}
@Test(groups = { "Functional" })
- public void testGetVisibleContigs()
+ public void testVisibleContigsIterator()
{
HiddenColumns cs = new HiddenColumns();
- List<int[]> visible = cs.getVisibleContigs(3, 10);
- assertEquals("[3, 9]", Arrays.toString(visible.get(0)));
+ Iterator<int[]> visible = cs.getVisContigsIterator(3, 10);
+ int[] region = visible.next();
+ assertEquals("[3, 9]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
cs.hideColumns(3, 6);
cs.hideColumns(8, 9);
// Test both ends visible region
// start position is inclusive, end position exclusive
- visible = cs.getVisibleContigs(1, 13);
- assertEquals("[1, 2]", Arrays.toString(visible.get(0)));
- assertEquals("[7, 7]", Arrays.toString(visible.get(1)));
- assertEquals("[10, 11]", Arrays.toString(visible.get(2)));
+ visible = cs.getVisContigsIterator(1, 13);
+ region = visible.next();
+ assertEquals("[1, 2]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[7, 7]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[10, 11]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
// Test start hidden, end visible
- visible = cs.getVisibleContigs(4, 14);
- assertEquals("[7, 7]", Arrays.toString(visible.get(0)));
- assertEquals("[10, 11]", Arrays.toString(visible.get(1)));
- assertEquals("[13, 13]", Arrays.toString(visible.get(2)));
+ visible = cs.getVisContigsIterator(4, 14);
+ region = visible.next();
+ assertEquals("[7, 7]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[10, 11]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[13, 13]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
// Test start hidden, end hidden
- visible = cs.getVisibleContigs(3, 10);
- assertEquals("[7, 7]", Arrays.toString(visible.get(0)));
+ visible = cs.getVisContigsIterator(3, 10);
+ region = visible.next();
+ assertEquals("[7, 7]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
// Test start visible, end hidden
- visible = cs.getVisibleContigs(0, 13);
- assertEquals("[0, 2]", Arrays.toString(visible.get(0)));
- assertEquals("[7, 7]", Arrays.toString(visible.get(1)));
- assertEquals("[10, 11]", Arrays.toString(visible.get(2)));
+ visible = cs.getVisContigsIterator(0, 13);
+ region = visible.next();
+ assertEquals("[0, 2]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[7, 7]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[10, 11]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
// Test empty result
- visible = cs.getVisibleContigs(4, 6);
- assertEquals(0, visible.size());
+ visible = cs.getVisContigsIterator(4, 6);
+ assertFalse(visible.hasNext());
}
@Test(groups = { "Functional" })
false);
// confirm that original contigs are as expected
- List<int[]> visible = hidden.getVisibleContigs(0, 25);
- assertEquals("[0, 14]", Arrays.toString(visible.get(0)));
- assertEquals("[18, 24]", Arrays.toString(visible.get(1)));
+ Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25);
+ int[] region = visible.next();
+ assertEquals("[0, 14]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[18, 24]", Arrays.toString(region));
// propagate insertions
HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
view);
// confirm that the contigs have changed to account for the gaps
- visible = result.getVisibleContigs(0, 25);
- assertEquals("[0, 10]", Arrays.toString(visible.get(0)));
- assertEquals("[14, 24]", Arrays.toString(visible.get(1)));
+ visible = result.getVisContigsIterator(0, 25);
+ region = visible.next();
+ assertEquals("[0, 10]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[14, 24]", Arrays.toString(region));
// confirm the alignment has been changed so that the other sequences have
// gaps inserted where the columns are hidden
false);
// confirm that original contigs are as expected
- List<int[]> visible = hidden.getVisibleContigs(0, 20);
- assertEquals("[0, 6]", Arrays.toString(visible.get(0)));
- assertEquals("[11, 19]", Arrays.toString(visible.get(1)));
+ Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20);
+ int[] region = visible.next();
+ assertEquals("[0, 6]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[11, 19]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
// propagate insertions
HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
view);
// confirm that the contigs have changed to account for the gaps
- visible = result.getVisibleContigs(0, 20);
- assertEquals("[0, 4]", Arrays.toString(visible.get(0)));
- assertEquals("[7, 19]", Arrays.toString(visible.get(1)));
+ visible = result.getVisContigsIterator(0, 20);
+ region = visible.next();
+ assertEquals("[0, 4]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[7, 19]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
// confirm the alignment has been changed so that the other sequences have
// gaps inserted where the columns are hidden