00001 /* 00002 Last changed Time-stamp: <2005-11-03 11:24:14 raim> 00003 $Id: options.h,v 1.2 2005/11/03 11:04:00 raimc Exp $ 00004 */ 00005 #ifndef _OPTIONS_H_ 00006 #define _OPTIONS_H_ 00007 00008 /* Command-line Options */ 00009 typedef struct _Options { 00010 char ExeName[256]; /* name of executable */ 00011 char GvFormat[64]; /* output format for graph drawings */ 00012 char ModelFile[256]; /* model file name */ 00013 char ModelPath[256]; /* path to the model file */ 00014 char Parameter[64]; /* Paramter for variation in batch process 00015 or variable for sensitivity analysis*/ 00016 char Schema11[64]; /* name of schema L1v1 file */ 00017 char Schema12[64]; /* name of schema L1v2 file */ 00018 char Schema21[64]; /* name of schema L1v3 file */ 00019 char SchemaPath[256]; /* path to schema files */ 00020 double Time; /* Time to which model is integrated */ 00021 double PrintStep; /* Number of output steps from 0 to 'Time' */ 00022 double Error; /* absolute tolerance in Cvode integration */ 00023 double RError; /* relative tolerance in Cvode integration */ 00024 double Mxstep; /* maximum step number for CVode integration */ 00025 int Determinant; /* Calculate and print determinant of the 00026 jacobian matrix */ 00027 int DrawReactions; /* Calculate a graph of the reaction network */ 00028 int DrawJacobian; /* Calculate a graph of species interaction 00029 as determined by the jacobian matrix */ 00030 int HaltOnEvent; /* stop integration if event is detected */ 00031 int InterActive; /* Start program in interactive mode */ 00032 int Jacobian; /* Do not use jacobian matrix for integration */ 00033 int Sensitivity; /* Activate Sensitivity Analysis */ 00034 int PrintAll; /* Print all given results instead of only one */ 00035 int PrintJacobian; /* Print out time course of the jacobian matrix */ 00036 int PrintReactions; /* Print out time course of the reaction rates */ 00037 int PrintModel; /* Print out model, ODEs and jacobian expressions */ 00038 int PrintODEsToSBML; /* Construct ODE model and print out SBML */ 00039 int PrintOnTheFly; /* Print species concentration during integration */ 00040 int Wheel; /* Print progress wheel */ 00041 int PrintRates; /* Print time course of the ODE values */ 00042 int PrintMessage; /* Print messages of integration procedure */ 00043 int SteadyState; /* Check for steady states during integration */ 00044 int Validate; /* Validate SBML model before doing anything else */ 00045 int Write; /* Print results to file instead of stdout */ 00046 int Xmgrace; /* Print results to XMGrace instead of stdout */ 00047 } Options; 00048 00049 Options Opt; 00050 00051 void 00052 decodeCML(int argc, char *argv[]); 00053 void 00054 initializeOptions(void); 00055 void 00056 usage (int status); 00057 00058 #endif 00059 00060 /* End of file */
1.4.4