+
+ @Test(groups = "Functional")
+ public void getGenomicRangesFromFeatures()
+ {
+
+ }
+
+ /**
+ * Test the method that appends a single allele's reverse complement to a
+ * string buffer
+ */
+ @Test(groups = "Functional")
+ public void testReverseComplementAllele()
+ {
+ StringBuilder sb = new StringBuilder();
+ EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
+ EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
+ EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
+ EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
+ EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
+ assertEquals("C,c,G,A,T", sb.toString());
+
+ sb = new StringBuilder();
+ EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
+ EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
+ EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
+ assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
+ }
+
+ /**
+ * Test the method that computes the reverse complement of the alleles in a
+ * sequence_variant feature
+ */
+ @Test(groups = "Functional")
+ public void testReverseComplementAlleles()
+ {
+ String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
+ SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
+ 1, 2, 0f, null);
+ sf.setValue("alleles", alleles);
+ sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
+
+ EnsemblSeqProxy.reverseComplementAlleles(sf);
+ String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
+ // verify description is updated with reverse complement
+ assertEquals(revcomp, sf.getDescription());
+ // verify alleles attribute is updated with reverse complement
+ assertEquals(revcomp, sf.getValue("alleles"));
+ // verify attributes string is updated with reverse complement
+ assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
+ }
+
+ @Test(groups = "Functional")
+ public void testSortFeatures()
+ {
+ SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
+ SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
+ SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
+ SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
+ SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
+
+ // sort by start position ascending (forward strand)
+ // sf2 and sf3 tie and should not be reordered by sorting
+ EnsemblSeqProxy.sortFeatures(sfs, true);
+ assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
+
+ // sort by end position descending (reverse strand)
+ EnsemblSeqProxy.sortFeatures(sfs, false);
+ assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
+ }
+}