public List<Gene> getRelatedGenesByScore()
throws ApplicationException, DataStoreException, NoRelatedGenesInfoException {
options = runGeneManiaAlgorithm();
final Map<Gene, Double> scores = options.getScores();
ArrayList<Gene> relatedGenes = new ArrayList<Gene>(scores.keySet());
Collections.sort(
relatedGenes,
new Comparator<Gene>() {
public int compare(Gene gene1, Gene gene2) {
return -Double.compare(scores.get(gene1), scores.get(gene2));
}
});
return relatedGenes;
}
private Map<Long, Double> filterGeneScores(Map<Long, Double> scores, SearchResult options) {
Map<Long, Gene> queryGenes = options.getQueryGenes();
double maxScore = 0;
for (Map.Entry<Long, Double> entry : scores.entrySet()) {
if (queryGenes.containsKey(entry.getKey())) {
continue;
}
maxScore = Math.max(maxScore, entry.getValue());
}
Map<Long, Double> filtered = new HashMap<Long, Double>();
for (Map.Entry<Long, Double> entry : scores.entrySet()) {
long nodeId = entry.getKey();
double score = entry.getValue();
filtered.put(entry.getKey(), queryGenes.containsKey(nodeId) ? maxScore : score);
}
return filtered;
}