Exemplos de SBMLConverter em C++ (Cpp)

Exemplo n.º 1

Arquivo: TestCompFlatteningUnknownPackageRefs.cpp Projeto: copasi/copasi-dependencies

SBMLDocument* TestFlattenedUnknownValidateNoStrip(string file1, string file2)
{
  string filename(TestDataDirectory);
  
  ConversionProperties props;
  
  props.addOption("flatten comp");
  props.addOption("basePath", filename);
  props.addOption("performValidation", true);
  props.addOption("stripUnflattenablePackages", false);
  props.addOption("abortIfUnflattenable", "none");

  SBMLConverter* converter = 
    SBMLConverterRegistry::getInstance().getConverterFor(props);
  
  // load document
  string cfile = filename + file1;  
  SBMLDocument* doc = readSBMLFromFile(cfile.c_str());

  // fail if there is no model (readSBMLFromFile always returns a valid document)
  fail_unless(doc->getModel() != NULL);

  converter->setDocument(doc);
  int result = converter->convert();

  // fail if conversion was not valid
  fail_unless(result == LIBSBML_OPERATION_SUCCESS);

  string newModel = writeSBMLToStdString(doc);

  string ffile = filename + file2;
  SBMLDocument* fdoc = readSBMLFromFile(ffile.c_str());
  string flatModel = writeSBMLToStdString(fdoc);
  
  fail_unless(flatModel == newModel);

  delete fdoc;
  delete converter;

  return doc;
}

Exemplo n.º 2

Arquivo: TestCompFlatteningNewFlags.cpp Projeto: TheCoSMoCompany/biopredyn

END_TEST


START_TEST(test_comp_flatten_abort_reqd_only_6)
{
  ConversionProperties* props = new ConversionProperties();
  
  props->addOption("flatten comp");
  
  props->addOption("stripUnflattenablePackages", false);

  SBMLConverter* converter = 
    SBMLConverterRegistry::getInstance().getConverterFor(*props);
  
  // load document
  string dir(TestDataDirectory);
  string fileName = dir + "unknown1.xml";  
  SBMLDocument* doc = readSBMLFromFile(fileName.c_str());

  // fail if there is no model 
  //(but we have the unrecognised package error)
  fail_unless(doc->getNumErrors() == 1);
  fail_unless(doc->getModel() != NULL);
  fail_unless(doc->getErrorLog()->contains(UnrequiredPackagePresent) == true);

  converter->setDocument(doc);
  int result = converter->convert();

  fail_unless( result == LIBSBML_OPERATION_SUCCESS);

  string newModel = writeSBMLToString(doc);

  string ffile = dir + "unknown1_flat_stay.xml";
  SBMLDocument* fdoc = readSBMLFromFile(ffile.c_str());
  string flatModel = writeSBMLToString(fdoc);
  fail_unless(flatModel == newModel);

  delete doc;
  delete fdoc;
  delete converter;
}

Exemplo n.º 3

Arquivo: TestSBMLConverterRegistry.cpp Projeto: 0u812/libsbml.js.frozen

END_TEST

START_TEST (test_conversion_registry_getByIndex)
{

  int numConverters = SBMLConverterRegistry::getInstance().getNumConverters();

  for (int i = 0; i < numConverters; i++)
  {
    SBMLConverter *converter = SBMLConverterRegistry::getInstance().getConverterByIndex(i);

    fail_unless(converter != NULL);
    fail_unless(converter->getDefaultProperties().hasOption("none") == false);
    
    ConversionProperties props = converter->getDefaultProperties();

    
    delete converter;
  }


}

Exemplo n.º 4

Arquivo: TestCompFlatteningNewFlags.cpp Projeto: TheCoSMoCompany/biopredyn

END_TEST


START_TEST(test_comp_flatten_abort_all_3)
{
  ConversionProperties* props = new ConversionProperties();
  
  props->addOption("flatten comp");
  
  // checking the default
  props->addOption("abortIfUnflattenable", "all");
  props->addOption("stripUnflattenablePackages", false);

  SBMLConverter* converter = 
    SBMLConverterRegistry::getInstance().getConverterFor(*props);
  
  // load document
  string dir(TestDataDirectory);
  string fileName = dir + "unknown2.xml";  
  SBMLDocument* doc = readSBMLFromFile(fileName.c_str());

  // fail if there is no model 
  //(but we have the unrecognised package error)
  fail_unless(doc->getNumErrors() == 1);
  fail_unless(doc->getModel() != NULL);
  fail_unless(doc->getErrorLog()->contains(RequiredPackagePresent) == true);

  converter->setDocument(doc);
  int result = converter->convert();

  fail_unless( result == LIBSBML_OPERATION_FAILED);

  fail_unless(doc->getNumErrors() == 2);
  fail_unless(doc->getErrorLog()->contains(RequiredPackagePresent) == true);
  fail_unless(doc->getErrorLog()->contains(CompFlatteningNotRecognisedReqd) == true);

  delete doc;
  delete converter;
}

Exemplo n.º 5

Arquivo: flattenModel.cpp Projeto: 0u812/roadrunner-backup

int main(int argc,char** argv)
{
  bool leavePorts = false;
  if (argc < 3)
  {
    cout << usage << endl;
    return 1;
  }
  else if (argc == 3)
  {
    if ( string("-p") == string(argv[1]) )
    {
      cout << usage << endl;
      return 1;
    }       
  }

  int  argIndex = 1;
  
  if ( string("-p") == string(argv[1]) )
  {
    leavePorts = true;
    ++argIndex;
  }     

  if (SBMLExtensionRegistry::isPackageEnabled("comp") == false)
  {
    cerr << "The version of libsbml being used does not have the comp"
      << " package code enabled" << endl;
    return 1;
  }

  const char* inputFile   = argv[argIndex];
  const char* outputFile  = argv[argIndex+1];

  SBMLDocument* document = readSBML(inputFile);

  if (document->getNumErrors() > 0)
  {
    cerr << "Encountered the following SBML errors:" << endl;
    document->printErrors(cerr);
    return 1;
  }

  ConversionProperties* props = new ConversionProperties();
  
  props->addOption("flatten comp");
  props->addOption("leavePorts", leavePorts);

  SBMLConverter* converter = 
             SBMLConverterRegistry::getInstance().getConverterFor(*props);
  

  converter->setDocument(document);
  
  int result = converter->convert();

  if (result != LIBSBML_OPERATION_SUCCESS)
  {
    cerr << "Conversion failed\n";
    document->printErrors();
  }

  writeSBML(document, outputFile);

}