+++ /dev/null
-/*
- * 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 <http://www.gnu.org/licenses/>.
- * 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));
- }
-}
git://source.jalview.org / jalview.git / blobdiff