assertEquals(2, cs.findColumnPosition(5));
}
+ /**
+ * Test the code used to locate the reference sequence ruler origin
+ */
+ @Test(groups = { "Functional" })
+ public void testLocateVisibleBoundsofSequence()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
+ assertEquals(2, seq.findIndex(seq.getStart()));
+
+ // 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(cs.locateVisibleBoundsOfSequence(seq)));
+
+ // hidden column on gap after end of sequence - should not affect bounds
+ cs.hideColumns(13);
+ 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(cs.locateVisibleBoundsOfSequence(seq)));
+
+ cs.revealAllHiddenColumns();
+ // hidden column on gap before beginning of sequence - should vis bounds by
+ // one
+ cs.hideColumns(0);
+ 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(cs.locateVisibleBoundsOfSequence(seq)));
+
+ cs.revealAllHiddenColumns();
+ // hide columns around most of sequence - leave one residue remaining
+ cs.hideColumns(1, 3);
+ cs.hideColumns(6, 11);
+ assertEquals("-D",
+ 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(cs.locateVisibleBoundsOfSequence(seq)));
+ cs.revealAllHiddenColumns();
+
+ // hide whole sequence - should just get location of hidden region
+ // 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(cs.locateVisibleBoundsOfSequence(seq)));
+
+ }
+
+ @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")});
+ ColumnSelection cs = new ColumnSelection();
+ cs.hideInsertionsFor(al.getSequenceAt(0));
+ assertEquals(
+ "G",
+ ""
+ + al.getSequenceAt(0).getCharAt(
+ cs.adjustForHiddenColumns(9)));
+
+
+ }
@Test(groups = { "Functional" })
public void testHideColumns()
{
}
/**
+ * 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 the method that reveals a range of hidden columns given the start
* column of the range
*/
cs.invertColumnSelection(1, 9);
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);
+ cs.hideColumns(3);
+ cs.hideColumns(7);
+ cs.hideColumns(5,9);
+
+ // same selections added in a different order
+ ColumnSelection cs2 = new ColumnSelection();
+ cs2.addElement(1);
+ cs2.addElement(513);
+ cs2.addElement(0);
+
+ // with no hidden columns
+ assertFalse(cs.equals(cs2));
+ assertFalse(cs2.equals(cs));
+
+ // with hidden columns added in a different order
+ cs2.hideColumns(6, 9);
+ cs2.hideColumns(5, 8);
+ cs2.hideColumns(3);
+
+ 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.hideColumns(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
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSelection()
+ {
+ ColumnSelection cs = new ColumnSelection();
+ int[] sel = { 4, 3, 7, 21 };
+ for (int col : sel)
+ {
+ cs.addElement(col);
+ }
+ List<Integer> selected = cs.getSelected();
+ assertEquals(4, selected.size());
+ int i = 0;
+ for (int col : sel)
+ {
+ assertEquals(col, selected.get(i++).intValue());
+ }
+
+ cs.removeElement(7);
+ cs.addElement(1);
+ cs.removeElement(4);
+ selected = cs.getSelected();
+ assertEquals(3, selected.size());
+ assertEquals(3, selected.get(0).intValue());
+ assertEquals(21, selected.get(1).intValue());
+ assertEquals(1, selected.get(2).intValue());
+ }
}
git://source.jalview.org / jalview.git / blobdiff