Examples with GeneCoexpressionNodeDegreeValueObject ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject used on opensource projects

Example 1 with GeneCoexpressionNodeDegreeValueObject

use of ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject in project Gemma by PavlidisLab.

the class LinkAnalysisServiceTest method checkResults.

private int checkResults(Collection<BioAssaySet> ees, int expectedMinimumMaxSupport) {
    boolean foundOne = false;
    int maxSupport = 0;
    Taxon mouse = taxonService.findByCommonName("mouse");
    Collection<Gene> genesWithLinks = new ArrayList<>();
    int totalLinks = 0;
    // numdatasetstesting will not be set so we won't bother checking.
    assertTrue(!geneCoexpressionService.getCoexpression(ee, true).isEmpty());
    Collection<CoexpressionValueObject> eeResults = geneCoexpressionService.getCoexpression(ee, false);
    assertTrue(!eeResults.isEmpty());
    for (CoexpressionValueObject coex : eeResults) {
        this.checkResult(coex);
    }
    Map<Long, GeneCoexpressionNodeDegreeValueObject> nodeDegrees = geneCoexpressionService.getNodeDegrees(EntityUtils.getIds(geneService.loadAll()));
    assertTrue(!nodeDegrees.isEmpty());
    // experiment-major query
    Map<Long, List<CoexpressionValueObject>> allLinks = geneCoexpressionService.findCoexpressionRelationships(mouse, new HashSet<Long>(), EntityUtils.getIds(ees), ees.size(), 10, false);
    assertTrue(!allLinks.isEmpty());
    for (Long g : allLinks.keySet()) {
        for (CoexpressionValueObject coex : allLinks.get(g)) {
            this.checkResult(coex);
        }
    }
    for (Gene gene : geneService.loadAll(mouse)) {
        Collection<CoexpressionValueObject> links = geneCoexpressionService.findCoexpressionRelationships(gene, EntityUtils.getIds(ees), 1, 0, false);
        if (links == null || links.isEmpty()) {
            continue;
        }
        assertEquals(geneCoexpressionService.findCoexpressionRelationships(gene, Collections.singleton(ee.getId()), 0, false).size(), geneCoexpressionService.countLinks(ee, gene).intValue());
        GeneCoexpressionNodeDegreeValueObject nodeDegree = geneCoexpressionService.getNodeDegree(gene);
        if (links.size() != nodeDegree.getLinksWithMinimumSupport(1)) {
            log.info(nodeDegree);
            assertEquals("Node degree check failed for gene " + gene, links.size(), nodeDegree.getLinksWithMinimumSupport(1).intValue());
        }
        assertTrue(nodeDegree.getLinksWithMinimumSupport(1) >= nodeDegree.getLinksWithMinimumSupport(2));
        totalLinks += links.size();
        log.debug(links.size() + " hits for " + gene);
        for (CoexpressionValueObject coex : links) {
            this.checkResult(coex);
            if (coex.getNumDatasetsSupporting() > maxSupport) {
                maxSupport = coex.getNumDatasetsSupporting();
            }
        }
        foundOne = true;
        if (genesWithLinks.size() == 5) {
            // without specifying stringency
            Map<Long, List<CoexpressionValueObject>> multiGeneResults = geneCoexpressionService.findCoexpressionRelationships(mouse, EntityUtils.getIds(genesWithLinks), EntityUtils.getIds(ees), 100, false);
            if (multiGeneResults.isEmpty()) {
                // noinspection ConstantConditions // these strange structures are to help with debugger.
                assertTrue(!multiGeneResults.isEmpty());
            }
            for (Long id : multiGeneResults.keySet()) {
                for (CoexpressionValueObject coex : multiGeneResults.get(id)) {
                    this.checkResult(coex);
                }
            }
            // with stringency specified, quick.
            Map<Long, List<CoexpressionValueObject>> multiGeneResults2 = geneCoexpressionService.findCoexpressionRelationships(mouse, EntityUtils.getIds(genesWithLinks), EntityUtils.getIds(ees), ees.size(), 100, true);
            if (multiGeneResults.size() != multiGeneResults2.size()) {
                assertEquals(multiGeneResults.size(), multiGeneResults2.size());
            }
            for (Long id : multiGeneResults2.keySet()) {
                for (CoexpressionValueObject coex : multiGeneResults2.get(id)) {
                    this.checkResult(coex);
                }
            }
        }
        genesWithLinks.add(gene);
    }
    assertTrue(foundOne);
    Map<Long, List<CoexpressionValueObject>> mygeneresults = geneCoexpressionService.findInterCoexpressionRelationships(mouse, EntityUtils.getIds(genesWithLinks), EntityUtils.getIds(ees), 1, false);
    if (mygeneresults.isEmpty()) {
        // noinspection ConstantConditions // these strange structures are to help with debugger.
        assertTrue(!mygeneresults.isEmpty());
    }
    for (Long id : mygeneresults.keySet()) {
        for (CoexpressionValueObject coex : mygeneresults.get(id)) {
            this.checkResult(coex);
        }
    }
    assertTrue(maxSupport >= expectedMinimumMaxSupport);
    return totalLinks;
}

Example 2 with GeneCoexpressionNodeDegreeValueObject

use of ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject in project Gemma by PavlidisLab.

the class CoexpressionNodeDegreeValueObjectTest method testa.

@Test
public void testa() {
    Gene g = Gene.Factory.newInstance();
    g.setId(1L);
    g.setOfficialName("foo");
    GeneCoexpressionNodeDegree nd = GeneCoexpressionNodeDegree.Factory.newInstance(g);
    GeneCoexpressionNodeDegreeValueObject t = new GeneCoexpressionNodeDegreeValueObject(nd);
    t.increment(1, true);
    t.increment(2, true);
    assertEquals(2, t.getLinksWithMinimumSupport(1, true).intValue());
    assertEquals(1, t.getLinksWithExactSupport(1, true).intValue());
    t.increment(1, true);
    t.increment(2, true);
    assertEquals(4, t.getLinksWithMinimumSupport(1, true).intValue());
    assertEquals(2, t.getLinksWithMinimumSupport(2, true).intValue());
    assertEquals(2, t.getLinksWithExactSupport(1, true).intValue());
    assertEquals(3, t.asIntArrayPos().length);
    assertEquals(0, t.asIntArrayPos()[0]);
    assertEquals(2, t.asIntArrayPos()[1]);
    assertEquals(2, t.asIntArrayPos()[2]);
}

Example 3 with GeneCoexpressionNodeDegreeValueObject

use of ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject in project Gemma by PavlidisLab.

the class GeneServiceImpl method loadFullyPopulatedValueObject.

@Override
@Transactional(readOnly = true)
public GeneValueObject loadFullyPopulatedValueObject(Long id) {
    Gene gene = this.geneDao.load(id);
    if (gene == null) {
        return null;
    }
    gene = this.geneDao.thaw(gene);
    GeneValueObject gvo = GeneValueObject.convert2ValueObject(gene);
    Collection<GeneAlias> aliasObjects = gene.getAliases();
    Collection<String> aliasStrings = new ArrayList<>();
    for (GeneAlias ga : aliasObjects) {
        aliasStrings.add(ga.getAlias());
    }
    gvo.setAliases(aliasStrings);
    if (gene.getMultifunctionality() != null) {
        gvo.setMultifunctionalityRank(gene.getMultifunctionality().getRank());
    }
    Long compositeSequenceCount = this.getCompositeSequenceCountById(id);
    gvo.setCompositeSequenceCount(compositeSequenceCount.intValue());
    Integer platformCount = this.geneDao.getPlatformCountById(id);
    gvo.setPlatformCount(platformCount);
    Collection<GeneSet> geneSets = this.geneSetSearch.findByGene(gene);
    Collection<GeneSetValueObject> gsVos = new ArrayList<>();
    // noinspection CollectionAddAllCanBeReplacedWithConstructor // Constructor can't handle subclasses
    gsVos.addAll(geneSetValueObjectHelper.convertToLightValueObjects(geneSets, false));
    gvo.setGeneSets(gsVos);
    Collection<Gene> geneHomologues = this.homologeneService.getHomologues(gene);
    geneHomologues = this.thawLite(geneHomologues);
    Collection<GeneValueObject> homologues = this.loadValueObjects(geneHomologues);
    gvo.setHomologues(homologues);
    Collection<PhenotypeAssociation> pas = gene.getPhenotypeAssociations();
    Collection<CharacteristicValueObject> cVos = new HashSet<>();
    for (PhenotypeAssociation pa : pas) {
        cVos.addAll(CharacteristicValueObject.characteristic2CharacteristicVO(pa.getPhenotypes()));
    }
    gvo.setPhenotypes(cVos);
    if (gvo.getNcbiId() != null) {
        SearchSettingsImpl s = new SearchSettingsImpl();
        s.setTermUri("http://purl.org/commons/record/ncbi_gene/" + gvo.getNcbiId());
        s.noSearches();
        s.setSearchExperiments(true);
        Map<Class<?>, List<SearchResult>> r = searchService.search(s);
        if (r.containsKey(ExpressionExperiment.class)) {
            List<SearchResult> hits = r.get(ExpressionExperiment.class);
            gvo.setAssociatedExperimentCount(hits.size());
        }
    }
    GeneCoexpressionNodeDegreeValueObject nodeDegree = coexpressionService.getNodeDegree(gene);
    if (nodeDegree != null) {
        gvo.setNodeDegreesPos(nodeDegree.asIntArrayPos());
        gvo.setNodeDegreesNeg(nodeDegree.asIntArrayNeg());
        gvo.setNodeDegreePosRanks(nodeDegree.asDoubleArrayPosRanks());
        gvo.setNodeDegreeNegRanks(nodeDegree.asDoubleArrayNegRanks());
    }
    return gvo;
}

Example 4 with GeneCoexpressionNodeDegreeValueObject

use of ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject in project Gemma by PavlidisLab.

the class GeneCoexpressionSearchServiceImpl method populateNodeDegrees.

/**
 * Populate node degree. Note that this ignores the datasets that were used in the query - the statistics are for
 * 'all' data sets.
 */
private void populateNodeDegrees(CoexpressionMetaValueObject result) {
    StopWatch timer = new StopWatch();
    timer.start();
    Collection<Long> allUsedGenes = new HashSet<>();
    for (CoexpressionValueObjectExt coexp : result.getResults()) {
        allUsedGenes.add(coexp.getQueryGene().getId());
        allUsedGenes.add(coexp.getFoundGene().getId());
    }
    Map<Long, GeneCoexpressionNodeDegreeValueObject> nodeDegrees = new HashMap<>();
    if (allUsedGenes.size() > 0) {
        nodeDegrees = coexpressionService.getNodeDegrees(allUsedGenes);
    }
    for (CoexpressionValueObjectExt coexp : result.getResults()) {
        // if node degree info is out of date.
        if (!nodeDegrees.containsKey(coexp.getQueryGene().getId()) || !nodeDegrees.containsKey(coexp.getFoundGene().getId())) {
            continue;
        }
        GeneCoexpressionNodeDegreeValueObject queryGeneNodeDegree = nodeDegrees.get(coexp.getQueryGene().getId());
        GeneCoexpressionNodeDegreeValueObject foundGeneNodeDegree = nodeDegrees.get(coexp.getFoundGene().getId());
        boolean pos = coexp.getNegSupp() == 0;
        coexp.setQueryGeneNodeDegree(queryGeneNodeDegree.getLinksWithMinimumSupport(coexp.getSupport(), pos));
        coexp.setFoundGeneNodeDegree(foundGeneNodeDegree.getLinksWithMinimumSupport(coexp.getSupport(), pos));
        coexp.setQueryGeneNodeDegreeRank(queryGeneNodeDegree.getRankAtMinimumSupport(coexp.getSupport(), pos));
        coexp.setFoundGeneNodeDegreeRank(foundGeneNodeDegree.getRankAtMinimumSupport(coexp.getSupport(), pos));
    }
    assert result.getSummaries() != null;
    for (Long g : nodeDegrees.keySet()) {
        if (!result.getSummaries().containsKey(g))
            continue;
        result.getSummaries().get(g).setCoexpNodeDegree(nodeDegrees.get(g));
    }
    if (timer.getTime() > 100) {
        GeneCoexpressionSearchServiceImpl.log.info("Populate node degree for " + result.getResults().size() + ": " + timer.getTime() + "ms");
    }
}

Example 5 with GeneCoexpressionNodeDegreeValueObject

use of ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject in project Gemma by PavlidisLab.

the class CoexpressionDaoImpl method updateNodeDegree.

@Override
@Transactional
public GeneCoexpressionNodeDegreeValueObject updateNodeDegree(Gene g, GeneCoexpressionNodeDegree nd) {
    Session sess = this.getSessionFactory().getCurrentSession();
    List<CoexpressionValueObject> hits = this.getCoexpression(g);
    /*
         * We have to reset the support.
         */
    GeneCoexpressionNodeDegreeValueObject gcndvo = new GeneCoexpressionNodeDegreeValueObject(nd);
    gcndvo.clear();
    assert gcndvo.getMaxSupportNeg() == 0;
    for (CoexpressionValueObject hit : hits) {
        if (hit.isPositiveCorrelation()) {
            gcndvo.increment(hit.getNumDatasetsSupporting(), true);
        } else {
            gcndvo.increment(hit.getNumDatasetsSupporting(), false);
        }
    }
    assert gcndvo.total() == hits.size();
    GeneCoexpressionNodeDegree entity = gcndvo.toEntity();
    nd.setLinkCountsPositive(entity.getLinkCountsPositive());
    nd.setLinkCountsNegative(entity.getLinkCountsNegative());
    if (CoexpressionDaoImpl.log.isDebugEnabled())
        CoexpressionDaoImpl.log.debug("gene=" + g.getId() + " pos=" + StringUtils.join(ArrayUtils.toObject(nd.getLinkCountsPositive()), " ") + " neg=" + StringUtils.join(ArrayUtils.toObject(nd.getLinkCountsNegative()), " "));
    sess.update(nd);
    // might not be necessary, but presumption is data is stale now...
    this.gene2GeneCoexpressionCache.remove(g.getId());
    this.geneTestedInCache.remove(g.getId());
    return gcndvo;
}