//**********************************************************************************************************************
vector<string> ClearcutCommand::setParameters(){
try {
CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pphylip);
CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pfasta);
CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pverbose);
CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pquiet);
CommandParameter pversion("version", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pversion);
CommandParameter pseed("seed", "String", "", "", "*", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnorandom);
CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshuffle);
CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pneighbor);
CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpblen);
CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpdist);
CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pDNA);
CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pprotein);
CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pjukes);
CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkimura);
CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pstdout);
CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pntrees);
CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "","",false,false); parameters.push_back(pmatrixout);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "ClearcutCommand", "setParameters");
exit(1);
}
}
int prirup( void )
{
int sus ;
char userirup[10];
sus = 0 ;
fgets(userirup, 10, stdin);
if ( (!strcmp(userirup, "c\n") ) ||
(!strcmp(userirup, "t\n") ) ||
(!strcmp(userirup, "cycle\n")) ||
(!strcmp(userirup, "time\n") ) ) {
printtc() ;
} else if ( (!strcmp(userirup, "r\n") ) ||
(!strcmp(userirup, "rad\n")) ) {
printrc() ;
} else if (!strcmp(userirup, "wdmp\n")) {
sus = 1 ;
} else if (!strcmp(userirup, "wgdmp\n")) {
sus = 2 ;
} else if ( (!strcmp(userirup, "stop\n") ) ||
(!strcmp(userirup, "pause\n")) ) {
sus = -1 ;
pccsoff = 1 ;
} else if ( (!strcmp(userirup, "quit\n")) ||
(!strcmp(userirup, "end\n") ) ) {
sus = -2 ;
pccsoff = 1 ;
} else if ( (!strcmp(userirup, "?\n") ) ||
(!strcmp(userirup, "h\n") ) ||
(!strcmp(userirup, "help\n")) ) {
PRINT(stdout,"Help for Run Interrupt Commands:\n");
PRINT(stdout," c, t, cycle, time : Print timestep info\n");
PRINT(stdout," r, rad : Print radiation info\n");
#ifdef SILO
PRINT(stdout," wdmp, wgdmp : Dump restart or graphics file\n");
#endif
PRINT(stdout," stop, pause : Suspend run & accept commands\n");
PRINT(stdout," quit, end : Terminate execution completely\n");
PRINT(stdout," ?, h, help : Display this help info\n");
PRINT(stdout," v, version : Print compile version info\n");
} else if ( (!strcmp(userirup, "v\n") ) ||
(!strcmp(userirup, "version\n")) ) {
pversion();
} else if (strcmp(userirup, "\n")) {
/* PRINT(stdout, "%s %s", "Unknown interrupt command:", userirup); */
}
return(sus) ;
}