import jalview.gui.JvOptionPane;
import jalview.util.Comparison;
-import java.util.ArrayList;
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();
- int[] visible = cs.getVisibleContigs(3, 10);
- assertEquals("[3, 9]", Arrays.toString(visible));
+ 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, 7, 7, 10, 11]", Arrays.toString(visible));
+ 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, 10, 11, 13, 13]", Arrays.toString(visible));
+ 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));
+ 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, 7, 7, 10, 11]", Arrays.toString(visible));
+ 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("[]", Arrays.toString(visible));
+ visible = cs.getVisContigsIterator(4, 6);
+ assertFalse(visible.hasNext());
}
@Test(groups = { "Functional" })
HiddenColumns cs = new HiddenColumns();
cs.hideColumns(10, 11);
cs.hideColumns(5, 7);
+ Iterator<int[]> regions = cs.iterator();
assertEquals("[5, 7]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
HiddenColumns cs2 = new HiddenColumns(cs);
+ regions = cs2.iterator();
assertTrue(cs2.hasHiddenColumns());
- assertEquals(2, cs2.getHiddenColumnsCopy().size());
+ assertEquals(2, cs2.getNumberOfRegions());
// hidden columns are held in column order
assertEquals("[5, 7]",
- Arrays.toString(cs2.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
assertEquals("[10, 11]",
- Arrays.toString(cs2.getHiddenColumnsCopy().get(1)));
+ Arrays.toString(regions.next()));
+ }
+
+ @Test(groups = "Functional")
+ public void testCopyConstructor2()
+ {
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideColumns(10, 11);
+ cs.hideColumns(5, 7);
+
+ HiddenColumns cs2 = new HiddenColumns(cs, 3, 9, 1);
+ assertTrue(cs2.hasHiddenColumns());
+ Iterator<int[]> regions = cs2.iterator();
+
+ // only [5,7] returned, offset by 1
+ assertEquals("[4, 6]",
+ Arrays.toString(regions.next()));
+ assertEquals(3, cs2.getSize());
+
+ cs2 = new HiddenColumns(cs, 8, 15, 4);
+ regions = cs2.iterator();
+ assertTrue(cs2.hasHiddenColumns());
+
+ // only [10,11] returned, offset by 4
+ assertEquals("[6, 7]",
+ Arrays.toString(regions.next()));
+ assertEquals(2, cs2.getSize());
+
+ cs2 = new HiddenColumns(cs, 6, 10, 4);
+ assertFalse(cs2.hasHiddenColumns());
}
/**
ColumnSelection colsel = new ColumnSelection();
HiddenColumns cs = al.getHiddenColumns();
colsel.hideSelectedColumns(5, al.getHiddenColumns());
- List<int[]> hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
+ Iterator<int[]> regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[5, 5]", Arrays.toString(regions.next()));
colsel.hideSelectedColumns(3, al.getHiddenColumns());
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(2, hidden.size());
+ regions = cs.iterator();
+ assertEquals(2, cs.getNumberOfRegions());
// two hidden ranges, in order:
- assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
- assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
- assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
+ assertEquals("[3, 3]", Arrays.toString(regions.next()));
+ assertEquals("[5, 5]", Arrays.toString(regions.next()));
// hiding column 4 expands [3, 3] to [3, 4]
// and merges to [5, 5] to make [3, 5]
colsel.hideSelectedColumns(4, al.getHiddenColumns());
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[3, 5]", Arrays.toString(regions.next()));
// clear hidden columns (note they are added to selected)
cs.revealAllHiddenColumns(colsel);
// it is now actually null but getter returns an empty list
- assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+ assertEquals(0, cs.getNumberOfRegions());
cs.hideColumns(3, 6);
- hidden = cs.getHiddenColumnsCopy();
- int[] firstHiddenRange = hidden.get(0);
+ regions = cs.iterator();
+ int[] firstHiddenRange = regions.next();
assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
// adding a subrange of already hidden should do nothing
cs.hideColumns(4, 5);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
cs.hideColumns(3, 5);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
cs.hideColumns(4, 6);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
cs.hideColumns(3, 6);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals("[3, 6]",
- Arrays.toString(cs.getHiddenColumnsCopy().get(0)));
+ Arrays.toString(regions.next()));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(2, 4);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[2, 4]", Arrays.toString(regions.next()));
// extend contiguous with 2 positions overlap
cs.hideColumns(3, 5);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[2, 5]", Arrays.toString(regions.next()));
// extend contiguous with 1 position overlap
cs.hideColumns(5, 6);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[2, 6]", Arrays.toString(regions.next()));
// extend contiguous with overlap both ends:
cs.hideColumns(1, 7);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[1, 7]", Arrays.toString(regions.next()));
}
/**
HiddenColumns cs = new HiddenColumns();
cs.hideColumns(49, 59);
cs.hideColumns(69, 79);
- List<int[]> hidden = cs.getHiddenColumnsCopy();
- assertEquals(2, hidden.size());
- assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
- assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));
+ Iterator<int[]> regions = cs.iterator();
+ assertEquals(2, cs.getNumberOfRegions());
+ assertEquals("[49, 59]", Arrays.toString(regions.next()));
+ assertEquals("[69, 79]", Arrays.toString(regions.next()));
cs.hideColumns(48, 80);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[48, 80]", Arrays.toString(regions.next()));
/*
* another...joining hidden ranges
cs.hideColumns(50, 60);
// hiding 21-49 should merge to one range
cs.hideColumns(21, 49);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(1, hidden.size());
- assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
+ regions = cs.iterator();
+ assertEquals(1, cs.getNumberOfRegions());
+ assertEquals("[10, 60]", Arrays.toString(regions.next()));
/*
* another...left overlap, subsumption, right overlap,
cs.hideColumns(60, 70);
cs.hideColumns(15, 45);
- hidden = cs.getHiddenColumnsCopy();
- assertEquals(2, hidden.size());
- assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
- assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
+ regions = cs.iterator();
+ assertEquals(2, cs.getNumberOfRegions());
+ assertEquals("[10, 50]", Arrays.toString(regions.next()));
+ assertEquals("[60, 70]", Arrays.toString(regions.next()));
}
@Test(groups = { "Functional" })
one.set(1);
cs = new HiddenColumns();
cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ assertEquals(1, cs.getNumberOfRegions());
one.set(2);
cs = new HiddenColumns();
cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ assertEquals(1, cs.getNumberOfRegions());
one.set(3);
cs = new HiddenColumns();
cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ assertEquals(1, cs.getNumberOfRegions());
// split
one.clear(2);
cs = new HiddenColumns();
cs.hideMarkedBits(one);
- assertEquals(2, cs.getHiddenColumnsCopy().size());
+ assertEquals(2, cs.getNumberOfRegions());
assertEquals(0, cs.adjustForHiddenColumns(0));
assertEquals(2, cs.adjustForHiddenColumns(1));
cs = new HiddenColumns();
cs.hideMarkedBits(one);
- assertEquals(1, cs.getHiddenColumnsCopy().size());
+ assertEquals(1, cs.getNumberOfRegions());
assertEquals(0, cs.adjustForHiddenColumns(0));
assertEquals(1, cs.adjustForHiddenColumns(1));
}
@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
- int[] oldcontigs = hidden.getVisibleContigs(0, 25);
- int[] testcontigs = { 0, 14, 18, 24 };
- assertTrue(Arrays.equals(oldcontigs, testcontigs));
+ 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
- int[] newcontigs = result.getVisibleContigs(0, 25);
- testcontigs[1] = 10;
- testcontigs[2] = 14;
- assertTrue(Arrays.equals(newcontigs, testcontigs));
+ 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
- int[] oldcontigs = hidden.getVisibleContigs(0, 20);
- int[] testcontigs = { 0, 6, 11, 19 };
- assertTrue(Arrays.equals(oldcontigs, testcontigs));
+ 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
- int[] newcontigs = result.getVisibleContigs(0, 20);
- testcontigs[1] = 4;
- testcontigs[2] = 7;
- assertTrue(Arrays.equals(newcontigs, testcontigs));
+ 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
}
@Test(groups = "Functional")
- public void testGetHiddenColumnsCopy()
+ public void testIterator()
{
HiddenColumns h = new HiddenColumns();
- ArrayList<int[]> result = h.getHiddenColumnsCopy();
- assertTrue(result.isEmpty());
+ Iterator<int[]> result = h.iterator();
+ assertFalse(result.hasNext());
h.hideColumns(5, 10);
- result = h.getHiddenColumnsCopy();
- assertEquals(1, result.size());
- assertEquals(5, result.get(0)[0]);
- assertEquals(10, result.get(0)[1]);
+ result = h.iterator();
+ int[] next = result.next();
+ assertEquals(5, next[0]);
+ assertEquals(10, next[1]);
+ assertFalse(result.hasNext());
h.hideColumns(22, 23);
- result = h.getHiddenColumnsCopy();
- assertEquals(2, result.size());
- assertEquals(5, result.get(0)[0]);
- assertEquals(10, result.get(0)[1]);
- assertEquals(22, result.get(1)[0]);
- assertEquals(23, result.get(1)[1]);
+ result = h.iterator();
+ next = result.next();
+ assertEquals(5, next[0]);
+ assertEquals(10, next[1]);
+ next = result.next();
+ assertEquals(22, next[0]);
+ assertEquals(23, next[1]);
+ assertFalse(result.hasNext());
// test for only one hidden region at start of alignment
ColumnSelection sel = new ColumnSelection();
h.revealAllHiddenColumns(sel);
h.hideColumns(0, 1);
- result = h.getHiddenColumnsCopy();
- assertEquals(1, result.size());
- assertEquals(0, result.get(0)[0]);
- assertEquals(1, result.get(0)[1]);
+ result = h.iterator();
+ next = result.next();
+ assertEquals(0, next[0]);
+ assertEquals(1, next[1]);
+ assertFalse(result.hasNext());
}
@Test(groups = "Functional")
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);
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