X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FDnaTest.java;h=18515174a4e971d12db4e4b91336d54132dd75f1;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=55908dd9ca94970c6136bdff9fd0b0a1de99127a;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java index 55908dd..1851517 100644 --- a/test/jalview/analysis/DnaTest.java +++ b/test/jalview/analysis/DnaTest.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.analysis; import static org.testng.AssertJUnit.assertEquals; @@ -9,6 +29,7 @@ import jalview.datamodel.AlignedCodon; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.gui.AlignViewport; import jalview.io.FormatAdapter; @@ -94,7 +115,7 @@ public class DnaTest * * @throws IOException */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testTranslateCdna_withUntranslatableCodons() throws IOException { @@ -103,8 +124,7 @@ 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 +136,7 @@ public class DnaTest * * @throws IOException */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testTranslateCdna_withUntranslatableCodonsAndHiddenColumns() throws IOException { @@ -148,23 +168,22 @@ public class DnaTest } /** - * Test simple translation to Amino Acids (with STOP codons translated to X). + * Test simple translation to Amino Acids (with STOP codons translated to *). * * @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( - "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYYXXX", + "AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***", aa); } @@ -173,7 +192,7 @@ 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 +202,7 @@ 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 +211,7 @@ 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 +220,7 @@ 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 +277,7 @@ 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 +286,14 @@ 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 +301,7 @@ 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 +317,8 @@ 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 +328,7 @@ 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"); @@ -436,11 +451,92 @@ 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()); assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString()); assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString()); } + + /** + * Test dna complementing + */ + @Test(groups = "Functional") + public void testGetComplement() + { + assertEquals('t', Dna.getComplement('a')); + assertEquals('T', Dna.getComplement('A')); + assertEquals('a', Dna.getComplement('t')); + assertEquals('A', Dna.getComplement('T')); + assertEquals('c', Dna.getComplement('g')); + assertEquals('C', Dna.getComplement('G')); + assertEquals('g', Dna.getComplement('c')); + assertEquals('G', Dna.getComplement('C')); + // note uU --> aA but not vice versa + assertEquals('a', Dna.getComplement('u')); + assertEquals('A', Dna.getComplement('U')); + // ambiguity codes, see http://www.bioinformatics.org/sms/iupac.html + assertEquals('r', Dna.getComplement('y')); + assertEquals('R', Dna.getComplement('Y')); + assertEquals('y', Dna.getComplement('r')); + assertEquals('Y', Dna.getComplement('R')); + assertEquals('k', Dna.getComplement('m')); + assertEquals('K', Dna.getComplement('M')); + assertEquals('m', Dna.getComplement('k')); + assertEquals('M', Dna.getComplement('K')); + assertEquals('b', Dna.getComplement('v')); + assertEquals('B', Dna.getComplement('V')); + assertEquals('v', Dna.getComplement('b')); + assertEquals('V', Dna.getComplement('B')); + assertEquals('d', Dna.getComplement('h')); + assertEquals('D', Dna.getComplement('H')); + assertEquals('h', Dna.getComplement('d')); + assertEquals('H', Dna.getComplement('D')); + assertEquals('Q', Dna.getComplement('Q')); + } + + @Test(groups = "Functional") + public void testReverseSequence() + { + String seq = "-Ac-GtU--rYkMbVdHNX-"; + String seqRev = new StringBuilder(seq).reverse().toString(); + + // reverse: + SequenceI reversed = Dna.reverseSequence("Seq1", seq, false); + assertEquals(1, reversed.getStart()); + assertEquals(15, reversed.getEnd()); + assertEquals(20, reversed.getLength()); + assertEquals(seqRev, reversed.getSequenceAsString()); + assertEquals("Seq1|rev", reversed.getName()); + + // reverse complement: + SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true); + assertEquals("-XNDhBvKmRy--AaC-gT-", revcomp.getSequenceAsString()); + assertEquals("Seq1|revcomp", revcomp.getName()); + } + + @Test(groups = "Functional") + public void testReverseCdna() + { + String seq = "-Ac-GtU--rYkMbVdHNX-"; + String seqRev = new StringBuilder(seq).reverse().toString(); + String seqDs = seq.replaceAll("-", ""); + String seqDsRev = new StringBuilder(seqDs).reverse().toString(); + + SequenceI dna = new Sequence("Seq1", seq); + Alignment al = new Alignment(new SequenceI[] { dna }); + al.createDatasetAlignment(); + assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence() + .getSequenceAsString()); + + ColumnSelection cs = new ColumnSelection(); + AlignViewportI av = new AlignViewport(al, cs); + Dna testee = new Dna(av, new int[] { 0, al.getWidth() - 1 }); + AlignmentI reversed = testee.reverseCdna(false); + assertEquals(1, reversed.getHeight()); + assertEquals(seqRev, reversed.getSequenceAt(0).getSequenceAsString()); + assertEquals(seqDsRev, reversed.getSequenceAt(0).getDatasetSequence() + .getSequenceAsString()); + } }