Examples with AminoAcidCode org.nextprot.api.commons.bio.AminoAcidCode used on opensource projects

Example 26 with AminoAcidCode

use of org.nextprot.api.commons.bio.AminoAcidCode in project nextprot-api by calipho-sib.

the class SequenceVariantHGVSParseDelinsTest method testParseDeletionMultiAndInsertionMulti.

@Test
public void testParseDeletionMultiAndInsertionMulti() throws Exception {
    SequenceVariation pm = format.parse("p.D419_R420delinsSSDG");
    Assert.assertEquals(AminoAcidCode.ASPARTIC_ACID, pm.getVaryingSequence().getFirstAminoAcid());
    Assert.assertEquals(AminoAcidCode.ARGININE, pm.getVaryingSequence().getLastAminoAcid());
    Assert.assertEquals(419, pm.getVaryingSequence().getFirstAminoAcidPos());
    Assert.assertEquals(420, pm.getVaryingSequence().getLastAminoAcidPos());
    Assert.assertEquals(SequenceChange.Type.DELETION_INSERTION, pm.getSequenceChange().getType());
    Assert.assertArrayEquals(AminoAcidCode.valueOfAminoAcidCodeSequence("SSDG"), (AminoAcidCode[]) pm.getSequenceChange().getValue());
}

Example 27 with AminoAcidCode

use of org.nextprot.api.commons.bio.AminoAcidCode in project nextprot-api by calipho-sib.

the class SequenceVariantHGVSParseDelinsTest method testParseDeletionMultiAasAndInsertion1.

@Test
public void testParseDeletionMultiAasAndInsertion1() throws Exception {
    SequenceVariation pm = format.parse("p.L330_A331delinsF");
    Assert.assertEquals(AminoAcidCode.LEUCINE, pm.getVaryingSequence().getFirstAminoAcid());
    Assert.assertEquals(AminoAcidCode.ALANINE, pm.getVaryingSequence().getLastAminoAcid());
    Assert.assertEquals(330, pm.getVaryingSequence().getFirstAminoAcidPos());
    Assert.assertEquals(331, pm.getVaryingSequence().getLastAminoAcidPos());
    Assert.assertEquals(SequenceChange.Type.DELETION_INSERTION, pm.getSequenceChange().getType());
    Assert.assertArrayEquals(AminoAcidCode.valueOfAminoAcidCodeSequence("F"), (AminoAcidCode[]) pm.getSequenceChange().getValue());
}

Example 28 with AminoAcidCode

use of org.nextprot.api.commons.bio.AminoAcidCode in project nextprot-api by calipho-sib.

the class SequenceVariantHGVSParseInsertionTest method testParseInsertionsVariants2.

@Test
public void testParseInsertionsVariants2() throws ParseException {
    format = new SequenceVariantHGVSFormat(ParsingMode.PERMISSIVE);
    SequenceVariation pm = format.parse("p.Lys722_Ala723insTyrLys");
    assertProteinSequenceVariation(pm, AminoAcidCode.LYSINE, AminoAcidCode.ALANINE, 722);
    Assert.assertEquals(SequenceChange.Type.INSERTION, pm.getSequenceChange().getType());
    Assert.assertArrayEquals(AminoAcidCode.valueOfAminoAcidCodeSequence("YK"), (AminoAcidCode[]) pm.getSequenceChange().getValue());
    Assert.assertEquals(722, ((Insertion) pm.getSequenceChange()).getInsertAfterPos());
}