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JAL-3143 unit tests updated for code changes!
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 25 Oct 2018 19:27:16 +0000
(20:27 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Thu, 25 Oct 2018 19:27:16 +0000
(20:27 +0100)
test/jalview/ext/ensembl/EnsemblCdnaTest.java
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test/jalview/ext/ensembl/EnsemblCdsTest.java
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test/jalview/ext/ensembl/EnsemblGeneTest.java
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test/jalview/ext/ensembl/EnsemblGenomeTest.java
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diff --git
a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index
c9d8deb
..
9e9d9a4
100644
(file)
--- a/
test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/
test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@
-79,19
+79,19
@@
public class EnsemblCdnaTest
// exon at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
null);
// exon at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("-");
genomic.addSequenceFeature(sf);
// exon (sub-type) at (start + exon_variant) length 101
sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
sf.setStrand("-");
genomic.addSequenceFeature(sf);
// exon (sub-type) at (start + exon_variant) length 101
sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("-");
genomic.addSequenceFeature(sf);
// exon belonging to a different transcript doesn't count
sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
sf.setStrand("-");
genomic.addSequenceFeature(sf);
// exon belonging to a different transcript doesn't count
sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
- sf.setValue("Parent", "transcript:anotherOne");
+ sf.setValue("Parent", "anotherOne");
genomic.addSequenceFeature(sf);
// transcript feature doesn't count
genomic.addSequenceFeature(sf);
// transcript feature doesn't count
@@
-134,19
+134,19
@@
public class EnsemblCdnaTest
// exon at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
null);
// exon at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// exon (sub-type) at (start + exon_variant) length 101
sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// exon (sub-type) at (start + exon_variant) length 101
sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// exon belonging to a different transcript doesn't count
sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// exon belonging to a different transcript doesn't count
sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
- sf.setValue("Parent", "transcript:anotherOne");
+ sf.setValue("Parent", "anotherOne");
genomic.addSequenceFeature(sf);
// transcript feature doesn't count
genomic.addSequenceFeature(sf);
// transcript feature doesn't count
@@
-226,14
+226,14
@@
public class EnsemblCdnaTest
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
- sf.setValue("Parent", "transcript:" + accId);
+ sf.setValue("Parent", accId);
assertTrue(testee.retainFeature(sf, accId));
// test is not case-sensitive
assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
// feature with wrong parent is not retained
assertTrue(testee.retainFeature(sf, accId));
// test is not case-sensitive
assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
// feature with wrong parent is not retained
- sf.setValue("Parent", "transcript:XYZ");
+ sf.setValue("Parent", "XYZ");
assertFalse(testee.retainFeature(sf, accId));
}
assertFalse(testee.retainFeature(sf, accId));
}
@@
-253,30
+253,30
@@
public class EnsemblCdnaTest
// exon with wrong parent: not valid
SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null);
// exon with wrong parent: not valid
SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf2.setValue("Parent", "transcript:XYZ");
+ sf2.setValue("Parent", "XYZ");
seq.addSequenceFeature(sf2);
// exon with right parent is valid
SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null);
seq.addSequenceFeature(sf2);
// exon with right parent is valid
SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf3.setValue("Parent", "transcript:" + accId);
+ sf3.setValue("Parent", accId);
seq.addSequenceFeature(sf3);
// exon sub-type with right parent is valid
SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 1, 2, 0f,
null);
seq.addSequenceFeature(sf3);
// exon sub-type with right parent is valid
SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 1, 2, 0f,
null);
- sf4.setValue("Parent", "transcript:" + accId);
+ sf4.setValue("Parent", accId);
seq.addSequenceFeature(sf4);
// transcript not valid:
SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
seq.addSequenceFeature(sf4);
// transcript not valid:
SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
- sf5.setValue("Parent", "transcript:" + accId);
+ sf5.setValue("Parent", accId);
seq.addSequenceFeature(sf5);
// CDS not valid:
SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
seq.addSequenceFeature(sf5);
// CDS not valid:
SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
- sf6.setValue("Parent", "transcript:" + accId);
+ sf6.setValue("Parent", accId);
seq.addSequenceFeature(sf6);
List<SequenceFeature> sfs = new EnsemblCdna()
seq.addSequenceFeature(sf6);
List<SequenceFeature> sfs = new EnsemblCdna()
diff --git
a/test/jalview/ext/ensembl/EnsemblCdsTest.java
b/test/jalview/ext/ensembl/EnsemblCdsTest.java
index
a44ab7f
..
e7574eb
100644
(file)
--- a/
test/jalview/ext/ensembl/EnsemblCdsTest.java
+++ b/
test/jalview/ext/ensembl/EnsemblCdsTest.java
@@
-78,19
+78,19
@@
public class EnsemblCdsTest
// CDS at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
null);
// CDS at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// CDS (sub-type) at (start + 10500) length 101
sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// CDS (sub-type) at (start + 10500) length 101
sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// CDS belonging to a different transcript doesn't count
sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// CDS belonging to a different transcript doesn't count
sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
- sf.setValue("Parent", "transcript:anotherOne");
+ sf.setValue("Parent", "anotherOne");
genomic.addSequenceFeature(sf);
// exon feature doesn't count
genomic.addSequenceFeature(sf);
// exon feature doesn't count
@@
-135,16
+135,16
@@
public class EnsemblCdsTest
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is retained
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is retained
- sf = new SequenceFeature("CDS_psequence_variantredicted", "", 20000,
+ sf = new SequenceFeature("anotherType", "", 20000,
20500, 0f, null);
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
20500, 0f, null);
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
- sf.setValue("Parent", "transcript:" + accId);
+ sf.setValue("Parent", accId);
assertTrue(testee.retainFeature(sf, accId));
// feature with wrong parent is not retained
assertTrue(testee.retainFeature(sf, accId));
// feature with wrong parent is not retained
- sf.setValue("Parent", "transcript:XYZ");
+ sf.setValue("Parent", "XYZ");
assertFalse(testee.retainFeature(sf, accId));
}
assertFalse(testee.retainFeature(sf, accId));
}
@@
-164,29
+164,29
@@
public class EnsemblCdsTest
// cds with wrong parent not valid
SequenceFeature sf2 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
// cds with wrong parent not valid
SequenceFeature sf2 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
- sf2.setValue("Parent", "transcript:XYZ");
+ sf2.setValue("Parent", "XYZ");
seq.addSequenceFeature(sf2);
// cds with right parent is valid
SequenceFeature sf3 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
seq.addSequenceFeature(sf2);
// cds with right parent is valid
SequenceFeature sf3 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
- sf3.setValue("Parent", "transcript:" + accId);
+ sf3.setValue("Parent", accId);
seq.addSequenceFeature(sf3);
// cds sub-type with right parent is valid
SequenceFeature sf4 = new SequenceFeature("CDS_predicted", "", 1, 2, 0f,
null);
seq.addSequenceFeature(sf3);
// cds sub-type with right parent is valid
SequenceFeature sf4 = new SequenceFeature("CDS_predicted", "", 1, 2, 0f,
null);
- sf4.setValue("Parent", "transcript:" + accId);
+ sf4.setValue("Parent", accId);
seq.addSequenceFeature(sf4);
// transcript not valid:
SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
seq.addSequenceFeature(sf4);
// transcript not valid:
SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
- sf5.setValue("Parent", "transcript:" + accId);
+ sf5.setValue("Parent", accId);
seq.addSequenceFeature(sf5);
// exon not valid:
SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
seq.addSequenceFeature(sf5);
// exon not valid:
SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf6.setValue("Parent", "transcript:" + accId);
+ sf6.setValue("Parent", accId);
seq.addSequenceFeature(sf6);
List<SequenceFeature> sfs = new EnsemblCds().getIdentifyingFeatures(seq,
seq.addSequenceFeature(sf6);
List<SequenceFeature> sfs = new EnsemblCds().getIdentifyingFeatures(seq,
diff --git
a/test/jalview/ext/ensembl/EnsemblGeneTest.java
b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index
446b4f7
..
8b1e840
100644
(file)
--- a/
test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/
test/jalview/ext/ensembl/EnsemblGeneTest.java
@@
-81,7
+81,7
@@
public class EnsemblGeneTest
// gene at (start + 10500) length 101
SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
null);
// gene at (start + 10500) length 101
SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
null);
- sf.setValue("ID", "gene:" + geneId);
+ sf.setValue("id", geneId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
@@
-113,7
+113,7
@@
public class EnsemblGeneTest
// gene at (start + 10500) length 101
SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
null);
// gene at (start + 10500) length 101
SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
null);
- sf.setValue("ID", "gene:" + geneId);
+ sf.setValue("id", geneId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
@@
-146,30
+146,30
@@
public class EnsemblGeneTest
// transcript feature
SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
20500, 0f, null);
// transcript feature
SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
20500, 0f, null);
- sf1.setValue("Parent", "gene:" + geneId);
- sf1.setValue("transcript_id", "transcript1");
+ sf1.setValue("Parent", geneId);
+ sf1.setValue("id", "transcript1");
genomic.addSequenceFeature(sf1);
// transcript sub-type feature
SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
0f, null);
genomic.addSequenceFeature(sf1);
// transcript sub-type feature
SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
0f, null);
- sf2.setValue("Parent", "gene:" + geneId);
- sf2.setValue("transcript_id", "transcript2");
+ sf2.setValue("Parent", geneId);
+ sf2.setValue("id", "transcript2");
genomic.addSequenceFeature(sf2);
// NMD_transcript_variant treated like transcript in Ensembl
SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
22000, 22500, 0f, null);
// id matching should not be case-sensitive
genomic.addSequenceFeature(sf2);
// NMD_transcript_variant treated like transcript in Ensembl
SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
22000, 22500, 0f, null);
// id matching should not be case-sensitive
- sf3.setValue("Parent", "gene:" + geneId.toLowerCase());
- sf3.setValue("transcript_id", "transcript3");
+ sf3.setValue("Parent", geneId.toLowerCase());
+ sf3.setValue("id", "transcript3");
genomic.addSequenceFeature(sf3);
// transcript for a different gene - ignored
SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
0f, null);
genomic.addSequenceFeature(sf3);
// transcript for a different gene - ignored
SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
0f, null);
- sf4.setValue("Parent", "gene:XYZ");
- sf4.setValue("transcript_id", "transcript4");
+ sf4.setValue("Parent", "XYZ");
+ sf4.setValue("id", "transcript4");
genomic.addSequenceFeature(sf4);
EnsemblGene testee = new EnsemblGene();
genomic.addSequenceFeature(sf4);
EnsemblGene testee = new EnsemblGene();
@@
-196,24
+196,24
@@
public class EnsemblGeneTest
EnsemblGene testee = new EnsemblGene();
SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
null);
EnsemblGene testee = new EnsemblGene();
SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
null);
- sf.setValue("ID", "gene:" + geneId);
+ sf.setValue("id", geneId);
assertFalse(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
assertFalse(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
- sf.setValue("Parent", "gene:" + geneId);
+ sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
null);
assertTrue(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "gene:" + geneId);
+ sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
0f, null);
assertTrue(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
0f, null);
- sf.setValue("Parent", "gene:" + geneId);
+ sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
assertTrue(testee.retainFeature(sf, geneId));
- sf.setValue("Parent", "gene:XYZ");
+ sf.setValue("Parent", "ßXYZ");
assertFalse(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
assertFalse(testee.retainFeature(sf, geneId));
sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
@@
-235,28
+235,28
@@
public class EnsemblGeneTest
seq.addSequenceFeature(sf1);
// gene with wrong ID not valid
seq.addSequenceFeature(sf1);
// gene with wrong ID not valid
- SequenceFeature sf2 = new SequenceFeature("gene", "", 1, 2, 0f, null);
- sf2.setValue("ID", "gene:XYZ");
+ SequenceFeature sf2 = new SequenceFeature("gene", "a", 1, 2, 0f, null);
+ sf2.setValue("id", "XYZ");
seq.addSequenceFeature(sf2);
// gene with right ID is valid
seq.addSequenceFeature(sf2);
// gene with right ID is valid
- SequenceFeature sf3 = new SequenceFeature("gene", "", 1, 2, 0f, null);
- sf3.setValue("ID", "gene:" + accId);
+ SequenceFeature sf3 = new SequenceFeature("gene", "b", 1, 2, 0f, null);
+ sf3.setValue("id", accId);
seq.addSequenceFeature(sf3);
// gene sub-type with right ID is valid
SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
seq.addSequenceFeature(sf3);
// gene sub-type with right ID is valid
SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
- sf4.setValue("ID", "gene:" + accId);
+ sf4.setValue("id", accId);
seq.addSequenceFeature(sf4);
// transcript not valid:
SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
seq.addSequenceFeature(sf4);
// transcript not valid:
SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
- sf5.setValue("ID", "gene:" + accId);
+ sf5.setValue("id", accId);
seq.addSequenceFeature(sf5);
// exon not valid:
SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
seq.addSequenceFeature(sf5);
// exon not valid:
SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf6.setValue("ID", "gene:" + accId);
+ sf6.setValue("id", accId);
seq.addSequenceFeature(sf6);
List<SequenceFeature> sfs = new EnsemblGene()
seq.addSequenceFeature(sf6);
List<SequenceFeature> sfs = new EnsemblGene()
diff --git
a/test/jalview/ext/ensembl/EnsemblGenomeTest.java
b/test/jalview/ext/ensembl/EnsemblGenomeTest.java
index
72ee492
..
11140f9
100644
(file)
--- a/
test/jalview/ext/ensembl/EnsemblGenomeTest.java
+++ b/
test/jalview/ext/ensembl/EnsemblGenomeTest.java
@@
-77,13
+77,13
@@
public class EnsemblGenomeTest
// transcript at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
20500, 0f, null);
// transcript at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
20500, 0f, null);
- sf.setValue("ID", "transcript:" + transcriptId);
+ sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// transcript (sub-type) at (start + 10500) length 101
sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// transcript (sub-type) at (start + 10500) length 101
sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
- sf.setValue("ID", "transcript:" + transcriptId);
+ sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
@@
-91,13
+91,13
@@
public class EnsemblGenomeTest
// although strictly it is a sequence_variant in SO
sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
0f, null);
// although strictly it is a sequence_variant in SO
sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
0f, null);
- sf.setValue("ID", "transcript:" + transcriptId);
+ sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// transcript with a different ID doesn't count
sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// transcript with a different ID doesn't count
sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
- sf.setValue("ID", "transcript:anotherOne");
+ sf.setValue("id", "anotherOne");
genomic.addSequenceFeature(sf);
// parent of transcript feature doesn't count
genomic.addSequenceFeature(sf);
// parent of transcript feature doesn't count
@@
-150,11
+150,11
@@
public class EnsemblGenomeTest
assertTrue(testee.retainFeature(sf, accId));
// other feature with correct parent is kept
assertTrue(testee.retainFeature(sf, accId));
// other feature with correct parent is kept
- sf.setValue("Parent", "transcript:" + accId);
+ sf.setValue("Parent", accId);
assertTrue(testee.retainFeature(sf, accId));
// other feature with wrong parent is not kept
assertTrue(testee.retainFeature(sf, accId));
// other feature with wrong parent is not kept
- sf.setValue("Parent", "transcript:XYZ");
+ sf.setValue("Parent", "XYZ");
assertFalse(testee.retainFeature(sf, accId));
}
assertFalse(testee.retainFeature(sf, accId));
}
@@
-174,36
+174,37
@@
public class EnsemblGenomeTest
seq.addSequenceFeature(sf1);
// transcript with wrong ID not valid
seq.addSequenceFeature(sf1);
// transcript with wrong ID not valid
- SequenceFeature sf2 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ // NB change desc to avoid rejection of duplicate feature!
+ SequenceFeature sf2 = new SequenceFeature("transcript", "a", 1, 2, 0f,
null);
null);
- sf2.setValue("ID", "transcript");
+ sf2.setValue("id", "transcript");
seq.addSequenceFeature(sf2);
// transcript with right ID is valid
seq.addSequenceFeature(sf2);
// transcript with right ID is valid
- SequenceFeature sf3 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ SequenceFeature sf3 = new SequenceFeature("transcript", "b", 1, 2, 0f,
null);
null);
- sf3.setValue("ID", "transcript:" + accId);
+ sf3.setValue("id", accId);
seq.addSequenceFeature(sf3);
// transcript sub-type with right ID is valid
SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
seq.addSequenceFeature(sf3);
// transcript sub-type with right ID is valid
SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
- sf4.setValue("ID", "transcript:" + accId);
+ sf4.setValue("id", accId);
seq.addSequenceFeature(sf4);
// Ensembl treats NMD_transcript_variant as if a transcript
SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
1, 2, 0f, null);
seq.addSequenceFeature(sf4);
// Ensembl treats NMD_transcript_variant as if a transcript
SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
1, 2, 0f, null);
- sf5.setValue("ID", "transcript:" + accId);
+ sf5.setValue("id", accId);
seq.addSequenceFeature(sf5);
// gene not valid:
SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
seq.addSequenceFeature(sf5);
// gene not valid:
SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
- sf6.setValue("ID", "transcript:" + accId);
+ sf6.setValue("id", accId);
seq.addSequenceFeature(sf6);
// exon not valid:
SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
seq.addSequenceFeature(sf6);
// exon not valid:
SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
- sf7.setValue("ID", "transcript:" + accId);
+ sf7.setValue("id", accId);
seq.addSequenceFeature(sf7);
List<SequenceFeature> sfs = new EnsemblGenome()
seq.addSequenceFeature(sf7);
List<SequenceFeature> sfs = new EnsemblGenome()