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

Example 31 with GeneValueObject

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

the class GeneController method loadAllenBrainImages.

/**
 * AJAX NOTE: this method updates the value object passed in
 */
public Collection<ImageValueObject> loadAllenBrainImages(Long geneId) {
    Collection<ImageValueObject> images = new ArrayList<>();
    GeneValueObject gene = geneService.loadValueObjectById(geneId);
    String queryGeneSymbol = gene.getOfficialSymbol();
    GeneValueObject mouseGene = gene;
    boolean usingHomologue = false;
    if (!gene.getTaxonCommonName().equals("mouse")) {
        mouseGene = this.homologeneService.getHomologueValueObject(geneId, "mouse");
        usingHomologue = true;
    }
    if (mouseGene != null) {
        Collection<ImageSeries> imageSeries;
        try {
            imageSeries = allenBrainAtlasService.getRepresentativeSaggitalImages(mouseGene.getOfficialSymbol());
            String abaGeneUrl = allenBrainAtlasService.getGeneUrl(mouseGene.getOfficialSymbol());
            Collection<Image> representativeImages = allenBrainAtlasService.getImagesFromImageSeries(imageSeries);
            images = ImageValueObject.convert2ValueObjects(representativeImages, abaGeneUrl, new GeneValueObject(mouseGene), queryGeneSymbol, usingHomologue);
        } catch (IOException e) {
            log.warn("Could not get ABA data: " + e);
        }
    }
    return images;
}