Copasi2SBMLTranslator Class Reference

#include <SBWTranslator.h>

Public Member Functions
	Copasi2SBMLTranslator ()
virtual	~Copasi2SBMLTranslator ()

Static Public Member Functions
static void	registerMethods (SystemsBiologyWorkbench::MethodTable< Copasi2SBMLTranslator > &table)
static std::string	translate (const std::string &sbmlString)
static std::string	translateFileToSBML (const std::string &fileName)
static std::string	translateToSBML (const std::string &copasiString)

Protected Member Functions
SystemsBiologyWorkbench::DataBlockWriter	getAuthor (SystemsBiologyWorkbench::Module from, SystemsBiologyWorkbench::DataBlockReader reader)
SystemsBiologyWorkbench::DataBlockWriter	getCopyright (SystemsBiologyWorkbench::Module from, SystemsBiologyWorkbench::DataBlockReader reader)
SystemsBiologyWorkbench::DataBlockWriter	getDescription (SystemsBiologyWorkbench::Module from, SystemsBiologyWorkbench::DataBlockReader reader)
SystemsBiologyWorkbench::DataBlockWriter	getFileExtension (SystemsBiologyWorkbench::Module from, SystemsBiologyWorkbench::DataBlockReader reader)
SystemsBiologyWorkbench::DataBlockWriter	getFileType (SystemsBiologyWorkbench::Module from, SystemsBiologyWorkbench::DataBlockReader reader)
SystemsBiologyWorkbench::DataBlockWriter	getName (SystemsBiologyWorkbench::Module from, SystemsBiologyWorkbench::DataBlockReader reader)
SystemsBiologyWorkbench::DataBlockWriter	getURL (SystemsBiologyWorkbench::Module from, SystemsBiologyWorkbench::DataBlockReader reader)
SystemsBiologyWorkbench::DataBlockWriter	getVersion (SystemsBiologyWorkbench::Module from, SystemsBiologyWorkbench::DataBlockReader reader)
SystemsBiologyWorkbench::DataBlockWriter	translate (SystemsBiologyWorkbench::Module from, SystemsBiologyWorkbench::DataBlockReader reader)
SystemsBiologyWorkbench::DataBlockWriter	translateFileToSBML (SystemsBiologyWorkbench::Module from, SystemsBiologyWorkbench::DataBlockReader reader)
SystemsBiologyWorkbench::DataBlockWriter	translateToSBML (SystemsBiologyWorkbench::Module from, SystemsBiologyWorkbench::DataBlockReader reader)

Static Private Attributes
static int	mLevel = 3
static int	mVersion = 1

Detailed Description

Definition at line 16 of file SBWTranslator.h.

Constructor & Destructor Documentation

Copasi2SBMLTranslator::Copasi2SBMLTranslator

(

)

Definition at line 35 of file SBWTranslator.cpp.

{
}

Copasi2SBMLTranslator::~Copasi2SBMLTranslator ( )

virtual

Definition at line 38 of file SBWTranslator.cpp.

{
}

Member Function Documentation

DataBlockWriter Copasi2SBMLTranslator::getAuthor ( SystemsBiologyWorkbench::Module  from, SystemsBiologyWorkbench::DataBlockReader  reader  )

protected

Definition at line 110 of file SBWTranslator.cpp.

Referenced by registerMethods().

{
  static string author("Frank T. Bergmann");
  return DataBlockWriter() << author;
}

DataBlockWriter Copasi2SBMLTranslator::getCopyright ( SystemsBiologyWorkbench::Module  from, SystemsBiologyWorkbench::DataBlockReader  reader  )

protected

Definition at line 120 of file SBWTranslator.cpp.

Referenced by registerMethods().

{
  static string copy("(c) 2012 COPASI Team");
  return DataBlockWriter() << copy;
}

DataBlockWriter Copasi2SBMLTranslator::getDescription ( SystemsBiologyWorkbench::Module  from, SystemsBiologyWorkbench::DataBlockReader  reader  )

protected

Definition at line 115 of file SBWTranslator.cpp.

Referenced by registerMethods().

{
  static string description("This converter converts a COPASI model to an SBML file");
  return DataBlockWriter();
}

DataBlockWriter Copasi2SBMLTranslator::getFileExtension ( SystemsBiologyWorkbench::Module  from, SystemsBiologyWorkbench::DataBlockReader  reader  )

protected

Definition at line 130 of file SBWTranslator.cpp.

Referenced by registerMethods().

{
  static string extension(".cps");
  return DataBlockWriter() << extension;
}

DataBlockWriter Copasi2SBMLTranslator::getFileType ( SystemsBiologyWorkbench::Module  from, SystemsBiologyWorkbench::DataBlockReader  reader  )

protected

Definition at line 135 of file SBWTranslator.cpp.

Referenced by registerMethods().

{
  static string fileType("COPASI file");
  return DataBlockWriter() << fileType;
}

DataBlockWriter Copasi2SBMLTranslator::getName ( SystemsBiologyWorkbench::Module  from, SystemsBiologyWorkbench::DataBlockReader  reader  )

protected

Definition at line 98 of file SBWTranslator.cpp.

Referenced by registerMethods().

{
  static string name("Copasi2SBML Translator");
  return DataBlockWriter();
}

DataBlockWriter Copasi2SBMLTranslator::getURL ( SystemsBiologyWorkbench::Module  from, SystemsBiologyWorkbench::DataBlockReader  reader  )

protected

Definition at line 125 of file SBWTranslator.cpp.

Referenced by registerMethods().

{
  static string url("http://copasi.org");
  return DataBlockWriter() << url;
}

DataBlockWriter Copasi2SBMLTranslator::getVersion ( SystemsBiologyWorkbench::Module  from, SystemsBiologyWorkbench::DataBlockReader  reader  )

protected

Definition at line 104 of file SBWTranslator.cpp.

References CVersion::VERSION.

Referenced by registerMethods().

{
  static string version(CVersion::VERSION.getVersion());
  return DataBlockWriter() << version;
}

void Copasi2SBMLTranslator::registerMethods ( SystemsBiologyWorkbench::MethodTable< Copasi2SBMLTranslator > &  table )

static

Definition at line 42 of file SBWTranslator.cpp.

References getAuthor(), getCopyright(), getDescription(), getFileExtension(), getFileType(), getName(), getURL(), getVersion(), translate(), translateFileToSBML(), and translateToSBML().

{
  table.addMethod(&Copasi2SBMLTranslator::getName,            "string getName()", false, "Return the name of this importer");
  table.addMethod(&Copasi2SBMLTranslator::getVersion,         "string getVersion()", false, "Return the version of this importer");
  table.addMethod(&Copasi2SBMLTranslator::getAuthor,          "string getAuthor()", false, "Return the corresponding author for this importer");
  table.addMethod(&Copasi2SBMLTranslator::getDescription,       "string getDescription()", false, "Return a description for this importer");
  table.addMethod(&Copasi2SBMLTranslator::getName,        "string getDisplayName()", false, "Return the display name for this importer.");
  table.addMethod(&Copasi2SBMLTranslator::getCopyright,       "string getCopyright()", false, "Return the copyright for this importer");
  table.addMethod(&Copasi2SBMLTranslator::getURL,           "string getURL()", false, "Return a URL for this reporter.");
  table.addMethod(&Copasi2SBMLTranslator::getFileExtension,            "string getFileExtension()", false, "Returns the file extension as a string");
  table.addMethod(&Copasi2SBMLTranslator::getFileType,                 "string getFileType()", false, "Returns a string describing the type of file");
  table.addMethod(&Copasi2SBMLTranslator::translate,          "string translate(string)", false, "Translate SBML string to COPASI.");
  table.addMethod(&Copasi2SBMLTranslator::translateToSBML,          "string translateToSBML(string)", false, "Translate COPASI string to SBML.");
  table.addMethod(&Copasi2SBMLTranslator::translateFileToSBML,          "string translateFileToSBML(string)", false, "Translate COPASI string to SBML.");
}

std::string Copasi2SBMLTranslator::translate ( const std::string &  sbmlString )

static

Definition at line 67 of file SBWTranslator.cpp.

References CCopasiRootContainer::addDatamodel(), CDirEntry::fileName(), COptions::getValue(), CCopasiDataModel::importSBMLFromString(), CCopasiRootContainer::init(), CDirEntry::makePathAbsolute(), CDirEntry::remove(), and CCopasiDataModel::saveModel().

Referenced by registerMethods().

{
  CCopasiRootContainer::init(0, NULL);
  CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();
  pDataModel->importSBMLFromString(sbmlString);

  string tempDir;
  COptions::getValue("Tmp", tempDir);
  string tempFile = "tmp.cps";
  CDirEntry::makePathAbsolute(tempFile, tempDir);
  tempFile = CDirEntry::fileName(tempFile);
  pDataModel->saveModel(tempFile, NULL, true);
  std::ifstream ifs(tempFile.c_str());
  std::string str((std::istreambuf_iterator<char>(ifs)), std::istreambuf_iterator<char>());
  ifs.close();
  CDirEntry::remove(tempFile);
  return str;
}

SystemsBiologyWorkbench::DataBlockWriter Copasi2SBMLTranslator::translate ( SystemsBiologyWorkbench::Module  from, SystemsBiologyWorkbench::DataBlockReader  reader  )

protected

std::string Copasi2SBMLTranslator::translateFileToSBML ( const std::string &  fileName )

static

Definition at line 58 of file SBWTranslator.cpp.

References CCopasiRootContainer::addDatamodel(), CCopasiDataModel::exportSBMLToString(), CCopasiRootContainer::init(), and CCopasiDataModel::loadModel().

Referenced by main(), and registerMethods().

{
  CCopasiRootContainer::init(0, NULL);
  CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();
  pDataModel->loadModel(fileName, NULL);
  string sbml = pDataModel->exportSBMLToString(NULL, mLevel, mVersion);
  return sbml;
}

SystemsBiologyWorkbench::DataBlockWriter Copasi2SBMLTranslator::translateFileToSBML ( SystemsBiologyWorkbench::Module  from, SystemsBiologyWorkbench::DataBlockReader  reader  )

protected

std::string Copasi2SBMLTranslator::translateToSBML ( const std::string &  copasiString )

static

Definition at line 86 of file SBWTranslator.cpp.

References CCopasiRootContainer::addDatamodel(), CCopasiDataModel::exportSBMLToString(), COptions::getPWD(), CCopasiRootContainer::init(), and CCopasiDataModel::loadModel().

Referenced by registerMethods().

{
  CCopasiRootContainer::init(0, NULL);
  CCopasiDataModel* pDataModel = CCopasiRootContainer::addDatamodel();

  istringstream str(copasiString);

  pDataModel->loadModel(str, COptions::getPWD(), NULL);
  string sbml = pDataModel->exportSBMLToString(NULL, mLevel, mVersion);
  return sbml;
}

SystemsBiologyWorkbench::DataBlockWriter Copasi2SBMLTranslator::translateToSBML ( SystemsBiologyWorkbench::Module  from, SystemsBiologyWorkbench::DataBlockReader  reader  )

protected

Member Data Documentation

int Copasi2SBMLTranslator::mLevel = 3

staticprivate

Definition at line 44 of file SBWTranslator.h.

int Copasi2SBMLTranslator::mVersion = 1

staticprivate

Definition at line 45 of file SBWTranslator.h.

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The documentation for this class was generated from the following files:

• SBWTranslator.h
• SBWTranslator.cpp