* overflow from add
*/
ResidueCount rc = new ResidueCount(true);
+ rc.addGap();
rc.put('A', Short.MAX_VALUE - 1);
assertFalse(rc.isCountingInts());
rc.add('A');
rc.add('A');
assertTrue(rc.isCountingInts());
assertEquals(rc.getCount('a'), Short.MAX_VALUE + 1);
+ rc.add('A');
+ assertTrue(rc.isCountingInts());
+ assertEquals(rc.getCount('a'), Short.MAX_VALUE + 2);
+ assertEquals(rc.getGapCount(), 1);
+ rc.addGap();
+ assertEquals(rc.getGapCount(), 2);
/*
* overflow from put
rc.put('G', Short.MAX_VALUE + 1);
assertTrue(rc.isCountingInts());
assertEquals(rc.getCount('g'), Short.MAX_VALUE + 1);
+ rc.put('G', 1);
+ assertTrue(rc.isCountingInts());
+ assertEquals(rc.getCount('g'), 1);
+
+ /*
+ * underflow from put
+ */
+ rc = new ResidueCount(true);
+ rc.put('G', Short.MIN_VALUE - 1);
+ assertTrue(rc.isCountingInts());
+ assertEquals(rc.getCount('g'), Short.MIN_VALUE - 1);
}
/**
rc.put('J', 4);
assertTrue(rc.isUsingOtherData());
+ assertEquals(rc.getCount('J'), 4);
+ rc.add('j');
+ assertEquals(rc.getCount('J'), 5);
}
@Test(groups = "Functional")
@Test(groups = "Functional")
public void testGetModalCount()
{
- ResidueCount rc = new ResidueCount();
+ ResidueCount rc = new ResidueCount(true);
rc.add('c');
rc.add('g');
rc.add('c');
assertEquals(rc.getModalCount(), Short.MAX_VALUE + 1);
// modal count is in the 'other data' counts
- rc = new ResidueCount();
+ rc = new ResidueCount(false);
rc.add('Q');
rc.add('{');
rc.add('{');
@Test(groups = "Functional")
public void testGetResiduesForCount()
{
- ResidueCount rc = new ResidueCount();
+ ResidueCount rc = new ResidueCount(true);
rc.add('c');
rc.add('g');
rc.add('c');
assertEquals(rc.getResiduesForCount(-1), "");
// modal count is in the 'short overflow' counts
- rc = new ResidueCount();
+ rc = new ResidueCount(true);
rc.add('c');
rc.put('g', Short.MAX_VALUE);
rc.add('G');
assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "G");
assertEquals(rc.getResiduesForCount(1), "C");
+
+ // peptide modal count is in the 'short overflow' counts
+ rc = new ResidueCount(false);
+ rc.add('c');
+ rc.put('p', Short.MAX_VALUE);
+ rc.add('P');
+ assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "P");
+ assertEquals(rc.getResiduesForCount(1), "C");
// modal count is in the 'other data' counts
rc = new ResidueCount();
}
@Test(groups = "Functional")
- public void testGetSymbolCounts()
+ public void testGetSymbolCounts_nucleotide()
{
- ResidueCount rc = new ResidueCount();
- rc.add('q');
+ ResidueCount rc = new ResidueCount(true);
+ rc.add('g');
rc.add('c');
- rc.add('Q');
+ rc.add('G');
rc.add('J'); // 'otherData'
- rc.add('q');
- rc.add('x');
+ rc.add('g');
+ rc.add('N');
+ rc.put('[', 0); // 'otherdata'
SymbolCounts sc = rc.getSymbolCounts();
- Assert.assertArrayEquals(new char[] { 'C', 'Q', 'X', 'J' }, sc.symbols);
- Assert.assertArrayEquals(new int[] { 1, 3, 1, 1 }, sc.values);
+ Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'J', '[' },
+ sc.symbols);
+ Assert.assertArrayEquals(new int[] { 1, 3, 1, 1, 0 }, sc.values);
// now with overflow to int counts
- rc.put('g', Short.MAX_VALUE);
- rc.add('g');
+ rc.put('U', Short.MAX_VALUE);
+ rc.add('u');
sc = rc.getSymbolCounts();
- Assert.assertArrayEquals(new char[] { 'C', 'G', 'Q', 'X', 'J' },
+ Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'U', 'J', '[' },
sc.symbols);
- Assert.assertArrayEquals(new int[] { 1, 32768, 3, 1, 1 }, sc.values);
+ Assert.assertArrayEquals(new int[] { 1, 3, 1, 32768, 1, 0 }, sc.values);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetSymbolCounts_peptide()
+ {
+ ResidueCount rc = new ResidueCount(false);
+ rc.add('W');
+ rc.add('q');
+ rc.add('W');
+ rc.add('Z'); // 'otherData'
+ rc.add('w');
+ rc.add('L');
+
+ SymbolCounts sc = rc.getSymbolCounts();
+ Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
+ Assert.assertArrayEquals(new int[] { 1, 1, 3, 1 }, sc.values);
+
+ // now with overflow to int counts
+ rc.put('W', Short.MAX_VALUE);
+ rc.add('W');
+ sc = rc.getSymbolCounts();
+ Assert.assertArrayEquals(new char[] { 'L', 'Q', 'W', 'Z' }, sc.symbols);
+ Assert.assertArrayEquals(new int[] { 1, 1, 32768, 1 }, sc.values);
}
@Test(groups = "Functional")
rc.add('g');
assertEquals(rc.toString(), "[ C:1 G:32768 Q:2 {:1 ]");
}
+
+ @Test(groups = "Functional")
+ public void testGetTooltip()
+ {
+ ResidueCount rc = new ResidueCount();
+
+ // no counts!
+ assertEquals(rc.getTooltip(20, 1), "");
+
+ /*
+ * count 7 C, 6 K, 7 Q, 10 P, 9 W, 1 F (total 40)
+ */
+ for (int i = 0; i < 7; i++)
+ {
+ rc.add('c');
+ rc.add('q');
+ }
+ for (int i = 0; i < 10; i++)
+ {
+ rc.add('p');
+ }
+ for (int i = 0; i < 9; i++)
+ {
+ rc.add('W');
+ }
+ for (int i = 0; i < 6; i++)
+ {
+ rc.add('K');
+ }
+ rc.add('F');
+
+ assertEquals(rc.getTooltip(40, 0),
+ "P 25%; W 22%; C 17%; Q 17%; K 15%; F 2%");
+
+ assertEquals(rc.getTooltip(30, 1),
+ "P 33.3%; W 30.0%; C 23.3%; Q 23.3%; K 20.0%; F 3.3%");
+ }
+
+ @Test(groups = "Functional")
+ public void testPut()
+ {
+ ResidueCount rc = new ResidueCount();
+ rc.put('q', 3);
+ assertEquals(rc.getCount('Q'), 3);
+ rc.put(' ', 4);
+ assertEquals(rc.getGapCount(), 4);
+ rc.put('.', 5);
+ assertEquals(rc.getGapCount(), 5);
+ rc.put('-', 6);
+ assertEquals(rc.getGapCount(), 6);
+
+ rc.put('?', 5);
+ assertEquals(rc.getCount('?'), 5);
+ rc.put('?', 6);
+ rc.put('!', 7);
+ assertEquals(rc.getCount('?'), 6);
+ assertEquals(rc.getCount('!'), 7);
+ }
}