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

Example 21 with SequenceVariation

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

the class SequenceVariantHGVSParseDeletionTest method testParseRangeDeletionCode3.

@Test
public void testParseRangeDeletionCode3() throws Exception {
    SequenceVariation pm = format.parse("p.Lys487_Leu498del");
    Assert.assertEquals(AminoAcidCode.LYSINE, pm.getVaryingSequence().getFirstAminoAcid());
    Assert.assertEquals(AminoAcidCode.LEUCINE, pm.getVaryingSequence().getLastAminoAcid());
    Assert.assertEquals(487, pm.getVaryingSequence().getFirstAminoAcidPos());
    Assert.assertEquals(498, pm.getVaryingSequence().getLastAminoAcidPos());
    Assert.assertEquals(SequenceChange.Type.DELETION, pm.getSequenceChange().getType());
}

Example 22 with SequenceVariation

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

the class SequenceVariantHGVSParseDeletionTest method testParseAADeletion.

@Test
public void testParseAADeletion() throws Exception {
    SequenceVariation pm = format.parse("p.K73del");
    Assert.assertEquals(AminoAcidCode.LYSINE, pm.getVaryingSequence().getFirstAminoAcid());
    Assert.assertEquals(73, pm.getVaryingSequence().getFirstAminoAcidPos());
    Assert.assertEquals(SequenceChange.Type.DELETION, pm.getSequenceChange().getType());
}

Example 23 with SequenceVariation

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

the class SequenceVariantHGVSParseDelinsTest method testParseDeletion1AaAndInsertion1.

// /// DELETION FOLLOWED BY INSERTIONS
@Test
public void testParseDeletion1AaAndInsertion1() throws Exception {
    SequenceVariation pm = format.parse("p.T399delinsL");
    Assert.assertEquals(AminoAcidCode.THREONINE, pm.getVaryingSequence().getFirstAminoAcid());
    Assert.assertEquals(399, pm.getVaryingSequence().getFirstAminoAcidPos());
    Assert.assertEquals(SequenceChange.Type.DELETION_INSERTION, pm.getSequenceChange().getType());
    Assert.assertArrayEquals(AminoAcidCode.valueOfAminoAcidCodeSequence("L"), (AminoAcidCode[]) pm.getSequenceChange().getValue());
}

Example 24 with SequenceVariation

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

the class SequenceVariantHGVSParseDelinsTest method testParseDeletionMultiAasAndInsertion1Code3.

@Test
public void testParseDeletionMultiAasAndInsertion1Code3() throws Exception {
    SequenceVariation pm = format.parse("p.Leu330_Ala331delinsPhe");
    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 25 with SequenceVariation

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

the class SequenceVariantHGVSParseDelinsTest method testParseAANonStandardDelins1.

@Test
public void testParseAANonStandardDelins1() throws Exception {
    format = new SequenceVariantHGVSFormat(ParsingMode.PERMISSIVE);
    SequenceVariation pm = format.parse("p.T399>L");
    Assert.assertEquals(AminoAcidCode.THREONINE, pm.getVaryingSequence().getFirstAminoAcid());
    Assert.assertEquals(399, pm.getVaryingSequence().getFirstAminoAcidPos());
    Assert.assertEquals(SequenceChange.Type.DELETION_INSERTION, pm.getSequenceChange().getType());
    Assert.assertArrayEquals(AminoAcidCode.valueOfAminoAcidCodeSequence("L"), (AminoAcidCode[]) pm.getSequenceChange().getValue());
}