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

Example 1 with IsoformSpecificity

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

the class MasterIsoformMappingServiceIntegrationTest method shouldReturnIsoformsInProperOrder.

@Test
public void shouldReturnIsoformsInProperOrder() {
    List<IsoformSpecificity> specs = this.mimService.findMasterIsoformMappingByEntryName("NX_Q8WZ42");
    int i = 0;
    for (IsoformSpecificity spec : specs) {
        i++;
        // TITIN has Iso 1, Iso 2, ... Iso 13
        assertTrue(spec.getIsoformMainName().equals("Iso " + i));
    }
    assertTrue(true);
}

Example 2 with IsoformSpecificity

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

the class MasterIsoformMappingServiceIntegrationTest method shouldReturn2IsoformsWith2MappingPositionsEach.

@Test
public void shouldReturn2IsoformsWith2MappingPositionsEach() {
    List<IsoformSpecificity> specs = this.mimService.findMasterIsoformMappingByEntryName("NX_P26439");
    assertTrue(specs.size() == 2);
    IsoformSpecificity spec;
    spec = specs.get(0);
    assertTrue(spec.getIsoformAc().equals("NX_P26439-1"));
    assertTrue(spec.getIsoformMainName().equals("Iso 1"));
    assertTrue(spec.getPositions().size() == 2);
    spec = specs.get(1);
    assertTrue(spec.getIsoformAc().equals("NX_P26439-2"));
    assertTrue(spec.getIsoformMainName().equals("Iso 2"));
    assertTrue(spec.getPositions().size() == 2);
}

Example 3 with IsoformSpecificity

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

the class MasterIsoformMappingDaoIntegrationTest method shouldReturn_4_Mappings.

@Test
public void shouldReturn_4_Mappings() {
    List<IsoformSpecificity> specs = mimdao.findIsoformMappingByMaster("NX_P26439");
    // for each of the 2 isoform we have 2 mapping positions: 2 x 2 = 4
    assertTrue(specs.size() == 4);
    for (IsoformSpecificity spec : specs) {
        // is set later by service
        assertTrue(spec.getIsoformMainName() == null);
        assertTrue(spec.getIsoformAc() != null);
        // we expect one position item by row and thus by IsoformSpecificity
        assertTrue(spec.getPositions().size() == 1);
        System.out.println(spec.toString());
    }
}

Example 4 with IsoformSpecificity

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

the class MasterIsoformMappingServiceImpl method findMasterIsoformMappingByEntryName.

@Override
@Cacheable("master-isoform-mapping")
public List<IsoformSpecificity> findMasterIsoformMappingByEntryName(String entryName) {
    // - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    // build a map between isoform unique name and isoform main name
    // - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    List<Isoform> isoforms = isoformService.findIsoformsByEntryName(entryName);
    Map<String, String> unique2mainName = new HashMap<String, String>();
    for (Isoform iso : isoforms) {
        String mainName = iso.getMainEntityName().getValue();
        unique2mainName.put(iso.getUniqueName(), mainName);
    }
    // - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    // group partial mappings obtained from DAO by isoform and set isoform name
    // - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    Map<String, IsoformSpecificity> map = new HashMap<String, IsoformSpecificity>();
    List<IsoformSpecificity> specs = masterIsoformMappingDao.findIsoformMappingByMaster(entryName);
    for (IsoformSpecificity tmpSpec : specs) {
        String ac = tmpSpec.getIsoformAc();
        if (!map.containsKey(ac))
            map.put(ac, new IsoformSpecificity(null, ac));
        IsoformSpecificity spec = map.get(ac);
        // replace unique name with main name
        spec.setIsoformMainName(unique2mainName.get(ac));
        spec.addPosition(tmpSpec.getPositions().get(0));
    }
    List<IsoformSpecificity> list = new ArrayList<IsoformSpecificity>(map.values());
    Collections.sort(list);
    // returns a immutable list when the result is cacheable (this prevents modifying the cache, since the cache returns a reference) copy on read and copy on write is too much time consuming
    return new ImmutableList.Builder<IsoformSpecificity>().addAll(list).build();
}