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1 : efrank 1.1 #ifndef _SBWFACTORY_H
2 :     #define _SBWFACTORY_H
3 :     //***********************************************************************
4 :     // Reconstruction Readout Interface via SBW.
5 :     //
6 :     // Description:
7 :     //
8 :     // Connects to SBW server to obtain RecoElem hierarchy & reactions.
9 :     //
10 :     //
11 :     // Author List:
12 :     // Ed Frank, efrank@mcs.anl.gov
13 :     //
14 :     // History:
15 :     // 07 Juoy 03 efrank, hwang First Version
16 :     //
17 :     //
18 :     //***********************************************************************
19 :    
20 :     #include <string>
21 :     #include <vector>
22 : efrank 1.2 #include <string>
23 :    
24 :     #include "SBW.h" //should be replaceable with fwd declare but dosn't work?
25 :     #include "sbml/SBMLReader.h"
26 :     #include "sbml/SBMLTypes.h"
27 : efrank 1.1
28 :     using namespace SystemsBiologyWorkbench;
29 :    
30 :     class RecoElem;
31 :     class Reaction;
32 :    
33 :     class SbwFactory {
34 :     public:
35 :     SbwFactory( );
36 :     virtual ~SbwFactory() {}
37 :    
38 :     // This actually reads the whole tree starting at the specified location.
39 :    
40 :     RecoElem* getRecoElemById( unsigned int procId);
41 : efrank 1.2 RecoElem* getRecoElemFromSbmlFile( const char* filename );
42 :     RecoElem* getRecoElemFromSbmlFile( const std::string& filename );
43 :    
44 : efrank 1.4 void writeSbmlFile( RecoElem& re, const char* filename);
45 :     void buildSbmlModelFromRecoElem( Model_t* d, RecoElem& re);
46 : efrank 1.1
47 :     private:
48 :     RecoElem* sbwToRecoElem( DataBlockReader& r );
49 :     void unpackRx( DataBlockReader& rIn, vector<Reaction>& rxns );
50 :    
51 : efrank 1.2 RecoElem* SBMLtoRecoElem(Model_t* m);
52 : efrank 1.5 void inreaction(Model_t* theModel, Reaction_t* r, vector<Reaction>& rxns);
53 : efrank 1.2 void getReactionModifier(Reaction_t* r,
54 :     vector<string>& enzymeList );
55 : efrank 1.5 void buildSpeciesMap( map<string, Species_t*>& specesMap,
56 :     set<string>& names );
57 :     void addInOuts( const vector<string>& names,
58 :     const vector<int>& stoich,
59 :     Model_t* model,
60 :     map<string, Species_t*>& speciesMap,
61 :     SpeciesReference_t* (*createFn)(Model_t*) );
62 :     void addModifiers( const vector<string>& names,
63 :     Model_t* model,
64 :     map<string, Species_t*>& speciesMap);
65 : efrank 1.1 };
66 :    
67 :     #endif /* _BSSFACTORY_H */

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