From ea06798f6752c3156ed4618d4b706821e681b353 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 17 Jun 2013 10:21:32 +0100 Subject: [PATCH] test for JAL-1312 --- test/jalview/analysis/DnaTranslation.java | 98 +++++++++++++++++++++++++++++ 1 file changed, 98 insertions(+) create mode 100644 test/jalview/analysis/DnaTranslation.java diff --git a/test/jalview/analysis/DnaTranslation.java b/test/jalview/analysis/DnaTranslation.java new file mode 100644 index 0000000..a58131c --- /dev/null +++ b/test/jalview/analysis/DnaTranslation.java @@ -0,0 +1,98 @@ +package jalview.analysis; + +import static org.junit.Assert.*; +import jalview.datamodel.ColumnSelection; + +import java.io.IOException; + +import org.junit.AfterClass; +import org.junit.BeforeClass; +import org.junit.Test; +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"; + @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()); + } + } catch (IOException x) + { + x.printStackTrace(); + fail("Unexpected IOException ("+x.getMessage()+") - check test environment"); + } + } + +} -- 1.7.10.2