コード例 #1
0
 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;
 }
コード例 #2
0
 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;
 }
コード例 #3
0
  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;
  }