import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import java.util.List;
+
import org.testng.annotations.Test;
public class DBRefUtilsTest
SequenceI seq = new Sequence("Seq1", "ABCD");
DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
"1WRI A; 7-80;");
+ // TODO: correct PDBEntry and PDB DBRef accessions need to be generated for
+ // PDB ref in Stockholm
+
DBRefEntry[] refs = seq.getDBRefs();
assertEquals(1, refs.length);
assertSame(ref, refs[0]);
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
- DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
- ref2, ref3, ref4, ref5 }, target);
- assertEquals(3, matches.length);
- assertSame(ref1, matches[0]);
- assertSame(ref2, matches[1]);
- assertSame(ref5, matches[2]);
+ List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
+ ref1, ref2, ref3, ref4, ref5 }, target);
+ assertEquals(3, matches.size());
+ assertSame(ref1, matches.get(0));
+ assertSame(ref2, matches.get(1));
+ assertSame(ref5, matches.get(2));
}
/**
new int[] { 1, 1 }, 2, 2));
ref3.setMap(map3);
- DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
- ref2, ref3 }, target);
- assertEquals(2, matches.length);
- assertSame(ref1, matches[0]);
- assertSame(ref2, matches[1]);
+ List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
+ ref1, ref2, ref3 }, target);
+ assertEquals(2, matches.size());
+ assertSame(ref1, matches.get(0));
+ assertSame(ref2, matches.get(1));
}
/**
@Test(groups = { "Functional" })
public void testSearchRefs_accessionid()
{
-
+
DBRefEntry ref1 = new DBRefEntry("Uniprot", "1", "A1234"); // matches
DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1234"); // matches
// constructor does not upper-case accession id
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
-
- DBRefEntry[] dbrefs = new DBRefEntry[] { ref1,
- ref2, ref3, ref4, ref5 };
- DBRefEntry[] matches = DBRefUtils.searchRefs(dbrefs, "A1234");
- assertEquals(3, matches.length);
- assertSame(ref1, matches[0]);
- assertSame(ref2, matches[1]);
- assertSame(ref5, matches[2]);
+
+ DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5 };
+ List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
+ assertEquals(3, matches.size());
+ assertSame(ref1, matches.get(0));
+ assertSame(ref2, matches.get(1));
+ assertSame(ref5, matches.get(2));
}
/**
public void testSearchRefs_wildcardAccessionid()
{
DBRefEntry target = new DBRefEntry("EMBL", "2", null);
-
+
DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // matches
// constructor changes embl to EMBL
DBRefEntry ref2 = new DBRefEntry("embl", "1", "A1235"); // matches
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
1 }, 1, 1)));
-
- DBRefEntry[] matches = DBRefUtils.searchRefs(new DBRefEntry[] { ref1,
- ref2, ref3, ref4, ref5 }, target);
- assertEquals(4, matches.length);
- assertSame(ref1, matches[0]);
- assertSame(ref2, matches[1]);
- assertSame(ref3, matches[2]);
- assertSame(ref5, matches[3]);
+
+ List<DBRefEntry> matches = DBRefUtils.searchRefs(new DBRefEntry[] {
+ ref1, ref2, ref3, ref4, ref5 }, target);
+ assertEquals(4, matches.size());
+ assertSame(ref1, matches.get(0));
+ assertSame(ref2, matches.get(1));
+ assertSame(ref3, matches.get(2));
+ assertSame(ref5, matches.get(3));
}
}