Source Code for Module libModelSimilarity.fake_annotations

 1  #!/usr/bin/env python 
 2   
 3 -class ModelElementsAnnotations: 
 4      ''' 
 5      Represents all L{ElementAnnotations}s (each contains a list of L{Annotation}s) 
 6      functions that operate on multiple L{ElementAnnotations}s 
 7      ''' 
 8 -    def __init__(self,list_of_annotations): 
 9          ''' 
10          Read the SBML file elements that could be annoated. 
11          Elements are stored as L{ElementAnnotations}s 
12          @param suppress_errors:  
13          @type suppress_errors: bool  
14          ''' 
15          self._annotationElements =  [ElementAnnotations(x) for x in list_of_annotations] 
16          self.libsbml_model = None 
17          self.libsbml_document = None 
18   
19 -    def getElementAnnotations(self): 
20          ''' 
21          return a list of L{ElementAnnotations} that can contain MIRIAM annotations 
22          @return: return all annotatable elements of the model 
23          @rtype: [L{ElementAnnotations}] 
24          ''' 
25          return self._annotationElements 
26   
27 -class ElementAnnotations: 
28 -    def __init__(self, annotations): 
29          self._annotations = annotations 
30          self.libsbml_element = FakeLibsbmlElement(annotations[0].id) 
31          self.type = 'species' 
32 -    def getAnnotations(self): 
33          return self._annotations 
34   
35 -class FakeLibsbmlElement: 
36 -    def __init__(self,id,name=""): 
37          self.id   = id 
38          self.name = name or id 
39 -    def getId(self): 
40          return self.id 
41 -    def getName(self): 
42          return self.name 
43 -    def getElementName(self): 
44          return 'species' 
45   
46 -class Annotation: 
47 -    def __init__(self, db, id, qualifier): 
48          self.db = db 
49          self.id = id 
50          self.qualifier = qualifier 
51   
52  if __name__ == "__main__": 
53      import cluster 
54      cluster.similarity_measure_version = 4 
55      cluster.apply_caching = False 
56      da=cluster.DatabaseAnnotation() 
57      da.load_from_path("curated/") 
58      ma = cluster.ModelAnnotation(ModelElementsAnnotations([[Annotation("ChEBI","CHEBI:17234","is")], 
59                                                             [Annotation("ChEBI","CHEBI:4170","is")], 
60                                                             [Annotation("ChEBI","CHEBI:28013","is")], 
61                                                             [Annotation("ChEBI","CHEBI:16108","is")], 
62                                                             [Annotation("KEGG Compound","C00197","is")], 
63                                                             [Annotation("KEGG Compound","C00031","is")] 
64                                                             ]),"current query") 
65      ma = cluster.ModelAnnotation(ModelElementsAnnotations([[Annotation("KEGG Compound","C00002","is") 
66                                                             ]]),"current query") 
67      print da.compare_model_annotation_object(ma) 
68      #print da.compare_to_file("bmtest/BIOMD0000000211.xml") 
69