Examples with Substitution org.nextprot.api.commons.bio.variation.prot.impl.seqchange.Substitution used on opensource projects

Example 6 with Substitution

use of org.nextprot.api.commons.bio.variation.prot.impl.seqchange.Substitution in project nextprot-api by calipho-sib.

the class SequenceVariantHGVSParseSubstitutionTest method testParseSubstitution.

// /// SUBSTITUTIONS
@Test
public void testParseSubstitution() throws Exception {
    SequenceVariation pm = format.parse("p.R54C");
    Assert.assertEquals(AminoAcidCode.ARGININE, pm.getVaryingSequence().getFirstAminoAcid());
    Assert.assertEquals(AminoAcidCode.ARGININE, pm.getVaryingSequence().getLastAminoAcid());
    Assert.assertEquals(54, pm.getVaryingSequence().getFirstAminoAcidPos());
    Assert.assertEquals(54, pm.getVaryingSequence().getLastAminoAcidPos());
    Assert.assertTrue(pm.getSequenceChange() instanceof Substitution);
    Assert.assertEquals(AminoAcidCode.CYSTEINE, pm.getSequenceChange().getValue());
}