From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 2 Oct 2016 11:27:30 +0000 (+0100)
Subject: JAL-2210 first pass at attempting to fix CrossRef tests due to removal of sequence... 
X-Git-Tag: Release_2_10_0~20^2~11
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=6405be60655fe096cdbff89cccf0a5b12f8b7e80

JAL-2210 first pass at attempting to fix CrossRef tests due to removal of sequence ID matcher based fallback for discovering crossrefs.
---

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 24ddb34..50f38b6 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(4, found.length);
+    assertEquals(3, found.length);
     assertSame(ref1, found[0]);
     assertSame(ref2, found[1]);
     assertSame(ref4, found[2]);
-    assertSame(ref9, found[3]);
+    // assertSame(ref9, found[3]); ENSEMBL not protein
   }
 
   /**
@@ -402,11 +402,14 @@ public class CrossRefTest
   public void testFindXrefSequences_withFetch()
   {
     SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
-    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
-    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P30419"));
-    dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
+    dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2"));
+    dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419"));
+    dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314"));
     final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
+    pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+
     final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
+    pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
 
     /*
      * argument false suppresses adding DAS sources
@@ -471,7 +474,7 @@ public class CrossRefTest
      * 'spliced transcript' with CDS ranges
      */
     SequenceI braf002 = new Sequence("ENST00000497784", "gCAGGCtaTCTGTTCaa");
-    braf002.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
+    braf002.addDBRef(new DBRefEntry("UNIPROT", "ENSEMBL|0", "H7C5K3"));
     braf002.addSequenceFeature(new SequenceFeature("CDS", "", 2, 6, 0f,
             null));
     braf002.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, 0f,
@@ -483,8 +486,9 @@ public class CrossRefTest
      * which happens to be true for Uniprot,PDB,EMBL but not Pfam,Rfam,Ensembl 
      */
     final SequenceI pep1 = new Sequence("UNIPROT|P15056", "MAAL");
+    pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056"));
     final SequenceI pep2 = new Sequence("UNIPROT|H7C5K3", "QALF");
-
+    pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
     /*
      * argument false suppresses adding DAS sources
      * todo: define an interface type SequenceFetcherI and mock that