import java.io.File;
import java.io.IOException;
import java.net.MalformedURLException;
-import java.util.Arrays;
import java.util.List;
import java.util.Set;
File dataFile = new File("test/jalview/io/J03321.gb");
FileParse fp = new FileParse(dataFile.getAbsolutePath(),
DataSourceType.FILE);
- FlatFile parser = new GenBankFile(fp, "GenBankTest");
- parser.parse();
+ EMBLLikeFlatFile parser = new GenBankFile(fp, "GenBankTest");
List<SequenceI> seqs = parser.getSeqs();
assertEquals(seqs.size(), 1);
* xref to self : 1
* protein products: 8
*/
- List<DBRefEntry> dbrefs = Arrays.asList(seq.getDBRefs());
+ List<DBRefEntry> dbrefs = seq.getDBRefs();
assertEquals(dbrefs.size(), 9);
// xref to 'self':
assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
assertEquals(dbref.getAccessionId(), "AAA91574.1");
mapping = dbref.getMap();
- mapTo = mapping.getTo();
+ mapTo = mapping.getTo();
assertEquals(mapTo.getName(), "AAA91574.1");
// the /product qualifier transfers to protein product description
assertEquals(mapTo.getDescription(), "hypothetical protein");