Exemplo n.º 1
0
        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);
        }
Exemplo n.º 2
0
        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);
        }