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);
}
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 void test_SBMLWriter_L3_create()
{
SBMLWriter w = new SBMLWriter();
assertTrue(w != null);
w = null;
}
/// <summary>
/// Converts the current binary model to an SBML 3.1 Qual document and writes it to a file.
/// </summary>
public void WriteToSbmlFile(BinaryModel model, string outputPath)
{
var outputSbmlDocument = ToSbmlQualDocument(model);
var writer = new SBMLWriter();
writer.writeSBML(outputSbmlDocument, outputPath);
}
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);
}
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_SBMLWriter_L3_setProgramVersion()
{
SBMLWriter w = new SBMLWriter();
assertTrue(w != null);
int i = w.setProgramVersion("sss");
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
i = w.setProgramVersion("");
assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS);
w = null;
}
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);
}
static void testWriteCompressedSBML(SBMLDocument d, string file)
{
if (SBMLWriter.hasZlib())
{
//
// write/read gzip file
//
string cfile = file + ".gz";
try
{
if (libsbml.writeSBML(d, cfile) == 0)
{
ERR("[WriteCompressedSBML] Error: cannot write " + file + ".gz");
}
else
{
OK();
}
}
catch (Exception e)
{
ERR("[WriteCompressedSBML] (" + cfile + ") Error: Exception thrown : " + e.Message);
}
//
// write/read zip file
//
cfile = file + ".zip";
try
{
if (libsbml.writeSBML(d, cfile) == 0)
{
ERR("[WriteCompressedSBML] Error: cannot write " + file + ".zip");
}
else
{
OK();
}
}
catch (Exception e)
{
ERR("[WriteCompressedSBML] (" + cfile + ") Error: Exception thrown : " + e.Message);
}
}
if (SBMLWriter.hasBzip2())
{
//
// write/read bzip2 file
//
string cfile = file + ".bz2";
try
{
if (libsbml.writeSBML(d, cfile) == 0)
{
ERR("[WriteCompressedSBML] Error: cannot write " + cfile);
}
else
{
if (libsbml.readSBML(cfile) == null)
{
ERR("[WriteCompressedSBML] Error: failed to read " + cfile);
}
else
{
OK();
}
}
}
catch (Exception e)
{
ERR("[WriteCompressedSBML] (" + cfile + ") Error: Exception thrown : " + e.Message);
}
}
}
