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

Example 61 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatDuplicationSimpleCode3.

@Test
public void testFormatDuplicationSimpleCode3() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcid(AminoAcidCode.CYSTEINE, 76).thenDuplicate().build();
    Assert.assertEquals("p.Cys76dup", format.format(pm, AminoAcidCode.CodeType.THREE_LETTER));
}

Example 62 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatInitiationExtensionCode3.

@Test
public void testFormatInitiationExtensionCode3() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcid(AminoAcidCode.METHIONINE, 1).thenInitiationExtension(-12, AminoAcidCode.VALINE).build();
    Assert.assertEquals("p.Met1Valext-12", format.format(pm, AminoAcidCode.CodeType.THREE_LETTER));
}

Example 63 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatFrameshiftCode3.

@Test
public void testFormatFrameshiftCode3() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcid(AminoAcidCode.METHIONINE, 682).thenFrameshift(AminoAcidCode.ALANINE, 2).build();
    Assert.assertEquals("p.Met682AlafsTer2", format.format(pm, AminoAcidCode.CodeType.THREE_LETTER));
}

Example 64 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatDeletionMultiAasAndInsertion1.

@Test
public void testFormatDeletionMultiAasAndInsertion1() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcidRange(AminoAcidCode.LEUCINE, 330, AminoAcidCode.ALANINE, 331).thenDeleteAndInsert(AminoAcidCode.PHENYLALANINE).build();
    Assert.assertEquals("p.L330_A331delinsF", format.format(pm));
}

Example 65 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatDeletionMultiAndInsertionMultiCode3.

@Test
public void testFormatDeletionMultiAndInsertionMultiCode3() 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.Asp419_Arg420delinsSerSerAspGly", format.format(pm, AminoAcidCode.CodeType.THREE_LETTER));
}