- String[][] codonVariants = new String[][] { { "A" }, { "G" }, { "T" } };
-
- /*
- * AGT codes for S - this is not included in the variants returned
- */
- List<String> variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
- assertEquals("[]", variants.toString());
-
- // S is reported if it differs from the current value (A):
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "A");
- assertEquals("[S]", variants.toString());
-
- /*
- * synonymous variant is not reported
- */
- codonVariants = new String[][] { { "A" }, { "G" }, { "C", "T" } };
- // AGC and AGT both code for S
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "s");
- assertEquals("[]", variants.toString());
-
- /*
- * equivalent variants are only reported once
- */
- codonVariants = new String[][] { { "C" }, { "T" },
- { "A", "C", "G", "T" } };
- // CTA CTC CTG CTT all code for L
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
- assertEquals("[L]", variants.toString());
-
- /*
- * vary codons 1 and 2; variant products are sorted and non-redundant
- */
- codonVariants = new String[][] { { "a", "C" }, { "g", "T" }, { "A" } };
- // aga ata cga cta code for R, I, R, L
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
- assertEquals("[I, L, R]", variants.toString());
-
- /*
- * vary codons 2 and 3
- */
- codonVariants = new String[][] { { "a" }, { "g", "T" }, { "A", "c" } };
- // aga agc ata atc code for R, S, I, I
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
- assertEquals("[I, R]", variants.toString());
-
- /*
- * vary codons 1 and 3
- */
- codonVariants = new String[][] { { "a", "t" }, { "a" }, { "t", "g" } };
- // aat aag tat tag code for N, K, Y, STOP - STOP sorted to end
- variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
- assertEquals("[K, N, Y, STOP]", variants.toString());
+ 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());
+ }