X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FDnaTest.java;h=c8f07ec52128f165866b4a9be5bae2662427d7ff;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=765ec2bbf69b3f804dcbae809288b8eb4eaadc45;hpb=4099019578bbeb81b76154922851ada38fb0017d;p=jalview.git diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java index 765ec2b..c8f07ec 100644 --- a/test/jalview/analysis/DnaTest.java +++ b/test/jalview/analysis/DnaTest.java @@ -1,3 +1,23 @@ +/* + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.analysis; import static org.testng.AssertJUnit.assertEquals; @@ -94,7 +114,7 @@ public class DnaTest * * @throws IOException */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testTranslateCdna_withUntranslatableCodons() throws IOException { @@ -103,8 +123,7 @@ public class DnaTest "FASTA"); ColumnSelection cs = new ColumnSelection(); AlignViewportI av = new AlignViewport(alf, cs); - Dna dna = new Dna(av, new int[] - { 0, alf.getWidth() - 1 }); + Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 }); AlignmentI translated = dna.translateCdna(); assertNotNull("Couldn't do a full width translation of test data.", translated); @@ -116,7 +135,7 @@ public class DnaTest * * @throws IOException */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns() throws IOException { @@ -152,15 +171,14 @@ public class DnaTest * * @throws IOException */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testTranslateCdna_simple() throws IOException { AlignmentI alf = new FormatAdapter().readFile(fasta, FormatAdapter.PASTE, "FASTA"); ColumnSelection cs = new ColumnSelection(); AlignViewportI av = new AlignViewport(alf, cs); - Dna dna = new Dna(av, new int[] - { 0, alf.getWidth() - 1 }); + Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 }); AlignmentI translated = dna.translateCdna(); String aa = translated.getSequenceAt(0).getSequenceAsString(); assertEquals( @@ -173,7 +191,7 @@ public class DnaTest * * @throws IOException */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testTranslateCdna_hiddenColumns() throws IOException { AlignmentI alf = new FormatAdapter().readFile(fasta, @@ -183,8 +201,7 @@ public class DnaTest cs.hideColumns(24, 35); // hide codons 9-12 cs.hideColumns(177, 191); // hide codons 60-64 AlignViewportI av = new AlignViewport(alf, cs); - Dna dna = new Dna(av, new int[] - { 0, alf.getWidth() - 1 }); + Dna dna = new Dna(av, new int[] { 0, alf.getWidth() - 1 }); AlignmentI translated = dna.translateCdna(); String aa = translated.getSequenceAt(0).getSequenceAsString(); assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa); @@ -193,7 +210,7 @@ public class DnaTest /** * Use this test to help debug into any cases of interest. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testCompareCodonPos_oneOnly() { assertFollows("-AA--A", "G--GG"); // 2 shifted seq2, 3 shifted seq1 @@ -202,7 +219,7 @@ public class DnaTest /** * Tests for method that compares 'alignment' of two codon position triplets. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testCompareCodonPos() { /* @@ -259,7 +276,7 @@ public class DnaTest * reorders the cDNA and retranslates, and verifies that the translations are * the same (apart from ordering). */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testTranslateCdna_sequenceOrderIndependent() { /* @@ -268,16 +285,14 @@ public class DnaTest AlignmentI cdna = new DnaAlignmentGenerator().generate(12, 8, 97, 5, 5); ColumnSelection cs = new ColumnSelection(); AlignViewportI av = new AlignViewport(cdna, cs); - Dna dna = new Dna(av, new int[] - { 0, cdna.getWidth() - 1 }); + Dna dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 }); AlignmentI translated = dna.translateCdna(); /* * Jumble the cDNA sequences and translate. */ SequenceI[] sorted = new SequenceI[cdna.getHeight()]; - final int[] jumbler = new int[] - { 6, 7, 3, 4, 2, 0, 1, 5 }; + final int[] jumbler = new int[] { 6, 7, 3, 4, 2, 0, 1, 5 }; int seqNo = 0; for (int i : jumbler) { @@ -285,8 +300,7 @@ public class DnaTest } AlignmentI cdnaReordered = new Alignment(sorted); av = new AlignViewport(cdnaReordered, cs); - dna = new Dna(av, new int[] - { 0, cdna.getWidth() - 1 }); + dna = new Dna(av, new int[] { 0, cdna.getWidth() - 1 }); AlignmentI translated2 = dna.translateCdna(); /* @@ -302,8 +316,8 @@ public class DnaTest { final String translation1 = translated.getSequenceAt( originalSequenceIndex).getSequenceAsString(); - final String translation2 = translated2.getSequenceAt(sortedSequenceIndex) - .getSequenceAsString(); + final String translation2 = translated2.getSequenceAt( + sortedSequenceIndex).getSequenceAsString(); assertEquals(translation2, translation1); sortedSequenceIndex++; } @@ -313,7 +327,7 @@ public class DnaTest * Test that all the cases in testCompareCodonPos have a 'symmetric' * comparison (without checking the actual comparison result). */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testCompareCodonPos_isSymmetric() { assertSymmetric("AAA", "GGG"); @@ -436,7 +450,7 @@ public class DnaTest /** * Weirdly, maybe worth a test to prove the helper method of this test class. */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testConvertCodon() { assertEquals("[0, 1, 2]", convertCodon("AAA").toString());