int scan_main(SSL *ssl)
{
int order;
system("clear");
order = Mlist();
switch(order)
{
case CSCL: scan_local_files();break;
case CSCS: scan_serv_files(ssl,order);break;
case CSCLS: scan_all(ssl);break;
default: fprintf(stderr,"No such option!\n");
return -1;
}
return 0;
}
int MyCalculateDiversity(vector<vector<vector<int> > > AlleleList, vector<int> ActiveMaxAllelesList, std::string Standardize, double& RandomActiveDiversity, double& AltRandomActiveDiversity)
{
/*AlleleList structure:
Pop1..r
locusarray1..n */
int CoreSize = AlleleList.size();
int NumLoci = AlleleList[0].size();
int i, j, M;
unsigned int k;
vector<int> CurrLoc;
vector<int> Mlist(NumLoci);
set<int> AlleleSet;
if (NumLoci == 0)
{
RandomActiveDiversity = -1;
AltRandomActiveDiversity = -1;
}
else
{
//use set to eliminate redundancies
for (i=0;i<NumLoci;i++)
{
//3. pass alleles from the same locus into a single set, for all populations in core, to remove redundancies
AlleleSet.clear(); //clear AlleleSet
for (j=0;j<CoreSize;j++)
{
CurrLoc = AlleleList[j][i];
for (k=0;k<CurrLoc.size();++k)
{
AlleleSet.insert(CurrLoc[k]); //locus i for all population j
}
}
if (AlleleSet.size() == 0) M=0;
else M=AlleleSet.size();
Mlist[i] = M;
}
//5. standardize the M values to the maximum possible number of alleles at that locus,
//and add them up to get final estimate of standardized allelic diversity in the core.
//Then divide by the number of loci to get a number that is comparable across data sets.
//calculate the standardized allelic diversity
double SAD;
double SADtemp = 0; //SADtemp is the summed value of standardized M across all loci for a single subcore
for (i=0;i<NumLoci;i++)
{
SADtemp = SADtemp + ( (double) Mlist[i] / (double) ActiveMaxAllelesList[i] );
}
SAD = SADtemp / NumLoci;
//calculate M by simply adding up the Mlist
M = 0;
for (k=0;k<Mlist.size();++k)
{
M = M + Mlist[k];
}
//6. Determine the way variables are updated so that the value for the desired optimality
//criterion is RandomActiveDiversity, while the other is AltRandomActiveDiversity.
//This way, the output can contain information on both M+ and M criteria,
//although only one will be used for optimization.
if (Standardize == "yes")
{
RandomActiveDiversity = SAD;
AltRandomActiveDiversity = M;
}
else if (Standardize == "no")
{
RandomActiveDiversity = M;
AltRandomActiveDiversity = SAD;
}
}
return 0;
}
/* void Ucommand (void) -------------------------
*
* OS/0 command processor.
*
* Before spawning/calling this process, set the
* external variable CurrentTerm to the number
* of the terminal you want the command processor to
* run on. Note that CurrentTerm is incremented by
* the command processor after it "uses" the value.
* This allows Ucommand to be spawned in a loop.
*
* This command interpreter was designed to be both
* spawned and called. It is suggested that terms
* 1-3 be spawned, then term 1 be called directly.
* This way when the "bye" command is issued at a terminal
* greater than 0 the system will not shut down.
*/
void Ucommand (void)
{
int TermNum = (CurrentTerm++) ;
ARG Args ;
char *Cmd ;
char *user ;
char *prompt ;
char *buf ;
int NumChars, CmdNum, i ;
short bLoggedIn = FALSE ;
Cmd = (char*) malloc (sizeof(char)*256) ;
user = (char*) malloc (sizeof(char)*256) ;
prompt = (char*) malloc (sizeof(char)*256) ;
buf = (char*) malloc (sizeof(char)*256) ;
tprint (" Command processor %d active\n", TermNum) ;
sprintf (buf, "\aOS/0 Mail - Copyright (c) 1990, Charles Kindel and Sandy Smith.\n") ;
Writeterm (buf, strlen (buf), TermNum) ;
sprintf (buf, "\tCommand processor %d active\n", TermNum) ;
Writeterm (buf, strlen (buf), TermNum) ;
sprintf (buf, "Available commands:\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
for (i = 0 ; i < NCMDS ; i++)
{
sprintf (buf, "\t%s\n", cmdnames[i]) ;
Writeterm (buf, strlen(buf), TermNum) ;
}
strcpy (user, "OS/0") ;
while (TRUE)
{
if (!bLoggedIn && TermNum)
sprintf (prompt, "\x1b[1mType \"login <username>\" to get started:\x1b[0m ") ;
else
sprintf (prompt, "\x1b[1m[%s]\x1b[0m ", user) ;
Writeterm (prompt, strlen(prompt), TermNum) ;
NumChars = Readterm (Cmd, CMDSIZE, TermNum) ;
CmdNum = CmdToNum (Cmd, &Args) ;
if (bEcho)
{
/* echo cmd to terminal */
for (i = 0 ; i <= Args.num ; i++)
{
sprintf (buf, "%s ", Args.arg[i]) ;
Writeterm (buf, strlen(buf), TermNum) ;
}
Writeterm ("\n", 1, TermNum) ;
}
switch (CmdNum)
{
case CECHO :
if (TermNum)
{
sprintf (buf, "\aYou must be logged in to use that command!\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
break ;
}
if (Args.num)
{
if (!strcmp (Args.arg[1], "on"))
bEcho = TRUE ;
else
if (!strcmp (Args.arg[1], "off"))
bEcho = FALSE ;
else
{
sprintf (buf, "The usage for the echo command is : \"echo [on|off]\"\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
break ;
}
}
else
{
sprintf (buf, "\techo is %s\n", bEcho ? "on" : "off") ;
Writeterm (buf, strlen(buf), TermNum) ;
}
break ;
case CHELP :
sprintf (buf, "Available commands:\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
for (i = 0 ; i < NCMDS ; i++)
{
sprintf (buf, "\t%s\n", cmdnames[i]) ;
Writeterm (buf, strlen(buf), TermNum) ;
}
break ;
case CLIST :
if (bLoggedIn || !TermNum)
Mlist (TermNum) ;
else
{
sprintf (buf, "\aYou must be logged in to use that command!\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
break ;
}
break ;
case CADDUSER:
Madduser (TermNum, &Args) ;
break ;
case CLOGIN :
if (bLoggedIn)
{
Mlogout (TermNum, user, &Args) ;
strcpy (user, "OS/0") ;
}
if (Mlogin (TermNum, user, &Args))
bLoggedIn = TRUE ;
break ;
case CLOGOUT :
if (!bLoggedIn)
{
sprintf (buf, "\aNo one is logged in!\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
break ;
}
bLoggedIn = !Mlogout (TermNum, user, &Args) ;
strcpy (user, "OS/0") ;
break ;
case CMAIL :
if (!bLoggedIn)
{
sprintf (buf, "\aYou must be logged in to use that command!\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
break ;
}
MMail (TermNum, user, &Args) ;
break ;
case CCMD :
if (!bLoggedIn && TermNum)
{
sprintf (buf, "\aYou must be logged in to use that command!\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
break ;
}
if (Args.num != 1)
{
sprintf (buf, "\aThe usage for \"cmd\" is: cmd <time>\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
break ;
}
sprintf (buf, "Executing a psuedo-command...\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
Delay (atoi(Args.arg[1]) / 10) ;
break ;
case CDIR :
if (bLoggedIn || !TermNum)
Udir (TermNum) ;
else
{
sprintf (buf, "\aYou must be logged in to use that command!\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
}
break ;
case CTIME:
if (bLoggedIn || !TermNum)
{
sprintf (buf, "The current time is %d\n", Get_Time_of_Day()) ;
Writeterm (buf, strlen(buf), TermNum) ;
}
else
{
sprintf (buf, "\aYou must be logged in to use that command!\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
}
break ;
case CDEL:
if (TermNum) /* check to see if were on term 0 */
{
sprintf (buf, "\aFiles can be deleted from Terminal 0 only.\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
break ;
}
for (i = 1 ; i <= Args.num ; i++)
{
if (!(strcmp (Args.arg[i], ".")) || (-1 == Uremove (Args.arg[i])))
{
sprintf (buf, "\t%s does not exist.\n", Args.arg[i]) ;
Writeterm (buf, strlen(buf), TermNum) ;
}
sprintf (buf, "\t%s deleted.\n", Args.arg[i]) ;
Writeterm (buf, strlen(buf), TermNum) ;
}
break ;
case CFORMAT :
if (TermNum) /* check to see if were on term 0 */
{
sprintf (buf, "\aThe disk can be formatted from Terminal 0 only.\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
break ;
}
Uformat (INODESPACE) ;
break ;
case CTYPE :
if (TermNum && !bLoggedIn)
{
sprintf (buf, "\aYou must be logged in to use this command!\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
break ;
}
Ctype (TermNum, &Args) ;
break ;
case CBYE :
if (TermNum) /* check to see if were on term 0 */
{
sprintf (buf, "\aThe system can only be shut down from Terminal 0.\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
break ;
}
sprintf (buf, "Shutting down the OS/0 file system!\n") ;
Writeterm (buf, strlen(buf), TermNum) ;
for (i = 1 ; i < 4 ; i++)
{
sprintf (buf, "\n\a\a\aNotice! The OS/0 file system is going down in 10 seconds!\n") ;
Writeterm (buf, strlen(buf), i) ;
}
Delay (10) ;
free (Cmd) ;
free (user) ;
free (prompt) ;
free (buf) ;
Terminate () ;
break ;
default :
if (strlen(Cmd))
{
sprintf (buf, "\a\"%s\" is an invalid command!\n", Cmd) ;
Writeterm (buf, strlen(buf), TermNum) ;
}
break ;
}
}
} /* Ucommand */
