+ * Test the method that hides a specified column including any adjacent
+ * selected columns. This is a convenience method for the case where multiple
+ * column regions are selected and then hidden using menu option View | Hide |
+ * Selected Columns.
+ */
+ @Test(groups = { "Functional" })
+ public void testHideColumns_withSelection()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+ ColumnSelection cs = new ColumnSelection();
+ // select columns 4-6
+ cs.addElement(4);
+ cs.addElement(5);
+ cs.addElement(6);
+ // hide column 5 (and adjacent):
+ cs.hideSelectedColumns(5, al.getHiddenColumns());
+ // 4,5,6 now hidden:
+ Iterator<int[]> regions = al.getHiddenColumns().iterator();
+ assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+ assertEquals("[4, 6]", Arrays.toString(regions.next()));
+ // none now selected:
+ assertTrue(cs.getSelected().isEmpty());
+
+ // repeat, hiding column 4 (5 and 6)
+ al = gen.generate(50, 20, 123, 5, 5);
+ cs = new ColumnSelection();
+ cs.addElement(4);
+ cs.addElement(5);
+ cs.addElement(6);
+ cs.hideSelectedColumns(4, al.getHiddenColumns());
+ regions = al.getHiddenColumns().iterator();
+ assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+ assertEquals("[4, 6]", Arrays.toString(regions.next()));
+ assertTrue(cs.getSelected().isEmpty());
+
+ // repeat, hiding column (4, 5 and) 6
+ al = gen.generate(50, 20, 123, 5, 5);
+ cs = new ColumnSelection();
+ cs.addElement(4);
+ cs.addElement(5);
+ cs.addElement(6);
+ cs.hideSelectedColumns(6, al.getHiddenColumns());
+ regions = al.getHiddenColumns().iterator();
+ assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+ assertEquals("[4, 6]", Arrays.toString(regions.next()));
+ assertTrue(cs.getSelected().isEmpty());
+
+ // repeat, with _only_ adjacent columns selected
+ al = gen.generate(50, 20, 123, 5, 5);
+ cs = new ColumnSelection();
+ cs.addElement(4);
+ cs.addElement(6);
+ cs.hideSelectedColumns(5, al.getHiddenColumns());
+ regions = al.getHiddenColumns().iterator();
+ assertEquals(1, al.getHiddenColumns().getNumberOfRegions());
+ assertEquals("[4, 6]", Arrays.toString(regions.next()));
+ assertTrue(cs.getSelected().isEmpty());
+ }
+
+ /**
+ * Test the method that hides all (possibly disjoint) selected column ranges
+ */
+ @Test(groups = { "Functional" })
+ public void testHideSelectedColumns()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+ ColumnSelection cs = new ColumnSelection();
+ int[] sel = { 2, 3, 4, 7, 8, 9, 20, 21, 22 };
+ for (int col : sel)
+ {
+ cs.addElement(col);
+ }
+
+ HiddenColumns cols = al.getHiddenColumns();
+ cols.hideColumns(15, 18);
+
+ cs.hideSelectedColumns(al);
+ assertTrue(cs.getSelected().isEmpty());
+ Iterator<int[]> regions = cols.iterator();
+ assertEquals(4, cols.getNumberOfRegions());
+ assertEquals("[2, 4]", Arrays.toString(regions.next()));
+ assertEquals("[7, 9]", Arrays.toString(regions.next()));
+ assertEquals("[15, 18]", Arrays.toString(regions.next()));
+ assertEquals("[20, 22]", Arrays.toString(regions.next()));
+ }
+
+ /**
+ * Test the method that gets runs of selected columns ordered by column. If
+ * this fails, HideSelectedColumns may also fail
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSelectedRanges()
+ {
+ /*
+ * getSelectedRanges returns ordered columns regardless
+ * of the order in which they are added
+ */
+ ColumnSelection cs = new ColumnSelection();
+ int[] sel = { 4, 3, 7, 21, 9, 20, 8, 22, 2 };
+ for (int col : sel)
+ {
+ cs.addElement(col);
+ }
+ List<int[]> range;
+ range = cs.getSelectedRanges();
+ assertEquals(3, range.size());
+ assertEquals("[2, 4]", Arrays.toString(range.get(0)));
+ assertEquals("[7, 9]", Arrays.toString(range.get(1)));
+ assertEquals("[20, 22]", Arrays.toString(range.get(2)));
+ cs.addElement(0);
+ cs.addElement(1);
+ range = cs.getSelectedRanges();
+ assertEquals(3, range.size());
+ assertEquals("[0, 4]", Arrays.toString(range.get(0)));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testInvertColumnSelection()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(50, 20, 123, 5, 5);
+
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(4);
+ cs.addElement(6);
+ cs.addElement(8);
+
+ HiddenColumns cols = al.getHiddenColumns();
+ cols.hideColumns(3, 3);
+ cols.hideColumns(6, 6);
+
+ // invert selection from start (inclusive) to end (exclusive)
+ cs.invertColumnSelection(2, 9, al);
+ assertEquals("[2, 5, 7]", cs.getSelected().toString());
+
+ cs.invertColumnSelection(1, 9, al);
+ assertEquals("[1, 4, 8]", cs.getSelected().toString());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testMaxColumnSelection()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(0);
+ cs.addElement(513);
+ cs.addElement(1);
+ assertEquals(513, cs.getMax());
+ cs.removeElement(513);
+ assertEquals(1, cs.getMax());
+ cs.removeElement(1);
+ assertEquals(0, cs.getMax());
+ cs.addElement(512);
+ cs.addElement(513);
+ assertEquals(513, cs.getMax());
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testMinColumnSelection()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(0);
+ cs.addElement(513);
+ cs.addElement(1);
+ assertEquals(0, cs.getMin());
+ cs.removeElement(0);
+ assertEquals(1, cs.getMin());
+ cs.addElement(0);
+ assertEquals(0, cs.getMin());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testEquals()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(0);
+ cs.addElement(513);
+ cs.addElement(1);
+
+ // same selections added in a different order
+ ColumnSelection cs2 = new ColumnSelection();
+ cs2.addElement(1);
+ cs2.addElement(513);
+ cs2.addElement(0);
+
+ assertTrue(cs.equals(cs2));
+ assertTrue(cs.equals(cs));
+ assertTrue(cs2.equals(cs));
+ assertTrue(cs2.equals(cs2));
+
+ cs2.addElement(12);
+ assertFalse(cs.equals(cs2));
+ assertFalse(cs2.equals(cs));
+
+ cs2.removeElement(12);
+ assertTrue(cs.equals(cs2));
+ }
+
+ /*
+ cs2.hideSelectedColumns(88);
+ assertFalse(cs.equals(cs2));
+ /*
+ * unhiding a column adds it to selection!
+ */
+ /* cs2.revealHiddenColumns(88);
+ assertFalse(cs.equals(cs2));
+ cs.addElement(88);
+ assertTrue(cs.equals(cs2));
+ */
+
+ /**
+ * Test the method that returns selected columns, in the order in which they
+ * were added