From: Jim Procter Date: Mon, 17 Jun 2013 14:10:22 +0000 (+0100) Subject: JAL-1312 formatting and more comprehensive test X-Git-Tag: Jalview_2_9~240^2~6 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=7e463aa5bd5225620ab909fb4890aa4a98b4a3af JAL-1312 formatting and more comprehensive test --- diff --git a/test/jalview/analysis/DnaTranslation.java b/test/jalview/analysis/DnaTranslation.java index a58131c..d29ee15 100644 --- a/test/jalview/analysis/DnaTranslation.java +++ b/test/jalview/analysis/DnaTranslation.java @@ -13,86 +13,114 @@ import org.junit.runner.RunWith; public class DnaTranslation { - private static String JAL_1312_example_align_fasta = - ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n" - +"ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n" - +"GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n" - +"GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n" - +"TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n" - +">gi|27804621|gb|AY178912.1|/1-259\n" - +"-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n" - +"AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n" - +"GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" - +"TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n" - +">gi|27804623|gb|AY178913.1|/1-259\n" - +"-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n" - +"AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n" - +"GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" - +"TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n" - +">gi|27804627|gb|AY178915.1|/1-260\n" - +"-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n" - +"GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n" - +"GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n" - +"TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n" - +">gi|27804631|gb|AY178917.1|/1-261\n" - +"-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n" - +"GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n" - +"GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" - +"TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n" - +">gi|27804635|gb|AY178919.1|/1-261\n" - +"-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n" - +"AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n" - +"GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" - +"TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n" - +">gi|27804641|gb|AY178922.1|/1-261\n" - +"-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n" - +"GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n" - +"GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" - +"TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n" - +">gi|27804647|gb|AY178925.1|/1-261\n" - +"-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n" - +"GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n" - +"GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n" - +"TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n" - +">gi|27804649|gb|AY178926.1|/1-261\n" - +"-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n" - +"GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n" - +"GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n" - +"TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n" - +">gi|27804653|gb|AY178928.1|/1-261\n" - +"-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n" - +"GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n" - +"GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n" - +"TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n" - +">gi|27804659|gb|AY178931.1|/1-261\n" - +"-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n" - +"GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n" - +"GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" - +"TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n"; + private static String JAL_1312_example_align_fasta = ">B.FR.83.HXB2_LAI_IIIB_BRU_K03455/45-306\n" + + "ATGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAATTAAAACATATAGTATGGGCAAGCAG\n" + + "GGAGCTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATACTGGGACA\n" + + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAGTAGCAACCCTCTATTG\n" + + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAC\n" + + ">gi|27804621|gb|AY178912.1|/1-259\n" + + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n" + + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGGACA\n" + + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" + + "TGTTCATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAT\n" + + ">gi|27804623|gb|AY178913.1|/1-259\n" + + "-TGGGAGAA-ATTCGGTT-CGGCCAGGGGGAAAGAAAAAATATCAGTTAAAACATATAGTATGGGCAAGCAG\n" + + "AGAGCTAGAACGATTCGCAGTTAACCCTGGCCTTTTAGAGACATCACAAGGCTGTAGACAAATACTGGAACA\n" + + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" + + "TGTTCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n" + + ">gi|27804627|gb|AY178915.1|/1-260\n" + + "-TGGGAAAA-ATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n" + + "GGAGCTAGAACGATTCGCAGTTAACCCTGGCCTGTTAGAAACATCAGAAGGTTGTAGACAAATATTGGGACA\n" + + "GCTACAACCATCCCTTGAGACAGGATCAGAAGAACTTAAATCATTATWTAATACCATAGCAGTCCTCTATTG\n" + + "TGTACATCAAAGGATAGATATAAAAGACACCAAGGAAGCTTTAGAG\n" + + ">gi|27804631|gb|AY178917.1|/1-261\n" + + "-TGGGAAAAAATTCGGTTGAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n" + + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACACCAGAAGGCTGTAGACAAATACTGGGACA\n" + + "GCTACAACCGTCCCTTCAGACAGGATCGGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" + + "TGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAGGCTTTAGAC\n" + + ">gi|27804635|gb|AY178919.1|/1-261\n" + + "-TGGGAGAGAATTCGGTTACGGCCAGGAGGAAAGAAAAAATATAAATTGAAACATATAGTATGGGCAGGCAG\n" + + "AGAGCTAGATCGATTCGCAGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAGATATTGGGACA\n" + + "GCTACAACCGTCCCTTAAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" + + "TGTACATCAAAGGATAGATGTAAAAGACACCAAGGAAGCTTTAGAT\n" + + ">gi|27804641|gb|AY178922.1|/1-261\n" + + "-TGGGAGAAAATTCGGTTACGGCCAGGGGGAAAGAAAAGATATAAGTTAAAACATATAGTATGGGCAAGCAG\n" + + "GGAGCTAGAACGATTCGCAGTCAACCCTGGCCTGTTAGAAACATCAGAAGGCTGCAGACAAATACTGGGACA\n" + + "GTTACACCCATCCCTTCATACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" + + "TGTGCATCAAAGGATAGAAGTAAAAGACACCAAGGAAGCTTTAGAC\n" + + ">gi|27804647|gb|AY178925.1|/1-261\n" + + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATCAATTAAAACATGTAGTATGGGCAAGCAG\n" + + "GGAACTAGAACGATTCGCAGTTAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n" + + "GCTACAACCATCCCTTCAGACAGGATCAGAGGAACTTAAATCATTATTTAATACAGTAGCAGTCCTCTATTG\n" + + "TGTACATCAAAGAATAGATGTAAAAGACACCAAGGAAGCTCTAGAA\n" + + ">gi|27804649|gb|AY178926.1|/1-261\n" + + "-TGGGAAAAAATTCGGTTAAGGCCAGGGGGAAAGAAAAAATATAAGTTAAAACATATAGTATGGGCAAGCAG\n" + + "GGAGCTAGAACGATTCGCGGTCAATCCTGGCCTGTTAGAAACATCAGAAGGCTGTAGACAACTACTGGGACA\n" + + "GTTACAACCATCCCTTCAGACAGGATCAGAAGAACTCAAATCATTATATAATACAATAGCAACCCTCTATTG\n" + + "TGTGCATCAAAGGATAGAGATAAAAGACACCAAGGAAGCCTTAGAT\n" + + ">gi|27804653|gb|AY178928.1|/1-261\n" + + "-TGGGAAAGAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAATTAAAACATATAGTATGGGCAAGCAG\n" + + "GGAGCTAGACCGATTCGCACTTAACCCCGGCCTGTTAGAAACATCAGAAGGCTGTAGACAAATATTGGGACA\n" + + "GCTACAATCGTCCCTTCAGACAGGATCAGAAGAACTTAGATCACTATATAATACAGTAGCAGTCCTCTATTG\n" + + "TGTGCATCAAAAGATAGATGTAAAAGACACCAAGGAAGCCTTAGAC\n" + + ">gi|27804659|gb|AY178931.1|/1-261\n" + + "-TGGGAAAAAATTCGGTTACGGCCAGGAGGAAAGAAAAGATATAAATTAAAACATATAGTATGGGCAAGCAG\n" + + "GGAGCTAGAACGATTYGCAGTTAATCCTGGCCTTTTAGAAACAGCAGAAGGCTGTAGACAAATACTGGGACA\n" + + "GCTACAACCATCCCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGTAGCAACCCTCTATTG\n" + + "TGTACATCAAAGGATAGAGATAAAAGACACCAAGGAAGCTTTAGAA\n"; + + @Test - public void translationWithUntranslatableCodonsTest() { - // Corner case for this test is the presence of codons after codons that were not translated. - try { - jalview.datamodel.AlignmentI alf = new jalview.io.FormatAdapter().readFile(JAL_1312_example_align_fasta, jalview.io.FormatAdapter.PASTE, "FASTA"); - int vwidth=15; // translate in 15 base stretches - for (int ipos=0;ipos+vwidth0) { cs.hideColumns(0,ipos-1); } - cs.hideColumns(ipos+vwidth,alf.getWidth()); - int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth()); - String[] sel = cs.getVisibleSequenceStrings(0, alf.getWidth(), alf.getSequencesArray()); - jalview.datamodel.AlignmentI transAlf = jalview.analysis.Dna.CdnaTranslate(alf.getSequencesArray(), sel, - vcontigs, alf.getGapCharacter(),null, alf.getWidth(), null); - - assertTrue("Translation failed (ipos="+ipos+") No alignment data.",transAlf!=null); - assertTrue("Translation failed (ipos="+ipos+") Empty algnment.",transAlf.getHeight()>0); - assertTrue("Translation failed (ipos="+ipos+") Translated "+transAlf.getHeight()+" sequences from "+alf.getHeight()+" sequences",alf.getHeight()==transAlf.getHeight()); - } + public void translationWithUntranslatableCodonsTest() + { + // Corner case for this test is the presence of codons after codons that + // were not translated. + jalview.datamodel.AlignmentI alf = null; + try + { + alf = new jalview.io.FormatAdapter().readFile(JAL_1312_example_align_fasta, + jalview.io.FormatAdapter.PASTE, "FASTA"); } catch (IOException x) { x.printStackTrace(); - fail("Unexpected IOException ("+x.getMessage()+") - check test environment"); + fail("Unexpected IOException (" + x.getMessage() + + ") - check test environment"); } - } + { + // full translation + ColumnSelection cs = new jalview.datamodel.ColumnSelection(); + assertNotNull("Couldn't do a full width translation of test data.", + jalview.analysis.Dna.CdnaTranslate( + alf.getSequencesArray(), + cs.getVisibleSequenceStrings(0, alf.getWidth(), + alf.getSequencesArray()), new int[] + { 0, alf.getWidth() - 1 }, alf.getGapCharacter(), + null, alf.getWidth(), null)); + } + int vwidth = 15; // translate in 15 base stretches + for (int ipos = 0; ipos + vwidth < alf.getWidth(); ipos += vwidth) + { + ColumnSelection cs = new jalview.datamodel.ColumnSelection(); + if (ipos > 0) + { + cs.hideColumns(0, ipos - 1); + } + cs.hideColumns(ipos + vwidth, alf.getWidth()); + int[] vcontigs = cs.getVisibleContigs(0, alf.getWidth()); + String[] sel = cs.getVisibleSequenceStrings(0, alf.getWidth(), + alf.getSequencesArray()); + jalview.datamodel.AlignmentI transAlf = jalview.analysis.Dna + .CdnaTranslate(alf.getSequencesArray(), sel, vcontigs, + alf.getGapCharacter(), null, alf.getWidth(), null); + assertTrue("Translation failed (ipos=" + ipos + + ") No alignment data.", transAlf != null); + assertTrue("Translation failed (ipos=" + ipos + ") Empty algnment.", + transAlf.getHeight() > 0); + assertTrue("Translation failed (ipos=" + ipos + ") Translated " + + transAlf.getHeight() + " sequences from " + alf.getHeight() + + " sequences", alf.getHeight() == transAlf.getHeight()); + } + + } }