/**
* If no experiments were specified, inject into statisticsQuery a superset of all experiments for
* which stats exist across all attributes
*
* @param statisticsQuery
* @param statisticsStorage
*/
private static void setQueryExperiments(
StatisticsQueryCondition statisticsQuery, StatisticsStorage statisticsStorage) {
Set<ExperimentInfo> exps = statisticsQuery.getExperiments();
if (exps
.isEmpty()) { // No experiments conditions were specified - assemble a superset of all
// experiments for which stats exist across all attributes
for (EfAttribute attr : statisticsQuery.getAttributes()) {
Map<ExperimentInfo, ConciseSet> expsToStats =
getStatisticsForAttribute(statisticsQuery.getStatisticsType(), attr, statisticsStorage);
if (expsToStats != null) exps.addAll(expsToStats.keySet());
}
statisticsQuery.inExperiments(exps);
}
}
/**
* @param orAttributes
* @param statType
* @param minExperiments minimum experiment count restriction for this clause
* @param statisticsStorage - used to retrieve orAttributes, needed finding experiment counts in
* bit index
* @return StatisticsQueryOrConditions representing orAttributes
*/
public static StatisticsQueryOrConditions<StatisticsQueryCondition> getStatisticsOrQuery(
final List<Attribute> orAttributes,
final StatisticsType statType,
int minExperiments,
final StatisticsStorage statisticsStorage) {
StatisticsQueryOrConditions<StatisticsQueryCondition> orConditions =
new StatisticsQueryOrConditions<StatisticsQueryCondition>();
orConditions.setMinExperiments(minExperiments);
// LinkedHashMap used to maintain ordering of processing of experiments in multi-Attribute,
// multi-Experiment bit index queries to
// retrieve sorted lists of experiments to be plotted on the gene page.
Map<ExperimentInfo, Set<EfAttribute>> allExpsToAttrs =
new LinkedHashMap<ExperimentInfo, Set<EfAttribute>>();
for (Attribute attr : orAttributes) {
attr.getAttributeToExperimentMappings(statisticsStorage, allExpsToAttrs);
}
// Now process allExpsToAttrs - for all efo terms in orAttributes, grouping into one
// StatisticsQueryCondition
// attributes from potentially different efoTerms for one experiment. This has the effect of
// counting a given
// experiment only once for an OR collection of Attributes.
for (Map.Entry<ExperimentInfo, Set<EfAttribute>> expToAttr : allExpsToAttrs.entrySet()) {
StatisticsQueryCondition cond = new StatisticsQueryCondition(statType);
if (expToAttr.getKey() != EfAttribute.ALL_EXPERIMENTS)
// For efv Attributes we span all experiments
cond.inExperiments(Collections.singletonList(expToAttr.getKey()));
for (EfAttribute attr : expToAttr.getValue()) {
cond.inAttribute(attr);
}
orConditions.orCondition(cond);
}
return orConditions;
}