X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;fp=test%2Fjalview%2Futil%2FDBRefUtilsTest.java;h=f92e454d83ba0932e11e50c62a9d2721613add1b;hb=4898f0ae429e0c61ddba72ca46be89b34bb4df8b;hp=0368d1ebb697f99bcef122c8f6a76b30a71e5153;hpb=5a6ac5b535856903629234ad43a71319a91ebee5;p=jalview.git diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java index 0368d1e..f92e454 100644 --- a/test/jalview/util/DBRefUtilsTest.java +++ b/test/jalview/util/DBRefUtilsTest.java @@ -33,6 +33,7 @@ import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.gui.JvOptionPane; +import java.util.Arrays; import java.util.List; import org.testng.annotations.BeforeClass; @@ -62,25 +63,25 @@ public class DBRefUtilsTest DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346"); // Source is converted to upper-case by this constructor! DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347"); - DBRefEntry[] dbrefs = new DBRefEntry[] { ref1, ref2, ref3 }; + List dbrefs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3 }); String[] sources = new String[] { "EMBL", "UNIPROT" }; - DBRefEntry[] selected = DBRefUtils.selectRefs(dbrefs, sources); - assertEquals(3, selected.length); - assertSame(ref1, selected[0]); - assertSame(ref2, selected[1]); - assertSame(ref3, selected[2]); + List selected = DBRefUtils.selectRefs(dbrefs, sources); + assertEquals(3, selected.size()); + assertSame(ref1, selected.get(0)); + assertSame(ref2, selected.get(1)); + assertSame(ref3, selected.get(2)); sources = new String[] { "EMBL" }; selected = DBRefUtils.selectRefs(dbrefs, sources); - assertEquals(1, selected.length); - assertSame(ref1, selected[0]); + assertEquals(1, selected.size()); + assertSame(ref1, selected.get(0)); sources = new String[] { "UNIPROT" }; selected = DBRefUtils.selectRefs(dbrefs, sources); - assertEquals(2, selected.length); - assertSame(ref2, selected[0]); - assertSame(ref3, selected[1]); + assertEquals(2, selected.size()); + assertSame(ref2, selected.get(0)); + assertSame(ref3, selected.get(1)); sources = new String[] { "EMBLCDS" }; selected = DBRefUtils.selectRefs(dbrefs, sources); @@ -88,10 +89,10 @@ public class DBRefUtilsTest sources = new String[] { "embl", "uniprot" }; selected = DBRefUtils.selectRefs(dbrefs, sources); - assertEquals(3, selected.length); - assertSame(ref1, selected[0]); - assertSame(ref2, selected[1]); - assertSame(ref3, selected[2]); + assertEquals(3, selected.size()); + assertSame(ref1, selected.get(0)); + assertSame(ref2, selected.get(1)); + assertSame(ref3, selected.get(2)); } /** @@ -128,13 +129,18 @@ public class DBRefUtilsTest { SequenceI seq = new Sequence("Seq1", "ABCD"); DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890"); - DBRefEntry[] refs = seq.getDBRefs(); - assertEquals(1, refs.length); - assertSame(ref, refs[0]); + List refs = seq.getDBRefs(); + assertEquals(1, refs.size()); + assertSame(ref, refs.get(0)); assertEquals("EMBL", ref.getSource()); assertEquals("1.2", ref.getVersion()); assertEquals("a7890", ref.getAccessionId()); assertTrue(seq.getAllPDBEntries().isEmpty()); + SequenceI seq2 = new Sequence("Seq2", "ABCD"); + // Check that whitespace doesn't confuse parseToDbRef + DBRefEntry ref2 = DBRefUtils.parseToDbRef(seq2, "EMBL", "1.2", + " a7890"); + assertEquals(ref, ref2); } /** @@ -149,9 +155,9 @@ public class DBRefUtilsTest // 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]); + List refs = seq.getDBRefs(); + assertEquals(1, refs.size()); + assertSame(ref, refs.get(0)); assertEquals("PDB", ref.getSource()); assertEquals("1.2", ref.getVersion()); // DBRef id is pdbId + chain code @@ -184,8 +190,9 @@ public class DBRefUtilsTest ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1, 1 }, 1, 1))); - List matches = DBRefUtils.searchRefs(new DBRefEntry[] { - ref1, ref2, ref3, ref4, ref5 }, target); + List matches = DBRefUtils.searchRefs( + Arrays.asList(new DBRefEntry[] { + ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL); assertEquals(3, matches.size()); assertSame(ref1, matches.get(0)); assertSame(ref2, matches.get(1)); @@ -217,8 +224,9 @@ public class DBRefUtilsTest new int[] { 1, 1 }, 2, 2)); ref3.setMap(map3); - List matches = DBRefUtils.searchRefs(new DBRefEntry[] { - ref1, ref2, ref3 }, target); + List matches = DBRefUtils.searchRefs( + Arrays.asList(new DBRefEntry[] { + ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL); assertEquals(2, matches.size()); assertSame(ref1, matches.get(0)); assertSame(ref2, matches.get(1)); @@ -242,7 +250,8 @@ public class DBRefUtilsTest 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 }; + List dbrefs = Arrays.asList(new DBRefEntry[] { + ref1, ref2, ref3, ref4, ref5 }); List matches = DBRefUtils.searchRefs(dbrefs, "A1234"); assertEquals(3, matches.size()); assertSame(ref1, matches.get(0)); @@ -270,8 +279,9 @@ public class DBRefUtilsTest ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1, 1 }, 1, 1))); - List matches = DBRefUtils.searchRefs(new DBRefEntry[] { - ref1, ref2, ref3, ref4, ref5 }, target); + List matches = DBRefUtils.searchRefs( + Arrays.asList(new DBRefEntry[] { + ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL); assertEquals(4, matches.size()); assertSame(ref1, matches.get(0)); assertSame(ref2, matches.get(1));