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JAL-2232 some fix / partial fix of failing tests
bug/JAL-2210_hack_for_Release_2_10
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 4 Oct 2016 13:55:59 +0000
(14:55 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 4 Oct 2016 13:55:59 +0000
(14:55 +0100)
test/jalview/analysis/CrossRefTest.java
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diff --git
a/test/jalview/analysis/CrossRefTest.java
b/test/jalview/analysis/CrossRefTest.java
index
50f38b6
..
759f527
100644
(file)
--- 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);
* 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(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);
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
/*
* 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);
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");
*/
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");
new MapList(map2)));
x07547.addDBRef(dbref7);
DBRefEntry dbref8 = new DBRefEntry("UNIPROT", "0", "B0BCM4");