public static void Main(string[] args)
{
if (args.Length != 2)
{
string myname = Path.GetFileName(Environment.GetCommandLineArgs()[0]);
Console.WriteLine("Usage: {0} input-filename output-filename", myname);
Environment.Exit(1);
}
string inputFile = args[0];
string outputFile = args[1];
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
Environment.Exit(1);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument sbmlDoc = reader.readSBML(inputFile);
if ( sbmlDoc.getNumErrors() > 0)
{
sbmlDoc.printErrors();
Console.WriteLine("[Error] Cannot read {0}", inputFile);
Environment.Exit(1);
}
writer.writeSBML(sbmlDoc, outputFile);
Console.WriteLine("[OK] Echoed {0} to {1}", inputFile, outputFile);
}
public static void Main(String[] args)
{
if (args.Length < 2 || args.Length > 3)
{
Console.WriteLine("Usage: FlattenModel [-p] input-filename output-filename");
Console.WriteLine(" -p : list unused ports");
Environment.Exit(2);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
bool leavePorts = false;
SBMLDocument doc;
if (args.Length == 2)
{
doc = reader.readSBML(args[0]);
}
else
{
doc = reader.readSBML(args[1]);
leavePorts = true;
}
if (doc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
doc.printErrors();
}
else
{
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to flatten */
props.addOption("flatten comp", true, "flatten comp");
/* add an option to leave ports if the user has requested this */
props.addOption("leavePorts", leavePorts, "unused ports should be listed in the flattened model");
/* perform the conversion */
int result = doc.convert(props);
if (result != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine("conversion failed ... ({0})", result);
doc.printErrors();
Environment.Exit(3);
}
if (args.Length == 2)
{
writer.writeSBML(doc, args[1]);
}
else
{
writer.writeSBML(doc, args[2]);
}
}
}
public static void Main(string[] args)
{
if (args.Length != 2)
{
string myname = Path.GetFileName(Environment.GetCommandLineArgs()[0]);
Console.WriteLine("Usage: {0} input-filename output-filename", myname);
Environment.Exit(1);
}
string inputFile = args[0];
string outputFile = args[1];
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
Environment.Exit(1);
}
var now = DateTime.Now.Ticks;
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument sbmlDoc = reader.readSBML(inputFile);
if ( sbmlDoc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
sbmlDoc.printErrors();
Console.WriteLine("[Error] Cannot read {0}", inputFile);
Environment.Exit(1);
}
Console.WriteLine("Read {0} in {1}", inputFile, new TimeSpan(DateTime.Now.Ticks - now).TotalMilliseconds);
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to convert a model with
L3 FBC to L2 with COBRA annotation */
props.addOption("convert fbc to cobra", true, "Convert FBC model to Cobra model");
now = DateTime.Now.Ticks;
/* perform the conversion */
int result = sbmlDoc.convert(props);
if (result != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine ("conversion failed ... ");
Environment.Exit(3);
}
writer.writeSBML(sbmlDoc, outputFile);
Console.WriteLine("[OK] converted to FBC from {0} and wrote to {1} (in {2} msec)", inputFile, outputFile, new TimeSpan(DateTime.Now.Ticks - now).TotalMilliseconds);
}
internal static HandleRef getCPtrAndDisown(SBMLWriter obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return(ptr);
}
public static void Main(string[] args)
{
if (args.Length != 3)
{
string myname = Path.GetFileName(Environment.GetCommandLineArgs()[0]);
Console.WriteLine("Usage: {0} input-filename package-to-strip output-filename", myname);
Environment.Exit(1);
}
string inputFile = args[0];
string packageToStrip = args[1];
string outputFile = args[2];
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
Environment.Exit(1);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument sbmlDoc = reader.readSBML(inputFile);
if ( sbmlDoc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
sbmlDoc.printErrors();
Console.WriteLine("[Error] Cannot read {0}", inputFile);
Environment.Exit(1);
}
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to strip a given package */
props.addOption("stripPackage", true, "Strip SBML Level 3 package constructs from the model");
/* add an option with the package we want to remove */
props.addOption("package", packageToStrip, "Name of the SBML Level 3 package to be stripped");
/* perform the conversion */
if (sbmlDoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine ("conversion failed ... ");
Environment.Exit(3);
}
writer.writeSBML(sbmlDoc, outputFile);
Console.WriteLine("[OK] Stripped package '{0}' from {1} and wrote to {2}", packageToStrip, inputFile, outputFile);
}
public static void Main(string[] args)
{
if (args.Length != 2)
{
string myname = Path.GetFileName(Environment.GetCommandLineArgs()[0]);
Console.WriteLine("Usage: {0} input-filenameoutput-filename", myname);
Environment.Exit(1);
}
string inputFile = args[0];
string outputFile = args[1];
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
Environment.Exit(1);
}
SBMLReader reader = new SBMLReader();
SBMLWriter writer = new SBMLWriter();
SBMLDocument sbmlDoc = reader.readSBML(inputFile);
if ( sbmlDoc.getErrorLog().getNumFailsWithSeverity(libsbml.LIBSBML_SEV_ERROR) > 0)
{
sbmlDoc.printErrors();
Console.WriteLine("[Error] Cannot read {0}", inputFile);
Environment.Exit(1);
}
/* create a new conversion properties structure */
ConversionProperties props = new ConversionProperties();
/* add an option that we want to promote parameters */
props.addOption("promoteLocalParameters", true, "Promotes all Local Parameters to Global ones");
/* perform the conversion */
if (sbmlDoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS)
{
Console.WriteLine ("conversion failed ... ");
Environment.Exit(3);
}
writer.writeSBML(sbmlDoc, outputFile);
Console.WriteLine("[OK] promoted paramters from {0} and wrote to {1}", inputFile, outputFile);
}
internal static HandleRef getCPtrAndDisown(SBMLWriter obj)
{
HandleRef ptr = new HandleRef(null, IntPtr.Zero);
if (obj != null)
{
ptr = obj.swigCPtr;
obj.swigCMemOwn = false;
}
return ptr;
}
internal static HandleRef getCPtr(SBMLWriter obj)
{
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
internal static HandleRef getCPtr(SBMLWriter obj)
{
return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr);
}
public void test_SBMLWriter_L3_setProgramName()
{
SBMLWriter w = new SBMLWriter();
assertTrue( w != null );
int i = w.setProgramName( "sss");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
i = w.setProgramName("");
assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS );
w = null;
}
public void test_SBMLWriter_L3_create()
{
SBMLWriter w = new SBMLWriter();
assertTrue( w != null );
w = null;
}
public void test_WriteL3SBML_error()
{
SBMLDocument d = new SBMLDocument();
SBMLWriter w = new SBMLWriter();
assertEquals( false, w.writeSBML(d, "/tmp/impossible/path/should/fail") );
assertTrue( d.getNumErrors() == 1 );
assertTrue( d.getError(0).getErrorId() == libsbml.XMLFileUnwritable );
d = null;
w = null;
}
public void test_SBase_appendNotesWithGlobalNamespace()
{
string notes = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" + "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" xmlns:html=\"http://www.w3.org/1999/xhtml\" level=\"2\" version=\"4\">\n" + " <model id=\"test\" name=\"name\">\n" + " <notes>\n" + " <html:p>DATE: 2010/12/08 13:00:00</html:p>\n" + " <html:p>VERSION: 0.99</html:p>\n" + " <html:p>TAXONOMY: 9606</html:p>\n" + " </notes>\n" + " </model>\n" + "</sbml>\n";
SBMLDocument sbmlDoc = new SBMLDocument (2, 4);
sbmlDoc.getNamespaces ().@add ("http://www.w3.org/1999/xhtml", "html");
Model sbmlModel = sbmlDoc.createModel ();
sbmlModel.setId ("test");
sbmlModel.setName ("name");
setOrAppendNotes (sbmlModel, "<html:p>DATE: 2010/12/08 13:00:00</html:p>");
setOrAppendNotes (sbmlModel, "<html:p>VERSION: 0.99</html:p>");
setOrAppendNotes (sbmlModel, "<html:p>TAXONOMY: 9606</html:p>");
SBMLWriter ttt = new SBMLWriter ();
string documentString = ttt.writeToString (sbmlDoc);
assertTrue ((notes == documentString));
}
