import jalview.util.MapList;
import jalview.ws.SequenceFetcher;
import jalview.ws.SequenceFetcherFactory;
+import jalview.ws.params.InvalidArgumentException;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import org.testng.annotations.AfterClass;
DBRefEntry ref8 = new DBRefEntry("PFAM", "1", "A123");
// ENSEMBL is a source of either dna or protein sequence data
DBRefEntry ref9 = new DBRefEntry("ENSEMBL", "1", "A123");
- DBRefEntry[] refs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5,
- ref6, ref7, ref8, ref9 };
+ List<DBRefEntry> refs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5,
+ ref6, ref7, ref8, ref9 });
/*
* Just the DNA refs:
*/
- DBRefEntry[] found = DBRefUtils.selectDbRefs(true, refs);
- assertEquals(4, found.length);
- assertSame(ref5, found[0]);
- assertSame(ref6, found[1]);
- assertSame(ref7, found[2]);
- assertSame(ref9, found[3]);
+ List<DBRefEntry> found = DBRefUtils.selectDbRefs(true, refs);
+ assertEquals(4, found.size());
+ assertSame(ref5, found.get(0));
+ assertSame(ref6, found.get(1));
+ assertSame(ref7, found.get(2));
+ assertSame(ref9, found.get(3));
/*
* Just the protein refs:
*/
found = DBRefUtils.selectDbRefs(false, refs);
- assertEquals(4, found.length);
- assertSame(ref1, found[0]);
- assertSame(ref2, found[1]);
- assertSame(ref4, found[2]);
- assertSame(ref9, found[3]);
+ assertEquals(4, found.size());
+ assertSame(ref1, found.get(0));
+ assertSame(ref2, found.get(1));
+ assertSame(ref4, found.get(2));
+ assertSame(ref9, found.get(3));
}
/**
* and others to dna coding databases
*/
sources.clear();
- seq.setDBRefs(null);
+ seq.setDBRefs(null);
seq.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234"));
seq.addDBRef(new DBRefEntry("EMBLCDS", "0", "E2347"));
SequenceI seq2 = new Sequence("Seq2", "MGKYQARLSS");
CrossRef testee = new CrossRef(al.getSequencesArray(), al);
AlignedCodonFrame acf = new AlignedCodonFrame();
boolean found = testee.searchDataset(true, dna1, dbref, result, acf,
- true);
+ true, DBRefUtils.SEARCH_MODE_FULL);
assertFalse(found);
assertTrue(result.isEmpty());
assertTrue(acf.isEmpty());
acf = new AlignedCodonFrame();
dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result,
- acf, false); // search dataset with a protein xref from a dna
+ acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein xref from a dna
// sequence to locate the protein product
assertTrue(found);
assertEquals(1, result.size());
acf = new AlignedCodonFrame();
dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result,
- acf, false); // search dataset with a protein's direct dbref to
+ acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein's direct dbref to
// locate dna sequences with matching xref
assertTrue(found);
assertEquals(1, result.size());
/*
* verify mappings added to Uniprot-to-EMBL dbrefs
*/
- Mapping mapping = p0ce19.getDBRefs()[0].getMap();
+ Mapping mapping = p0ce19.getDBRefs().get(0).getMap();
assertSame(j03321, mapping.getTo());
- mapping = p0ce19.getDBRefs()[1].getMap();
+ mapping = p0ce19.getDBRefs().get(1).getMap();
assertSame(x06707, mapping.getTo());
- mapping = p0ce20.getDBRefs()[0].getMap();
+ mapping = p0ce20.getDBRefs().get(0).getMap();
assertSame(j03321, mapping.getTo());
- mapping = p0ce20.getDBRefs()[1].getMap();
+ mapping = p0ce20.getDBRefs().get(1).getMap();
assertSame(x06707, mapping.getTo());
/*
* verify dbrefs on EMBL are mapped to alignment seqs
*/
- assertSame(p0ce19, j03321.getDBRefs()[0].getMap().getTo());
- assertSame(p0ce20, j03321.getDBRefs()[1].getMap().getTo());
- assertSame(p0ce19, x06707.getDBRefs()[0].getMap().getTo());
- assertSame(p0ce20, x06707.getDBRefs()[1].getMap().getTo());
+
+ assertSame(p0ce19, j03321.getDBRefs().get(0).getMap().getTo());
+ assertSame(p0ce20, j03321.getDBRefs().get(1).getMap().getTo());
+ assertSame(p0ce19, x06707.getDBRefs().get(0).getMap().getTo());
+ assertSame(p0ce20, x06707.getDBRefs().get(1).getMap().getTo());
/*
* verify new dbref on EMBL dbref mapping is copied to the
* original Uniprot sequence
*/
- assertEquals(4, p0ce19.getDBRefs().length);
- assertEquals("PIR", p0ce19.getDBRefs()[3].getSource());
- assertEquals("S01875", p0ce19.getDBRefs()[3].getAccessionId());
+ assertEquals(4, p0ce19.getDBRefs().size());
+ assertEquals("PIR", p0ce19.getDBRefs().get(3).getSource());
+ assertEquals("S01875", p0ce19.getDBRefs().get(3).getAccessionId());
}
@Test(groups = "Functional")