Examples with BioSequenceService ubic.gemma.persistence.service.genome.biosequence.BioSequenceService used on opensource projects

Example 1 with BioSequenceService

use of ubic.gemma.persistence.service.genome.biosequence.BioSequenceService in project Gemma by PavlidisLab.

the class GenericGenelistDesignGenerator method processOptions.

@Override
protected void processOptions() {
    super.processOptions();
    geneService = this.getBean(GeneService.class);
    arrayDesignAnnotationService = this.getBean(ArrayDesignAnnotationService.class);
    TaxonService taxonService = this.getBean(TaxonService.class);
    bioSequenceService = this.getBean(BioSequenceService.class);
    arrayDesignService = this.getBean(ArrayDesignService.class);
    compositeSequenceService = this.getBean(CompositeSequenceService.class);
    annotationAssociationService = this.getBean(AnnotationAssociationService.class);
    externalDatabaseService = this.getBean(ExternalDatabaseService.class);
    arrayDesignReportService = this.getBean(ArrayDesignReportService.class);
    if (this.hasOption('t')) {
        this.taxon = this.setTaxonByName(taxonService);
    }
    if (this.hasOption("ncbiids")) {
        this.useNCBIIds = true;
    } else if (this.hasOption("ensembl")) {
        this.useEnsemblIds = true;
    }
    if (useNCBIIds && useEnsemblIds) {
        throw new IllegalArgumentException("Choose one of ensembl or ncbi ids or gene symbols");
    }
}

Example 2 with BioSequenceService

use of ubic.gemma.persistence.service.genome.biosequence.BioSequenceService in project Gemma by PavlidisLab.

the class BioSequencePersistTest method onTearDownInTransaction.

@After
public void onTearDownInTransaction() {
    BioSequenceService bss = this.getBean(BioSequenceService.class);
    bss.remove(bs);
}