Examples with GeneCoexpressionNodeDegreeValueObject ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject used on opensource projects

Example 6 with GeneCoexpressionNodeDegreeValueObject

use of ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject in project Gemma by PavlidisLab.

the class CoexpressionServiceImpl method updateNodeDegree.

private void updateNodeDegree(Gene g, TreeMap<Integer, Map<Long, Integer>> forRanksPos, TreeMap<Integer, Map<Long, Integer>> forRanksNeg) {
    GeneCoexpressionNodeDegreeValueObject updatedVO = this.updateNodeDegree(g);
    if (CoexpressionServiceImpl.log.isDebugEnabled())
        CoexpressionServiceImpl.log.debug(updatedVO.toString());
    /*
         * Positive
         */
    Long id = updatedVO.getGeneId();
    for (Integer i = 0; i < updatedVO.asIntArrayPos().length; i++) {
        if (!forRanksPos.containsKey(i)) {
            forRanksPos.put(i, new HashMap<Long, Integer>());
        }
        // note this is the cumulative value.
        assert !forRanksPos.get(i).containsKey(id);
        forRanksPos.get(i).put(id, updatedVO.getLinksWithMinimumSupport(i, true));
    }
    /*
         * Negative
         */
    for (Integer i = 0; i < updatedVO.asIntArrayNeg().length; i++) {
        if (!forRanksNeg.containsKey(i)) {
            forRanksNeg.put(i, new HashMap<Long, Integer>());
        }
        // note this is the cumulative value.
        assert !forRanksNeg.get(i).containsKey(id);
        forRanksNeg.get(i).put(id, updatedVO.getLinksWithMinimumSupport(i, false));
    }
}