COPASI API  4.16.103
CMMLOutput.h
Go to the documentation of this file.
1 // Begin CVS Header
2 // $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/model/CMMLOutput.h,v $
3 // $Revision: 1.3 $
4 // $Name: $
5 // $Author: shoops $
6 // $Date: 2011/03/07 19:30:51 $
7 // End CVS Header
8 
9 // Copyright (C) 2011 - 2010 by Pedro Mendes, Virginia Tech Intellectual
10 // Properties, Inc., University of Heidelberg, and The University
11 // of Manchester.
12 // All rights reserved.
13 
14 // Copyright (C) 2001 - 2007 by Pedro Mendes, Virginia Tech Intellectual
15 // Properties, Inc. and EML Research, gGmbH.
16 // All rights reserved.
17 
18 // Copyright 2005 by Pedro Mendes, Virginia Tech Intellectual
19 // Properties, Inc. and EML Research, gGmbH.
20 // All rights reserved.
21 
22 #ifndef CMML_H
23 #define CMML_H
24 
25 #include <sstream>
26 #include <set>
27 #include <vector>
28 #include "copasi.h"
29 
30 class CModel;
31 class CMetab;
32 class CModelEntity;
33 class CReaction;
34 
35 /**
36  * This class handles the output of the differential equations as presentation MathML
37  */
39 {
40 
41 public:
42  CMMLOutput();
43 
44  static void writeDifferentialEquations(std::ostream & mml, CModel * model, bool localParameterNumbers, bool expand, bool expandFull);
45 
46 private:
47  static void writeLHS(std::ostream & out, const std::string & metabName,
48  const std::string & compName, size_t l);
49 
50  static void writeRHS(std::ostream & out, const CMetab* pMetab, const CReaction* pReac,
51  bool numbers, bool expand, bool expandFull,
52  size_t l);
53 
54  //list keys of all reactions that have the metab in their balances
55  static std::set<std::string> listReactionsForMetab(const CModel* model,
56  const std::string & key);
57 
58  static void createParameterMapping(const CReaction* pReac,
59  std::vector<std::vector<std::string> > & params,
60  bool numbers);
61 
62  static void writeLHS_ModelValue(std::ostream & out,
63  const std::string & valueName, size_t l);
64 
65  static void writeRHS_ModelEntity(std::ostream & out,
66  const CModelEntity* pEntity,
67  bool expandFull, size_t l);
68 
69  //std::ostringstream mml;
70 };
71 
72 #endif
static void writeRHS_ModelEntity(std::ostream &out, const CModelEntity *pEntity, bool expandFull, size_t l)
Definition: CMMLOutput.cpp:256
Definition: CMetab.h:178
static void writeLHS(std::ostream &out, const std::string &metabName, const std::string &compName, size_t l)
Definition: CMMLOutput.cpp:37
static void createParameterMapping(const CReaction *pReac, std::vector< std::vector< std::string > > &params, bool numbers)
Definition: CMMLOutput.cpp:142
static std::set< std::string > listReactionsForMetab(const CModel *model, const std::string &key)
Definition: CMMLOutput.cpp:512
static void writeRHS(std::ostream &out, const CMetab *pMetab, const CReaction *pReac, bool numbers, bool expand, bool expandFull, size_t l)
Definition: CMMLOutput.cpp:61
Definition: CModel.h:50
static void writeDifferentialEquations(std::ostream &mml, CModel *model, bool localParameterNumbers, bool expand, bool expandFull)
Definition: CMMLOutput.cpp:279
static void writeLHS_ModelValue(std::ostream &out, const std::string &valueName, size_t l)
Definition: CMMLOutput.cpp:242