use of ubic.gemma.core.analysis.report.ArrayDesignReportService 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");
}
}
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