import java.util.ArrayList;
import java.util.Arrays;
+ import java.util.BitSet;
import java.util.Collections;
import java.util.Enumeration;
import java.util.List;
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.
*
{
this.sequence = seq.toCharArray();
checkValidRange();
+ sequenceChanged();
}
@Override
return this.description;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#findIndex(int)
+ /**
+ * {@inheritDoc}
*/
@Override
public int findIndex(int pos)
{
- // returns the alignment position for a residue
+ /*
+ * use a valid, hopefully nearby, cursor if available
+ */
+ if (isValidCursor(cursor))
+ {
+ 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++;
}
- if ((j == end) && (j < pos))
+ if (j == end && j < pos)
{
return end + 1;
}
- else
+
+ 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)
+ {
+ 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 (!isValidCursor(curs))
+ {
+ /*
+ * 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)
{
- return i;
+ 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;
}
+ /**
+ * {@inheritDoc}
+ */
@Override
- public int findPosition(int i)
+ public int findPosition(final int column)
{
+ /*
+ * use a valid, hopefully nearby, cursor if available
+ */
+ if (isValidCursor(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;
+ }
+
+ /*
+ * update the cursor to the last residue position found (if any)
+ * (converting column position to base 1)
+ */
+ if (lastPosFound != 0)
+ {
+ 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.
+ *
+ * @param col
+ * @param curs
+ * @return
+ */
+ protected int findPosition(final int col, SequenceCursor curs)
+ {
+ if (!isValidCursor(curs))
+ {
+ /*
+ * wrong or invalidated cursor, compute de novo
+ */
+ return findPosition(col - 1);// ugh back to base 0
+ }
+
+ if (curs.columnPosition == col)
+ {
+ cursor = curs; // in case this method becomes public
+ 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;
+ int lastFoundPosition = curs.residuePosition;
+ int lastFoundPositionColumn = curs.columnPosition;
+
+ 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;
+ 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
+ * or beyond the length of the sequence (see JAL-2562)
+ */
+ if (delta > 0 && (gapped || column >= sequence.length))
+ {
+ 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 (!isValidCursor(curs))
+ {
+ /*
+ * 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
*
}
@Override
+ public BitSet getInsertionsAsBits()
+ {
+ BitSet map = new BitSet();
+ int lastj = -1, j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ((j < seqlen))
+ {
+ if (jalview.util.Comparison.isGap(sequence[j]))
+ {
+ if (lastj == -1)
+ {
+ lastj = j;
+ }
+ }
+ else
+ {
+ if (lastj != -1)
+ {
+ map.set(lastj, j);
+ lastj = -1;
+ }
+ }
+ j++;
+ }
+ if (lastj != -1)
+ {
+ map.set(lastj, j);
+ lastj = -1;
+ }
+ return map;
+ }
+
+ @Override
public void deleteChars(int i, int j)
{
int newstart = start, newend = end;
start = newstart;
end = newend;
sequence = tmp;
+ sequenceChanged();
}
@Override
}
sequence = tmp;
+ sequenceChanged();
}
@Override
}
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 sequenceChanged()
+ {
+ changeCount++;
+ }
}
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
import jalview.datamodel.PDBEntry.Type;
import jalview.gui.JvOptionPane;
import jalview.util.MapList;
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
+ import java.util.BitSet;
import java.util.List;
import java.util.Vector;
assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
+
+ BitSet gapfield = aseq.getInsertionsAsBits();
+ BitSet expectedgaps = new BitSet();
+ expectedgaps.set(2, 5);
+ expectedgaps.set(6, 9);
+
+ assertEquals(6, expectedgaps.cardinality());
+
+ assertEquals("getInsertionsAsBits didn't mark expected number of gaps",
+ 6, gapfield.cardinality());
+
+ assertEquals("getInsertionsAsBits not correct.", expectedgaps, gapfield);
}
@Test(groups = ("Functional"))
@Test(groups = { "Functional" })
public void testFindIndex()
{
+ /*
+ * call sequenceChanged() after each test to invalidate any cursor,
+ * forcing the 1-arg findIndex to be executed
+ */
SequenceI sq = new Sequence("test", "ABCDEF");
assertEquals(0, sq.findIndex(0));
+ sq.sequenceChanged();
assertEquals(1, sq.findIndex(1));
+ sq.sequenceChanged();
assertEquals(5, sq.findIndex(5));
+ sq.sequenceChanged();
assertEquals(6, sq.findIndex(6));
+ sq.sequenceChanged();
assertEquals(6, sq.findIndex(9));
sq = new Sequence("test/8-13", "-A--B-C-D-E-F--");
assertEquals(2, sq.findIndex(8));
+ sq.sequenceChanged();
assertEquals(5, sq.findIndex(9));
+ sq.sequenceChanged();
assertEquals(7, sq.findIndex(10));
// before start returns 0
+ sq.sequenceChanged();
assertEquals(0, sq.findIndex(0));
+ sq.sequenceChanged();
assertEquals(0, sq.findIndex(-1));
// beyond end returns last residue column
+ sq.sequenceChanged();
assertEquals(13, sq.findIndex(99));
}
/**
- * Tests for the method that returns a dataset sequence position (base 1) for
+ * Tests for the method that returns a dataset sequence position (start..) for
* an aligned column position (base 0).
*/
@Test(groups = { "Functional" })
public void testFindPosition()
{
- SequenceI sq = new Sequence("test", "ABCDEF");
- assertEquals(1, sq.findPosition(0));
- assertEquals(6, sq.findPosition(5));
+ /*
+ * call sequenceChanged() after each test to invalidate any cursor,
+ * forcing the 1-arg findPosition to be executed
+ */
+ SequenceI sq = new Sequence("test/8-13", "ABCDEF");
+ assertEquals(8, sq.findPosition(0));
+ // Sequence should now hold a cursor at [8, 0]
+ SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ int token = (int) PA.getValue(sq, "changeCount");
+ assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
+
+ sq.sequenceChanged();
+
+ /*
+ * find F13 at column offset 5, cursor should update to [13, 6]
+ */
+ assertEquals(13, sq.findPosition(5));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(++token, (int) PA.getValue(sq, "changeCount"));
+ assertEquals(new SequenceCursor(sq, 13, 6, token), cursor);
+
// assertEquals(-1, seq.findPosition(6)); // fails
- sq = new Sequence("test", "AB-C-D--");
- assertEquals(1, sq.findPosition(0));
- assertEquals(2, sq.findPosition(1));
+ sq = new Sequence("test/8-11", "AB-C-D--");
+ token = (int) PA.getValue(sq, "changeCount"); // 0
+ assertEquals(8, sq.findPosition(0));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
+
+ sq.sequenceChanged();
+ assertEquals(9, sq.findPosition(1));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
+
+ sq.sequenceChanged();
// gap position 'finds' residue to the right (not the left as per javadoc)
- assertEquals(3, sq.findPosition(2));
- assertEquals(3, sq.findPosition(3));
- assertEquals(4, sq.findPosition(4));
- assertEquals(4, sq.findPosition(5));
+ // cursor is set to the last residue position found [B 2]
+ assertEquals(10, sq.findPosition(2));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
+
+ sq.sequenceChanged();
+ assertEquals(10, sq.findPosition(3));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
+
+ sq.sequenceChanged();
+ // column[4] is the gap after C - returns D11
+ // cursor is set to [C 4]
+ assertEquals(11, sq.findPosition(4));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
+
+ sq.sequenceChanged();
+ assertEquals(11, sq.findPosition(5)); // D
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
+
+ sq.sequenceChanged();
// returns 1 more than sequence length if off the end ?!?
- assertEquals(5, sq.findPosition(6));
- assertEquals(5, sq.findPosition(7));
+ assertEquals(12, sq.findPosition(6));
- sq = new Sequence("test", "--AB-C-DEF--");
- assertEquals(1, sq.findPosition(0));
- assertEquals(1, sq.findPosition(1));
- assertEquals(1, sq.findPosition(2));
- assertEquals(2, sq.findPosition(3));
- assertEquals(3, sq.findPosition(4));
- assertEquals(3, sq.findPosition(5));
- assertEquals(4, sq.findPosition(6));
- assertEquals(4, sq.findPosition(7));
- assertEquals(5, sq.findPosition(8));
- assertEquals(6, sq.findPosition(9));
- assertEquals(7, sq.findPosition(10));
- assertEquals(7, sq.findPosition(11));
+ sq.sequenceChanged();
+ assertEquals(12, sq.findPosition(7));
+
+ sq = new Sequence("test/8-13", "--AB-C-DEF--");
+ assertEquals(8, sq.findPosition(0));
+
+ sq.sequenceChanged();
+ assertEquals(8, sq.findPosition(1));
+
+ sq.sequenceChanged();
+ assertEquals(8, sq.findPosition(2));
+
+ sq.sequenceChanged();
+ assertEquals(9, sq.findPosition(3));
+
+ sq.sequenceChanged();
+ assertEquals(10, sq.findPosition(4));
+
+ sq.sequenceChanged();
+ assertEquals(10, sq.findPosition(5));
+
+ sq.sequenceChanged();
+ assertEquals(11, sq.findPosition(6));
+
+ sq.sequenceChanged();
+ assertEquals(11, sq.findPosition(7));
+
+ sq.sequenceChanged();
+ assertEquals(12, sq.findPosition(8));
+
+ sq.sequenceChanged();
+ assertEquals(13, sq.findPosition(9));
+
+ sq.sequenceChanged();
+ assertEquals(14, sq.findPosition(10));
+
+ /*
+ * findPosition for column beyond sequence length
+ * returns 1 more than last residue position
+ */
+ sq.sequenceChanged();
+ assertEquals(14, sq.findPosition(11));
+ sq.sequenceChanged();
+ assertEquals(14, sq.findPosition(99));
}
@Test(groups = { "Functional" })
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)));
+ int token = (int) PA.getValue(sq, "changeCount"); // 0
+ SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 13, 10, token), cursor);
+
+ // find A pos given F
+ assertEquals(8, sq.findPosition(2, new SequenceCursor(sq, 13, 10, 0)));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 8, 2, token), cursor);
+
+ // find C pos given C
+ assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 10, 6, 0)));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 10, 6, token), cursor);
+
+ // 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)
+ // returns B9; cursor is updated to [B 5]
+ assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, 0)));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 9, 5, token), cursor);
+
+ // find 'residue' for column 8 given cursor for D (so working right)
+ // returns E12; cursor is updated to [D 7]
+ assertEquals(12, sq.findPosition(8, new SequenceCursor(sq, 11, 7, 0)));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 11, 7, token), cursor);
+
+ // find 'residue' for column 12 given cursor for B
+ // returns 1 more than last residue position; cursor is updated to [F 10]
+ assertEquals(14, sq.findPosition(12, new SequenceCursor(sq, 9, 5, 0)));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 13, 10, token), cursor);
+
+ /*
+ * findPosition for column beyond length of sequence
+ * returns 1 more than the last residue position
+ * cursor is set to last real residue position [F 10]
+ */
+ assertEquals(14, sq.findPosition(99, new SequenceCursor(sq, 8, 2, 0)));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 13, 10, token), cursor);
+
+ /*
+ * and the case without a trailing gap
+ */
+ sq = new Sequence("test/8-13", "-A--BCD-EF");
+ // first find C from A
+ assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 8, 2, 0)));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 10, 6, token), cursor);
+ // now 'find' 99 from C
+ // cursor is set to [F 10]
+ assertEquals(14, sq.findPosition(99, cursor));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 13, 10, token), cursor);
+ }
+
+ @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);
+ }
+
+ @Test
+ public void testIsValidCursor()
+ {
+ Sequence sq = new Sequence("Seq", "ABC--DE-F", 8, 13);
+ assertFalse(sq.isValidCursor(null));
+
+ /*
+ * cursor is valid if it has valid sequence ref and changeCount token
+ * and positions within the range of the sequence
+ */
+ int changeCount = (int) PA.getValue(sq, "changeCount");
+ SequenceCursor cursor = new SequenceCursor(sq, 13, 1, changeCount);
+ assertTrue(sq.isValidCursor(cursor));
+
+ /*
+ * column position outside [0 - length-1] is rejected
+ */
+ cursor = new SequenceCursor(sq, 13, -1, changeCount);
+ assertFalse(sq.isValidCursor(cursor));
+ cursor = new SequenceCursor(sq, 13, 9, changeCount);
+ assertFalse(sq.isValidCursor(cursor));
+ cursor = new SequenceCursor(sq, 7, 8, changeCount);
+ assertFalse(sq.isValidCursor(cursor));
+ cursor = new SequenceCursor(sq, 14, 2, changeCount);
+ assertFalse(sq.isValidCursor(cursor));
+
+ /*
+ * wrong sequence is rejected
+ */
+ cursor = new SequenceCursor(null, 13, 1, changeCount);
+ assertFalse(sq.isValidCursor(cursor));
+ cursor = new SequenceCursor(new Sequence("Seq", "abc"), 13, 1,
+ changeCount);
+ assertFalse(sq.isValidCursor(cursor));
+
+ /*
+ * wrong token value is rejected
+ */
+ cursor = new SequenceCursor(sq, 13, 1, changeCount + 1);
+ assertFalse(sq.isValidCursor(cursor));
+ cursor = new SequenceCursor(sq, 13, 1, changeCount - 1);
+ assertFalse(sq.isValidCursor(cursor));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFindPosition_withCursorAndEdits()
+ {
+ 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)));
+ int token = (int) PA.getValue(sq, "changeCount"); // 0
+ SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 13, 10, token), cursor);
+
+ /*
+ * setSequence should invalidate the cursor cached by the sequence
+ */
+ sq.setSequence("-A-BCD-EF---"); // one gap removed
+ assertEquals(8, sq.getStart()); // sanity check
+ assertEquals(11, sq.findPosition(5)); // D11
+ // cursor should now be at [D 6]
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
+
+ /*
+ * deleteChars should invalidate the cached cursor
+ */
+ sq.deleteChars(2, 5); // delete -BC
+ assertEquals("-AD-EF---", sq.getSequenceAsString());
+ assertEquals(8, sq.getStart()); // sanity check
+ assertEquals(10, sq.findPosition(4)); // E10
+ // cursor should now be at [E 5]
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 10, 5, ++token), cursor);
+
+ /*
+ * Edit to insert gaps should invalidate the cached cursor
+ * insert 2 gaps at column[3] to make -AD---EF---
+ */
+ SequenceI[] seqs = new SequenceI[] { sq };
+ AlignmentI al = new Alignment(seqs);
+ new EditCommand().appendEdit(Action.INSERT_GAP, seqs, 3, 2, al, true);
+ assertEquals("-AD---EF---", sq.getSequenceAsString());
+ assertEquals(10, sq.findPosition(4)); // E10
+ // cursor should now be at [D 3]
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 9, 3, ++token), cursor);
+
+ /*
+ * insertCharAt should invalidate the cached cursor
+ * insert CC at column[4] to make -AD-CC--EF---
+ */
+ sq.insertCharAt(4, 2, 'C');
+ assertEquals("-AD-CC--EF---", sq.getSequenceAsString());
+ assertEquals(13, sq.findPosition(9)); // F13
+ // cursor should now be at [F 10]
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals(new SequenceCursor(sq, 13, 10, ++token), cursor);
+ }
}
git://source.jalview.org / jalview.git / commitdiff