Examples with GeneValueObject ubic.gemma.model.genome.gene.GeneValueObject used on opensource projects

Example 26 with GeneValueObject

use of ubic.gemma.model.genome.gene.GeneValueObject in project Gemma by PavlidisLab.

the class PhenotypeAssociationDaoImpl method findGenesForPhenotype.

@Override
public Map<GeneValueObject, OntologyTerm> findGenesForPhenotype(OntologyTerm term, Long taxon, boolean includeIEA) {
    Collection<OntologyTerm> children = term.getChildren(false);
    Map<String, OntologyTerm> uris = new HashMap<>();
    uris.put(term.getUri(), term);
    for (OntologyTerm c : children) {
        uris.put(c.getUri(), c);
    }
    assert !uris.isEmpty();
    Session sess = this.getSessionFactory().getCurrentSession();
    String q = "select distinct ph.gene, p.valueUri, p.evidenceCode " + " from PhenotypeAssociation ph join ph.phenotypes p where p.valueUri in (:t)";
    Query query = sess.createQuery(q);
    Map<GeneValueObject, OntologyTerm> result = new HashMap<>();
    query.setParameterList("t", uris.keySet());
    List<?> list = query.list();
    for (Object o : list) {
        Object[] oa = (Object[]) o;
        Gene g = (Gene) oa[0];
        if (!taxon.equals(g.getTaxon().getId()))
            continue;
        String uri = (String) oa[1];
        GOEvidenceCode ev = (GOEvidenceCode) oa[2];
        if (!includeIEA && ev != null && ev.equals(GOEvidenceCode.IEA)) {
            continue;
        }
        GeneValueObject gvo = new GeneValueObject(g);
        OntologyTerm otForUri = uris.get(uri);
        assert otForUri != null;
        /*
             * only clobber if this term is more specific
             */
        if (result.containsKey(gvo) && otForUri.getParents(false).contains(otForUri)) {
            continue;
        }
        result.put(gvo, otForUri);
    }
    return result;
}

Example 27 with GeneValueObject

use of ubic.gemma.model.genome.gene.GeneValueObject in project Gemma by PavlidisLab.

the class DEDVController method format4File.

/**
 * Converts the given map into a tab delimited String
 */
private String format4File(Map<ExpressionExperimentValueObject, Map<Long, Collection<DoubleVectorValueObject>>> result) {
    StringBuilder converted = new StringBuilder();
    // Saves us from loading genes
    Map<Long, GeneValueObject> genes = new HashMap<>();
    // unnecessarily
    converted.append("# Generated by Gemma\n# ").append(new Date()).append("\n");
    converted.append(ExpressionDataFileService.DISCLAIMER + "#\n");
    for (ExpressionExperimentValueObject ee : result.keySet()) {
        boolean didHeaderForEe = false;
        Collection<Long> geneIds = result.get(ee).keySet();
        for (Long geneId : geneIds) {
            GeneValueObject gene;
            if (genes.containsKey(geneId)) {
                gene = genes.get(geneId);
            } else {
                gene = geneService.loadValueObjectById(geneId);
                genes.put(geneId, gene);
            }
            String geneName = gene.getOfficialSymbol();
            Collection<DoubleVectorValueObject> vecs = result.get(ee).get(geneId);
            for (DoubleVectorValueObject dedv : vecs) {
                if (!didHeaderForEe) {
                    converted.append(makeHeader(dedv));
                    didHeaderForEe = true;
                }
                converted.append(geneName).append("\t").append(gene.getOfficialName()).append("\t");
                converted.append(dedv.getDesignElement().getName()).append("\t");
                if (dedv.getData() != null || dedv.getData().length != 0) {
                    for (double data : dedv.getData()) {
                        converted.append(String.format("%.3f", data)).append("\t");
                    }
                    // remove the trailing tab
                    converted.deleteCharAt(converted.length() - 1);
                }
                converted.append("\n");
            }
        }
        converted.append("\n");
    }
    converted.append("\r\n");
    return converted.toString();
}

Example 28 with GeneValueObject

use of ubic.gemma.model.genome.gene.GeneValueObject in project Gemma by PavlidisLab.

the class DEDVController method makeVisCollection.

/**
 * Takes the DEDVs and put them in point objects and normalize the values. returns a map of eeid to visValueObject.
 * Currently removes multiple hits for same gene. Tries to pick best DEDV.
 */
private VisualizationValueObject[] makeVisCollection(Collection<DoubleVectorValueObject> dedvs, Collection<Long> genes, Map<Long, Collection<Long>> validatedProbes, Map<Long, LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>> layouts) {
    Map<Long, List<DoubleVectorValueObject>> vvoMap = new HashMap<>();
    // Organize by expression experiment
    if (dedvs == null || dedvs.isEmpty())
        return new VisualizationValueObject[1];
    for (DoubleVectorValueObject dvvo : dedvs) {
        // FIXME: we can probably use this information, and do away with carrying so much Layout information around?
        // assert dvvo.isReorganized() && dvvo.getBioAssayDimension().isReordered(); // not always true!!
        ExpressionExperimentValueObject ee = dvvo.getExpressionExperiment();
        if (!vvoMap.containsKey(ee.getId())) {
            vvoMap.put(ee.getId(), new ArrayList<DoubleVectorValueObject>());
        }
        vvoMap.get(ee.getId()).add(dvvo);
    }
    List<GeneValueObject> geneValueObjects;
    if (genes == null || genes.isEmpty()) {
        geneValueObjects = new ArrayList<>(getGeneValueObjectsUsed(dedvs).values());
    } else {
        geneValueObjects = getGeneValueObjectList(new ArrayList<>(genes));
    }
    StopWatch timer = new StopWatch();
    timer.start();
    VisualizationValueObject[] result = new VisualizationValueObject[vvoMap.keySet().size()];
    // Create collection of visualizationValueObject for flotr on js side
    int i = 0;
    for (Long ee : vvoMap.keySet()) {
        Collection<Long> validatedProbeList = null;
        if (validatedProbes != null) {
            validatedProbeList = validatedProbes.get(ee);
        }
        Collection<DoubleVectorValueObject> vectors = vvoMap.get(ee);
        VisualizationValueObject vvo = new VisualizationValueObject(vectors, geneValueObjects, validatedProbeList);
        if (vectors.size() > 0) {
            getSampleNames(vectors, vvo, layouts);
            if (vectors.size() > 0 && layouts != null && !layouts.isEmpty() && layouts.containsKey(ee)) {
                // Set up the experimental designinfo so we can show it above the graph.
                LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>> layout = layouts.get(ee);
                this.prepareFactorsForFrontEndDisplay(vvo, layout);
            }
        }
        /*
             * Set up the experimental design info so we can show it above the graph.
             */
        if (layouts != null && layouts.get(ee) != null) {
            vvo.setUpFactorProfiles(layouts.get(ee));
        }
        result[i] = vvo;
        i++;
    }
    long time = timer.getTime();
    if (time > 1000) {
        log.info("Created vis value objects in: " + time);
    }
    return result;
}

Example 29 with GeneValueObject

use of ubic.gemma.model.genome.gene.GeneValueObject in project Gemma by PavlidisLab.

the class GeneController method loadGeneDetails.

/**
 * AJAX used for gene page
 */
public GeneValueObject loadGeneDetails(Long geneId) {
    // return geneCoreService.loadGeneDetails( geneId );
    GeneValueObject gvo = geneCoreService.loadGeneDetails(geneId);
    Collection<EvidenceValueObject<? extends PhenotypeAssociation>> collEVO = phenotypeAssociationManagerService.findEvidenceByGeneId(geneId, new HashSet<String>(), new EvidenceFilter(gvo.getTaxonId(), false, null));
    Iterator<EvidenceValueObject<? extends PhenotypeAssociation>> iter = collEVO.iterator();
    Collection<CharacteristicValueObject> collFilteredDVO = new HashSet<>();
    while (iter.hasNext()) {
        EvidenceValueObject evo = iter.next();
        if (!evo.isHomologueEvidence())
            collFilteredDVO.addAll(evo.getPhenotypes());
    }
    gvo.setPhenotypes(collFilteredDVO);
    gvo.setNumGoTerms(this.findGOTerms(geneId).size());
    return gvo;
}

Example 30 with GeneValueObject

use of ubic.gemma.model.genome.gene.GeneValueObject in project Gemma by PavlidisLab.

the class GeneController method show.

@RequestMapping(value = { "/showGene.html", "/" }, method = RequestMethod.GET)
public ModelAndView show(HttpServletRequest request, HttpServletResponse response) {
    String idString = request.getParameter("id");
    String ncbiId = request.getParameter("ncbiid");
    String geneName = request.getParameter("name");
    String taxonName = request.getParameter("taxon");
    String ensemblId = request.getParameter("ensemblId");
    GeneValueObject geneVO = null;
    try {
        if (StringUtils.isNotBlank(idString)) {
            Long id = Long.parseLong(idString);
            geneVO = geneService.loadValueObjectById(id);
            if (geneVO == null) {
                addMessage(request, "object.notfound", new Object[] { "Gene " + id });
                return new ModelAndView("index");
            }
        } else if (StringUtils.isNotBlank(ncbiId)) {
            geneVO = geneService.findByNCBIIdValueObject(Integer.parseInt(ncbiId));
        } else if (StringUtils.isNotBlank(ensemblId)) {
            @SuppressWarnings("unchecked") Collection<Gene> foundGenes = Collections.singleton(geneService.findByEnsemblId(ensemblId));
            if (foundGenes.size() == 1) {
                Gene gene = foundGenes.iterator().next();
                if (gene != null) {
                    geneVO = geneService.loadValueObjectById(gene.getId());
                }
            }
        } else if (StringUtils.isNotBlank(geneName) && StringUtils.isNotBlank(taxonName)) {
            Taxon taxon = taxonService.findByCommonName(taxonName);
            if (taxon != null) {
                Gene gene = geneService.findByOfficialSymbol(geneName, taxon);
                if (gene != null) {
                    geneVO = geneService.loadValueObjectById(gene.getId());
                }
            }
        }
    } catch (NumberFormatException e) {
        addMessage(request, "object.notfound", new Object[] { "Gene" });
        return new ModelAndView("index");
    }
    if (geneVO == null) {
        addMessage(request, "object.notfound", new Object[] { "Gene" });
        return new ModelAndView("index");
    }
    Long id = geneVO.getId();
    assert id != null;
    ModelAndView mav = new ModelAndView("gene.detail");
    mav.addObject("geneId", id);
    mav.addObject("geneOfficialSymbol", geneVO.getOfficialSymbol());
    mav.addObject("geneOfficialName", geneVO.getOfficialName());
    mav.addObject("geneNcbiId", geneVO.getNcbiId());
    mav.addObject("geneTaxonCommonName", geneVO.getTaxonCommonName());
    mav.addObject("geneTaxonId", geneVO.getTaxonId());
    return mav;
}