- added basic Java API and example for it

- reconsidered on what functions to expose

CMakeLists.txt

@@ -41,8 +41,53 @@ find_path(LIBSBML_INCLUDE_DIR
 )
 
 
+###############################################################################
+#
+# Need some variables set up, such as the name for the libSBML
+# library and the Path and file separator characters. The
+# MISC_PREFIX variable will cause libsbml bindings, examples and
+# documentation to be installed in PREFIX/${MISC_PREFIX}.
+#
+
+if(UNIX OR CYGWIN)
+    set(PATH_SEP "/")
+    set(FILE_SEP ":")
+else()
+    set(PATH_SEP "\\")
+    set(FILE_SEP ";")
+endif()
+
 set(EXTRA_LIBS "" CACHE STRING "List of additional libraries to link against." )
 
+option(WITH_CSHARP   "Generate C# language bindings."     OFF)
+option(WITH_JAVA     "Generate Java language bindings."   OFF)
+
+
+###############################################################################
+#
+# Find the C# compiler to use and set name for resulting library
+#
+
+if(WITH_CSHARP)
+    find_program(CSHARP_COMPILER
+        NAMES gmcs csc
+        PATHS C:/Windows/Microsoft.NET/Framework/v2.0.50727/ /usr/bin /usr/local/bin
+        DOC "The file name of the C# compiler."
+        )
+    if(UNIX)
+    else()
+        if(CMAKE_SIZEOF_VOID_P EQUAL 4)
+            # mark libsbml library as x86
+            set(CSHARP_EXTRA_ARGS -platform:x86 )
+        elseif(CMAKE_SIZEOF_VOID_P EQUAL 8)
+            # mark libsbml library as x64
+            set(CSHARP_EXTRA_ARGS -platform:x64 )
+        endif()
+    endif()
+
+endif(WITH_CSHARP)
+
+
 if(WIN32 AND NOT CYGWIN)
  add_definitions(-DLIBSBML_EXPORTS -DWIN32)
  if(MSVC)
@@ -107,9 +152,19 @@ message(STATUS
                 
  C   FLAGS      : ${CMAKE_C_FLAGS}
  CXX FLAGS      : ${CMAKE_CXX_FLAGS}
- Extra Libs     : ${EXTRA_LIBS}
- 
+ Extra Libs     : ${EXTRA_LIBS} 
  
 """
 )
 
+if(WITH_CSHARP)
+    message(STATUS "  Using C#                      = ${CSHARP_COMPILER}")
+endif()
+
+if(WITH_JAVA)
+    message(STATUS "  Using Java                    = ${Java_JAVA_EXECUTABLE}")
+endif()
+
+add_subdirectory(bindings)
+
+

SpatialSBML/spatialsimulator.cpp

@@ -804,6 +804,11 @@ void freeRInfo(vector<reactionInfo*> &rInfoList)
   }
 }
 
+int SpatialSimulator::getVariableLength() const
+{
+return (Zindex -1) * Yindex * Xindex + (Yindex-1) * Xindex + Xindex-1;
+}
+
 void reversePolishRK(reactionInfo *&rInfo, variableInfo *&sInfo, int Xindex, int Yindex, int Zindex, double dt, int m, materialType mType, bool inVol, diffCInfo **dci)
 {
   int X, Y, Z, i;
@@ -1114,13 +1119,37 @@ Parameter* SpatialSimulator::getDiffusionCoefficientForSpecies(const std::string
   return NULL;
 }
 
+  SpatialSimulator::SpatialSimulator():
+  Xdiv(100), Ydiv(100), Zdiv(1), model(NULL), volDimension(0), memDimension(0)
+  {
+  }
+  void SpatialSimulator::initFromFile(const std::string &fileName, int xdim, int ydim, int zdim/*=1*/)
+  {
+	SBMLDocument*doc = readSBMLFromFile(fileName.c_str());
+	initFromModel(doc, xdim, ydim, zdim);
+  }
+  void SpatialSimulator::initFromString(const std::string &sbml, int xdim, int ydim, int zdim/*=1*/)
+  {
+    SBMLDocument*doc = readSBMLFromString(sbml.c_str());
+	initFromModel(doc, xdim, ydim, zdim);
+  }
+
+
 SpatialSimulator::SpatialSimulator(SBMLDocument* doc, int xdim, int ydim, int zdim /*=1*/) :
   Xdiv(xdim), Ydiv(ydim), Zdiv(zdim), model(NULL), volDimension(0), memDimension(0)
 {
+  initFromModel(doc, xdim, ydim, zdim);
+}
+
+void SpatialSimulator::initFromModel(SBMLDocument* doc, int xdim, int ydim, int zdim/*=1*/)
+  {
   unsigned int i, j, k;
   int X = 0, Y = 0, Z = 0, index = 0;	  
   int numOfASTNodes = 0;
 
+  Xdiv = xdim;
+  Ydiv = ydim;
+  Zdiv = zdim;
 
   //sbml core
   ASTNode *ast;
@@ -2627,6 +2656,11 @@ double* SpatialSimulator::getGeometry(const std::string &compartmentId, int &len
   return info->isDomain;
 }
 
+int SpatialSimulator::getGeometryLength() const
+{
+return numOfVolIndexes;
+}
+
 boundaryType* SpatialSimulator::getBoundaryType(const std::string &compartmentId, int &length)
 {
   analyticVolInfo* info = searchAvolInfoByCompartment(avolInfoList, compartmentId.c_str());
@@ -2641,6 +2675,21 @@ int* SpatialSimulator::getBoundary(const std::string &compartmentId, int &length
   return info->isBoundary;
 }
 
+double SpatialSimulator::getVariableAt(const std::string& variable, int x, int y, int z)
+{  
+  variableInfo *sInfo = searchInfoById(varInfoList, variable.c_str());
+  if (sInfo == NULL)
+  {
+    return 0.0;
+  }
+
+  int index = getIndexForPosition(x, y);
+  if (index == -1)
+	return 0.0;
+
+  return sInfo->value[index];
+}
+
 double* SpatialSimulator::getVariable(const std::string &speciesId, int &length)
 {
   variableInfo *sInfo = searchInfoById(varInfoList, speciesId.c_str());

SpatialSBML/spatialsimulator.h

@@ -6,8 +6,10 @@
 #include <string>
 #include <vector>
 
-LIBSBML_CPP_NAMESPACE_BEGIN
+#ifndef SWIG
 
+LIBSBML_CPP_NAMESPACE_BEGIN
+# endif
 class SBMLDocument;
 class Model;
 class Species;
@@ -22,20 +24,28 @@ class ListOfCompartments;
 class ListOfReactions;
 class ListOfParameters;
 class ListOfRules;
-
+#ifndef SWIG
 LIBSBML_CPP_NAMESPACE_END
 
+
 typedef enum _boundaryType {
   Xp = 0, Xm, Yp, Ym, Zp, Zm
 } boundaryType;
 
+# endif
 #include "spatialstructs.h"
 
 
 class SpatialSimulator 
 {
 public: 
-  SpatialSimulator(SBMLDocument* doc, int xdim, int ydim, int zdim=1);
+  SpatialSimulator();
+  void initFromFile(const std::string &fileName, int xdim, int ydim, int zdim=1);
+  void initFromString(const std::string &sbml, int xdim, int ydim, int zdim=1);
+#ifndef SWIG
+  void initFromModel(SBMLDocument* doc, int xdim, int ydim, int zdim=1);
+  SpatialSimulator(SBMLDocument* doc, int xdim, int ydim, int zdim=1);  
+#endif
   virtual ~SpatialSimulator();
 
   void setGnuplotExecutable(const std::string &location);
@@ -49,31 +59,48 @@ class SpatialSimulator
 
   void setParameterUniformly(const std::string &id, double value);
   void setParameter(const std::string &id, double value);
-  void setParameterUniformly(variableInfo *species, double value);
   int getIndexForPosition(double x, double y);
+#ifndef SWIG
+  void setParameterUniformly(variableInfo *species, double value);
+#endif
+#ifndef SWIG
   // return the values for the given variable (as 1d) flat array
   double* getVariable(const std::string &speciesId, int &length);
   double* getGeometry(const std::string &compartmentId, int &length);
+
   boundaryType* getBoundaryType(const std::string &compartmentId, int &length);
+
   int* getBoundary(const std::string &compartmentId, int &length);
   double* getX(int &length);
   double* getY(int &length);
   double* getZ(int &length);
+#endif
 
+  int getVariableLength() const;
+  int getGeometryLength() const;
   int getXDim() const { return Xdiv;}
   int getYDim() const { return Ydiv;}
   int getZDim() const { return Zdiv;}
 
+  double getVariableAt(const std::string& variable, int x, int y, int z=0);
+
+#ifndef SWIG
+
+
   // for comparison allow the old stuff to run too
   static int runOldMain(int argc, const char* argv[]);
 
-  const Model* getModel() const;
 
+  const Model* getModel() const;
   void deleteValuesOutsideDomain(variableInfo *info );
+
+#endif
+
   void deleteValuesOutsideDomain(const std::string& id);
 
 private:
 
+#ifndef SWIG
   Parameter* getDiffusionCoefficientForSpecies(const std::string& id, int index=0);
 
   // prints all values from the current point;
@@ -125,7 +152,7 @@ class SpatialSimulator
   ListOfReactions *lor    ;
   ListOfParameters *lop   ;
   ListOfRules *lorules    ;
-
+#endif
 };
 
 #endif //SPATIAL_SIMULATOR_H 

SpatialSBML/spatialstructs.h

@@ -4,7 +4,6 @@
 using namespace std;
 LIBSBML_CPP_NAMESPACE_USE;
 
-
 typedef enum _materialTYpe {
   reactants = 0, products
 }materialType;

bindings/CMakeLists.txt

@@ -0,0 +1,36 @@
+###############################################################################
+#
+# Description       : CMake build script for spatialSBML language bindings
+# Original author(s): Frank Bergmann <[email protected]>
+# Organization      : California Institute of Technology
+#
+###############################################################################
+
+find_program(SWIG_EXECUTABLE
+    NAMES swig
+    PATHS
+       c:/swigwin-2.0.8
+       c:/swigwin-2.0.7
+       c:/swigwin-2.0.4
+       c:/swigwin-2.0.2
+       c:/swigwin-2.0.1
+       c:/swigwin-2.0.0
+       /usr/local/bin
+       /opt/local/bin
+       /usr/bin
+    DOC "The file name of the swig executable."
+    )
+set(SWIG_EXTRA_ARGS)
+
+
+#
+# and build selected language bindings
+#
+
+if(WITH_CSHARP)
+add_subdirectory(csharp)
+endif()
+
+if(WITH_JAVA)
+add_subdirectory(java)
+endif()