From b45b78bfc90750c57a947ba64e47d43de36100f1 Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 4 Oct 2016 14:55:59 +0100 Subject: [PATCH] JAL-2232 some fix / partial fix of failing tests --- test/jalview/analysis/CrossRefTest.java | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java index 50f38b6..759f527 100644 --- a/test/jalview/analysis/CrossRefTest.java +++ b/test/jalview/analysis/CrossRefTest.java @@ -80,11 +80,11 @@ public class CrossRefTest * Just the protein refs: */ found = DBRefUtils.selectDbRefs(false, refs); - assertEquals(3, found.length); + assertEquals(4, found.length); assertSame(ref1, found[0]); assertSame(ref2, found[1]); assertSame(ref4, found[2]); - // assertSame(ref9, found[3]); ENSEMBL not protein + assertSame(ref9, found[3]); } /** @@ -121,8 +121,9 @@ public class CrossRefTest seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350")); sources = new CrossRef(new SequenceI[] { seq }, al) .findXrefSourcesForSequences(false); - assertEquals(4, sources.size()); - assertEquals("[EMBL, EMBLCDS, GENEDB, ENSEMBL]", sources.toString()); + // method is patched to remove EMBL from the sources to match + assertEquals(3, sources.size()); + assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString()); /* * add a sequence to the alignment which has a dbref to UNIPROT|A1234 @@ -140,8 +141,9 @@ public class CrossRefTest al.addSequence(seq2); sources = new CrossRef(new SequenceI[] { seq, seq2 }, al) .findXrefSourcesForSequences(false); - assertEquals(3, sources.size()); - assertEquals("[EMBLCDS, EMBL, GENEDB]", sources.toString()); + // method removed EMBL from sources to match + assertEquals(2, sources.size()); + assertEquals("[EMBLCDS, GENEDB]", sources.toString()); } /** @@ -624,7 +626,7 @@ public class CrossRefTest */ final SequenceI x07547 = new Sequence("EMBL|X07547", "cccAAACCCTTTGGG"); DBRefEntry dbref7 = new DBRefEntry("UNIPROT", "0", "P0CE20"); - dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), + dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), new MapList(map2))); x07547.addDBRef(dbref7); DBRefEntry dbref8 = new DBRefEntry("UNIPROT", "0", "B0BCM4"); -- 1.7.10.2