Source Code for Module libTI2.model.additional_information_handler

 1  #!/usr/bin/env python 
 2  import os.path,libsbml 
 3   
 4   
 5 -class additional_information_handler: 
 6 -    def __generate_temporary_filename__(self,fn): 
 7          return ".".join(fn.split(".")[:-1])+os.path.sep+"steady_state.xml" 
 8   
 9 -    def __file_exists_check__(self): 
10          if not self.modelInstance.reload_cached_file: 
11              self.exists = False 
12              return 
13          try: 
14              if self.filename == "temp.xml": raise IOError() 
15              f = file(self.filename,"r") 
16              f.close() 
17              self.exists = True 
18          except IOError: 
19              self.exists = False 
20           
21 -    def __init__(self,modelInstance): 
22          self.modelInstance = modelInstance 
23          self.filename = self.__generate_temporary_filename__(self.modelInstance.filename) 
24          self.__file_exists_check__() 
25   
26 -    def __write_steady_state_values_to_document__(self,document,steady_state_values): 
27          if not self.exists: 
28              for species in document.getModel().getListOfSpecies(): 
29                  if species.getId() not in steady_state_values: 
30                      # species not simulated 
31                      continue 
32                  val = steady_state_values[species.getId()] 
33                  if species.isSetInitialConcentration(): 
34                      species.setInitialConcentration(val) 
35                  elif species.isSetInitialAmount(): 
36                      species.setInitialAmount(val) 
37   
38 -    def write_file(self,steady_state_values,filename=None): 
39          if not filename: filename = self.filename 
40          document = self.modelInstance.sbmldoc.clone() 
41          self.__write_steady_state_values_to_document__(document,steady_state_values) 
42          libsbml.writeSBML( document, filename ) 
43