/// <summary>
/// The program is to be invoked with two arguments, the input and output file.
/// </summary>
/// <param name="args">command line arguments</param>
/// <returns>0 in case of no errors</returns>
public static int Main(string[] args)
{
if (args.Length != 2)
{
Console.WriteLine("{0}Usage: setIdFromNames filename output{0}{0}", Environment.NewLine);
return(1);
}
string filename = args[0];
string output = args[1];
// read the document
long start = DateTime.Now.Ticks;
SBMLDocument document = libsbml.readSBMLFromFile(filename);
long stop = DateTime.Now.Ticks;
Console.WriteLine();
Console.WriteLine(" filename: {0}", filename);
Console.WriteLine(" read time (ms): {0}", TimeSpan.FromTicks(stop - start).TotalMilliseconds);
// stop in case of serious errors
long errors = document.getNumErrors(libsbml.LIBSBML_SEV_ERROR);
if (errors > 0)
{
Console.WriteLine(" error(s): {0}", errors);
document.printErrors();
return((int)errors);
}
// get a list of all elements, as we will need to know all identifiers
// so that we don't create duplicates.
SBaseList allElements = document.getListOfAllElements();
// get a list of all ids
var allIds = getAllIds(allElements);
// create the transformer with the ids
var trans = new SetIdFromNames(allIds);
// rename the identifiers (using the elements we already gathered before)
start = DateTime.Now.Ticks;
document.getModel().renameIDs(allElements, trans);
stop = DateTime.Now.Ticks;
Console.WriteLine(" rename time (ms): {0}", TimeSpan.FromTicks(stop - start).TotalMilliseconds);
// write to file
start = DateTime.Now.Ticks;
libsbml.writeSBMLToFile(document, output);
stop = DateTime.Now.Ticks;
Console.WriteLine(" write time (ms): {0}", TimeSpan.FromTicks(stop - start).TotalMilliseconds);
Console.WriteLine();
// if we got here all went well ...
return(0);
}
/// <summary>
/// The program is to be invoked with one argument, the input file.
/// </summary>
/// <param name="args">command line arguments</param>
/// <returns>0 in case of no errors</returns>
public static int Main(string[] args)
{
if (args.Length != 1)
{
Console.WriteLine("{0}Usage: getAllElementsWithNotes filename{0}{0}", Environment.NewLine);
return(1);
}
string filename = args[0];
// read the document
long start = DateTime.Now.Ticks;
SBMLDocument document = libsbml.readSBMLFromFile(filename);
long stop = DateTime.Now.Ticks;
Console.WriteLine();
Console.WriteLine(" filename: {0}", filename);
Console.WriteLine(" read time (ms): {0}", TimeSpan.FromTicks(stop - start).TotalMilliseconds);
// stop in case of serious errors
long errors = document.getNumErrors(libsbml.LIBSBML_SEV_ERROR);
if (errors > 0)
{
Console.WriteLine(" error(s): {0}", errors);
document.printErrors();
return((int)errors);
}
// create the filter we want to use
var filter = new NotesFilter();
// get a list of all elements with notes
start = DateTime.Now.Ticks;
Console.WriteLine(" searching ......:");
SBaseList allElements = document.getListOfAllElements(filter);
stop = DateTime.Now.Ticks;
Console.WriteLine(" search time (ms): {0}", TimeSpan.FromTicks(stop - start).TotalMilliseconds);
Console.WriteLine();
Console.WriteLine(" elements with notes: {0}", allElements.getSize());
Console.WriteLine();
// if we got here all went well ...
return(0);
}