import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.fail;
-import static org.testng.AssertJUnit.assertNull;
import java.io.File;
import java.io.IOException;
import java.util.List;
import java.util.Set;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.Sequence.DBModList;
public class EmblFlatFileTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ Cache.initLogger();
+ }
+
/**
* A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
* one of them reverse strand
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((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1579);
- assertEquals(ranges.get(0)[1], 2934);
+ assertEquals(ranges.get(0)[1], 2931); // excludes stop 2934
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 451);
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 2928);
- assertEquals(ranges.get(0)[1], 3992);
+ assertEquals(ranges.get(0)[1], 3989); // excludes stop 3992
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 354);
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 4054);
- assertEquals(ranges.get(0)[1], 4848);
+ assertEquals(ranges.get(0)[1], 4845); // excludes stop 4848
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 264);
assertEquals(ranges.get(0)[0], 7022);
assertEquals(ranges.get(0)[1], 7502);
assertEquals(ranges.get(1)[0], 1);
- assertEquals(ranges.get(1)[1], 437);
+ assertEquals(ranges.get(1)[1], 434); // excludes stop at 437
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 305);
// complement(488..1480)
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1480);
- assertEquals(ranges.get(0)[1], 488);
+ assertEquals(ranges.get(0)[1], 491); // // excludes stop at 488
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 330);
}
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);
// exact length match:
assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons));
- // match if we assume exons include stop codon not in protein:
- assertSame(exons, EmblFlatFile.adjustForProteinLength(5, exons));
-
+ // patch from JAL-3725 in EmblXmlSource propagated to Flatfile
+ // match if we assume exons include stop codon not in protein:
+ int[] truncated = EmblFlatFile.adjustForProteinLength(5, exons);
+ assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 35]");
+
// truncate last exon by 6bp
- int[] truncated = EmblFlatFile.adjustForProteinLength(4, exons);
- assertEquals("[11, 15, 21, 25, 31, 32]", Arrays.toString(truncated));
+ truncated = EmblFlatFile.adjustForProteinLength(4, exons);
+ assertEquals(Arrays.toString(truncated),"[11, 15, 21, 25, 31, 32]");
// remove last exon and truncate preceding by 1bp (so 3bp in total)
truncated = EmblFlatFile.adjustForProteinLength(3, exons);
- assertEquals("[11, 15, 21, 24]", Arrays.toString(truncated));
+ assertEquals(Arrays.toString(truncated),"[11, 15, 21, 24]");
// exact removal of exon case:
exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
truncated = EmblFlatFile.adjustForProteinLength(4, exons);
- assertEquals("[11, 15, 21, 27]", Arrays.toString(truncated));
+ assertEquals(Arrays.toString(truncated), "[11, 15, 21, 27]");
// what if exons are too short for protein?
truncated = EmblFlatFile.adjustForProteinLength(7, exons);