+/*
+ * 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 jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ComparisonTest
{
- @Test(groups ={ "Functional" })
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @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(groups ={ "Functional" })
- public void testIsNucleotide() {
+ @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[]
+ 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 }));
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
- assertTrue(Comparison.isNucleotide(new SequenceI[]
- { seq }));
+ assertTrue(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 }));
+ 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");
/*
- * 90% DNA:
+ * 90% DNA but one protein sequence - expect false
*/
- 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 } }));
+ 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:
+ * 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 } }));
+ 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 }));
+ assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
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(groups ={ "Functional" })
- 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 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