*/
package jalview.datamodel;
+import static org.testng.Assert.assertNull;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import jalview.analysis.AlignmentGenerator;
import jalview.gui.JvOptionPane;
import java.util.Arrays;
+import java.util.BitSet;
import java.util.List;
+import java.util.Random;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
}
/**
+ * Test the method which counts the number of hidden columns
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSize()
+ {
+ HiddenColumns hidden = new HiddenColumns();
+ assertEquals(0, hidden.getSize());
+
+ hidden.hideColumns(3, 5);
+ assertEquals(3, hidden.getSize());
+
+ hidden.hideColumns(8, 8);
+ assertEquals(4, hidden.getSize());
+
+ hidden.hideColumns(9, 14);
+ assertEquals(10, hidden.getSize());
+
+ ColumnSelection cs = new ColumnSelection();
+ hidden.revealAllHiddenColumns(cs);
+ assertEquals(0, hidden.getSize());
+ }
+
+ /**
* Test the method that finds the visible column position of an alignment
* column, allowing for hidden columns.
*/
HiddenColumns cs = new HiddenColumns();
cs.hideColumns(10, 11);
cs.hideColumns(5, 7);
- assertEquals("[5, 7]", Arrays.toString(cs.getListOfCols().get(0)));
+ assertEquals("[5, 7]",
+ Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0)));
HiddenColumns cs2 = new HiddenColumns(cs);
assertTrue(cs2.hasHiddenColumns());
- assertEquals(2, cs2.getListOfCols().size());
+ assertEquals(2, cs2.getHiddenColumnsCopyAsList().size());
// hidden columns are held in column order
- assertEquals("[5, 7]", Arrays.toString(cs2.getListOfCols().get(0)));
- assertEquals("[10, 11]", Arrays.toString(cs2.getListOfCols().get(1)));
+ assertEquals("[5, 7]",
+ Arrays.toString(cs2.getHiddenColumnsCopyAsList().get(0)));
+ assertEquals("[10, 11]",
+ Arrays.toString(cs2.getHiddenColumnsCopyAsList().get(1)));
}
/**
Arrays.toString(cs.locateVisibleBoundsOfSequence(seq)));
// hidden column on gap after end of sequence - should not affect bounds
- colsel.hideSelectedColumns(13, al);
+ colsel.hideSelectedColumns(13, al.getHiddenColumns());
assertEquals(
Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 1,
seq.findIndex(seq.getEnd()) - 1, seq.getStart(),
cs.revealAllHiddenColumns(colsel);
// hidden column on gap before beginning of sequence - should vis bounds by
// one
- colsel.hideSelectedColumns(0, al);
+ colsel.hideSelectedColumns(0, al.getHiddenColumns());
assertEquals(
Arrays.toString(new int[] { seq.findIndex(seq.getStart()) - 2,
seq.findIndex(seq.getEnd()) - 2, seq.getStart(),
ColumnSelection colsel = new ColumnSelection();
HiddenColumns cs = al.getHiddenColumns();
- colsel.hideSelectedColumns(5, al);
- List<int[]> hidden = cs.getListOfCols();
+ colsel.hideSelectedColumns(5, al.getHiddenColumns());
+ List<int[]> hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
assertEquals("[5, 5]", Arrays.toString(hidden.get(0)));
- colsel.hideSelectedColumns(3, al);
+ colsel.hideSelectedColumns(3, al.getHiddenColumns());
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(2, hidden.size());
// two hidden ranges, in order:
- assertSame(hidden, cs.getListOfCols());
+ assertEquals(hidden.size(), cs.getHiddenColumnsCopyAsList().size());
assertEquals("[3, 3]", Arrays.toString(hidden.get(0)));
assertEquals("[5, 5]", Arrays.toString(hidden.get(1)));
// hiding column 4 expands [3, 3] to [3, 4]
// and merges to [5, 5] to make [3, 5]
- colsel.hideSelectedColumns(4, al);
- hidden = cs.getListOfCols();
+ colsel.hideSelectedColumns(4, al.getHiddenColumns());
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
assertEquals("[3, 5]", Arrays.toString(hidden.get(0)));
// 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.getListOfCols().isEmpty());
+ assertTrue(cs.getHiddenColumnsCopyAsList().isEmpty());
cs.hideColumns(3, 6);
- hidden = cs.getListOfCols();
+ hidden = cs.getHiddenColumnsCopyAsList();
int[] firstHiddenRange = hidden.get(0);
assertEquals("[3, 6]", Arrays.toString(firstHiddenRange));
// adding a subrange of already hidden should do nothing
cs.hideColumns(4, 5);
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
- assertSame(firstHiddenRange, cs.getListOfCols().get(0));
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0)));
cs.hideColumns(3, 5);
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
- assertSame(firstHiddenRange, cs.getListOfCols().get(0));
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0)));
cs.hideColumns(4, 6);
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
- assertSame(firstHiddenRange, cs.getListOfCols().get(0));
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0)));
cs.hideColumns(3, 6);
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
- assertSame(firstHiddenRange, cs.getListOfCols().get(0));
+ assertEquals("[3, 6]",
+ Arrays.toString(cs.getHiddenColumnsCopyAsList().get(0)));
cs.revealAllHiddenColumns(colsel);
cs.hideColumns(2, 4);
- hidden = cs.getListOfCols();
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
assertEquals("[2, 4]", Arrays.toString(hidden.get(0)));
// extend contiguous with 2 positions overlap
cs.hideColumns(3, 5);
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
assertEquals("[2, 5]", Arrays.toString(hidden.get(0)));
// extend contiguous with 1 position overlap
cs.hideColumns(5, 6);
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
assertEquals("[2, 6]", Arrays.toString(hidden.get(0)));
// extend contiguous with overlap both ends:
cs.hideColumns(1, 7);
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
assertEquals("[1, 7]", Arrays.toString(hidden.get(0)));
}
colsel.addElement(10);
cs.revealHiddenColumns(5, colsel);
// hidden columns list now null but getter returns empty list:
- assertTrue(cs.getListOfCols().isEmpty());
+ assertTrue(cs.getHiddenColumnsCopyAsList().isEmpty());
// 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.getListOfCols();
+ List<int[]> hidden = cs.getHiddenColumnsCopyAsList();
cs.revealHiddenColumns(6, colsel);
- assertSame(hidden, cs.getListOfCols());
+ assertEquals(hidden.size(), cs.getHiddenColumnsCopyAsList().size());
assertTrue(colsel.getSelected().isEmpty());
}
* revealing hidden columns adds them (in order) to the (unordered)
* selection list
*/
- assertTrue(cs.getListOfCols().isEmpty());
+ assertTrue(cs.getHiddenColumnsCopyAsList().isEmpty());
assertEquals("[11, 1, 2, 3, 5, 6, 7, 8]", colsel.getSelected()
.toString());
}
HiddenColumns cs = new HiddenColumns();
cs.hideColumns(49, 59);
cs.hideColumns(69, 79);
- List<int[]> hidden = cs.getListOfCols();
+ List<int[]> hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(2, hidden.size());
assertEquals("[49, 59]", Arrays.toString(hidden.get(0)));
assertEquals("[69, 79]", Arrays.toString(hidden.get(1)));
cs.hideColumns(48, 80);
- hidden = cs.getListOfCols();
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
assertEquals("[48, 80]", Arrays.toString(hidden.get(0)));
cs.hideColumns(50, 60);
// hiding 21-49 should merge to one range
cs.hideColumns(21, 49);
- hidden = cs.getListOfCols();
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(1, hidden.size());
assertEquals("[10, 60]", Arrays.toString(hidden.get(0)));
cs.hideColumns(60, 70);
cs.hideColumns(15, 45);
- hidden = cs.getListOfCols();
+ hidden = cs.getHiddenColumnsCopyAsList();
assertEquals(2, hidden.size());
assertEquals("[10, 50]", Arrays.toString(hidden.get(0)));
assertEquals("[60, 70]", Arrays.toString(hidden.get(1)));
}
+ @Test(groups = { "Functional" })
+ public void testHideBitset()
+ {
+ HiddenColumns cs;
+
+ BitSet one = new BitSet();
+
+ // one hidden range
+ one.set(1);
+ cs = new HiddenColumns();
+ cs.hideMarkedBits(one);
+ assertEquals(1, cs.getHiddenColumnsCopyAsList().size());
+
+ one.set(2);
+ cs = new HiddenColumns();
+ cs.hideMarkedBits(one);
+ assertEquals(1, cs.getHiddenColumnsCopyAsList().size());
+
+ one.set(3);
+ cs = new HiddenColumns();
+ cs.hideMarkedBits(one);
+ assertEquals(1, cs.getHiddenColumnsCopyAsList().size());
+
+ // split
+ one.clear(2);
+ cs = new HiddenColumns();
+ cs.hideMarkedBits(one);
+ assertEquals(2, cs.getHiddenColumnsCopyAsList().size());
+
+ assertEquals(0, cs.adjustForHiddenColumns(0));
+ assertEquals(2, cs.adjustForHiddenColumns(1));
+ assertEquals(4, cs.adjustForHiddenColumns(2));
+
+ // one again
+ one.clear(1);
+ cs = new HiddenColumns();
+ cs.hideMarkedBits(one);
+
+ assertEquals(1, cs.getHiddenColumnsCopyAsList().size());
+
+ assertEquals(0, cs.adjustForHiddenColumns(0));
+ assertEquals(1, cs.adjustForHiddenColumns(1));
+ assertEquals(2, cs.adjustForHiddenColumns(2));
+ assertEquals(4, cs.adjustForHiddenColumns(3));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetBitset()
+ {
+ BitSet toMark, fromMark;
+ long seed = -3241532;
+ Random number = new Random(seed);
+ for (int n = 0; n < 1000; n++)
+ {
+ // create a random bitfield
+ 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);
+
+ // see if we can recover bitfield
+ hc.markHiddenRegions(fromMark = new BitSet());
+ assertEquals(toMark, fromMark);
+ }
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFindHiddenRegionPositions()
+ {
+ HiddenColumns hc = new HiddenColumns();
+
+ List<Integer> positions = hc.findHiddenRegionPositions();
+ assertTrue(positions.isEmpty());
+
+ hc.hideColumns(3, 7);
+ hc.hideColumns(10, 10);
+ hc.hideColumns(14, 15);
+
+ positions = hc.findHiddenRegionPositions();
+ assertEquals(3, positions.size());
+ assertEquals(3, positions.get(0).intValue());
+ assertEquals(5, positions.get(1).intValue());
+ assertEquals(8, positions.get(2).intValue());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testRegionsToString()
+ {
+ HiddenColumns hc = new HiddenColumns();
+
+ String result = hc.regionsToString(",", "--");
+ assertEquals("", result);
+
+ hc.hideColumns(3, 7);
+ hc.hideColumns(10, 10);
+ hc.hideColumns(14, 15);
+
+ result = hc.regionsToString(",", "--");
+ assertEquals("3--7,10--10,14--15", result);
+ }
+
+ @Test(groups = "Functional")
+ public void getVisibleStartAndEndIndexTest()
+ {
+ Sequence seq = new Sequence("testSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+ AlignmentI align = new Alignment(new SequenceI[] { seq });
+ HiddenColumns hc = new HiddenColumns();
+
+ int[] startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+ assertEquals(0, startEnd[0]);
+ assertEquals(25, startEnd[1]);
+
+ hc.hideColumns(0, 0);
+ startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+ assertEquals(1, startEnd[0]);
+ assertEquals(25, startEnd[1]);
+
+ hc.hideColumns(6, 9);
+ hc.hideColumns(11, 12);
+ startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+ assertEquals(1, startEnd[0]);
+ assertEquals(25, startEnd[1]);
+
+ hc.hideColumns(24, 25);
+ startEnd = hc.getVisibleStartAndEndIndex(align.getWidth());
+ System.out.println(startEnd[0] + " : " + startEnd[1]);
+ assertEquals(1, startEnd[0]);
+ assertEquals(23, startEnd[1]);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetRegionWithEdgeAtRes()
+ {
+ HiddenColumns hc = new HiddenColumns();
+
+ int[] result = hc.getRegionWithEdgeAtRes(5);
+ assertNull(result);
+
+ hc.hideColumns(3, 7);
+ hc.hideColumns(10, 10);
+ hc.hideColumns(14, 15);
+
+ result = hc.getRegionWithEdgeAtRes(3);
+ assertEquals(3, result[0]);
+ assertEquals(7, result[1]);
+
+ result = hc.getRegionWithEdgeAtRes(5);
+ assertEquals(10, result[0]);
+ assertEquals(10, result[1]);
+
+ result = hc.getRegionWithEdgeAtRes(6);
+ assertNull(result);
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff