X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Fio%2FEmblFlatFileTest.java;h=7775c8f3c10c0da55da7f71f889f719688113ec0;hb=d85279450741df748b662ca0e7757a489b8c6d01;hp=c893c09bef9d8c26fd9429c68d3368c921ef2d4f;hpb=da62703518a88707b9144bc51e50d6af7093a7c7;p=jalview.git diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java index c893c09..7775c8f 100644 --- a/test/jalview/io/EmblFlatFileTest.java +++ b/test/jalview/io/EmblFlatFileTest.java @@ -47,7 +47,6 @@ public class EmblFlatFileTest File dataFile = new File("test/jalview/io/J03321.embl.txt"); FileParse fp = new FileParse(dataFile, DataSourceType.FILE); EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest"); - parser.parse(); List seqs = parser.getSeqs(); assertEquals(seqs.size(), 1); @@ -231,6 +230,22 @@ public class EmblFlatFileTest } assertEquals(uniprotCount, 8); } + /** + * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features, + * one of them reverse strand + * + * @throws MalformedURLException + * @throws IOException + */ + @Test(groups = "Functional") + public void testParseToRNA() throws MalformedURLException, IOException + { + File dataFile = new File("test/jalview/io/J03321_rna.embl.txt"); + FileParse fp = new FileParse(dataFile, DataSourceType.FILE); + EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest"); + List seqs = parser.getSeqs(); + assertTrue(seqs.get(0).getSequenceAsString().indexOf("u")>-1); + } @Test(groups = "Functional") public void testParse_codonStartNot1() @@ -263,7 +278,6 @@ public class EmblFlatFileTest + " ggatGcgtaa gttagacgaa attttgtctt tgcgcacaga 40\n"; FileParse fp = new FileParse(data, DataSourceType.PASTE); EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest"); - parser.parse(); List seqs = parser.getSeqs(); assertEquals(seqs.size(), 1); SequenceI seq = seqs.get(0);