old_contents: # 
  # Author    : Manuel Bernal Llinares
  # Project   : trackhub-creator
  # Timestamp : 02-08-2017 16:40
  # ---
  # © 2017 Manuel Bernal Llinares <mbdebian@gmail.com>
  # All rights reserved.
  # 
  
  """
  This module contains models for dealing with PoGo stuff
  """
  
  
  class PogoRunResult:
      def __init__(self):
          self.__ncbi_taxonomy_id = None
          self.__pogo_source_file_path = None
          self.__protein_sequence_file_path = None
          self.__gtf_file_path = None
          # Map<pogo_result_file_extension, pogo_result_file_path>
          self.__pogo_result_file_paths = {}
  
      def __init__(self,
                   ncbi_taxonomy_id,
                   pogo_source_file_path,
                   protein_sequence_file_path,
                   gtf_file_path):
          """
          Syntactic sugar constructor
          :param ncbi_taxonomy_id: ncbi taxonomy id for this PoGo run results
          :param pogo_source_file_path: path of the source file used to run PoGo
          """
          self.__init__()
          self.set_ncbi_taxonomy_id(ncbi_taxonomy_id)
          self.set_pogo_source_file_path(pogo_source_file_path)
          self.set_protein_sequence_file_path(protein_sequence_file_path)
          self.set_gtf_file_path(gtf_file_path)
  
      def __generate_pogo_result_file_paths(self):
          pass
  
      def set_ncbi_taxonomy_id(self, taxonomy_id):
          self.__ncbi_taxonomy_id = taxonomy_id
  
      def set_pogo_source_file_path(self, pogo_source_file_path):
          if not self.__pogo_source_file_path or (self.__pogo_source_file_path != pogo_source_file_path):
              self.__pogo_source_file_path = pogo_source_file_path
              # TODO - Regenerate pogo result file paths
  
      def set_protein_sequence_file_path(self, protein_sequence_file_path):
          self.__protein_sequence_file_path = protein_sequence_file_path
  
      def set_gtf_file_path(self, gtf_file_path):
          self.__gtf_file_path = gtf_file_path
  
      def add_pogo_result_file_path(self, pogo_result_file_path):
          self.__pogo_result_file_paths.add(pogo_result_file_path)
  
new_contents: # 
  # Author    : Manuel Bernal Llinares
  # Project   : trackhub-creator
  # Timestamp : 02-08-2017 16:40
  # ---
  # © 2017 Manuel Bernal Llinares <mbdebian@gmail.com>
  # All rights reserved.
  # 
  
  """
  This module contains models for dealing with PoGo stuff
  """
  
  
  class PogoRunResult:
      def __init__(self):
          self.__ncbi_taxonomy_id = None
          self.__pogo_source_file_path = None
          self.__protein_sequence_file_path = None
          self.__gtf_file_path = None
          # Map<pogo_result_file_extension, pogo_result_file_path>
          self.__pogo_result_file_paths = {}
  
      def __init__(self,
                   ncbi_taxonomy_id,
                   pogo_source_file_path,
                   protein_sequence_file_path,
                   gtf_file_path):
          """
          Syntactic sugar constructor
          :param ncbi_taxonomy_id: ncbi taxonomy id for this PoGo run results
          :param pogo_source_file_path: path of the source file used to run PoGo
          """
          self.__init__()
          self.set_ncbi_taxonomy_id(ncbi_taxonomy_id)
          self.set_pogo_source_file_path(pogo_source_file_path)
          self.set_protein_sequence_file_path(protein_sequence_file_path)
          self.set_gtf_file_path(gtf_file_path)
  
      def __generate_pogo_result_file_paths(self, pogo_source_file_path):
          pass
  
      def set_ncbi_taxonomy_id(self, taxonomy_id):
          self.__ncbi_taxonomy_id = taxonomy_id
  
      def set_pogo_source_file_path(self, pogo_source_file_path):
          if not self.__pogo_source_file_path or (self.__pogo_source_file_path != pogo_source_file_path):
              self.__pogo_source_file_path = pogo_source_file_path
              # Regenerate pogo result file paths
              self.__generate_pogo_result_file_paths(pogo_source_file_path)
  
      def set_protein_sequence_file_path(self, protein_sequence_file_path):
          self.__protein_sequence_file_path = protein_sequence_file_path
  
      def set_gtf_file_path(self, gtf_file_path):
          self.__gtf_file_path = gtf_file_path
  
      def add_pogo_result_file_path(self, pogo_result_file_path):
          self.__pogo_result_file_paths.add(pogo_result_file_path)
  
subject: call and refactor for __generate_pogo_result_file_paths