JAL-2656 JAL-3615 check response headers to test for gzipped url reply

[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
      */
-    DBRefEntry[] dbRefs = al.getSequenceAt(1).getDBRefs();
+    List<DBRefEntry> dbRefs = al.getSequenceAt(1).getDBRefs();
     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
      */
-    DBRefEntry[] dbRefs = al.getSequenceAt(3).getDBRefs();
+    List<DBRefEntry> dbRefs = al.getSequenceAt(3).getDBRefs();
     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(map.get("PolyPhen"), "Bad++"); // %3B%3B decoded
+    assertEquals(map.get("PolyPhen"), "Bad;;"); // %3B%3B decoded
 
     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
      */
-    DBRefEntry[] dbRefs = al.findName("transcript3").getDBRefs();
+    List<DBRefEntry> dbRefs = al.findName("transcript3").getDBRefs();
     SequenceI peptide = null;
     for (DBRefEntry dbref : dbRefs)
     {