private double[] computeEdgeWeightExtrema(RelatedGenesEngineResponseDto response) { double[] extrema = new double[] {1, 0}; for (NetworkDto network : response.getNetworks()) { for (InteractionDto interaction : network.getInteractions()) { double weight = interaction.getWeight() * network.getWeight(); if (extrema[0] > weight) { extrema[0] = weight; } if (extrema[1] < weight) { extrema[1] = weight; } } } return extrema; }
private EnrichmentEngineRequestDto createEnrichmentRequest( RelatedGenesEngineResponseDto response) { if (human.getOntology() == null) { return null; } EnrichmentEngineRequestDto request = new EnrichmentEngineRequestDto(); request.setProgressReporter(NullProgressReporter.instance()); request.setMinCategories(MIN_CATEGORIES); request.setqValueThreshold(Q_VALUE_THRESHOLD); request.setOrganismId(human.getId()); request.setOntologyId(human.getOntology().getId()); Set<Long> nodes = new HashSet<Long>(); for (NetworkDto network : response.getNetworks()) { for (InteractionDto interaction : network.getInteractions()) { nodes.add(interaction.getNodeVO1().getId()); nodes.add(interaction.getNodeVO2().getId()); } } request.setNodes(nodes); return request; }