code: private void processNetwork(final ProtoNetwork pn) {
          // Inject protein families
          ProtoNetwork pfamMerged = stage1(pn);
          // Inject named complexes
          ProtoNetwork ncMerged = stage2(pfamMerged);
          // Inject gene scaffolding
          ProtoNetwork geneMerged = stage3(ncMerged);
          // Inject homology knowledge
          ProtoNetwork orthoMerged = stage4(geneMerged);
          // Equivalence the network
          ProtoNetwork equived = stage5(orthoMerged);
          stage6(equived);
      }
docs: Runs the phase three stages over the input proto-network.
  
  @param pn Proto-network input by user