor, compute de novo
+ */
+ return findPosition(col - 1);// ugh back to base 0
+ }
+
+ if (curs.columnPosition == col)
+ {
+ return curs.residuePosition; // easy case :-)
+ }
+
+ /*
+ * move left or right to find pos from cursor position
+ */
+ int column = curs.columnPosition - 1; // to base 0
+ int newPos = curs.residuePosition;
+ int delta = curs.columnPosition > col ? -1 : 1;
+ boolean gapped = false;
+
+ 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;
+ }
+ }
+
+ /*
+ * hack to give position to the right if on a gap
+ * pending resolution of JAL-2562
+ */
+ if (delta > 0 && gapped)
+ {
+ newPos++;
+ }
+
+ return newPos;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public Range findPositions(int fromCol, int toCol)
+ {
+ if (cursor != null && cursor.sequence == this
+ && cursor.token == changeCount)
+ {
+ return findPositions(fromCol, toCol, cursor);
+ }
+
+ /*
+ * count residues before fromCol
+ */
+ int j = 0;
+ int count = 0;
+ int seqlen = sequence.length;
+ while (j < fromCol && j < seqlen)
+ {
+ if (!Comparison.isGap(sequence[j]))
+ {
+ count++;
+ }
+ j++;
+ }
+
+ /*
+ * find first and last residues between fromCol and toCol
+ */
+ int firstPos = 0;
+ int lastPos = 0;
+ boolean foundFirst = false;
+
+ while (j <= toCol && j < seqlen)
+ {
+ if (!Comparison.isGap(sequence[j]))
+ {
+ count++;
+ if (!foundFirst)
+ {
+ firstPos = count;
+ foundFirst = true;
+ }
+ lastPos = count;
+ }
+ j++;
+ }
+
+ if (firstPos == 0)
+ {
+ /*
+ * no residues in this range
+ */
+ return null;
+ }
+
+ /*
+ * adjust for sequence start coordinate
+ */
+ firstPos += start - 1;
+ lastPos += start - 1;
+
+ return new Range(firstPos, lastPos);
+ }
+
+ /**
+ * Returns the range of sequence positions included in the given alignment
+ * position range. If no positions are included (the range is entirely gaps),
+ * then returns null. The cursor parameter may provide a starting position in
+ * the neighbourhood of the search (which may be left of, right of, or
+ * overlapping the search region).
+ *
+ * @param fromCol
+ * start column of region (0..)
+ * @param toCol
+ * end column of region (0..)
+ * @param curs
+ * @return
+ */
+ protected Range findPositions(int fromCol, int toCol, SequenceCursor curs)
+ {
+ if (curs.sequence != this || curs.token != changeCount)
+ {
+ /*
+ * wrong or invalidated cursor, compute de novo
+ */
+ return findPositions(fromCol, toCol);
+ }
+
+ /*
+ * keep this simple...first step from cursor to fromCol...
+ */
+ final int seqlen = sequence.length;
+ int resNo = curs.residuePosition;
+ int col = curs.columnPosition - 1; // from base 1 to base 0
+ if (col != fromCol)
+ {
+ int delta = col > fromCol ? -1 : 1;
+ while (col != fromCol && col >= 0 && col < seqlen)
+ {
+ if (!Comparison.isGap(sequence[col]))
+ {
+ resNo += delta;
+ }
+ col += delta;
+ }
+ }
+
+ if (col < fromCol || col == seqlen)
+ {
+ /*
+ * sequence lies to the left of the target region
+ */
+ return null;
+ }
+
+ /*
+ * resNo is now the residue at fromCol (if not gapped), else the one
+ * before it (if delta == 1), else the one after (if delta == -1);
+ * we want the residue before fromCol
+ */
+ if (!Comparison.isGap(sequence[fromCol]))
+ {
+ resNo--;
+ }
+ else if (curs.columnPosition > fromCol)
+ {
+ resNo -= 2;
+ }
+
+ /*
+ * now first and last residues between fromCol and toCol
+ */
+ int firstPos = 0;
+ int lastPos = 0;
+ boolean foundFirst = false;
+
+ while (col <= toCol && col < seqlen)
+ {
+ if (!Comparison.isGap(sequence[col]))
+ {
+ resNo++;
+ if (!foundFirst)
+ {
+ firstPos = resNo;
+ foundFirst = true;
+ }
+ lastPos = resNo;
+ }
+ col++;
+ }
+
+ if (firstPos == 0)
+ {
+ /*
+ * no residues in this range
+ */
+ return null;
+ }
+
+ return new Range(firstPos, lastPos);
+ }
+
+ /**