X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FDnaTranslation.java;h=74ec4614e543f89b14bbd66502b039fa70a7e516;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=a58131c27db69cfe0c975a0ee4b8fc4126050a45;hpb=ea06798f6752c3156ed4618d4b706821e681b353;p=jalview.git
diff --git a/test/jalview/analysis/DnaTranslation.java b/test/jalview/analysis/DnaTranslation.java
index a58131c..74ec461 100644
--- a/test/jalview/analysis/DnaTranslation.java
+++ b/test/jalview/analysis/DnaTranslation.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.junit.Assert.*;
@@ -13,86 +31,114 @@ 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());
+ }
+
+ }
}