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

Example 1 with ChromosomalLocation

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

the class ChromosomalLocationComparatorTest method testCompare.

@Test
public void testCompare() throws Exception {
    ChromosomalLocationComparator comparator = new ChromosomalLocationComparator();
    List<ChromosomalLocation> list = ChromosomalLocationTest.newChromosomalLocations("19p15", "18", "19p15.3", "19p13", "19");
    ChromosomalLocation unk = new ChromosomalLocation();
    unk.setChromosome("unknown");
    unk.setBand("unknown");
    list.add(unk);
    ChromosomalLocation unkBand = new ChromosomalLocation();
    unkBand.setChromosome("X");
    unkBand.setBand("unknown");
    list.add(unkBand);
    ChromosomalLocation unkBand2 = new ChromosomalLocation();
    unkBand2.setChromosome("Y");
    unkBand2.setBand("");
    list.add(unkBand2);
    Collections.sort(list, comparator);
    assertChromosomalLocation(list.get(0), "18", "");
    assertChromosomalLocation(list.get(1), "19", "");
    assertChromosomalLocation(list.get(2), "19", "p13");
    assertChromosomalLocation(list.get(3), "19", "p15");
    assertChromosomalLocation(list.get(4), "19", "p15.3");
    assertChromosomalLocation(list.get(5), "X", "unknown");
    assertChromosomalLocation(list.get(6), "Y", "");
    assertChromosomalLocation(list.get(7), "unknown", "unknown");
}

Example 2 with ChromosomalLocation

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

the class GeneDaoIntegrationTest method buildChromosomalLocation.

private ChromosomalLocation buildChromosomalLocation(String displayName, String geneGeneNames, String masterGeneNames) {
    ChromosomalLocation loc = new ChromosomalLocation();
    loc.setDisplayName(displayName);
    loc.setGeneGeneNames(geneGeneNames);
    loc.setMasterGeneNames(masterGeneNames);
    return loc;
}

Example 3 with ChromosomalLocation

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

the class GeneDaoIntegrationTest method shouldGetSameValuesFromOldAndNewQueries.

@Test
public void shouldGetSameValuesFromOldAndNewQueries() {
    String entryName = "NX_A6NCW0";
    List<ChromosomalLocation> locs1;
    ChromosomalLocation loc1;
    List<ChromosomalLocation> locs2;
    ChromosomalLocation loc2;
    // old algorithm
    locs1 = geneDao.findChromosomalLocationsByEntryNameOld(entryName);
    Assert.assertEquals(1, locs1.size());
    loc1 = locs1.get(0);
    // new algorithm
    locs2 = geneDao.findChromosomalLocationsByEntryName(entryName);
    Assert.assertEquals(1, locs2.size());
    loc2 = locs1.get(0);
    // field content comparison
    Assert.assertEquals(loc1.getAccession(), loc2.getAccession());
    Assert.assertEquals(loc1.getBand(), loc2.getBand());
    Assert.assertEquals(loc1.getChromosome(), loc2.getChromosome());
    Assert.assertEquals(loc1.isGoldMapping(), loc2.isGoldMapping());
    Assert.assertEquals(loc1.getRecommendedName("old"), loc2.getRecommendedName("old"));
    Assert.assertEquals(loc1.getFirstPosition(), loc2.getFirstPosition());
    Assert.assertEquals(loc1.getLastPosition(), loc2.getLastPosition());
    Assert.assertEquals(loc1.getStrand(), loc2.getStrand());
}

Example 4 with ChromosomalLocation

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

the class GeneDaoIntegrationTest method shouldShowDifferenceBetweenOldAndNewImplementation.

@Test
public void shouldShowDifferenceBetweenOldAndNewImplementation() {
    ChromosomalLocation loc;
    // about 103 locations: Example: NX_A6NJ64
    // The displayName is null and displayName is not null
    loc = buildChromosomalLocation("RP11-166B2.1", "RP11-166B2.1", null);
    Assert.assertEquals("RP11-166B2.1", loc.getRecommendedName("old"));
    Assert.assertEquals("unknown", loc.getRecommendedName());
    // TODO find other example
    // about 3 locations: Example: NX_Q5VWM5
    // The displayName is the second option of the masterGeneNames and the second option of the geneGeneNames
    loc = buildChromosomalLocation("PRAMEF15", "PRAMEF9 PRAMEF15", "PRAMEF9 PRAMEF15");
    Assert.assertEquals("PRAMEF15", loc.getRecommendedName("old"));
    Assert.assertEquals("PRAMEF15", loc.getRecommendedName());
}

Example 5 with ChromosomalLocation

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

the class GeneDaoIntegrationTest method shouldHandleCaseWhenSomeOfMultipleUniProtNamesMatchesAreProvided.

// TODO: TO FIX BY PAM
@Ignore
@Test
public void shouldHandleCaseWhenSomeOfMultipleUniProtNamesMatchesAreProvided() {
    // Case 3 - about 237 locations
    ChromosomalLocation loc;
    // (a) In this example: NX_O14603, 2 gene names are in both geneGeneNameas and masterGeneNames: PRY2 PRY => NOT deterministic
    // getRecommendedName() returns the first found in the intersection, it is arbitrary,
    // the displayName could in this case make the choice deterministic
    loc = buildChromosomalLocation("PRY2", "PRY PRY2", "PRYP4 PRYP3 PRY2 PRY");
    Assert.assertEquals("PRY2", loc.getRecommendedName("old"));
    Assert.assertEquals("PRY", loc.getRecommendedName());
    // (b) In this example: NX_Q0WX57, a single gene name is both in geneGeneNameas and masterGeneNames: USP17L30 => deterministic.
    // But we see that the ENSG gene name (displayName) prefers the other geneName USP17J
    loc = buildChromosomalLocation("USP17J", "USP17J USP17L30", "USP17L30 USP17L25 USP17L29 USP17L28 USP17L27 USP17L26 USP17L24");
    Assert.assertEquals("USP17L30", loc.getRecommendedName("old"));
    Assert.assertEquals("USP17L30", loc.getRecommendedName());
    // (c) In this example NX_Q13066: no gene name are both in geneGeneNameas and masterGeneNames => NOT deterministic
    // We choose the first one in masterGeneNames
    loc = buildChromosomalLocation(null, null, "GAGE2C GAGE2B");
    Assert.assertEquals("GAGE2C", loc.getRecommendedName("old"));
    Assert.assertEquals("GAGE2C", loc.getRecommendedName());
    loc = buildChromosomalLocation("fakeGene", "fakeGene", "GAGE2C GAGE2B");
    Assert.assertEquals("GAGE2C", loc.getRecommendedName("old"));
    Assert.assertEquals("GAGE2C", loc.getRecommendedName());
    loc = buildChromosomalLocation("fakeGene", "fakeGene fakeGene2", "GAGE2C GAGE2B");
    Assert.assertEquals("GAGE2C", loc.getRecommendedName("old"));
    Assert.assertEquals("GAGE2C", loc.getRecommendedName());
}