int
main(int argc, char *argv[])
{
sparsegraph sg,sh,*this;
int n,codetype;
int argnum,i,j,outcode;
char *arg,sw;
boolean badargs;
boolean sswitch,gswitch,qswitch,vswitch,xswitch,Xswitch;
boolean pswitch,Lswitch,tswitch,yswitch,Yswitch;
long Lvalue;
double t;
char *infilename,*outfilename;
FILE *infile,*outfile;
nauty_counter nin,nout;
int status,xstatus,ystatus,tvalue,imin,imax;
DYNALLSTAT(int,ham1,ham1_sz);
DYNALLSTAT(int,ham2,ham2_sz);
HELP;
INITSEED;
ran_init(seed);
sswitch = gswitch = yswitch = qswitch = vswitch = FALSE;
tswitch = xswitch = Xswitch = Lswitch = pswitch = FALSE;
Yswitch = FALSE;
infilename = outfilename = NULL;
argnum = 0;
badargs = FALSE;
for (j = 1; !badargs && j < argc; ++j)
{
arg = argv[j];
if (arg[0] == '-' && arg[1] != '\0')
{
++arg;
while (*arg != '\0')
{
sw = *arg++;
SWBOOLEAN('s',sswitch)
else SWBOOLEAN('g',gswitch)
else SWBOOLEAN('q',qswitch)
else SWBOOLEAN('x',xswitch)
else SWBOOLEAN('y',yswitch)
else SWBOOLEAN('Y',Yswitch)
else SWBOOLEAN('X',Xswitch)
else SWBOOLEAN('v',vswitch)
else SWBOOLEAN('p',pswitch)
else SWLONG('L',Lswitch,Lvalue,"-L")
else SWINT('t',tswitch,tvalue,"-t")
else badargs = TRUE;
}
}
else
{
++argnum;
int
main(int argc, char *argv[])
{
sparsegraph sg;
int n,codetype;
int argnum,i,j,outcode,tvalue;
char *arg,sw;
boolean badargs;
boolean sswitch,gswitch,qswitch,Lswitch,tswitch,vswitch,uswitch;
long Lvalue;
double t;
char *infilename,*outfilename;
FILE *infile,*outfile;
nauty_counter nin,nout,nNO,nYES,nTIMEOUT;
int status;
DYNALLSTAT(int,cyc,cyc_sz);
HELP;
INITSEED;
ran_init(seed);
uswitch = sswitch = gswitch = Lswitch = qswitch = vswitch = tswitch = FALSE;
infilename = outfilename = NULL;
argnum = 0;
badargs = FALSE;
for (j = 1; !badargs && j < argc; ++j)
{
arg = argv[j];
if (arg[0] == '-' && arg[1] != '\0')
{
++arg;
while (*arg != '\0')
{
sw = *arg++;
SWBOOLEAN('s',sswitch)
else SWBOOLEAN('g',gswitch)
else SWBOOLEAN('u',uswitch)
else SWBOOLEAN('q',qswitch)
else SWBOOLEAN('v',vswitch)
else SWLONG('L',Lswitch,Lvalue,"-L")
else SWINT('t',tswitch,tvalue,"-t")
else badargs = TRUE;
}
}
else
{
++argnum;
/**
Main program.
@return error code or EXIT_SUCCESS if successful
*/
int main(int argc, char *argv[])
{
int i;
sys.input = NULL;
sys.output = NULL;
sys.needs_queue = FALSE;
sys.volume = 1.; // initial volume factor
sys.doubling_time = -1; // no growth at all
sys.doubling_time_std = 0; // the doubling time is exact
sys.last_division = NAN; // to distinguish from given division times
sys.growth_type = GROWTH_EXPONENTIAL;
sys.division_type = DIVIDE_HALF;
sys.output_stats = FALSE;
sys.output_conc = OUTPUT_AUTOMATIC;
sys.output_kaic = FALSE;
sys.output_phos = FALSE;
sys.output_quite = FALSE;
sys.species = NULL;
sys.tau_init = 0.;
// check command line parameters
while( TRUE )
{
static struct option long_options[] =
{
// These options set a flag.
{"a_bionmial", no_argument, 0, 'a'},
{"conc", no_argument, 0, 'c'},
{"exponential", no_argument, 0, 'e'},
{"linear", no_argument, 0, 'l'},
{"help", no_argument, 0, 'h'},
{"input", required_argument, 0, 'i'},
{"number", no_argument, 0, 'n'},
{"output", required_argument, 0, 'o'},
{"phos", no_argument, 0, 'p'},
{"quite", no_argument, 0, 'q'},
{"seed", optional_argument, 0, 's'},
{"total", no_argument, 0, 't'},
{"verbose", no_argument, 0, 'v'},
{"species", required_argument, 0, 1000},
};
// getopt_long stores the option index here.
int option_index = 0;
// parse the next option
i = getopt_long( argc, argv, "acehlnpqstv", long_options, &option_index );
// Detect the end of the options.
if( i == -1 )
break;
switch(i)
{
case 'a': // also --a_binomial
sys.division_type = DIVIDE_HALF;
break;
case 'c': // also --conc
sys.output_conc = OUTPUT_CONCENTRATION;
break;
case 'e': // also --exponential
sys.growth_type = GROWTH_EXPONENTIAL;
break;
case 'h': // also --help
show_help();
return EXIT_SUCCESS;
break;
case 'l': // also --linear
sys.growth_type = GROWTH_LINEAR;
break;
case 'i': // only --input
if( NULL == optarg )
{
fprintf( stderr, "If the option '--input' is given, a filename has to be added" );
return EXIT_FAILURE;
}
sys.input = malloc( ( strlen(optarg) + 1 ) * sizeof( char ) );
strcpy( sys.input, optarg );
break;
case 'n': // also --number
sys.output_conc = OUTPUT_COPYNUMBER;
break;
case 'o': // only --output
if( NULL == optarg )
{
fprintf( stderr, "If the option '--output' is given, a filename has to be added" );
return EXIT_FAILURE;
}
sys.output = malloc( ( strlen(optarg) + 1 ) * sizeof( char ) );
strcpy( sys.output, optarg );
printf( "files: %s - %s\n", sys.output, optarg );
break;
case 'p':
sys.output_phos = TRUE;
break;
case 'q':
sys.output_quite = TRUE;
break;
case 's':
if( NULL == optarg )
{
// init random number generator with seed based on current time
ran_init(0);
}
else
{
long seed;
if( 1 != sscanf( optarg, "%ld%*s", &seed ) )
{
fprintf( stderr, "If a value for '--seed' is given, it has to be a long integer number.\n" );
return EXIT_FAILURE;
}
ran_init( seed );
}
break;
case 't':
sys.output_kaic = TRUE;
break;
case 'v':
sys.output_stats = TRUE;
break;
case 1000: // only --species
if( NULL == optarg )
{
fprintf( stderr, "If the option '--species' is given, an identifier has to be added" );
return EXIT_FAILURE;
}
sys.species = malloc( ( strlen(optarg) + 1 ) * sizeof( char ) );
strcpy( sys.species, optarg );
break;
default:
abort();
}
}
// load data from files and initialize program
start();
// cleanup
return finish ();
}
void CreateRandColors(int n)
{
int i=0, ind0, ind1, ind2;
char aux[6];
ran_init(n);
for (i = 0; i<n; i++)
{
strcpy(NShape[i].color, "\0");
strcpy(aux, "\0");
ind1 = KRAN(4096);
NShape[i].labcol=(ind1/128) % 2;
for (ind0 = 0; ind0<3; ind0++)
{
ind2 = ind1 % 16;
ind1 = (ind1-ind2) / 16;
switch (ind2)
{
case 0:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "00");
strcat(NShape[i].color, aux);
break;
case 1:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "11");
strcat(NShape[i].color, aux);
break;
case 2:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "22");
strcat(NShape[i].color, aux);
break;
case 3:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "33");
strcat(NShape[i].color, aux);
break;
case 4:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "44");
strcat(NShape[i].color, aux);
break;
case 5:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "55");
strcat(NShape[i].color, aux);
break;
case 6:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "66");
strcat(NShape[i].color, aux);
break;
case 7:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "77");
strcat(NShape[i].color, aux);
break;
case 8:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "88");
strcat(NShape[i].color, aux);
break;
case 9:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "99");
strcat(NShape[i].color, aux);
break;
case 10:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "AA");
strcat(NShape[i].color, aux);
break;
case 11:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "BB");
strcat(NShape[i].color, aux);
break;
case 12:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "CC");
strcat(NShape[i].color, aux);
break;
case 13:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "DD");
strcat(NShape[i].color, aux);
break;
case 14:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "EE");
strcat(NShape[i].color, aux);
break;
case 15:
strcpy(aux, NShape[i].color);
strcpy(NShape[i].color, "FF");
strcat(NShape[i].color, aux);
break;
}
}
}
}
