- // create random alignment
- AlignmentGenerator gen = new AlignmentGenerator(false);
- AlignmentI al = gen.generate(50, 20, 123, 5, 5);
-
- HiddenColumns cs = al.getHiddenColumns();
- ColumnSelection colsel = new ColumnSelection();
-
- SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
- assertEquals(2, seq.findIndex(seq.getStart()));
-
- // no hidden columns
- assertEquals(
- Arrays.toString(new int[]
- { seq.findIndex(seq.getStart()) - 1, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- // hidden column on gap after end of sequence - should not affect bounds
- colsel.hideSelectedColumns(13, al.getHiddenColumns());
- assertEquals(
- Arrays.toString(new int[]
- { seq.findIndex(seq.getStart()) - 1, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- cs.revealAllHiddenColumns(colsel);
- // hidden column on gap before beginning of sequence - should vis bounds by
- // one
- colsel.hideSelectedColumns(0, al.getHiddenColumns());
- assertEquals(
- Arrays.toString(new int[]
- { seq.findIndex(seq.getStart()) - 2, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- cs.revealAllHiddenColumns(colsel);
- // hide columns around most of sequence - leave one residue remaining
- cs.hideColumns(1, 3);
- cs.hideColumns(6, 11);
- assertEquals("-D",
- cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
- { seq })[0]);
-
- assertEquals(
- Arrays.toString(
- new int[]
- { 1, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
- cs.revealAllHiddenColumns(colsel);
-
- // hide whole sequence - should just get location of hidden region
- // containing sequence
- cs.hideColumns(1, 11);
- assertEquals(
- Arrays.toString(
- new int[]
- { 0, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 15);
- assertEquals(Arrays
- .toString(new int[]
- { 0, seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
-
- SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(7, 17);
- assertEquals(
- Arrays.toString(
- new int[]
- { 0, seq2.findIndex(seq2.getStart()) - 1,
- seq2.findIndex(seq2.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(3, 17);
- assertEquals(
- Arrays.toString(
- new int[]
- { 0, seq2.findIndex(seq2.getStart()) - 1,
- seq2.findIndex(seq2.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(3, 19);
- assertEquals(
- Arrays.toString(
- new int[]
- { 0, seq2.findIndex(seq2.getStart()) - 1,
- seq2.findIndex(seq2.getEnd()) - 1 }),
- Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 0);
- int[] test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 1);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 2);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(1, 1);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 2, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(1, 2);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(1, 3);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 2);
- cs.hideColumns(5, 6);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 2);
- cs.hideColumns(5, 6);
- cs.hideColumns(9, 10);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 2);
- cs.hideColumns(7, 11);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(2, 4);
- cs.hideColumns(7, 11);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(2, 4);
- cs.hideColumns(7, 12);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 1, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(1, 11);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));
-
- cs.revealAllHiddenColumns(colsel);
- cs.hideColumns(0, 12);
- test = cs.locateVisibleBoundsOfSequence(seq);
- assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
- Arrays.toString(test));