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

Example 26 with SequenceVariation

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

the class SequenceVariantHGVSParseDelinsTest method testParseAANonStandardDelins3.

@Test
public void testParseAANonStandardDelins3() throws Exception {
    format = new SequenceVariantHGVSFormat(ParsingMode.PERMISSIVE);
    SequenceVariation pm = format.parse("p.W39_E40>*");
    Assert.assertEquals(AminoAcidCode.TRYPTOPHAN, pm.getVaryingSequence().getFirstAminoAcid());
    Assert.assertEquals(AminoAcidCode.GLUTAMIC_ACID, pm.getVaryingSequence().getLastAminoAcid());
    Assert.assertEquals(39, pm.getVaryingSequence().getFirstAminoAcidPos());
    Assert.assertEquals(40, pm.getVaryingSequence().getLastAminoAcidPos());
    Assert.assertEquals(SequenceChange.Type.DELETION_INSERTION, pm.getSequenceChange().getType());
    Assert.assertArrayEquals(AminoAcidCode.valueOfAminoAcidCodeSequence("*"), (AminoAcidCode[]) pm.getSequenceChange().getValue());
}

Example 27 with SequenceVariation

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

the class SequenceVariantHGVSParseDelinsTest method testParseDeletion1AaAndInsertion1Code3.

@Test
public void testParseDeletion1AaAndInsertion1Code3() throws Exception {
    SequenceVariation pm = format.parse("p.Thr399delinsLeu");
    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 28 with SequenceVariation

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

the class SequenceVariantHGVSParseDelinsTest method testParseAANonStandardDelins2.

@Test
public void testParseAANonStandardDelins2() throws Exception {
    format = new SequenceVariantHGVSFormat(ParsingMode.PERMISSIVE);
    SequenceVariation pm = format.parse("p.L330_A331>F");
    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 29 with SequenceVariation

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

the class SequenceVariantHGVSParseDelinsTest method testParseAANonStandardDelins4.

@Test
public void testParseAANonStandardDelins4() throws Exception {
    format = new SequenceVariantHGVSFormat(ParsingMode.PERMISSIVE);
    SequenceVariation pm = format.parse("p.D419_R420>SSDG");
    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 30 with SequenceVariation

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

the class SequenceVariantHGVSParseDuplicationTest method testParseDuplication.

@Test
public void testParseDuplication() throws Exception {
    SequenceVariation duplication = format.parse("p.Cys76_Glu79dup");
    Assert.assertEquals(AminoAcidCode.CYSTEINE, duplication.getVaryingSequence().getFirstAminoAcid());
    Assert.assertEquals(AminoAcidCode.GLUTAMIC_ACID, duplication.getVaryingSequence().getLastAminoAcid());
    Assert.assertEquals(76, duplication.getVaryingSequence().getFirstAminoAcidPos());
    Assert.assertEquals(79, duplication.getVaryingSequence().getLastAminoAcidPos());
    Assert.assertEquals(SequenceChange.Type.DUPLICATION, duplication.getSequenceChange().getType());
    Assert.assertEquals(79, duplication.getSequenceChange().getValue());
}