X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FComparisonTest.java;fp=test%2Fjalview%2Futil%2FComparisonTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=6f6841ddefecc1ae87fd9c816ff3f995fd6e9f6d;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/test/jalview/util/ComparisonTest.java b/test/jalview/util/ComparisonTest.java deleted file mode 100644 index 6f6841d..0000000 --- a/test/jalview/util/ComparisonTest.java +++ /dev/null @@ -1,215 +0,0 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 - * of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with Jalview. If not, see . - * The Jalview Authors are detailed in the 'AUTHORS' file. - */ -package jalview.util; - -import static org.testng.AssertJUnit.assertEquals; -import static org.testng.AssertJUnit.assertFalse; -import static org.testng.AssertJUnit.assertTrue; - -import jalview.datamodel.Sequence; -import jalview.datamodel.SequenceI; -import jalview.gui.JvOptionPane; - -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - -public class ComparisonTest -{ - - @BeforeClass(alwaysRun = true) - public void setUpJvOptionPane() - { - JvOptionPane.setInteractiveMode(false); - JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); - } - - @Test(groups = { "Functional" }) - public void testIsGap() - { - assertTrue(Comparison.isGap('-')); - assertTrue(Comparison.isGap('.')); - assertTrue(Comparison.isGap(' ')); - assertFalse(Comparison.isGap('X')); - assertFalse(Comparison.isGap('x')); - assertFalse(Comparison.isGap('*')); - assertFalse(Comparison.isGap('G')); - } - - /** - * Test for isNucleotide is that sequences in a dataset are more than 85% - * AGCTU. Test is not case-sensitive and ignores gaps. - */ - @Test(groups = { "Functional" }) - public void testIsNucleotide_sequences() - { - SequenceI seq = new Sequence("eightypercent", "agctuAGCPV"); - assertFalse(Comparison.isNucleotide(new SequenceI[] { seq })); - assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[] - { seq } })); - - seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV"); - assertFalse(Comparison.isNucleotide(new SequenceI[] { seq })); - - seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV"); - assertTrue(Comparison.isNucleotide(new SequenceI[] { seq })); - - seq = new Sequence("eightyfivepercentgapped", - "--agc--tuA--GCPV-a---gct-uA-GC---UV"); - assertFalse(Comparison.isNucleotide(new SequenceI[] { seq })); - - seq = new Sequence("nineypercentgapped", - "ag--ct-u-A---GC---g----Vag--c---tuAGCUV"); - assertTrue(Comparison.isNucleotide(new SequenceI[] { seq })); - - seq = new Sequence("allgap", "---------"); - assertFalse(Comparison.isNucleotide(new SequenceI[] { seq })); - - seq = new Sequence("DNA", "ACTugGCCAG"); - SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW"); - /* - * 90% DNA: - */ - assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq, - seq, seq, seq, seq, seq, seq, seq2 })); - assertTrue(Comparison.isNucleotide(new SequenceI[][] { - new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq }, - new SequenceI[] { seq, seq, seq, seq, seq, seq2 } })); - /* - * 80% DNA: - */ - assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq, - seq, seq, seq, seq, seq, seq2, seq2 })); - assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[] - { seq }, new SequenceI[] { seq, seq, seq }, - new SequenceI[] { seq, seq, seq, seq, seq2, seq2, null } })); - - seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt"); - // 12/14 = 85.7% - assertTrue(Comparison.isNucleotide(new SequenceI[] { seq })); - - assertFalse(Comparison.isNucleotide((SequenceI[]) null)); - assertFalse(Comparison.isNucleotide((SequenceI[][]) null)); - } - - /** - * Test the percentage identity calculation for two sequences - */ - @Test(groups = { "Functional" }) - public void testPID_includingGaps() - { - String seq1 = "ABCDEFG"; // extra length here is ignored - String seq2 = "abcdef"; - assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f); - - // comparison range defaults to length of first sequence - seq2 = "abcdefghijklmnopqrstuvwxyz"; - assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f); - - // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch - seq1 = "a--b-cdefh"; - seq2 = "a---bcdefg"; - int length = seq1.length(); - - // match gap-residue, match gap-gap: 9/10 identical - // TODO should gap-gap be included in a PID score? JAL-791 - assertEquals(90f, Comparison.PID(seq1, seq2, 0, length, true, false), - 0.001f); - // overloaded version of the method signature above: - assertEquals(90f, Comparison.PID(seq1, seq2), 0.001f); - - // don't match gap-residue, match gap-gap: 7/10 identical - // TODO should gap-gap be included in a PID score? - assertEquals(70f, Comparison.PID(seq1, seq2, 0, length, false, false), - 0.001f); - } - - @Test(groups = { "Functional" }) - public void testIsNucleotide() - { - assertTrue(Comparison.isNucleotide('a')); - assertTrue(Comparison.isNucleotide('A')); - assertTrue(Comparison.isNucleotide('c')); - assertTrue(Comparison.isNucleotide('C')); - assertTrue(Comparison.isNucleotide('g')); - assertTrue(Comparison.isNucleotide('G')); - assertTrue(Comparison.isNucleotide('t')); - assertTrue(Comparison.isNucleotide('T')); - assertTrue(Comparison.isNucleotide('u')); - assertTrue(Comparison.isNucleotide('U')); - assertFalse(Comparison.isNucleotide('-')); - assertFalse(Comparison.isNucleotide('P')); - } - - /** - * Test the percentage identity calculation for two sequences - */ - @Test(groups = { "Functional" }) - public void testPID_ungappedOnly() - { - // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch - // the extra length of seq1 is ignored - String seq1 = "a--b-cdefhr"; - String seq2 = "a---bcdefg"; - int length = seq1.length(); - - /* - * As currently coded, 'ungappedOnly' ignores gap-residue but counts - * gap-gap. Is this a bug - should gap-gap also be ignored, giving a PID of - * 5/6? - * - * Note also there is no variant of the calculation that penalises - * gap-residue i.e. counts it as a mismatch. This would give a score of 5/8 - * (if we ignore gap-gap) or 5/10 (if we count gap-gap as a match). - */ - // match gap-residue, match gap-gap: 7/8 identical - assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, true, true), - 0.001f); - - // don't match gap-residue with 'ungapped only' - same as above - assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, false, true), - 0.001f); - } - - @Test(groups = { "Functional" }) - public void testIsNucleotideSequence() - { - assertFalse(Comparison.isNucleotideSequence(null, true)); - assertTrue(Comparison.isNucleotideSequence("", true)); - assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", true)); - assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", false)); - assertFalse(Comparison.isNucleotideSequence("xAgGcCtTuU", false)); - assertFalse(Comparison.isNucleotideSequence("aAgGcCtTuUx", false)); - assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true)); - assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false)); - } - - @Test(groups = { "Functional" }) - public void testIsSameResidue() - { - assertTrue(Comparison.isSameResidue('a', 'a', false)); - assertTrue(Comparison.isSameResidue('a', 'a', true)); - assertTrue(Comparison.isSameResidue('A', 'a', false)); - assertTrue(Comparison.isSameResidue('a', 'A', false)); - - assertFalse(Comparison.isSameResidue('a', 'A', true)); - assertFalse(Comparison.isSameResidue('A', 'a', true)); - } -}