Examples with Annotation org.nextprot.api.core.domain.annotation.Annotation used on opensource projects

Example 21 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class ByAnnotationBioObjectComparatorTest method compareAnnotationsSameCatDiffCvName.

@Test
public void compareAnnotationsSameCatDiffCvName() throws Exception {
    Annotation refAnnot1 = new Annotation();
    refAnnot1.setAnnotationCategory(AnnotationCategory.GO_BIOLOGICAL_PROCESS);
    refAnnot1.setAnnotationHash("010a85141bf174a186aaf714676cb397");
    refAnnot1.setCvTermName("transmission of nerve impulse");
    Annotation refAnnot2 = new Annotation();
    refAnnot2.setAnnotationCategory(AnnotationCategory.GO_BIOLOGICAL_PROCESS);
    refAnnot2.setAnnotationHash("3bffa5c7f436f45d5c9a2aec4757a492");
    refAnnot2.setCvTermName("spike train");
    ByAnnotationBioObjectComparator comparator = new ByAnnotationBioObjectComparator(newHashMap(refAnnot1, refAnnot2));
    Annotation annotation1 = new Annotation();
    annotation1.setBioObject(mockBioObject(BioObject.BioType.ENTRY_ANNOTATION, BioObject.ResourceType.EXTERNAL, "010a85141bf174a186aaf714676cb397"));
    Annotation annotation2 = new Annotation();
    annotation2.setBioObject(mockBioObject(BioObject.BioType.ENTRY_ANNOTATION, BioObject.ResourceType.EXTERNAL, "3bffa5c7f436f45d5c9a2aec4757a492"));
    int cmp = comparator.compare(annotation1, annotation2);
    Assert.assertEquals(1, cmp);
}

Example 22 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class ByAnnotationBioObjectComparatorTest method compareAnnotationsSameBioObjects.

@Test
public void compareAnnotationsSameBioObjects() throws Exception {
    Annotation refAnnot1 = new Annotation();
    refAnnot1.setAnnotationCategory(AnnotationCategory.GO_BIOLOGICAL_PROCESS);
    refAnnot1.setAnnotationHash("010a85141bf174a186aaf714676cb397");
    refAnnot1.setCvTermName("transmission of nerve impulse");
    Annotation refAnnot2 = new Annotation();
    refAnnot2.setAnnotationCategory(AnnotationCategory.GO_BIOLOGICAL_PROCESS);
    refAnnot2.setAnnotationHash("3bffa5c7f436f45d5c9a2aec4757a492");
    refAnnot2.setCvTermName("transmission of nerve impulse");
    ByAnnotationBioObjectComparator comparator = new ByAnnotationBioObjectComparator(newHashMap(refAnnot1, refAnnot2));
    Annotation annotation1 = new Annotation();
    annotation1.setBioObject(mockBioObject(BioObject.BioType.ENTRY_ANNOTATION, BioObject.ResourceType.EXTERNAL, "010a85141bf174a186aaf714676cb397"));
    Annotation annotation2 = new Annotation();
    annotation2.setBioObject(mockBioObject(BioObject.BioType.ENTRY_ANNOTATION, BioObject.ResourceType.EXTERNAL, "3bffa5c7f436f45d5c9a2aec4757a492"));
    int cmp = comparator.compare(annotation1, annotation2);
    Assert.assertEquals(0, cmp);
}

Example 23 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class ByAnnotationVariantComparatorTest method compareVariantsSame.

@Test
public void compareVariantsSame() throws Exception {
    ByAnnotationVariantComparator comparator = new ByAnnotationVariantComparator();
    Annotation variant1 = mockAnnotationVariant(AnnotationCategory.VARIANT, "A", "V", new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-1", 14, 14), new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-4", 12, 12));
    Annotation variant2 = mockAnnotationVariant(AnnotationCategory.VARIANT, "A", "V", new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-1", 14, 14), new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-4", 12, 12));
    int cmp = comparator.compare(variant1, variant2);
    Assert.assertEquals(0, cmp);
}

Example 24 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class ByAnnotationVariantComparatorTest method compareVariantsMutagenesisSamePositionSameVariation.

@Test
public void compareVariantsMutagenesisSamePositionSameVariation() throws Exception {
    ByAnnotationVariantComparator comparator = new ByAnnotationVariantComparator();
    Annotation variant1 = mockAnnotationVariant(AnnotationCategory.VARIANT, "A", "V", new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-1", 14, 14), new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-4", 12, 12));
    Annotation variant2 = mockAnnotationVariant(AnnotationCategory.MUTAGENESIS, "A", "V", new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-1", 14, 14), new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-4", 12, 12));
    int cmp = comparator.compare(variant1, variant2);
    Assert.assertEquals(0, cmp);
}

Example 25 with Annotation

use of org.nextprot.api.core.domain.annotation.Annotation in project nextprot-api by calipho-sib.

the class ByAnnotationVariantComparatorTest method compareVariantsDiffEndingLocation.

@Test
public void compareVariantsDiffEndingLocation() throws Exception {
    ByAnnotationVariantComparator comparator = new ByAnnotationVariantComparator();
    Annotation variant1 = mockAnnotationVariant(AnnotationCategory.VARIANT, "X", "W", new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-1", 14, 14), new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-4", 12, 36));
    Annotation variant2 = mockAnnotationVariant(AnnotationCategory.VARIANT, "A", "V", new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-1", 14, 14), new ByIsoformPositionComparatorTest.TargetIsoform("NX_P51610-4", 12, 12));
    int cmp = comparator.compare(variant1, variant2);
    Assert.assertEquals(-1, cmp);
}