+++ /dev/null
-package jalview.analysis;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertTrue;
-
-import jalview.analysis.ResidueCount.SymbolCounts;
-
-import org.junit.Assert;
-import org.testng.annotations.Test;
-
-public class ResidueCountTest
-{
- /**
- * Test a mix of add and put for nucleotide counting
- */
- @Test(groups = "Functional")
- public void test_countNucleotide()
- {
- ResidueCount rc = new ResidueCount(true);
- assertEquals(rc.getCount('A'), 0);
- assertEquals(rc.getGapCount(), 0);
- // add then add
- assertEquals(rc.add('A'), 1);
- assertEquals(rc.add('a'), 2);
- // put then add
- rc.put('g', 3);
- assertEquals(rc.add('G'), 4);
- // add then put
- assertEquals(rc.add('c'), 1);
- rc.put('C', 4);
- assertEquals(rc.add('N'), 1);
-
- assertEquals(rc.getCount('a'), 2);
- assertEquals(rc.getCount('A'), 2);
- assertEquals(rc.getCount('G'), 4);
- assertEquals(rc.getCount('c'), 4);
- assertEquals(rc.getCount('T'), 0); // never seen
- assertEquals(rc.getCount('N'), 1);
- assertEquals(rc.getCount('?'), 0);
- assertEquals(rc.getCount('-'), 0);
-
- assertFalse(rc.isCountingInts());
- assertFalse(rc.isUsingOtherData());
- }
-
- /**
- * Test adding to gap count (either using addGap or add)
- */
- @Test(groups = "Functional")
- public void testAddGap()
- {
- ResidueCount rc = new ResidueCount(true);
- rc.addGap();
- rc.add('-');
- rc.add('.');
- rc.add(' ');
-
- assertEquals(rc.getGapCount(), 4);
- assertEquals(rc.getCount(' '), 4);
- assertEquals(rc.getCount('-'), 4);
- assertEquals(rc.getCount('.'), 4);
- assertFalse(rc.isUsingOtherData());
- assertFalse(rc.isCountingInts());
- }
-
- @Test(groups = "Functional")
- public void testOverflow()
- {
- /*
- * overflow from add
- */
- ResidueCount rc = new ResidueCount(true);
- rc.addGap();
- rc.put('A', Short.MAX_VALUE - 1);
- assertFalse(rc.isCountingInts());
- rc.add('A');
- assertFalse(rc.isCountingInts());
- 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 = new ResidueCount(true);
- 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);
- }
-
- /**
- * Test a mix of add and put for peptide counting
- */
- @Test(groups = "Functional")
- public void test_countPeptide()
- {
- ResidueCount rc = new ResidueCount(false);
- rc.put('q', 4);
- rc.add('Q');
- rc.add('X');
- rc.add('x');
- rc.add('W');
- rc.put('w', 7);
- rc.put('m', 12);
- rc.put('M', 13);
-
- assertEquals(rc.getCount('q'), 5);
- assertEquals(rc.getCount('X'), 2);
- assertEquals(rc.getCount('W'), 7);
- assertEquals(rc.getCount('m'), 13);
- assertEquals(rc.getCount('G'), 0);
- assertEquals(rc.getCount('-'), 0);
-
- assertFalse(rc.isCountingInts());
- assertFalse(rc.isUsingOtherData());
- }
-
- @Test(groups = "Functional")
- public void test_unexpectedPeptide()
- {
- ResidueCount rc = new ResidueCount(false);
- // expected characters (upper or lower case):
- String aas = "ACDEFGHIKLMNPQRSTVWXY";
- String lower = aas.toLowerCase();
- for (int i = 0; i < aas.length(); i++)
- {
- rc.put(aas.charAt(i), i);
- rc.add(lower.charAt(i));
- }
- for (int i = 0; i < aas.length(); i++)
- {
- assertEquals(rc.getCount(aas.charAt(i)), i + 1);
- }
- assertFalse(rc.isUsingOtherData());
-
- rc.put('J', 4);
- assertTrue(rc.isUsingOtherData());
- assertEquals(rc.getCount('J'), 4);
- rc.add('j');
- assertEquals(rc.getCount('J'), 5);
- }
-
- @Test(groups = "Functional")
- public void test_unexpectedNucleotide()
- {
- ResidueCount rc = new ResidueCount(true);
- // expected characters (upper or lower case):
- String nucs = "ACGTUN";
- String lower = nucs.toLowerCase();
- for (int i = 0; i < nucs.length(); i++)
- {
- rc.put(nucs.charAt(i), i);
- rc.add(lower.charAt(i));
- }
- for (int i = 0; i < nucs.length(); i++)
- {
- assertEquals(rc.getCount(nucs.charAt(i)), i + 1);
- }
- assertFalse(rc.isUsingOtherData());
-
- rc.add('J');
- assertTrue(rc.isUsingOtherData());
- }
-
- @Test(groups = "Functional")
- public void testGetModalCount()
- {
- ResidueCount rc = new ResidueCount(true);
- rc.add('c');
- rc.add('g');
- rc.add('c');
- assertEquals(rc.getModalCount(), 2);
-
- // modal count is in the 'short overflow' counts
- rc = new ResidueCount();
- rc.add('c');
- rc.put('g', Short.MAX_VALUE);
- rc.add('G');
- assertEquals(rc.getModalCount(), Short.MAX_VALUE + 1);
-
- // modal count is in the 'other data' counts
- rc = new ResidueCount(false);
- rc.add('Q');
- rc.add('{');
- rc.add('{');
- assertEquals(rc.getModalCount(), 2);
-
- // verify modal count excludes gap
- rc = new ResidueCount();
- rc.add('Q');
- rc.add('P');
- rc.add('Q');
- rc.addGap();
- rc.addGap();
- rc.addGap();
- assertEquals(rc.getModalCount(), 2);
- }
-
- @Test(groups = "Functional")
- public void testGetResiduesForCount()
- {
- ResidueCount rc = new ResidueCount(true);
- rc.add('c');
- rc.add('g');
- rc.add('c');
- assertEquals(rc.getResiduesForCount(2), "C");
- assertEquals(rc.getResiduesForCount(1), "G");
- assertEquals(rc.getResiduesForCount(3), "");
- assertEquals(rc.getResiduesForCount(0), "");
- assertEquals(rc.getResiduesForCount(-1), "");
-
- // modal count is in the 'short overflow' counts
- 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();
- rc.add('Q');
- rc.add('{');
- rc.add('{');
- assertEquals(rc.getResiduesForCount(1), "Q");
- assertEquals(rc.getResiduesForCount(2), "{");
-
- // residues share modal count
- rc = new ResidueCount();
- rc.add('G');
- rc.add('G');
- rc.add('c');
- rc.add('C');
- rc.add('U');
- assertEquals(rc.getResiduesForCount(1), "U");
- assertEquals(rc.getResiduesForCount(2), "CG");
-
- // expected and unexpected symbols share modal count
- rc = new ResidueCount();
- rc.add('G');
- rc.add('t');
- rc.add('[');
- rc.add('[');
- rc.add('t');
- rc.add('G');
- rc.add('c');
- rc.add('C');
- rc.add('U');
- assertEquals(rc.getResiduesForCount(1), "U");
- assertEquals(rc.getResiduesForCount(2), "CGT[");
- }
-
- @Test(groups = "Functional")
- public void testGetSymbolCounts_nucleotide()
- {
- ResidueCount rc = new ResidueCount(true);
- rc.add('g');
- rc.add('c');
- rc.add('G');
- rc.add('J'); // 'otherData'
- rc.add('g');
- rc.add('N');
- rc.put('[', 0); // 'otherdata'
-
- SymbolCounts sc = rc.getSymbolCounts();
- 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('U', Short.MAX_VALUE);
- rc.add('u');
- sc = rc.getSymbolCounts();
- Assert.assertArrayEquals(new char[] { 'C', 'G', 'N', 'U', 'J', '[' },
- sc.symbols);
- 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")
- public void testToString()
- {
- ResidueCount rc = new ResidueCount();
- rc.add('q');
- rc.add('c');
- rc.add('Q');
- assertEquals(rc.toString(), "[ C:1 Q:2 ]");
-
- // add 'other data'
- rc.add('{');
- assertEquals(rc.toString(), "[ C:1 Q:2 {:1 ]");
-
- // switch from short to int counting:
- rc.put('G', Short.MAX_VALUE);
- 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);
- }
-}
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