+ // 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);
+ }
+
+ @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"));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFindPositions()
+ {
+ SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
+
+ /*
+ * invalid inputs
+ */
+ assertNull(sq.findPositions(6, 5));
+ assertNull(sq.findPositions(0, 5));
+ assertNull(sq.findPositions(-1, 5));
+
+ /*
+ * all gapped ranges
+ */
+ assertNull(sq.findPositions(1, 1)); // 1-based columns
+ assertNull(sq.findPositions(5, 5));
+ assertNull(sq.findPositions(5, 6));
+ assertNull(sq.findPositions(5, 7));
+
+ /*
+ * all ungapped ranges
+ */
+ assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A
+ assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB
+ assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC
+ assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC
+
+ /*
+ * gap to ungapped range
+ */
+ assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC
+ assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE