AlignmentAnnotation[] tmp;
for (int s = 0; s < command.seqs.length; s++)
{
+ command.seqs[s].zapCursor();
+
if (modifyVisibility)
{
// Rows are only removed or added to sequence object.
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.
*
@Override
public int findIndex(int pos)
{
- // returns the alignment position for a residue
+ /*
+ * use a valid nearby cursor if available
+ */
+ if (cursor != null && cursor.sequence == this
+ && cursor.token == changeCount)
+ {
+ return findIndex(pos, cursor);
+ }
+
int j = start;
int i = 0;
// Rely on end being at least as long as the length of the sequence.
{
j++;
}
-
i++;
}
}
else
{
+ updateCursor(pos, i);
return i;
}
}
+ protected void updateCursor(int residuePos, int column)
+ {
+ // TODO probably want to synchronize this on something
+ cursor = new SequenceCursor(this, residuePos, column, 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 (curs.sequence != this || curs.token != changeCount)
+ {
+ /*
+ * 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)
+ {
+ 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);
+
+ return col;
+ }
+
@Override
- public int findPosition(int i)
+ public int findPosition(final int i)
{
+ /*
+ * use a valid nearby cursor if available
+ */
+ if (cursor != null && cursor.sequence == this
+ && cursor.token == changeCount)
+ {
+ return findPosition(i + 1, cursor);
+ }
+
int j = 0;
int pos = start;
int seqlen = sequence.length;
j++;
}
+ if (j == i && !Comparison.isGap(sequence[i]))
+ {
+ updateCursor(pos, i + 1);
+ }
+
return pos;
}
/**
+ * 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 firstPos = 0;
int lastPos = 0;
- int firstPosCol = 0;
boolean foundFirst = false;
while (j <= toCol && j < seqlen)
if (!foundFirst)
{
firstPos = count;
- firstPosCol = j;
foundFirst = true;
}
lastPos = count;
}
/**
+ * 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);
+ }
+
+ /**
* Returns an int array where indices correspond to each residue in the
* sequence and the element value gives its position in the alignment
*
}
return sequenceFeatureStore.findFeatures(from, to, types);
}
+
+ /**
+ * Invalidates any stale cursors (forcing recalculation) by incrementing the
+ * token that has to match the one presented by the cursor
+ */
+ @Override
+ public void zapCursor()
+ {
+ changeCount++;
+ }
}
--- /dev/null
+package jalview.datamodel;
+
+/**
+ * An immutable object representing one or more residue and corresponding
+ * alignment column positions for a sequence
+ */
+public class SequenceCursor
+{
+ /**
+ * the aligned sequence this cursor applies to
+ */
+ public final SequenceI sequence;
+
+ /**
+ * residue position in sequence (start...), 0 if undefined
+ */
+ public final int residuePosition;
+
+ /**
+ * column position (1...) corresponding to residuePosition, or 0 if undefined
+ */
+ public final int columnPosition;
+
+ /**
+ * a token which may be used to check whether this cursor is still valid for
+ * its sequence (allowing it to be ignored if the sequence has changed)
+ */
+ public final int token;
+
+ public SequenceCursor(SequenceI seq, int resPos, int column, int tok)
+ {
+ sequence = seq;
+ residuePosition = resPos;
+ columnPosition = column;
+ token = tok;
+ }
+}
* @return
*/
List<SequenceFeature> findFeatures(int from, int to, String... types);
+
+ /**
+ * Invalidate any cursors on the sequence (e.g. after an edit)
+ */
+ public void zapCursor();
}
{
SequenceI sq = new Sequence("test", "ABCDEF");
assertEquals(0, sq.findIndex(0));
+ PA.setValue(sq, "cursor", null);
assertEquals(1, sq.findIndex(1));
+ PA.setValue(sq, "cursor", null);
assertEquals(5, sq.findIndex(5));
+ PA.setValue(sq, "cursor", null);
assertEquals(6, sq.findIndex(6));
+ PA.setValue(sq, "cursor", null);
assertEquals(6, sq.findIndex(9));
sq = new Sequence("test/8-13", "-A--B-C-D-E-F--");
assertEquals(2, sq.findIndex(8));
+ PA.setValue(sq, "cursor", null);
assertEquals(5, sq.findIndex(9));
+ PA.setValue(sq, "cursor", null);
assertEquals(7, sq.findIndex(10));
// before start returns 0
+ PA.setValue(sq, "cursor", null);
assertEquals(0, sq.findIndex(0));
+ PA.setValue(sq, "cursor", null);
assertEquals(0, sq.findIndex(-1));
// beyond end returns last residue column
+ PA.setValue(sq, "cursor", null);
assertEquals(13, sq.findIndex(99));
-
}
/**
range = sq.findPositions(3, 7); // DE
assertEquals(new Range(11, 12), range);
}
+
+ @Test(groups = { "Functional" })
+ public void testFindIndex_withCursor()
+ {
+ Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
+
+ // find F given A
+ assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, 0)));
+
+ // find A given F
+ assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, 0)));
+
+ // find C given C
+ assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0)));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFindPosition_withCursor()
+ {
+ Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
+
+ // find F pos given A
+ assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0)));
+
+ // find A pos given F
+ assertEquals(8, sq.findPosition(2, new SequenceCursor(sq, 13, 10, 0)));
+
+ // find C pos given C
+ assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 10, 6, 0)));
+
+ // now the grey area - what residue position for a gapped column? JAL-2562
+
+ // find 'residue' for column 3 given cursor for D (so working left)
+ assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, 0)));
+
+ // find 'residue' for column 8 given cursor for D (so working right)
+ assertEquals(12, sq.findPosition(8, new SequenceCursor(sq, 11, 7, 0)));
+
+ // find 'residue' for column 12 given cursor for B
+ assertEquals(14, sq.findPosition(12, new SequenceCursor(sq, 9, 5, 0)));
+ }
+
+ @Test
+ public void testFindPositions_withCursor()
+ {
+ Sequence sq = new Sequence("Seq", "ABC--DE-F", 8, 13);
+
+ // find positions for columns 1-4 (BC--) given E cursor
+ Range range = sq.findPositions(1, 4, new SequenceCursor(sq, 12, 7, 0)); // BC
+ assertEquals(new Range(9, 10), range);
+
+ // repeat using B cursor
+ range = sq.findPositions(1, 4, new SequenceCursor(sq, 9, 2, 0)); // BC
+ assertEquals(new Range(9, 10), range);
+
+ // find positions for columns 2-4 (C--) given A cursor
+ range = sq.findPositions(2, 4, new SequenceCursor(sq, 8, 1, 0)); // C
+ assertEquals(new Range(10, 10), range);
+
+ // gapped region
+ assertNull(sq.findPositions(3, 4, new SequenceCursor(sq, 10, 3, 0)));
+ assertNull(sq.findPositions(3, 4, new SequenceCursor(sq, 12, 7, 0)));
+
+ // find positions for columns 2-6 (C--DE) given B cursor
+ range = sq.findPositions(2, 6, new SequenceCursor(sq, 9, 2, 0)); // CDE
+ assertEquals(new Range(10, 12), range);
+
+ // repeat using C as cursor
+ range = sq.findPositions(2, 6, new SequenceCursor(sq, 10, 3, 0));
+ assertEquals(new Range(10, 12), range);
+
+ // repeat using D as cursor
+ range = sq.findPositions(2, 6, new SequenceCursor(sq, 11, 6, 0));
+ assertEquals(new Range(10, 12), range);
+
+ // repeat using E as cursor
+ range = sq.findPositions(2, 6, new SequenceCursor(sq, 12, 7, 0));
+ assertEquals(new Range(10, 12), range);
+
+ // repeat using F as cursor
+ range = sq.findPositions(2, 6, new SequenceCursor(sq, 13, 9, 0));
+ assertEquals(new Range(10, 12), range);
+ }
}
git://source.jalview.org / jalview.git / commitdiff