import jalview.analysis.AlignmentGenerator;
import jalview.gui.JvOptionPane;
+import jalview.util.Comparison;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.List;
// test that without hidden columns, findColumnNToLeft returns
// position n to left of provided position
- int pos = cs.subtractVisibleColumns(3, 10);
+ long pos = cs.subtractVisibleColumns(3, 10);
assertEquals(7, pos);
// 0 returns same position
public void testGetVisibleContigs()
{
HiddenColumns cs = new HiddenColumns();
+
+ int[] visible = cs.getVisibleContigs(3, 10);
+ assertEquals("[]", Arrays.toString(visible));
+
cs.hideColumns(3, 6);
cs.hideColumns(8, 9);
cs.hideColumns(12, 12);
- // start position is inclusive, end position exclusive:
- int[] visible = cs.getVisibleContigs(1, 13);
+ // 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));
+ // Test start hidden, end visible
visible = cs.getVisibleContigs(4, 14);
assertEquals("[7, 7, 10, 11, 13, 13]", Arrays.toString(visible));
+ // Test start hidden, end hidden
visible = cs.getVisibleContigs(3, 10);
assertEquals("[7, 7]", Arrays.toString(visible));
+ // Test start visible, end hidden
+ visible = cs.getVisibleContigs(0, 13);
+ assertEquals("[0, 2, 7, 7, 10, 11]", Arrays.toString(visible));
+
+ // Test empty result
visible = cs.getVisibleContigs(4, 6);
assertEquals("[]", Arrays.toString(visible));
}
// no hidden columns
assertEquals(
- Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
+ 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.getEnd()) - 1, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
+ 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);
// one
colsel.hideSelectedColumns(0, al.getHiddenColumns());
assertEquals(
- Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 2,
- seq.findIndex(seq.getEnd()) - 2, seq.getStart(),
- seq.getEnd(), seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
+ 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);
cs.hideColumns(1, 3);
cs.hideColumns(6, 11);
assertEquals("-D",
- cs.getVisibleSequenceStrings(0, 5, new SequenceI[] { seq })[0]);
+ cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
+ { seq })[0]);
+
assertEquals(
- Arrays.toString(new int[] { 1, 1, 3, 3,
- seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
+ Arrays.toString(
+ new int[]
+ { 1, seq.findIndex(seq.getStart()) - 1,
+ seq.findIndex(seq.getEnd()) - 1 }),
Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
cs.revealAllHiddenColumns(colsel);
// containing sequence
cs.hideColumns(1, 11);
assertEquals(
- Arrays.toString(new int[] { 0, 1, 0, 0,
- seq.findIndex(seq.getStart()) - 1,
- seq.findIndex(seq.getEnd()) - 1 }),
+ 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));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 4);
+ cs.hideColumns(6, 12);
+ test = cs.locateVisibleBoundsOfSequence(seq);
+ assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
+ Arrays.toString(test));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 1);
+ cs.hideColumns(3, 12);
+ test = cs.locateVisibleBoundsOfSequence(seq);
+ assertEquals(Arrays.toString(new int[] { 0, 1, 11 }),
+ Arrays.toString(test));
+
+ // These tests cover different behaviour to original
+ // locateVisibleBoundsOfSequence
+ // Previously first values of each were 3,9 and 6 respectively.
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(3, 14);
+ cs.hideColumns(17, 19);
+ assertEquals(
+ Arrays.toString(
+ new int[]
+ { 3, seq2.findIndex(seq2.getStart()) - 1,
+ seq2.findIndex(seq2.getEnd()) - 1 }),
+ Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(3, 7);
+ cs.hideColumns(9, 14);
+ cs.hideColumns(17, 19);
+ assertEquals(
+ Arrays.toString(
+ new int[]
+ { 9, seq2.findIndex(seq2.getStart()) - 1,
+ seq2.findIndex(seq2.getEnd()) - 1 }),
+ Arrays.toString(cs.locateVisibleBoundsOfSequence(seq2)));
+
+ cs.revealAllHiddenColumns(colsel);
+ cs.hideColumns(0, 1);
+ cs.hideColumns(3, 4);
+ cs.hideColumns(6, 8);
+ cs.hideColumns(10, 12);
+ test = cs.locateVisibleBoundsOfSequence(seq);
+ assertEquals(Arrays.toString(new int[] { 6, 1, 11 }),
+ Arrays.toString(test));
+
}
@Test(groups = { "Functional" })
public void testLocateVisibleBoundsPathologicals()
{
// test some pathological cases we missed
- AlignmentI al = new Alignment(new SequenceI[] { new Sequence(
- "refseqGaptest", "KTDVTI----------NFI-----G----L") });
+ AlignmentI al = new Alignment(
+ new SequenceI[]
+ { new Sequence("refseqGaptest", "KTDVTI----------NFI-----G----L") });
HiddenColumns cs = new HiddenColumns();
cs.hideInsertionsFor(al.getSequenceAt(0));
- assertEquals(
- "G",
- ""
- + al.getSequenceAt(0).getCharAt(
- cs.adjustForHiddenColumns(9)));
+ assertEquals("G", ""
+ + al.getSequenceAt(0).getCharAt(cs.adjustForHiddenColumns(9)));
}
cs.hideColumns(5, 8);
colsel.addElement(10);
cs.revealHiddenColumns(5, colsel);
- // hidden columns list now null but getter returns empty list:
- assertTrue(cs.getHiddenColumnsCopy().isEmpty());
+
+ // hiddenColumns now empty
+ assertEquals(0, cs.getSize());
+
// revealed columns are marked as selected (added to selection):
assertEquals("[10, 5, 6, 7, 8]", colsel.getSelected().toString());
colsel = new ColumnSelection();
cs = new HiddenColumns();
cs.hideColumns(5, 8);
- List<int[]> hidden = cs.getHiddenColumnsCopy();
+
+ int prevSize = cs.getSize();
cs.revealHiddenColumns(6, colsel);
- assertEquals(hidden.size(), cs.getHiddenColumnsCopy().size());
+ assertEquals(prevSize, cs.getSize());
assertTrue(colsel.getSelected().isEmpty());
}
@Test(groups = { "Functional" })
public void testRevealAllHiddenColumns()
{
- HiddenColumns cs = new HiddenColumns();
+ HiddenColumns hidden = new HiddenColumns();
ColumnSelection colsel = new ColumnSelection();
- cs.hideColumns(5, 8);
- cs.hideColumns(2, 3);
+ hidden.hideColumns(5, 8);
+ hidden.hideColumns(2, 3);
colsel.addElement(11);
colsel.addElement(1);
- cs.revealAllHiddenColumns(colsel);
+ hidden.revealAllHiddenColumns(colsel);
/*
* revealing hidden columns adds them (in order) to the (unordered)
* selection list
*/
- assertTrue(cs.getHiddenColumnsCopy().isEmpty());
- assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", colsel.getSelected()
- .toString());
+
+ // hiddenColumns now empty
+ assertEquals(0, hidden.getSize());
+
+ assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]",
+ colsel.getSelected().toString());
}
@Test(groups = { "Functional" })
}
@Test(groups = { "Functional" })
- public void testGetBitset()
+ public void testMarkHiddenRegions()
{
BitSet toMark, fromMark;
long seed = -3241532;
for (int n = 0; n < 1000; n++)
{
// create a random bitfield
- toMark = BitSet.valueOf(new long[] { number.nextLong(),
- number.nextLong(), number.nextLong() });
+ toMark = BitSet
+ .valueOf(new long[]
+ { number.nextLong(), number.nextLong(), number.nextLong() });
toMark.set(n * number.nextInt(10), n * (25 + number.nextInt(25)));
HiddenColumns hc = new HiddenColumns();
hc.hideMarkedBits(toMark);
}
@Test(groups = "Functional")
- public void getVisibleStartAndEndIndexTest()
+ public void testGetVisibleStartAndEndIndexTest()
{
Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
AlignmentI align = new Alignment(new SequenceI[] { seq });
hc.hideColumns(10, 10);
hc.hideColumns(14, 15);
- result = hc.getRegionWithEdgeAtRes(3);
+ result = hc.getRegionWithEdgeAtRes(2);
assertEquals(3, result[0]);
assertEquals(7, result[1]);
result = hc.getRegionWithEdgeAtRes(6);
assertNull(result);
+
+ result = hc.getRegionWithEdgeAtRes(0);
+ assertNull(result);
+
+ result = hc.getRegionWithEdgeAtRes(7);
+ assertEquals(14, result[0]);
+ assertEquals(15, result[1]);
+
+ result = hc.getRegionWithEdgeAtRes(8);
+ assertEquals(14, result[0]);
+ assertEquals(15, result[1]);
}
@Test(groups = "Functional")
// create an alignment with no gaps - this will be the profile seq and other
// JPRED seqs
AlignmentGenerator gen = new AlignmentGenerator(false);
- AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
+ AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
// get the profileseq
SequenceI profileseq = al.getSequenceAt(0);
gappedseq.insertCharAt(6, al.getGapCharacter());
gappedseq.insertCharAt(7, al.getGapCharacter());
gappedseq.insertCharAt(8, al.getGapCharacter());
-
+
// create an alignment view with the gapped sequence
SequenceI[] seqs = new SequenceI[1];
seqs[0] = gappedseq;
false);
// confirm that original contigs are as expected
- int[] oldcontigs = hidden.getVisibleContigs(0, 20);
- int[] testcontigs = { 0, 14, 18, 19 };
+ int[] oldcontigs = hidden.getVisibleContigs(0, 25);
+ int[] testcontigs = { 0, 14, 18, 24 };
assertTrue(Arrays.equals(oldcontigs, testcontigs));
-
+
// 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);
+ int[] newcontigs = result.getVisibleContigs(0, 25);
testcontigs[1] = 10;
testcontigs[2] = 14;
assertTrue(Arrays.equals(newcontigs, testcontigs));
-
+
+ // confirm the alignment has been changed so that the other sequences have
+ // gaps inserted where the columns are hidden
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
+
+ }
+
+ @Test(groups = "Functional")
+ public void testPropagateInsertionsOverlap()
+ {
+ // test propagateInsertions where gaps and hiddenColumns overlap
+
+ // create an alignment with no gaps - this will be the profile seq and other
+ // JPRED seqs
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
+
+ // get the profileseq
+ SequenceI profileseq = al.getSequenceAt(0);
+ SequenceI gappedseq = new Sequence(profileseq);
+ gappedseq.insertCharAt(5, al.getGapCharacter());
+ gappedseq.insertCharAt(6, al.getGapCharacter());
+ gappedseq.insertCharAt(7, al.getGapCharacter());
+ gappedseq.insertCharAt(8, al.getGapCharacter());
+
+ // create an alignment view with the gapped sequence
+ SequenceI[] seqs = new SequenceI[1];
+ seqs[0] = gappedseq;
+ AlignmentI newal = new Alignment(seqs);
+
+ // hide columns so that some overlap with the gaps
+ HiddenColumns hidden = new HiddenColumns();
+ hidden.hideColumns(7, 10);
+
+ AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+ 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));
+
+ // 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));
+
+ // confirm the alignment has been changed so that the other sequences have
+ // gaps inserted where the columns are hidden
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
}
+
+ @Test(groups = "Functional")
+ public void testHasHiddenColumns()
+ {
+ HiddenColumns h = new HiddenColumns();
+
+ // new HiddenColumns2 has no hidden cols
+ assertFalse(h.hasHiddenColumns());
+
+ // some columns hidden, returns true
+ h.hideColumns(5, 10);
+ assertTrue(h.hasHiddenColumns());
+
+ // reveal columns, no hidden cols again
+ ColumnSelection sel = new ColumnSelection();
+ h.revealAllHiddenColumns(sel);
+ assertFalse(h.hasHiddenColumns());
+ }
+
+ @Test(groups = "Functional")
+ public void testHasManyHiddenColumns()
+ {
+ HiddenColumns h = new HiddenColumns();
+
+ // new HiddenColumns2 has no hidden cols
+ assertFalse(h.hasManyHiddenColumns());
+
+ // one set of columns hidden, returns false
+ h.hideColumns(5, 10);
+ assertFalse(h.hasManyHiddenColumns());
+
+ // two sets hidden, returns true
+ h.hideColumns(15, 17);
+ assertTrue(h.hasManyHiddenColumns());
+
+ // back to one block, asserts false
+ h.hideColumns(11, 14);
+ assertFalse(h.hasManyHiddenColumns());
+ }
+
+ @Test(groups = "Functional")
+ public void testAdjustForHiddenColumns()
+ {
+ HiddenColumns h = new HiddenColumns();
+ // returns input value when there are no hidden columns
+ assertEquals(10, h.adjustForHiddenColumns(10));
+
+ h.hideColumns(20, 30);
+ assertEquals(10, h.adjustForHiddenColumns(10));
+ assertEquals(20 + 11, h.adjustForHiddenColumns(20));
+ assertEquals(35 + 11, h.adjustForHiddenColumns(35));
+
+ h.hideColumns(5, 7);
+ assertEquals(10 + 3, h.adjustForHiddenColumns(10));
+ assertEquals(20 + 14, h.adjustForHiddenColumns(20));
+ assertEquals(35 + 14, h.adjustForHiddenColumns(35));
+
+ ColumnSelection sel = new ColumnSelection();
+ h.revealAllHiddenColumns(sel);
+ h.hideColumns(0, 1);
+ assertEquals(4, h.adjustForHiddenColumns(2));
+ }
+
+ /*@Test(groups = "Functional")
+ public void testCompensateForEdit()
+ {
+ HiddenColumns2 h = new HiddenColumns2();
+
+ ColumnSelection sel = new ColumnSelection();
+ assertNull(h.compensateForEdit(10, 3, sel));
+
+ h.hideColumns(3, 4);
+ List<int[]> result = h.compensateForEdit(10, 3, sel);
+ assertEquals(0, result.size());
+
+ // edit partially overlapping hidden
+
+ h = new HiddenColumns2();
+ h.hideColumns(15, 17);
+ result = h.compensateForEdit(10, 6, sel);
+ assertEquals(0, result.size());
+
+ HiddenColumns2 h2 = new HiddenColumns2();
+ h2.hideColumns(9, 11);
+ assertTrue(h.equals(h2));
+
+ // edit fully overlapping hidden
+
+ h = new HiddenColumns2();
+ h.hideColumns(15, 17);
+ result = h.compensateForEdit(10, 8, sel);
+ assertEquals(result.get(0)[0], 15);
+ assertEquals(result.get(0)[1], 17);
+ assertFalse(h.hasHiddenColumns());
+
+ // edit at start
+
+ h = new HiddenColumns2();
+ h.hideColumns(0, 3);
+ result = h.compensateForEdit(0, 4, sel);
+ assertEquals(0, result.size());
+ assertEquals(sel.getSelected().size(), 4);
+ assertFalse(h.hasHiddenColumns());
+ }*/
+
+ /*@Test(groups = "Functional")
+ public void testCompensateForDelEdits()
+ {
+ HiddenColumns2 h = new HiddenColumns2();
+ HiddenColumns2 h2 = new HiddenColumns2();
+
+ h.compensateForDelEdits(10, 3);
+ assertFalse(h.hasHiddenColumns());
+
+ h = new HiddenColumns2();
+ h.hideColumns(3, 4);
+ h.compensateForDelEdits(10, 3);
+ h2.hideColumns(3, 4);
+ assertTrue(h.equals(h2));
+
+ h = new HiddenColumns2();
+ h.hideColumns(15, 17);
+ h.compensateForDelEdits(10, 6);
+ h2 = new HiddenColumns2();
+ h2.hideColumns(9, 11);
+ assertTrue(h.equals(h2));
+
+ h = new HiddenColumns2();
+ h.hideColumns(15, 17);
+ h.compensateForDelEdits(10, 8);
+ h2 = new HiddenColumns2();
+ h2.hideColumns(7, 9);
+ assertTrue(h.equals(h2));
+
+ h = new HiddenColumns2();
+ h.hideColumns(0, 3);
+ h.compensateForDelEdits(0, 4);
+ h2 = new HiddenColumns2();
+ h2.hideColumns(0, 0);
+ assertTrue(h.equals(h2));
+ }*/
+
+ @Test(groups = "Functional")
+ public void testGetHiddenBoundaryLeft()
+ {
+ HiddenColumns h = new HiddenColumns();
+
+ // returns same value if no hidden cols
+ assertEquals(3, h.getHiddenBoundaryLeft(3));
+
+ h.hideColumns(5, 10);
+ assertEquals(10, h.getHiddenBoundaryLeft(15));
+ assertEquals(3, h.getHiddenBoundaryLeft(3));
+ assertEquals(7, h.getHiddenBoundaryLeft(7));
+
+ h.hideColumns(15, 20);
+ assertEquals(10, h.getHiddenBoundaryLeft(15));
+ assertEquals(20, h.getHiddenBoundaryLeft(21));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetHiddenBoundaryRight()
+ {
+ HiddenColumns h = new HiddenColumns();
+
+ // returns same value if no hidden cols
+ assertEquals(3, h.getHiddenBoundaryRight(3));
+
+ h.hideColumns(5, 10);
+ assertEquals(5, h.getHiddenBoundaryRight(3));
+ assertEquals(15, h.getHiddenBoundaryRight(15));
+ assertEquals(7, h.getHiddenBoundaryRight(7));
+
+ h.hideColumns(15, 20);
+ assertEquals(15, h.getHiddenBoundaryRight(7));
+ assertEquals(15, h.getHiddenBoundaryRight(14));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetHiddenColumnsCopy()
+ {
+ HiddenColumns h = new HiddenColumns();
+ ArrayList<int[]> result = h.getHiddenColumnsCopy();
+ assertTrue(result.isEmpty());
+
+ h.hideColumns(5, 10);
+ result = h.getHiddenColumnsCopy();
+ assertEquals(1, result.size());
+ assertEquals(5, result.get(0)[0]);
+ assertEquals(10, result.get(0)[1]);
+
+ 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]);
+
+ // 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]);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetVisibleSequenceStrings()
+ {
+ HiddenColumns h = new HiddenColumns();
+ SequenceI seq1 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
+ SequenceI seq2 = new Sequence("TEST2", "VICYHRNDTGA");
+ SequenceI[] seqs = new SequenceI[2];
+ seqs[0] = seq1;
+ seqs[1] = seq2;
+ String[] result = h.getVisibleSequenceStrings(5, 10, seqs);
+ assertEquals(2, result.length);
+ assertEquals("WKQES", result[0]);
+ assertEquals("RNDTG", result[1]);
+
+ h.hideColumns(6, 8);
+ result = h.getVisibleSequenceStrings(5, 10, seqs);
+ assertEquals(2, result.length);
+ assertEquals("WS", result[0]);
+ assertEquals("RG", result[1]);
+
+ SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
+ ColumnSelection sel = new ColumnSelection();
+ h.revealAllHiddenColumns(sel);
+ h.hideColumns(1, 3);
+ h.hideColumns(6, 11);
+ assertEquals("-D",
+ h.getVisibleSequenceStrings(0, 5, new SequenceI[]
+ { seq })[0]);
+ }
+
+ @Test(groups = "Functional")
+ public void testHideInsertionsFor()
+ {
+ HiddenColumns h = new HiddenColumns();
+ HiddenColumns h2 = new HiddenColumns();
+ SequenceI seq1 = new Sequence("TEST1", "GAL---MFW-KQESPVICY--HRNDT");
+ SequenceI seq2 = new Sequence("TEST1", "GALMFWKQESPVICYHRNDT");
+
+ h.hideInsertionsFor(seq2);
+ assertTrue(h.equals(h2));
+
+ h.hideInsertionsFor(seq1);
+ h2.hideColumns(3, 5);
+ h2.hideColumns(9, 9);
+ h2.hideColumns(19, 20);
+ assertTrue(h.equals(h2));
+ }
+
+ @Test(groups = "Functional")
+ public void testHideMarkedBits()
+ {
+ HiddenColumns h = new HiddenColumns();
+ HiddenColumns h2 = new HiddenColumns();
+
+ BitSet tohide = new BitSet(21);
+ h.hideMarkedBits(tohide);
+ assertTrue(h.equals(h2));
+
+ // NB in hideMarkedBits, the last bit is not set to hidden
+ tohide.set(3, 6);
+ tohide.set(9);
+ tohide.set(19, 21);
+ h.hideMarkedBits(tohide);
+
+ h2.hideColumns(3, 5);
+ h2.hideColumns(9, 9);
+ h2.hideColumns(19, 20);
+ assertTrue(h.equals(h2));
+ }
+
+ @Test(groups = "Functional")
+ public void testMakeVisibleAnnotation()
+ {
+ HiddenColumns h = new HiddenColumns();
+ Annotation[] anns = new Annotation[] { null, null, new Annotation(1),
+ new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+ new Annotation(5), new Annotation(6), new Annotation(7),
+ new Annotation(8) };
+ AlignmentAnnotation ann = new AlignmentAnnotation("an", "some an",
+ anns);
+
+ // without hidden cols, just truncates
+ h.makeVisibleAnnotation(3, 5, ann);
+ assertEquals(3, ann.annotations.length);
+ assertEquals(2.0f, ann.annotations[0].value);
+ assertEquals(3.0f, ann.annotations[1].value);
+ assertNull(ann.annotations[2]);
+
+ anns = new Annotation[] { null, null, new Annotation(1),
+ new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+ new Annotation(5), new Annotation(6), new Annotation(7),
+ new Annotation(8) };
+ ann = new AlignmentAnnotation("an", "some an", anns);
+ h.hideColumns(4, 7);
+ h.makeVisibleAnnotation(1, 9, ann);
+ assertEquals(5, ann.annotations.length);
+ assertNull(ann.annotations[0]);
+ assertEquals(1.0f, ann.annotations[1].value);
+ assertEquals(2.0f, ann.annotations[2].value);
+ assertEquals(5.0f, ann.annotations[3].value);
+ assertEquals(6.0f, ann.annotations[4].value);
+
+ anns = new Annotation[] { null, null, new Annotation(1),
+ new Annotation(2), new Annotation(3), null, null, new Annotation(4),
+ new Annotation(5), new Annotation(6), new Annotation(7),
+ new Annotation(8) };
+ ann = new AlignmentAnnotation("an", "some an", anns);
+ h.hideColumns(1, 2);
+ h.makeVisibleAnnotation(1, 9, ann);
+ assertEquals(3, ann.annotations.length);
+ assertEquals(2.0f, ann.annotations[0].value);
+ assertEquals(5.0f, ann.annotations[1].value);
+ assertEquals(6.0f, ann.annotations[2].value);
+ }
+
+ @Test(groups = "Functional")
+ public void testSubtractVisibleColumns()
+ {
+ HiddenColumns h = new HiddenColumns();
+ int result = h.subtractVisibleColumns(1, 10);
+ assertEquals(9, result);
+
+ h.hideColumns(7, 9);
+ result = h.subtractVisibleColumns(4, 10);
+ assertEquals(3, result);
+
+ h.hideColumns(14, 15);
+ result = h.subtractVisibleColumns(4, 10);
+ assertEquals(3, result);
+
+ result = h.subtractVisibleColumns(10, 17);
+ assertEquals(2, result);
+
+ result = h.subtractVisibleColumns(1, 7);
+ assertEquals(5, result);
+
+ result = h.subtractVisibleColumns(1, 8);
+ assertEquals(5, result);
+
+ result = h.subtractVisibleColumns(3, 15);
+ assertEquals(10, result);
+
+ ColumnSelection sel = new ColumnSelection();
+ h.revealAllHiddenColumns(sel);
+ h.hideColumns(0, 30);
+ result = h.subtractVisibleColumns(31, 13);
+ assertEquals(-18, result);
+
+ result = h.subtractVisibleColumns(31, 0);
+ assertEquals(-31, result);
+
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff