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JAL-3763 always make a new dataset sequence for CDS sequence
[jalview.git]
/
test
/
jalview
/
io
/
vcf
/
VCFLoaderTest.java
diff --git
a/test/jalview/io/vcf/VCFLoaderTest.java
b/test/jalview/io/vcf/VCFLoaderTest.java
index
97b609d
..
a719cc4
100644
(file)
--- a/
test/jalview/io/vcf/VCFLoaderTest.java
+++ b/
test/jalview/io/vcf/VCFLoaderTest.java
@@
-209,7
+209,7
@@
public class VCFLoaderTest
* verify SNP variant feature(s) computed and added to protein
* first codon AGC varies to ACC giving S/T
*/
* verify SNP variant feature(s) computed and added to protein
* first codon AGC varies to ACC giving S/T
*/
- DBRefEntry[] dbRefs = al.getSequenceAt(1).getDBRefs();
+ List<DBRefEntry> dbRefs = al.getSequenceAt(1).getDBRefs();
SequenceI peptide = null;
for (DBRefEntry dbref : dbRefs)
{
SequenceI peptide = null;
for (DBRefEntry dbref : dbRefs)
{
@@
-475,7
+475,7
@@
public class VCFLoaderTest
* verify variant feature(s) computed and added to protein
* last codon GCT varies to GGT giving A/G in the last peptide position
*/
* verify variant feature(s) computed and added to protein
* last codon GCT varies to GGT giving A/G in the last peptide position
*/
- DBRefEntry[] dbRefs = al.getSequenceAt(3).getDBRefs();
+ List<DBRefEntry> dbRefs = al.getSequenceAt(3).getDBRefs();
SequenceI peptide = null;
for (DBRefEntry dbref : dbRefs)
{
SequenceI peptide = null;
for (DBRefEntry dbref : dbRefs)
{
@@
-542,7
+542,7
@@
public class VCFLoaderTest
assertEquals(sf.getValue("alleles"), "C,T");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
assertEquals(sf.getValue("alleles"), "C,T");
map = (Map) sf.getValue("CSQ");
assertEquals(map.size(), 9);
- assertEquals(map.get("PolyPhen"), "Bad++"); // %3B%3B decoded
+ assertEquals(map.get("PolyPhen"), "Bad;;"); // %3B%3B decoded
sf = geneFeatures.get(2);
assertEquals(sf.getBegin(), 9);
sf = geneFeatures.get(2);
assertEquals(sf.getBegin(), 9);
@@
-635,7
+635,7
@@
public class VCFLoaderTest
* and GAG/GGG which is E/G in position 4
* the insertion variant is not transferred to the peptide
*/
* and GAG/GGG which is E/G in position 4
* the insertion variant is not transferred to the peptide
*/
- DBRefEntry[] dbRefs = al.findName("transcript3").getDBRefs();
+ List<DBRefEntry> dbRefs = al.findName("transcript3").getDBRefs();
SequenceI peptide = null;
for (DBRefEntry dbref : dbRefs)
{
SequenceI peptide = null;
for (DBRefEntry dbref : dbRefs)
{