public List<String> getRelatedGeneNamesByScore()
throws ApplicationException, DataStoreException, NoRelatedGenesInfoException {
List<String> geneNames = new ArrayList<String>();
Iterator<Gene> itr = getRelatedGenesByScore().iterator();
while (itr.hasNext()) {
geneNames.add(itr.next().getSymbol());
}
return geneNames;
}
public static List<String> getValidGenes(List<String> genes)
throws SAXException, DataStoreException, ApplicationException {
List<String> validGenes = new ArrayList();
for (String geneName : genes) {
if (validGene(geneName)) {
validGenes.add(geneName);
}
}
return validGenes;
}
public void setNetworks(Set<String> n) {
Map<InteractionNetworkGroup, Collection<InteractionNetwork>> groupMembers =
new HashMap<InteractionNetworkGroup, Collection<InteractionNetwork>>();
Collection<InteractionNetworkGroup> groups = human.getInteractionNetworkGroups();
Set<String> notHandled = n;
for (InteractionNetworkGroup group : groups) {
if (n.contains(group.getName())) {
notHandled.remove(group.getName());
List<InteractionNetwork> networkMembers = new ArrayList<InteractionNetwork>();
Collection<InteractionNetwork> networks = group.getInteractionNetworks();
for (InteractionNetwork network : networks) {
networkMembers.add(network);
}
if (networkMembers.size() > 0) {
groupMembers.put(group, networkMembers);
}
}
}
networks = groupMembers;
}