+package jalview.datamodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.util.MapList;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.Test;
+
+public class MappedFeaturesTest
+{
+ @Test
+ public void testFindProteinVariants()
+ {
+ /*
+ * scenario:
+ * dna/10-20 aCGTaGctGAa (codons CGT=R, GGA = G)
+ * mapping: 3:1 from [11-13,15,18-19] to peptide/1-2 RG
+ */
+ SequenceI from = new Sequence("dna/10-20", "ACGTAGCTGAA");
+ SequenceI to = new Sequence("peptide", "RG");
+ MapList map = new MapList(new int[] { 11, 13, 15, 15, 18, 19 },
+ new int[]
+ { 1, 2 }, 3, 1);
+ Mapping mapping = new Mapping(to, map);
+
+ /*
+ * variants
+ * C>T at dna11, consequence CGT>TGT=C
+ * T>C at dna13, consequence CGT>CGC synonymous
+ */
+ List<SequenceFeature> features = new ArrayList<>();
+ SequenceFeature sf1 = new SequenceFeature("sequence_variant", "C,T",
+ 11, 11, null);
+ sf1.setValue("alleles", "C,T");
+ features.add(sf1);
+ SequenceFeature sf2 = new SequenceFeature("sequence_variant", "T,C", 13,
+ 13, null);
+ sf2.setValue("alleles", "T,C");
+ features.add(sf2);
+
+ /*
+ * missense variant in first codon
+ */
+ MappedFeatures mf = new MappedFeatures(mapping, from, 1, 'R',
+ features);
+ String variant = mf.findProteinVariants(sf1);
+ assertEquals(variant, "p.Arg1Cys");
+
+ /*
+ * more than one alternative allele
+ * C>G consequence is GGT=G
+ * peptide variants as a comma-separated list
+ */
+ sf1.setValue("alleles", "C,T,G");
+ variant = mf.findProteinVariants(sf1);
+ assertEquals(variant, "p.Arg1Cys,p.Arg1Gly");
+
+ /*
+ * synonymous variant in first codon
+ * shown in HGVS notation on peptide
+ */
+ variant = mf.findProteinVariants(sf2);
+ assertEquals(variant, "c.13T>C(p.=)");
+
+ /*
+ * CSQ:HGVSp value is used if present
+ */
+ Map<String, String> csq = new HashMap<>();
+ csq.put("HGVSp", "hello:world");
+ sf2.setValue("CSQ", csq);
+ variant = mf.findProteinVariants(sf2);
+ assertEquals(variant, "world");
+
+ /*
+ * missense and indel variants in second codon
+ * - codon is GGA spliced from dna positions 15,18,19
+ * - SNP G>T in second position mutates GGA>G to GTA>V
+ * - indel variants are not computed or reported
+ */
+ mf = new MappedFeatures(mapping, from, 2, 'G', features);
+ features.clear();
+ SequenceFeature sf3 = new SequenceFeature("sequence_variant",
+ "G,-,CG,T", 18, 18, null);
+ sf3.setValue("alleles", "G,-,CG,T");
+ features.add(sf3);
+ variant = mf.findProteinVariants(sf3);
+ assertEquals(variant, "p.Gly2Val");
+
+ /*
+ * G>T in first position gives TGA Stop
+ * shown with HGVS notation as 'Ter'
+ */
+ SequenceFeature sf4 = new SequenceFeature("sequence_variant", "G,T", 15,
+ 15, null);
+ sf4.setValue("alleles", "G,-,CG,T");
+ features.add(sf4);
+ variant = mf.findProteinVariants(sf4);
+ assertEquals(variant, "p.Gly2Ter");
+
+ /*
+ * feature must be one of those in MappedFeatures
+ */
+ SequenceFeature sf9 = new SequenceFeature("sequence_variant", "G,C", 15,
+ 15, null);
+ variant = mf.findProteinVariants(sf9);
+ assertEquals(variant, "");
+ }
+}