Examples with DynamicEntity org.molgenis.data.support.DynamicEntity used on opensource projects

Example 41 with DynamicEntity

use of org.molgenis.data.support.DynamicEntity in project molgenis by molgenis.

the class GoNLAnnotatorTest method testAnnotate3.

@Test
public void testAnnotate3() {
    Entity entity3 = new DynamicEntity(emd);
    entity3.set(VcfAttributes.CHROM, "1");
    entity3.set(VcfAttributes.POS, 78383467);
    entity3.set(VcfAttributes.REF, "G");
    entity3.set(VcfAttributes.ALT, "A");
    Iterator<Entity> results = annotator.annotate(Collections.singletonList(entity3));
    assertTrue(results.hasNext());
    Entity resultEntity = results.next();
    assertFalse(results.hasNext());
    assertEquals(resultEntity.get(GONL_GENOME_AF), "0.8674698795180723");
    assertEquals(resultEntity.get(GONL_GENOME_GTC), "6|120|372");
}

Example 42 with DynamicEntity

use of org.molgenis.data.support.DynamicEntity in project molgenis by molgenis.

the class GoNLAnnotatorTest method testAnnotate7.

@Test
public void testAnnotate7() {
    Entity entity7 = new DynamicEntity(emd);
    entity7.set(VcfAttributes.CHROM, "15");
    entity7.set(VcfAttributes.POS, 66641732);
    entity7.set(VcfAttributes.REF, "G");
    entity7.set(VcfAttributes.ALT, "A,C,T");
    Iterator<Entity> results = annotator.annotate(Collections.singletonList(entity7));
    assertTrue(results.hasNext());
    Entity resultEntity = results.next();
    assertFalse(results.hasNext());
    assertEquals(resultEntity.get(GONL_GENOME_AF), ".,0.09538152610441768,.");
    assertEquals(resultEntity.get(GONL_GENOME_GTC), ".,412|77|9,.");
}

Example 43 with DynamicEntity

use of org.molgenis.data.support.DynamicEntity in project molgenis by molgenis.

the class GoNLAnnotatorTest method testAnnotate12.

@Test
public void testAnnotate12() {
    Entity entity12 = new DynamicEntity(emd);
    entity12.set(VcfAttributes.CHROM, "2");
    entity12.set(VcfAttributes.POS, 219142023);
    entity12.set(VcfAttributes.REF, "G");
    entity12.set(VcfAttributes.ALT, "A");
    Iterator<Entity> results = annotator.annotate(Collections.singletonList(entity12));
    assertTrue(results.hasNext());
    Entity resultEntity = results.next();
    assertFalse(results.hasNext());
    assertEquals(resultEntity.get(GONL_GENOME_AF), "0.9969879518072289");
    assertEquals(resultEntity.get(GONL_GENOME_GTC), "0|3|495");
}

Example 44 with DynamicEntity

use of org.molgenis.data.support.DynamicEntity in project molgenis by molgenis.

the class GoNLAnnotatorTest method testAnnotate15.

/**
 * Test for bugfix where alt allele in resource was trimmed too much causing index out of bounds.
 */
@Test
public void testAnnotate15() {
    Entity entity14 = new DynamicEntity(emd);
    entity14.set(VcfAttributes.CHROM, "1");
    entity14.set(VcfAttributes.POS, 28227207);
    entity14.set(VcfAttributes.REF, "A");
    entity14.set(VcfAttributes.ALT, "G");
    Iterator<Entity> results = annotator.annotate(Collections.singletonList(entity14));
    assertTrue(results.hasNext());
    Entity resultEntity = results.next();
    assertFalse(results.hasNext());
    assertNull(resultEntity.get(GONL_GENOME_AF));
    assertNull(resultEntity.get(GONL_GENOME_GTC));
}

Example 45 with DynamicEntity

use of org.molgenis.data.support.DynamicEntity in project molgenis by molgenis.

the class GoNLAnnotatorTest method testAnnotate9.

@Test
public void testAnnotate9() {
    Entity entity9 = new DynamicEntity(emd);
    entity9.set(VcfAttributes.CHROM, "X");
    entity9.set(VcfAttributes.POS, 79943569);
    entity9.set(VcfAttributes.REF, "T");
    entity9.set(VcfAttributes.ALT, "C");
    Iterator<Entity> results = annotator.annotate(Collections.singletonList(entity9));
    assertTrue(results.hasNext());
    Entity resultEntity = results.next();
    assertFalse(results.hasNext());
    assertEquals(resultEntity.get(GONL_GENOME_AF), "0.9989939637826962");
    assertEquals(resultEntity.get(GONL_GENOME_GTC), "0|1|496");
}