import java.util.Arrays;
import java.util.BitSet;
import java.util.Iterator;
-import java.util.List;
import java.util.Random;
import org.testng.annotations.BeforeClass;
}
@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" })
}
@Test(groups = { "Functional" })
- public void testFindHiddenRegionPositions()
- {
- HiddenColumns hc = new HiddenColumns();
-
- List<Integer> positions = hc.findHiddenRegionPositions(0, 20);
- assertTrue(positions.isEmpty());
-
- hc.hideColumns(3, 7);
- hc.hideColumns(10, 10);
- hc.hideColumns(14, 15);
-
- positions = hc.findHiddenRegionPositions(0, 20);
- assertEquals(3, positions.size());
- assertEquals(3, positions.get(0).intValue());
- assertEquals(5, positions.get(1).intValue());
- assertEquals(8, positions.get(2).intValue());
-
- positions = hc.findHiddenRegionPositions(7, 20);
- assertEquals(2, positions.size());
- assertEquals(5, positions.get(0).intValue());
- assertEquals(8, positions.get(1).intValue());
-
- positions = hc.findHiddenRegionPositions(11, 13);
- assertEquals(0, positions.size());
-
- positions = hc.findHiddenRegionPositions(7, 20);
- assertEquals(2, positions.size());
- assertEquals(5, positions.get(0).intValue());
- assertEquals(8, positions.get(1).intValue());
-
- positions = hc.findHiddenRegionPositions(0, 1);
- assertEquals(0, positions.size());
-
- positions = hc.findHiddenRegionPositions(17, 20);
- assertEquals(0, positions.size());
-
- positions = hc.findHiddenRegionPositions(10, 15);
- assertEquals(2, positions.size());
- assertEquals(5, positions.get(0).intValue());
- assertEquals(8, positions.get(1).intValue());
- }
-
- @Test(groups = { "Functional" })
public void testRegionsToString()
{
HiddenColumns hc = new HiddenColumns();
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
public void testBoundedIterator()
{
HiddenColumns h = new HiddenColumns();
- Iterator<int[]> it = h.getBoundedIterator(0, 10, false);
+ Iterator<int[]> it = h.getBoundedIterator(0, 10);
// no hidden columns = nothing to iterate over
assertFalse(it.hasNext());
// all regions are returned
h.hideColumns(3, 10);
h.hideColumns(14, 16);
- it = h.getBoundedIterator(0, 20, false);
+ it = h.getBoundedIterator(0, 20);
assertTrue(it.hasNext());
int[] next = it.next();
assertEquals(3, next[0]);
// [start,end] overlaps a region
// 1 region returned
- it = h.getBoundedIterator(5, 7, false);
+ it = h.getBoundedIterator(5, 7);
assertTrue(it.hasNext());
next = it.next();
assertEquals(3, next[0]);
// [start,end] fully contains 1 region and start of last
// - 2 regions returned
- it = h.getBoundedIterator(3, 15, false);
+ it = h.getBoundedIterator(3, 15);
assertTrue(it.hasNext());
next = it.next();
assertEquals(3, next[0]);
// [start,end] contains end of first region and whole of last region
// - 2 regions returned
- it = h.getBoundedIterator(4, 20, false);
+ it = h.getBoundedIterator(4, 20);
assertTrue(it.hasNext());
next = it.next();
assertEquals(3, next[0]);
public void testBoundedStartIterator()
{
HiddenColumns h = new HiddenColumns();
- Iterator<Integer> it = h.getBoundedStartIterator(0, 10, false);
+ Iterator<Integer> it = h.getBoundedStartIterator(0, 10);
// no hidden columns = nothing to iterate over
assertFalse(it.hasNext());
// all regions are returned
h.hideColumns(3, 10);
h.hideColumns(14, 16);
- it = h.getBoundedStartIterator(0, 20, false);
+ it = h.getBoundedStartIterator(0, 20);
assertTrue(it.hasNext());
int next = it.next();
assertEquals(3, next);
// [start,end] does not contain a start of a region
// no regions to iterate over
- it = h.getBoundedStartIterator(4, 5, false);
+ it = h.getBoundedStartIterator(4, 5);
assertFalse(it.hasNext());
// [start,end] fully contains 1 region and start of last
// - 2 regions returned
- it = h.getBoundedStartIterator(3, 7, false);
+ it = h.getBoundedStartIterator(3, 7);
assertTrue(it.hasNext());
next = it.next();
assertEquals(3, next);
// [start,end] contains whole of last region
// - 1 region returned
- it = h.getBoundedStartIterator(4, 20, false);
+ it = h.getBoundedStartIterator(4, 20);
assertTrue(it.hasNext());
next = it.next();
assertEquals(6, next);
assertFalse(it.hasNext());
}
-
- @Test(groups = "Functional")
- public void testVisRegionsIterator()
- {
- HiddenColumns h = new HiddenColumns();
- Iterator<int[]> it = h.getBoundedVisRegionIterator(0, 15);
-
- // no hidden columns = single visible contig
- assertTrue(it.hasNext());
- assertEquals("[0, 15]", Arrays.toString(it.next()));
-
- // hidden column region at start
- h.hideColumns(0, 5);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertTrue(it.hasNext());
- assertEquals("[6, 15]", Arrays.toString(it.next()));
-
- // hidden column region at end
- h = new HiddenColumns();
- h.hideColumns(8, 15);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertTrue(it.hasNext());
- assertEquals("[0, 7]", Arrays.toString(it.next()));
-
- // hidden column region across whole region
- h = new HiddenColumns();
- h.hideColumns(0, 20);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertFalse(it.hasNext());
-
- // hidden column region in middle
- h = new HiddenColumns();
- h.hideColumns(1, 14);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertTrue(it.hasNext());
- assertEquals("[0, 0]", Arrays.toString(it.next()));
- assertTrue(it.hasNext());
- assertEquals("[15, 15]", Arrays.toString(it.next()));
-
- // hidden column region just off either end
- h = new HiddenColumns();
- h.hideColumns(3, 14);
- it = h.getBoundedVisRegionIterator(4, 13);
- assertFalse(it.hasNext());
-
- // multiple regions
- h = new HiddenColumns();
- h.hideColumns(3, 5);
- h.hideColumns(7, 11);
- h.hideColumns(14, 19);
- h.hideColumns(24, 25);
- h.hideColumns(35, 39);
- it = h.getBoundedVisRegionIterator(8, 26);
- assertTrue(it.hasNext());
- assertEquals("[12, 13]", Arrays.toString(it.next()));
- assertTrue(it.hasNext());
- assertEquals("[20, 23]", Arrays.toString(it.next()));
- assertTrue(it.hasNext());
- assertEquals("[26, 26]", Arrays.toString(it.next()));
- assertFalse(it.hasNext());
- }
}
git://source.jalview.org / jalview.git / blobdiff