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Example 1 with ArrayDesignMapResultService

use of ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService in project Gemma by PavlidisLab.

the class ArrayDesignMapSummaryCli method doWork.

@Override
protected Exception doWork(String[] args) {
    Exception err = this.processCommandLine(args);
    if (err != null)
        return err;
    ArrayDesignMapResultService arrayDesignMapResultService = this.getBean(ArrayDesignMapResultService.class);
    for (ArrayDesign arrayDesign : this.arrayDesignsToProcess) {
        ArrayDesign thawed = this.thaw(arrayDesign);
        Collection<CompositeSequenceMapSummary> results = arrayDesignMapResultService.summarizeMapResults(thawed);
        System.out.println(CompositeSequenceMapSummary.HEADER);
        for (CompositeSequenceMapSummary summary : results) {
            System.out.println(summary);
        }
    }
    return null;
}
Also used : ArrayDesign(ubic.gemma.model.expression.arrayDesign.ArrayDesign) ArrayDesignMapResultService(ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService) CompositeSequenceMapSummary(ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary)

Aggregations

ArrayDesignMapResultService (ubic.gemma.core.analysis.sequence.ArrayDesignMapResultService)1 CompositeSequenceMapSummary (ubic.gemma.core.analysis.sequence.CompositeSequenceMapSummary)1 ArrayDesign (ubic.gemma.model.expression.arrayDesign.ArrayDesign)1