Examples with NonRetainedResult ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult used on opensource projects

Example 1 with NonRetainedResult

use of ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult in project Gemma by PavlidisLab.

the class DifferentialExpressionSearchTaskImpl method getDetailsForContrasts.

/**
 * Retrieve the details (contrasts) for results which meet the criterion. (PVALUE_CONTRAST_SELECT_THRESHOLD).
 * Requires a database hit.
 *
 * @param diffExResults results
 * @return map
 */
private Map<Long, ContrastsValueObject> getDetailsForContrasts(Collection<DiffExprGeneSearchResult> diffExResults) {
    StopWatch timer = new StopWatch();
    timer.start();
    List<Long> resultsWithContrasts = new ArrayList<>();
    for (DiffExprGeneSearchResult r : diffExResults) {
        if (r.getResultId() == null) {
            // it is a dummy result. It means there is no result for this gene in this resultset.
            continue;
        }
        // Here I am trying to avoid fetching them when there is no hope that the results will be interesting.
        if (r instanceof MissingResult || r instanceof NonRetainedResult || r.getCorrectedPvalue() > DifferentialExpressionSearchTaskImpl.PVALUE_CONTRAST_SELECT_THRESHOLD) {
            // Then it won't have contrasts; no need to fetch.
            continue;
        }
        resultsWithContrasts.add(r.getResultId());
    }
    Map<Long, ContrastsValueObject> detailedResults = new HashMap<>();
    if (!resultsWithContrasts.isEmpty()) {
        // uses a left join so it will have all the results.
        detailedResults = differentialExpressionResultService.loadContrastDetailsForResults(resultsWithContrasts);
    }
    timer.stop();
    if (timer.getTotalTimeMillis() > 1) {
        DifferentialExpressionSearchTaskImpl.log.info("Fetch contrasts for " + resultsWithContrasts.size() + " results: " + timer.getTotalTimeMillis() + "ms");
    }
    return detailedResults;
}