Examples with SequenceVariation org.nextprot.api.commons.bio.variation.prot.SequenceVariation used on opensource projects

Example 66 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatAADeletionCode3.

@Test
public void testFormatAADeletionCode3() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcid(AminoAcidCode.LYSINE, 73).thenDelete().build();
    Assert.assertEquals("p.Lys73del", format.format(pm, AminoAcidCode.CodeType.THREE_LETTER));
}

Example 67 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatSubstitutionCode3.

@Test
public void testFormatSubstitutionCode3() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcid(AminoAcidCode.ARGININE, 54).thenSubstituteWith(AminoAcidCode.CYSTEINE).build();
    Assert.assertEquals("p.Arg54Cys", format.format(pm, AminoAcidCode.CodeType.THREE_LETTER));
}

Example 68 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatDeletion1AaAndInsertion1.

@Test
public void testFormatDeletion1AaAndInsertion1() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcid(AminoAcidCode.THREONINE, 399).thenDeleteAndInsert(AminoAcidCode.LEUCINE).build();
    Assert.assertEquals("p.T399delinsL", format.format(pm));
}

Example 69 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatDeletionMultiAndInsertionMulti.

@Test
public void testFormatDeletionMultiAndInsertionMulti() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcidRange(AminoAcidCode.ASPARTIC_ACID, 419, AminoAcidCode.ARGININE, 420).thenDeleteAndInsert(AminoAcidCode.SERINE, AminoAcidCode.SERINE, AminoAcidCode.ASPARTIC_ACID, AminoAcidCode.GLYCINE).build();
    Assert.assertEquals("p.D419_R420delinsSSDG", format.format(pm));
}

Example 70 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatRangeDeletionCode3.

@Test
public void testFormatRangeDeletionCode3() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcidRange(AminoAcidCode.LYSINE, 487, AminoAcidCode.LEUCINE, 498).thenDelete().build();
    Assert.assertEquals("p.Lys487_Leu498del", format.format(pm, AminoAcidCode.CodeType.THREE_LETTER));
}