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<SequenceI> seqs = parser.getSeqs();
assertEquals(seqs.size(), 1);
}
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<SequenceI> seqs = parser.getSeqs();
+ assertTrue(seqs.get(0).getSequenceAsString().indexOf("u")>-1);
+ }
@Test(groups = "Functional")
public void testParse_codonStartNot1()
+ " ggatGcgtaa gttagacgaa attttgtctt tgcgcacaga 40\n";
FileParse fp = new FileParse(data, DataSourceType.PASTE);
EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
- parser.parse();
List<SequenceI> seqs = parser.getSeqs();
assertEquals(seqs.size(), 1);
SequenceI seq = seqs.get(0);