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

Example 16 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatExtensionCode3.

@Test
public void testFormatExtensionCode3() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcid(AminoAcidCode.STOP, 110).thenTerminationExtension(17, AminoAcidCode.GLUTAMINE).build();
    Assert.assertEquals("p.Ter110Glnext*17", format.format(pm, AminoAcidCode.CodeType.THREE_LETTER));
}

Example 17 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatSubstitution.

@Test
public void testFormatSubstitution() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcid(AminoAcidCode.ARGININE, 54).thenSubstituteWith(AminoAcidCode.CYSTEINE).build();
    Assert.assertEquals("p.R54C", format.format(pm));
}

Example 18 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatSubstitutionFixCode1.

@Test
public void testFormatSubstitutionFixCode1() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcid(AminoAcidCode.STOP, 104).thenSubstituteWith(AminoAcidCode.GLUTAMIC_ACID).build();
    Assert.assertEquals("p.*104E", format.format(pm));
}

Example 19 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatSubstitutionFixCode3.

@Test
public void testFormatSubstitutionFixCode3() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcid(AminoAcidCode.STOP, 104).thenSubstituteWith(AminoAcidCode.GLUTAMIC_ACID).build();
    Assert.assertEquals("p.Ter104Glu", format.format(pm, AminoAcidCode.CodeType.THREE_LETTER));
}

Example 20 with SequenceVariation

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

the class SequenceVariantHGVSFormatterTest method testFormatDuplicationCode3.

@Test
public void testFormatDuplicationCode3() throws Exception {
    SequenceVariation pm = new SequenceVariationImpl.FluentBuilding().selectAminoAcidRange(AminoAcidCode.CYSTEINE, 76, AminoAcidCode.GLUTAMIC_ACID, 79).thenDuplicate().build();
    Assert.assertEquals("p.Cys76_Glu79dup", format.format(pm, AminoAcidCode.CodeType.THREE_LETTER));
}