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Example 1 with AnnotationAssociationService

use of ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService 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");
    }
}
Also used : GeneService(ubic.gemma.core.genome.gene.service.GeneService) AnnotationAssociationService(ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService) ExternalDatabaseService(ubic.gemma.persistence.service.common.description.ExternalDatabaseService) TaxonService(ubic.gemma.persistence.service.genome.taxon.TaxonService) ArrayDesignAnnotationService(ubic.gemma.core.analysis.service.ArrayDesignAnnotationService) BioSequenceService(ubic.gemma.persistence.service.genome.biosequence.BioSequenceService) CompositeSequenceService(ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService) ArrayDesignService(ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService) ArrayDesignReportService(ubic.gemma.core.analysis.report.ArrayDesignReportService)

Aggregations

ArrayDesignReportService (ubic.gemma.core.analysis.report.ArrayDesignReportService)1 ArrayDesignAnnotationService (ubic.gemma.core.analysis.service.ArrayDesignAnnotationService)1 GeneService (ubic.gemma.core.genome.gene.service.GeneService)1 ExternalDatabaseService (ubic.gemma.persistence.service.common.description.ExternalDatabaseService)1 ArrayDesignService (ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService)1 CompositeSequenceService (ubic.gemma.persistence.service.expression.designElement.CompositeSequenceService)1 BioSequenceService (ubic.gemma.persistence.service.genome.biosequence.BioSequenceService)1 AnnotationAssociationService (ubic.gemma.persistence.service.genome.sequenceAnalysis.AnnotationAssociationService)1 TaxonService (ubic.gemma.persistence.service.genome.taxon.TaxonService)1