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kaitoii11kaitoii11
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changed libsbml namespace handling
1 parent 6e0f28e commit ea3ddc2

25 files changed

+69
-44
lines changed

‎astFunction.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
#include <vector>
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77
using namespace std;
8-
using namespace libsbml;
8+
LIBSBML_CPP_NAMESPACE_USE
99

1010
void parseAST(ASTNode *ast, reversePolishInfo *rpInfo, vector<variableInfo*> &varInfoList, int index_max)
1111
{

‎boundaryFunction.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
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#include <vector>
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using namespace std;
8-
using namespace libsbml;
8+
LIBSBML_CPP_NAMESPACE_USE
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1010
void setBoundaryType(Model *model, vector<variableInfo*> &varInfoList, vector<GeometryInfo*> &geoInfoList, int Xindex, int Yindex, int Zindex, unsigned int dimension)
1111
{

‎calcPDE.cpp

Lines changed: 1 addition & 1 deletion
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@@ -11,7 +11,7 @@
1111
#define stackMax 50
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1313
using namespace std;
14-
using namespace libsbml;
14+
LIBSBML_CPP_NAMESPACE_USE
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1616
void reversePolishInitial(vector<unsigned int> &indexList, reversePolishInfo *rpInfo, double *value, int numOfASTNodes, int Xindex, int Yindex, int Zindex, bool isAllArea)
1717
{

‎checkFunc.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
#include <iostream>
66
#include <vector>
77

8-
using namespace libsbml;
8+
LIBSBML_CPP_NAMESPACE_USE
99
using namespace std;
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1111
void checkGeometry(GeometryInfo* geoInfo, std::string plane, int* isD, int X, int Y, int Z, unsigned int Xindex, unsigned int Yindex, unsigned int Zindex) {

‎checkStability.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
#include <cmath>
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77
using namespace std;
8-
using namespace libsbml;
8+
LIBSBML_CPP_NAMESPACE_USE
99

1010
double checkDiffusionStab(variableInfo* sInfo, double deltaX, double deltaY, double deltaZ, int Xindex, int Yindex, double dt)
1111
{

‎freeFunction.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
#include <vector>
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88
using namespace std;
9-
using namespace libsbml;
9+
LIBSBML_CPP_NAMESPACE_USE
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1111
void freeVarInfo(vector<variableInfo*> &varInfoList)
1212
{

‎options.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
#include <iostream>
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using namespace std;
10-
using namespace libsbml;
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LIBSBML_CPP_NAMESPACE_USE
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1212
void printErrorMessage()
1313
{

‎outputFunction.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
#include <fstream>
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1010
using namespace std;
11-
using namespace libsbml;
11+
LIBSBML_CPP_NAMESPACE_USE
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1313
void outputTimeCourse(Model *model, vector<variableInfo*> &varInfoList, vector<const char*> memList, variableInfo *xInfo, variableInfo *yInfo, variableInfo *zInfo, double *sim_time, double end_time, double dt, unsigned int dimension, int Xindex, int Yindex, int Zindex, int file_num, string fname)
1414
{

‎outputHDF.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@
1212
#include <sstream>
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1414
using namespace H5;
15-
using namespace libsbml;
15+
LIBSBML_CPP_NAMESPACE_USE
1616
using namespace std;
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const string FILENAME = "TimeCourseData.h5";

‎outputImage.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@
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using namespace cv;
1919
using namespace std;
20-
using namespace libsbml;
20+
LIBSBML_CPP_NAMESPACE_USE
2121
Vec3b infVec(192, 192, 192);
2222
Vec3b nanVec(255, 192, 255);
2323

‎searchFunction.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
#include <vector>
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55
using namespace std;
6-
using namespace libsbml;
6+
LIBSBML_CPP_NAMESPACE_USE
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88
variableInfo* searchInfoById(vector<variableInfo*> &varInfoList, const char *varName)
99
{

‎setInfoFunction.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@
1010
#include <iostream>
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1212
using namespace std;
13-
using namespace libsbml;
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LIBSBML_CPP_NAMESPACE_USE
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void setCompartmentInfo(libsbml::Model *model, std::vector<variableInfo*> &varInfoList)
1616
{

‎spatialsim/astFunction.h

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -5,12 +5,14 @@
55
#include "sbml/SBMLTypes.h"
66
#include <vector>
77

8-
void rearrangeAST(libsbml::ASTNode *ast);
8+
LIBSBML_CPP_NAMESPACE_USE
99

10-
void countAST(libsbml::ASTNode *ast, int &numOfASTNode);
10+
void rearrangeAST(ASTNode *ast);
1111

12-
void parseAST(libsbml::ASTNode *ast, reversePolishInfo *rpInfo, std::vector<variableInfo*> &varInfoList, int index_max);
12+
void countAST(ASTNode *ast, int &numOfASTNode);
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14-
void parseDependence(const libsbml::ASTNode *ast, std::vector<variableInfo*> &dependence, std::vector<variableInfo*> &varInfoList);
14+
void parseAST(ASTNode *ast, reversePolishInfo *rpInfo, std::vector<variableInfo*> &varInfoList, int index_max);
15+
16+
void parseDependence(const ASTNode *ast, std::vector<variableInfo*> &dependence, std::vector<variableInfo*> &varInfoList);
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1618
#endif

‎spatialsim/boundaryFunction.h

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,8 @@
55
#include "sbml/SBMLTypes.h"
66
#include <vector>
77

8-
void setBoundaryType(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, std::vector<GeometryInfo*> &geoInfoList, int Xindex, int Yindex, int Zindex, unsigned int dimension);
8+
LIBSBML_CPP_NAMESPACE_USE
9+
10+
void setBoundaryType(Model *model, std::vector<variableInfo*> &varInfoList, std::vector<GeometryInfo*> &geoInfoList, int Xindex, int Yindex, int Zindex, unsigned int dimension);
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1012
#endif

‎spatialsim/checkFunc.h

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
#include "mystruct.h"
55
#include <vector>
66
#include <string>
7-
#
7+
88
void checkMemPosition(std::vector<GeometryInfo*> geoinfoList, unsigned int Xindex, unsigned int Yindex, unsigned int Zindex, unsigned int dimension);
99

1010
void checkGeometry(GeometryInfo* geoInfo, std::string plane, int* isD, int X, int Y, int Z, unsigned int Xindex, unsigned int Yindex, unsigned int Zindex);

‎spatialsim/freeFunction.h

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -5,8 +5,11 @@
55
#include <vector>
66

77
void freeVarInfo(std::vector<variableInfo*> &varInfoList);
8+
89
void freeAvolInfo(std::vector<GeometryInfo*> &geoInfoList);
10+
911
void freeRInfo(std::vector<reactionInfo*> &geoInfoList);
12+
1013
void freeAvolInfo(std::vector<GeometryInfo*> &geoInfoList);
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1215
#endif

‎spatialsim/initializeFunction.h

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Original file line numberDiff line numberDiff line change
@@ -4,7 +4,9 @@
44
#include "mystruct.h"
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66
void InitializeVarInfo(variableInfo *varInfo);
7+
78
void InitializeAVolInfo(GeometryInfo *geoInfo);
9+
810
void InitializeVoronoiInfo(voronoiInfo *vorI, int numOfVolIndexes);
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1012
#endif

‎spatialsim/mystruct.h

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,8 @@
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#include "sbml/packages/spatial/extension/SpatialModelPlugin.h"
66
#include <vector>
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8+
LIBSBML_CPP_NAMESPACE_USE
9+
810
typedef enum _materialTYpe {
911
reactants = 0, products
1012
}materialType;
@@ -45,8 +47,8 @@ typedef struct _GeometryInfo {
4547
const char *domainTypeId;
4648
const char *domainId;
4749
std::vector <const char *> domainIdList;
48-
libsbml::AdjacentDomains *adjacent0;
49-
libsbml::AdjacentDomains *adjacent1;
50+
AdjacentDomains *adjacent0;
51+
AdjacentDomains *adjacent1;
5052
_GeometryInfo *adjacentGeo1;
5153
_GeometryInfo *adjacentGeo2;
5254
boundaryType *bType;
@@ -61,9 +63,9 @@ typedef struct _GeometryInfo {
6163
}GeometryInfo;
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6365
typedef struct _variableInfo {
64-
libsbml::Species *sp;
65-
libsbml::Compartment *com;
66-
libsbml::Parameter *para;
66+
Species *sp;
67+
Compartment *com;
68+
Parameter *para;
6769
const char* id;
6870
double *value;
6971
double *delta;
@@ -85,7 +87,7 @@ typedef struct _reactionInfo {
8587
double *value;
8688
reversePolishInfo *rpInfo;
8789
bool isMemTransport;
88-
libsbml::Reaction *reaction;
90+
Reaction *reaction;
8991
std::vector<_variableInfo*> spRefList;
9092
std::vector<bool> isVariable;
9193
std::vector<double> srStoichiometry;

‎spatialsim/options.h

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,10 @@
44
#include "mystruct.h"
55
#include "sbml/SBMLTypes.h"
66

7-
optionList getOptionList(int argc, char **argv, libsbml::SBMLDocument *doc);
7+
LIBSBML_CPP_NAMESPACE_USE
8+
9+
optionList getOptionList(int argc, char **argv, SBMLDocument *doc);
10+
811
void printErrorMessage();
912

1013
#endif

‎spatialsim/outputFunction.h

Lines changed: 8 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -5,16 +5,18 @@
55
#include "sbml/SBMLTypes.h"
66
#include <vector>
77

8-
void outputTimeCourse(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *xInfo, variableInfo *yInfo, variableInfo *zInfo, double *sim_time, double end_time, double dt, unsigned int dimension, int Xindex, int Yindex, int Zindex, int file_num, std::string fname);
8+
LIBSBML_CPP_NAMESPACE_USE
99

10-
void outputTimeCourse_zslice(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *xInfo, variableInfo *yInfo, double *sim_time, double end_time, double dt, unsigned int dimension, int Xindex, int Yindex, int file_num, std::string fname, int zslice);
10+
void outputTimeCourse(Model *model, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *xInfo, variableInfo *yInfo, variableInfo *zInfo, double *sim_time, double end_time, double dt, unsigned int dimension, int Xindex, int Yindex, int Zindex, int file_num, std::string fname);
1111

12-
void outputTimeCourse_yslice(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *xInfo, variableInfo *zInfo, double *sim_time, double end_time, double dt, unsigned int dimension, int Xindex, int Yindex, int Zindex, int file_num, std::string fname, int yslice);
12+
void outputTimeCourse_zslice(Model *model, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *xInfo, variableInfo *yInfo, double *sim_time, double end_time, double dt, unsigned int dimension, int Xindex, int Yindex, int file_num, std::string fname, int zslice);
1313

14-
void outputTimeCourse_xslice(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *yInfo, variableInfo *zInfo, double *sim_time, double end_time, double dt, unsigned int dimension, int Xindex, int Yindex, int Zindex, int file_num, std::string fname, int xslice);
14+
void outputTimeCourse_yslice(Model *model, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *xInfo, variableInfo *zInfo, double *sim_time, double end_time, double dt, unsigned int dimension, int Xindex, int Yindex, int Zindex, int file_num, std::string fname, int yslice);
1515

16-
void createOutputImage(FILE *gp, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *xInfo, variableInfo *yInfo, variableInfo *zInfo, libsbml::ListOfSpecies *los, int Xindex, int Yindex, int Zindex, double Xsize, double Ysize, double Zsize, unsigned int dimension, double range_min, double range_max, double *sim_time, int file_num, std::string fname);
16+
void outputTimeCourse_xslice(Model *model, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *yInfo, variableInfo *zInfo, double *sim_time, double end_time, double dt, unsigned int dimension, int Xindex, int Yindex, int Zindex, int file_num, std::string fname, int xslice);
1717

18-
void createOutputSliceImage(FILE *gp, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *info1, variableInfo *info2, char dim1, char dim2, int Xindex, int Yindex, int Zindex, libsbml::ListOfSpecies *los, unsigned int dimension, double range_min, double range_max, double *sim_time, int file_num, std::string fname);
18+
void createOutputImage(FILE *gp, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *xInfo, variableInfo *yInfo, variableInfo *zInfo, ListOfSpecies *los, int Xindex, int Yindex, int Zindex, double Xsize, double Ysize, double Zsize, unsigned int dimension, double range_min, double range_max, double *sim_time, int file_num, std::string fname);
19+
20+
void createOutputSliceImage(FILE *gp, std::vector<variableInfo*> &varInfoList, std::vector<const char*> memList, variableInfo *info1, variableInfo *info2, char dim1, char dim2, int Xindex, int Yindex, int Zindex, ListOfSpecies *los, unsigned int dimension, double range_min, double range_max, double *sim_time, int file_num, std::string fname);
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2022
#endif

‎spatialsim/outputHDF.h

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@@ -6,12 +6,14 @@
66
#include <string>
77
#include <vector>
88

9-
void makeHDF(std::string fname, libsbml::ListOfSpecies* los);
9+
LIBSBML_CPP_NAMESPACE_USE
1010

11-
void make3DHDF(std::string fname, libsbml::ListOfSpecies* los);
11+
void makeHDF(std::string fname, ListOfSpecies* los);
1212

13-
void outputValueData(std::vector<variableInfo*> &varInfoList, libsbml::ListOfSpecies* los, int Xdiv, int Ydiv, int Zdiv, int dimension, int file_num, std::string fname);
13+
void make3DHDF(std::string fname, ListOfSpecies* los);
1414

15-
void output3D_uint8(std::vector<variableInfo*> &varInfoList, libsbml::ListOfSpecies* los, int Xdiv, int Ydiv, int Zdiv, int file_num, std::string fname, double range_max);
15+
void outputValueData(std::vector<variableInfo*> &varInfoList, ListOfSpecies* los, int Xdiv, int Ydiv, int Zdiv, int dimension, int file_num, std::string fname);
16+
17+
void output3D_uint8(std::vector<variableInfo*> &varInfoList, ListOfSpecies* los, int Xdiv, int Ydiv, int Zdiv, int file_num, std::string fname, double range_max);
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1719
#endif

‎spatialsim/outputImage.h

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Original file line numberDiff line numberDiff line change
@@ -6,11 +6,13 @@
66
#include <opencv2/opencv.hpp>
77
#include <vector>
88

9-
void outputImg(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, int* geo_edge, int Xdiv, int Ydiv, double minX, double maxX, double minY, double maxY, double t, double range_min, double range_max, std::string fname, int file_num);
9+
LIBSBML_CPP_NAMESPACE_USE
1010

11-
void outputImg_slice(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, int* geo_edge, int Xdiv, int Ydiv, int Zdiv, double min0, double max0, double min1, double max1, double t, double range_min, double range_max, std::string fname, int file_num, int slice, char slicedim);
11+
void outputImg(Model *model, std::vector<variableInfo*> &varInfoList, int* geo_edge, int Xdiv, int Ydiv, double minX, double maxX, double minY, double maxY, double t, double range_min, double range_max, std::string fname, int file_num);
1212

13-
void outputGrayImage(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, int* geo_edge, int Xdiv, int Ydiv, int Zdiv, double t, double range_min, double range_max, std::string fname, int file_num);
13+
void outputImg_slice(Model *model, std::vector<variableInfo*> &varInfoList, int* geo_edge, int Xdiv, int Ydiv, int Zdiv, double min0, double max0, double min1, double max1, double t, double range_min, double range_max, std::string fname, int file_num, int slice, char slicedim);
14+
15+
void outputGrayImage(Model *model, std::vector<variableInfo*> &varInfoList, int* geo_edge, int Xdiv, int Ydiv, int Zdiv, double t, double range_min, double range_max, std::string fname, int file_num);
1416

1517
void outputGeo3dImage(std::vector<GeometryInfo*> geoInfoList, int Xdiv, int Ydiv, int Zdiv, std::string fname);
1618

‎spatialsim/searchFunction.h

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -5,8 +5,11 @@
55
#include <vector>
66

77
variableInfo* searchInfoById(std::vector<variableInfo*> &varInfoList, const char *varName);
8+
89
GeometryInfo* searchAvolInfoByDomainType(std::vector<GeometryInfo*> &geoInfoList, const char *dtId);
10+
911
GeometryInfo* searchAvolInfoByDomain(std::vector<GeometryInfo*> &geoInfoList, const char *dId);
12+
1013
GeometryInfo* searchAvolInfoByCompartment(std::vector<GeometryInfo*> &geoInfoList, const char *cId);
1114

1215
#endif

‎spatialsim/setInfoFunction.h

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -5,15 +5,17 @@
55
#include "sbml/SBMLTypes.h"
66
#include <vector>
77

8-
void setCompartmentInfo(libsbml::Model *model, std::vector<variableInfo*> &varInfoList);
8+
LIBSBML_CPP_NAMESPACE_USE
99

10-
void setSpeciesInfo(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, unsigned int volDimension, unsigned int memDimension, int Xindex, int Yindex, int Zindex);
10+
void setCompartmentInfo(Model *model, std::vector<variableInfo*> &varInfoList);
1111

12-
void setParameterInfo(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, int Xdiv, int Ydiv, int Zdiv, double &Xsize, double &Ysize, double &Zsize, double &deltaX, double &deltaY, double &deltaZ, char *&xaxis, char *&yaxis, char *&zaxis);
12+
void setSpeciesInfo(Model *model, std::vector<variableInfo*> &varInfoList, unsigned int volDimension, unsigned int memDimension, int Xindex, int Yindex, int Zindex);
1313

14-
void setReactionInfo(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, std::vector<reactionInfo*> &rInfoList, std::vector<reactionInfo*> &fast_rInfoList, unsigned int numOfVolIndexes);
14+
void setParameterInfo(Model *model, std::vector<variableInfo*> &varInfoList, int Xdiv, int Ydiv, int Zdiv, double &Xsize, double &Ysize, double &Zsize, double &deltaX, double &deltaY, double &deltaZ, char *&xaxis, char *&yaxis, char *&zaxis);
1515

16-
void setRateRuleInfo(libsbml::Model *model, std::vector<variableInfo*> &varInfoList, std::vector<reactionInfo*> &rInfoList, unsigned int numOfVolIndexes);
16+
void setReactionInfo(Model *model, std::vector<variableInfo*> &varInfoList, std::vector<reactionInfo*> &rInfoList, std::vector<reactionInfo*> &fast_rInfoList, unsigned int numOfVolIndexes);
17+
18+
void setRateRuleInfo(Model *model, std::vector<variableInfo*> &varInfoList, std::vector<reactionInfo*> &rInfoList, unsigned int numOfVolIndexes);
1719

1820
normalUnitVector* setNormalAngle(std::vector<GeometryInfo*> &geoInfoList, double Xsize, double Ysize, double Zsize, int dimension, int Xindex, int Yindex, int Zindex, unsigned int numOfVolIndexes);
1921

‎spatialsimulator.cpp

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,7 @@
3232
#include <zlib.h>
3333
#include <sys/stat.h>
3434

35-
using namespace libsbml;
35+
LIBSBML_CPP_NAMESPACE_USE
3636
using namespace H5;
3737
using namespace cv;
3838
using namespace std;

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