void serverStart(char *files[], int fileCount)
/* Load DNA. Build up indexes, set up listing port, and fall into
* accept loop. */
{
struct blatzIndex *indexList = NULL;
int i;
int acceptor;
struct bzp *bzp = bzpDefault();
/* Daemonize self. */
bzpSetOptions(bzp);
/* Load up all sequences. */
for (i=0; i<fileCount; ++i)
{
struct dnaLoad *dl = dnaLoadOpen(files[i]);
struct blatzIndex *oneList = blatzIndexDl(dl, bzp->weight, bzp->unmask);
indexList = slCat(indexList, oneList);
dnaLoadClose(&dl);
}
bzpTime("Loaded and indexed %d sequences", slCount(indexList));
verbose(1, "Ready for queries\n");
/* Turn self into proper daemon. */
logDaemonize("blatzServer");
acceptor = netAcceptingSocket(port, 100);
serviceLoop(acceptor, bzp, indexList);
}
void usage()
/* Explain usage and exit. */
{
struct bzp *bzp = bzpDefault();
printf("blatzServer version %d - Set up in-memory server for\n", bzpVersion());
printf("cross-species DNA alignments\n");
printf("usage:\n");
printf(" blatzServer start file(s)\n");
printf("Starts up server. Files are either fasta files, nib files, 2bit files\n");
printf("or text files containing the names of the above files one per line.\n");
printf("It's important that the sequence be repeat masked with repeats in\n");
printf("lower case.\n");
printf("Options: (defaults are shown for numerical parameters)\n");
bzpServerOptionsHelp(bzp);
bzpClientOptionsHelp(bzp);
printf(" -debug Writes diagnostic output to console and no daemon fork\n");
printf(" -subnet=255.255.255.255 Restrict access to subnet\n");
printf(" -port=%d Use specified TCP/IP port\n", bzpDefaultPort);
printf(" -host=%s Query specified host\n", host);
printf(" -cpu=%d Use specified number of CPUs (processes)\n", cpuCount);
printf("Other uses:\n");
printf(" blatzServer stop\n");
printf(" this terminates server\n");
printf(" blatzServer status\n");
printf(" this prints status info including version\n");
noWarnAbort();
}
static void usage()
/* Explain usage and exit. */
{
struct bzp *bzp = bzpDefault();
printf("blatzClient version %d - Ask server to do\n", bzpVersion());
printf("cross-species DNA alignments and save results.\n");
printf("usage:\n");
printf(" blatzClient queryFile outputFile.\n");
printf("The queryFile can be in fasta, nib, or 2bit format or a \n");
printf("text file containing the names of the above files one per line.\n");
printf("It's important that the sequence be repeat masked with repeats in\n");
printf("lower case.\n");
printf("Options: (defaults are shown for numerical parameters)\n");
bzpClientOptionsHelp(bzp);
printf(" -port=%d Use specified TCP/IP port\n", bzpDefaultPort);
printf(" -host=%s Query specified host\n", host);
noWarnAbort();
}
int main(int argc, char *argv[])
/* Process command line. */
{
struct bzp *bzp = bzpDefault();
/* Do initialization. */
bzpTime(NULL);
dnaUtilOpen();
optionInit(&argc, argv, options);
if (argc != 4)
usage(bzp);
/* Fill in parameters from command line options. */
bzpSetOptions(bzp);
loadAndAlignAll(bzp, argv[1], argv[2], argv[3]);
/* If you were a turtle you'd be home right now. */
return 0;
}
