+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 org.junit.Test;
+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 org.testng.annotations.Test;
+
public class ComparisonTest
{
- @Test
+ @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() {
+ @Test(groups = { "Functional" })
+ public void testIsNucleotide()
+ {
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:
*/
- 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 } }));
+ 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 } }));
+ 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
+ @Test(groups = { "Functional" })
public void testPID_matchGaps()
{
String seq1 = "ABCDEF";