+/*
+ * 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.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-
-import org.junit.Test;
+import jalview.gui.JvOptionPane;
public class ComparisonTest
{
- @Test
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @BeforeMethod(alwaysRun = true)
+ public void loadProperties()
+ {
+ Cache.loadProperties("test/jalview/util/comparisonTestProps.jvprops");
+ }
+
+ @Test(groups = { "Functional" })
public void testIsGap()
{
assertTrue(Comparison.isGap('-'));
* Test for isNucleotide is that sequences in a dataset are more than 85%
* AGCTU. Test is not case-sensitive and ignores gaps.
*/
- @Test
- public void testIsNucleotide() {
- SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
- assertFalse(Comparison.isNucleotide(new SequenceI[]
- { seq }));
+ @Test(groups = { "Functional" })
+ public void testIsNucleotide_sequences()
+ {
+ SequenceI seq = new Sequence("eightypercent+fivepercent", "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("eightyfivepercent+tenpercent",
+ "agctuagcgVagctuagcuVE");
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
- seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
- assertTrue(Comparison.isNucleotide(new SequenceI[]
- { seq }));
+ seq = new Sequence(">nineyfivepercent+0percent",
+ "aagctuagcgEagctuagcua");
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+ seq = new Sequence("nineyfivepercent+0percent", "agctuagcgEagctuagcua");
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+ seq = new Sequence("nineyfivepercent+fivepercent",
+ "agctuagcgWagctuagcua");
+ assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+ seq = new Sequence("nineyfivepercent+tenpercent",
+ "agctuagcgEWWctuagcua");
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+ seq = new Sequence("eightyfivepercent+fifteenpercent",
+ "agctuagcgWWWctuagcua");
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
seq = new Sequence("eightyfivepercentgapped",
"--agc--tuA--GCPV-a---gct-uA-GC---UV");
- assertFalse(Comparison.isNucleotide(new SequenceI[]
- { seq }));
+ 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("ninetyfivepercentgapped",
+ "ag--ct-u-a---gc---g----aag--c---tuagcuV");
+ assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
seq = new Sequence("allgap", "---------");
- assertFalse(Comparison.isNucleotide(new SequenceI[]
- { seq }));
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
seq = new Sequence("DNA", "ACTugGCCAG");
SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
- assertTrue(Comparison.isNucleotide(new SequenceI[]
- { seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 })); // 90% DNA
- assertFalse(Comparison.isNucleotide(new SequenceI[]
- { seq, seq, seq, seq, seq, seq, seq, seq, seq2, seq2 })); // 80% DNA
+ /*
+ * 90% DNA but one protein sequence - expect false
+ */
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[]
+ { seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
+ new SequenceI[]
+ { seq, seq, seq, seq, seq, seq2 } }));
+ /*
+ * 80% DNA but one protein sequence - Expect false
+ */
+ 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 }));
+ String seqString = "aaatatatatgEcctgagtcgt";
+ seq = new Sequence("ShortProteinThatLooksLikeDNA", seqString);
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+ seq = new Sequence("LongProteinThatLooksLikeDNA", seqString.repeat(10));
+ assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
- assertFalse(Comparison.isNucleotide(null));
+ assertFalse(Comparison.isNucleotide((SequenceI[]) null));
+ assertFalse(Comparison.isNucleotide((SequenceI[][]) null));
}
/**
- * Test percentage identity calculation for two sequences.
+ * Test the percentage identity calculation for two sequences
*/
- @Test
- public void testPID_matchGaps()
+ @Test(groups = { "Functional" })
+ public void testPID_includingGaps()
{
- String seq1 = "ABCDEF";
+ String seq1 = "ABCDEFG"; // extra length here is ignored
String seq2 = "abcdef";
assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
seq2 = "abcdefghijklmnopqrstuvwxyz";
assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
- seq2 = "a---bcdef";
+ // 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(groups = { "Functional" })
+ public void testIsNucleotideAmbiguity()
+ {
+ assertTrue(Comparison.isNucleotide('b', true));
+ assertTrue(Comparison.isNucleotide('B', true));
+ assertTrue(Comparison.isNucleotide('d', true));
+ assertTrue(Comparison.isNucleotide('V', true));
+ assertTrue(Comparison.isNucleotide('M', true));
+ assertTrue(Comparison.isNucleotide('s', true));
+ assertTrue(Comparison.isNucleotide('W', true));
+ assertTrue(Comparison.isNucleotide('x', true));
+ assertTrue(Comparison.isNucleotide('Y', true));
+ assertTrue(Comparison.isNucleotide('r', true));
+ assertTrue(Comparison.isNucleotide('i', true));
+ assertFalse(Comparison.isNucleotide('-', true));
+ assertFalse(Comparison.isNucleotide('n', true));
+ assertFalse(Comparison.isNucleotide('P', true));
+ }
+
+ /**
+ * 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));
+ assertFalse(Comparison.isNucleotideSequence("gatactawgataca", false));
+ // including nucleotide ambiguity
+ assertTrue(
+ Comparison.isNucleotideSequence("gatacaWgataca", true, true));
+ assertFalse(
+ Comparison.isNucleotideSequence("gatacaEgataca", true, true));
+
+ // not quite all nucleotides and ambiguity codes
+ Sequence seq = new Sequence("Ambiguity DNA codes", "gatacagatacabve");
+ assertFalse(Comparison.isNucleotide(seq));
+ // all nucleotide and nucleotide ambiguity codes
+ seq = new Sequence("Ambiguity DNA codes", "gatacagatacabvt");
+ assertFalse(Comparison.isNucleotide(seq));
+ seq = new Sequence("Ambiguity DNA codes", "agatacabb");
+ assertFalse(Comparison.isNucleotide(seq));
+ // 55% nucleotide with only Xs or Ns
+ assertTrue(Comparison
+ .isNucleotide(new Sequence("dnaWithXs", "gatacaXXXX")));
+ assertTrue(Comparison
+ .isNucleotide(new Sequence("dnaWithXs", "gatacaNNNN")));
+ assertFalse(Comparison
+ .isNucleotide(new Sequence("dnaWithXs", "gatacXXXXX")));
+ assertFalse(Comparison
+ .isNucleotide(new Sequence("dnaWithXs", "gatacNNNNN")));
+ }
+
+ @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));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testNucleotideProportion()
+ {
+ assertFalse(Comparison.myShortSequenceNucleotideProportionCount(2, 3));
+ assertTrue(Comparison.myShortSequenceNucleotideProportionCount(3, 3));
+ assertFalse(Comparison.myShortSequenceNucleotideProportionCount(2, 4));
+ assertTrue(Comparison.myShortSequenceNucleotideProportionCount(3, 4));
+ assertFalse(
+ Comparison.myShortSequenceNucleotideProportionCount(17, 20));
+ assertTrue(Comparison.myShortSequenceNucleotideProportionCount(18, 20));
+ assertFalse(
+ Comparison.myShortSequenceNucleotideProportionCount(38, 50));
+ assertTrue(Comparison.myShortSequenceNucleotideProportionCount(39, 50));
+ assertFalse(
+ Comparison.myShortSequenceNucleotideProportionCount(54, 100));
+ assertTrue(
+ Comparison.myShortSequenceNucleotideProportionCount(55, 100));
}
}
git://source.jalview.org / jalview.git / blobdiff