Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

[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 87cf727..a719cc4 100644 (file)
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -3,7 +3,6 @@ package jalview.io.vcf;
 import static jalview.io.gff.SequenceOntologyI.SEQUENCE_VARIANT;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNull;
-import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
 import jalview.bin.Cache;
@@ -210,7 +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)
     {
@@ -476,7 +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)
     {
@@ -543,7 +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);
@@ -636,7 +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)
     {
@@ -762,16 +761,4 @@ public class VCFLoaderTest
     assertEquals(sf.getEnd(), 15);
     assertEquals(sf.getDescription(), "T,C");
   }
-
-  @Test(groups = "Functional")
-  public void testDecodeSpecialCharacters() throws IOException
-  {
-    String encoded = "hello world";
-    String decoded = VCFLoader.decodeSpecialCharacters(encoded);
-    assertSame(encoded, decoded); // no change needed
-
-    encoded = "ab%3Acd%3Bef%3Dgh%25ij%2Ckl%3A";
-    decoded = VCFLoader.decodeSpecialCharacters(encoded);
-    assertEquals(decoded, "ab:cd;ef=gh%ij,kl:");
-  }
 }
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