// change sequence, should trigger an update of cached result
sq.setSequence("ASDFASDFADSF");
assertTrue(sq.isProtein());
- /*
- * in situ change of sequence doesn't change hashcode :-O
- * (sequence should not expose internal implementation)
- */
- for (int i = 0; i < sq.getSequence().length; i++)
- {
- sq.getSequence()[i] = "acgtu".charAt(i % 5);
- }
- assertTrue(sq.isProtein()); // but it isn't
}
@Test(groups = { "Functional" })
SequenceI sq = new Sequence("test/8-13", "ABCDEF");
assertEquals(8, sq.findPosition(0));
// Sequence should now hold a cursor at [8, 0]
+ assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0",
+ PA.getValue(sq, "cursor").toString());
SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
int token = (int) PA.getValue(sq, "changeCount");
assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
/*
* find F13 at column offset 5, cursor should update to [13, 6]
+ * endColumn is found and saved in cursor
*/
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("test:Pos13:Col6:startCol1:endCol6:tok1",
+ PA.getValue(sq, "cursor").toString());
// assertEquals(-1, seq.findPosition(6)); // fails
assertEquals(8, sq.findPosition(0));
cursor = (SequenceCursor) PA.getValue(sq, "cursor");
assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
+ assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
assertEquals(9, sq.findPosition(1));
cursor = (SequenceCursor) PA.getValue(sq, "cursor");
assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
+ assertEquals("test:Pos9:Col2:startCol1:endCol0:tok1",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
// gap position 'finds' residue to the right (not the left as per javadoc)
assertEquals(10, sq.findPosition(2));
cursor = (SequenceCursor) PA.getValue(sq, "cursor");
assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
+ assertEquals("test:Pos9:Col2:startCol1:endCol0:tok2",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
assertEquals(10, sq.findPosition(3));
cursor = (SequenceCursor) PA.getValue(sq, "cursor");
assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
+ assertEquals("test:Pos10:Col4:startCol1:endCol0:tok3",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
// column[4] is the gap after C - returns D11
assertEquals(11, sq.findPosition(4));
cursor = (SequenceCursor) PA.getValue(sq, "cursor");
assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
+ assertEquals("test:Pos10:Col4:startCol1:endCol0:tok4",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
assertEquals(11, sq.findPosition(5)); // D
cursor = (SequenceCursor) PA.getValue(sq, "cursor");
assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
+ // lastCol has been found and saved in the cursor
+ assertEquals("test:Pos11:Col6:startCol1:endCol6:tok5",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
// returns 1 more than sequence length if off the end ?!?
sq.sequenceChanged();
assertEquals(12, sq.findPosition(7));
+ /*
+ * first findPosition should also set firstResCol in cursor
+ */
sq = new Sequence("test/8-13", "--AB-C-DEF--");
assertEquals(8, sq.findPosition(0));
+ assertNull(PA.getValue(sq, "cursor"));
sq.sequenceChanged();
assertEquals(8, sq.findPosition(1));
+ assertNull(PA.getValue(sq, "cursor"));
sq.sequenceChanged();
assertEquals(8, sq.findPosition(2));
+ assertEquals("test:Pos8:Col3:startCol3:endCol0:tok2",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
assertEquals(9, sq.findPosition(3));
+ assertEquals("test:Pos9:Col4:startCol3:endCol0:tok3",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
+ // column[4] is a gap, returns next residue pos (C10)
+ // cursor is set to last residue found [B]
assertEquals(10, sq.findPosition(4));
+ assertEquals("test:Pos9:Col4:startCol3:endCol0:tok4",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
assertEquals(10, sq.findPosition(5));
+ assertEquals("test:Pos10:Col6:startCol3:endCol0:tok5",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
+ // column[6] is a gap, returns next residue pos (D11)
+ // cursor is set to last residue found [C]
assertEquals(11, sq.findPosition(6));
+ assertEquals("test:Pos10:Col6:startCol3:endCol0:tok6",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
assertEquals(11, sq.findPosition(7));
+ assertEquals("test:Pos11:Col8:startCol3:endCol0:tok7",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
assertEquals(12, sq.findPosition(8));
+ assertEquals("test:Pos12:Col9:startCol3:endCol0:tok8",
+ PA.getValue(sq, "cursor").toString());
+ /*
+ * when the last residue column is found, it is set in the cursor
+ */
sq.sequenceChanged();
assertEquals(13, sq.findPosition(9));
+ assertEquals("test:Pos13:Col10:startCol3:endCol10:tok9",
+ PA.getValue(sq, "cursor").toString());
sq.sequenceChanged();
assertEquals(14, sq.findPosition(10));
+ assertEquals("test:Pos13:Col10:startCol3:endCol10:tok10",
+ PA.getValue(sq, "cursor").toString());
/*
* findPosition for column beyond sequence length
*/
sq.sequenceChanged();
assertEquals(14, sq.findPosition(11));
+ assertEquals("test:Pos13:Col10:startCol3:endCol10:tok11",
+ PA.getValue(sq, "cursor").toString());
+
sq.sequenceChanged();
assertEquals(14, sq.findPosition(99));
+ assertEquals("test:Pos13:Col10:startCol3:endCol10:tok12",
+ PA.getValue(sq, "cursor").toString());
+
+ /*
+ * gapped sequence ending in non-gap
+ */
+ sq = new Sequence("test/8-13", "--AB-C-DEF");
+ assertEquals(13, sq.findPosition(9));
+ assertEquals("test:Pos13:Col10:startCol3:endCol10:tok0",
+ PA.getValue(sq, "cursor").toString());
+ sq.sequenceChanged();
+ assertEquals(12, sq.findPosition(8));
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ // sequenceChanged() invalidates cursor.lastResidueColumn
+ cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals("test:Pos12:Col9:startCol3:endCol0:tok1",
+ cursor.toString());
+ // findPosition with cursor accepts base 1 column values
+ assertEquals(13, ((Sequence) sq).findPosition(10, cursor));
+ assertEquals(13, sq.findPosition(9)); // F13
+ // lastResidueColumn has now been found and saved in cursor
+ assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1",
+ PA.getValue(sq, "cursor").toString());
}
@Test(groups = { "Functional" })
{
Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
- // find F pos given A
+ // find F pos given A - lastCol gets set in cursor
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);
+ assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
+ PA.getValue(sq, "cursor").toString());
- // find A pos given F
+ // find A pos given F - first residue column is saved in cursor
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);
+ assertEquals("test:Pos8:Col2:startCol2:endCol10:tok0",
+ PA.getValue(sq, "cursor").toString());
- // find C pos given C
+ // find C pos given C (neither startCol nor endCol is set)
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);
+ assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0",
+ PA.getValue(sq, "cursor").toString());
// 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);
+ assertEquals("test:Pos9:Col5:startCol0:endCol0:tok0",
+ PA.getValue(sq, "cursor").toString());
// 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);
+ assertEquals("test:Pos11:Col7:startCol0:endCol0:tok0",
+ PA.getValue(sq, "cursor").toString());
// find 'residue' for column 12 given cursor for B
// returns 1 more than last residue position; cursor is updated to [F 10]
+ // lastCol position is saved in cursor
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);
+ assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
+ PA.getValue(sq, "cursor").toString());
/*
* findPosition for column beyond length of sequence
* 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);
+ assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
+ PA.getValue(sq, "cursor").toString());
/*
* 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);
+ SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+ assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0",
+ cursor.toString());
// now 'find' 99 from C
- // cursor is set to [F 10]
+ // cursor is set to [F 10] and saved lastCol
assertEquals(14, sq.findPosition(99, cursor));
- cursor = (SequenceCursor) PA.getValue(sq, "cursor");
- assertEquals(new SequenceCursor(sq, 13, 10, token), cursor);
+ assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
+ PA.getValue(sq, "cursor").toString());
}
@Test
assertTrue(sq.isValidCursor(cursor));
/*
- * column position outside [0 - length-1] is rejected
+ * column position outside [0 - length] is rejected
*/
cursor = new SequenceCursor(sq, 13, -1, changeCount);
assertFalse(sq.isValidCursor(cursor));
- cursor = new SequenceCursor(sq, 13, 9, changeCount);
+ cursor = new SequenceCursor(sq, 13, 10, changeCount);
assertFalse(sq.isValidCursor(cursor));
cursor = new SequenceCursor(sq, 7, 8, changeCount);
assertFalse(sq.isValidCursor(cursor));
cursor = (SequenceCursor) PA.getValue(sq, "cursor");
assertEquals(new SequenceCursor(sq, 13, 10, ++token), cursor);
}
+
+ @Test(groups = { "Functional" })
+ public void testGetSequence()
+ {
+ String seqstring = "-A--BCD-EF--";
+ Sequence sq = new Sequence("test/8-13", seqstring);
+ sq.createDatasetSequence();
+ assertTrue(Arrays.equals(sq.getSequence(), seqstring.toCharArray()));
+ assertTrue(Arrays.equals(sq.getDatasetSequence().getSequence(),
+ "ABCDEF".toCharArray()));
+
+ // verify a copy of the sequence array is returned
+ char[] theSeq = (char[]) PA.getValue(sq, "sequence");
+ assertNotSame(theSeq, sq.getSequence());
+ theSeq = (char[]) PA.getValue(sq.getDatasetSequence(), "sequence");
+ assertNotSame(theSeq, sq.getDatasetSequence().getSequence());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testReplace()
+ {
+ String seqstring = "-A--BCD-EF--";
+ SequenceI sq = new Sequence("test/8-13", seqstring);
+ assertEquals(0, PA.getValue(sq, "changeCount"));
+
+ assertEquals(0, sq.replace('A', 'A')); // same char
+ assertEquals(seqstring, sq.getSequenceAsString());
+ assertEquals(0, PA.getValue(sq, "changeCount"));
+
+ assertEquals(0, sq.replace('X', 'Y')); // not there
+ assertEquals(seqstring, sq.getSequenceAsString());
+ assertEquals(0, PA.getValue(sq, "changeCount"));
+
+ assertEquals(1, sq.replace('A', 'K'));
+ assertEquals("-K--BCD-EF--", sq.getSequenceAsString());
+ assertEquals(1, PA.getValue(sq, "changeCount"));
+
+ assertEquals(6, sq.replace('-', '.'));
+ assertEquals(".K..BCD.EF..", sq.getSequenceAsString());
+ assertEquals(2, PA.getValue(sq, "changeCount"));
+ }
}