void statusResponse(int sd, struct bzp *bzp, struct blatzIndex *indexList)
/* Respond to status message. */
{
FILE *f = netFileFromSocket(sd);
fprintf(f, "version: %d\n", bzpVersion());
fprintf(f, "indexed sequences: %d\n", slCount(indexList));
fprintf(f, "bases indexed: %lld\n", basesInIndexList(indexList));
fprintf(f, "weight: %d\n", bzp->weight);
fprintf(f, "rna: %s\n", trueFalseString(bzp->rna));
fprintf(f, "minScore: %d\n", bzp->minScore);
fprintf(f, "minGapless: %d\n", bzp->minGapless);
fprintf(f, "multiHits: %d\n", bzp->multiHits);
fprintf(f, "minChain: %d\n", bzp->minChain);
fprintf(f, "maxExtend: %d\n", bzp->maxExtend);
fprintf(f, "maxBandGap: %d\n", bzp->maxBandGap);
fprintf(f, "minExpand: %d\n", bzp->minExpand);
fprintf(f, "expandWindow: %d\n", bzp->expandWindow);
fprintf(f, "out: %s\n", bzp->out);
fprintf(f, "good queries: %d\n", goodQueryCount);
fprintf(f, "bad queries: %d\n", badQueryCount);
fprintf(f, "crashes: %d\n", crashCount);
fprintf(f, "cpus used: %d\n", cpusUsed);
carefulClose(&f);
}
void serverStatus()
/* Send status message to server and print result. */
{
int sd = netMustConnect(host, port);
FILE *f;
netSendString(sd, "status");
f = netFileFromSocket(sd);
copyOpenFile(f, stdout);
}
static void blatzClient(char *input, char *output)
/* Send query message and dna to server and print result. */
{
struct dnaLoad *dl = dnaLoadOpen(input);
struct dnaSeq *seq;
FILE *f = mustOpen(output, "w");
static struct optionSpec options[] = {
BZP_CLIENT_OPTIONS
};
int i;
while ((seq = dnaLoadNext(dl)) != NULL)
{
/* Connect */
int sd = netMustConnect(host, port);
FILE *sf = NULL;
/* Send query command. */
netSendString(sd, "query");
/* Send options. */
for (i=0; i<ArraySize(options); ++i)
sendOption(sd, options[i].name);
/* Send sequence. */
if (optionExists("rna") || optionExists("unmask"))
toUpperN(seq->dna, seq->size);
else
{
if (seqIsLower(seq))
warn("Sequence %s is all lower case, and thus ignored. Use -unmask "
"flag to unmask lower case sequence.", seq->name);
}
netSendString(sd, "seq");
netSendString(sd, seq->name);
netSendHugeString(sd, seq->dna);
verbose(1, "%s\n", seq->name);
dnaSeqFree(&seq);
/* Get and save response. */
sf = netFileFromSocket(sd);
copyOpenFile(sf, f);
carefulClose(&sf);
/* Close connection */
close(sd);
}
dnaLoadClose(&dl);
carefulClose(&f);
}
void queryResponse(int sd, struct bzp *bzp, struct blatzIndex *indexList)
/* Respond to query message - read options and dna from socket,
* and do alignment. */
{
struct bzp lbzp = *bzp;
struct dnaSeq *seq = NULL;
char buf[256], *line, *word;
char *out = NULL, *mafT = NULL, *mafQ = NULL;
/* First get options - overriding what got set at startup. */
for (;;)
{
if ((line = netGetString(sd, buf)) == NULL)
{
truncatedQuery(1);
return;
}
word = nextWord(&line);
line = skipLeadingSpaces(line);
if (sameString(word, "seq"))
break;
else if (sameString(word, "rna"))
lbzp.rna = TRUE;
else if (sameString(word, "minScore"))
lbzp.minScore = atoi(line);
else if (sameString(word, "minGapless"))
lbzp.minGapless = atoi(line);
else if (sameString(word, "multiHits"))
lbzp.multiHits = atoi(line);
else if (sameString(word, "minChain"))
lbzp.minChain = atoi(line);
else if (sameString(word, "maxExtend"))
lbzp.maxExtend = atoi(line);
else if (sameString(word, "maxBandGap"))
lbzp.maxBandGap = atoi(line);
else if (sameString(word, "minExpand"))
lbzp.minExpand = atoi(line);
else if (sameString(word, "expandWindow"))
lbzp.expandWindow = atoi(line);
else if (sameString(word, "out"))
lbzp.out = out = cloneString(line);
else if (sameString(word, "mafQ"))
lbzp.mafQ = mafQ = cloneString(line);
else if (sameString(word, "mafT"))
lbzp.mafT = mafT = cloneString(line);
}
/* Get DNA into seq*/
{
char *name = netGetString(sd, buf);
char *dna;
if (name == NULL)
{
truncatedQuery(2);
return;
}
dna = netGetHugeString(sd);
if (dna == NULL)
{
truncatedQuery(3);
return;
}
AllocVar(seq);
seq->dna = dna;
seq->size = strlen(dna);
seq->name = cloneString(name);
bzpTime("Received %d bases in %s", seq->size, seq->name);
if (lbzp.rna)
maskTailPolyA(seq->dna, seq->size);
}
/* Create alignments into chainList and write results. */
{
FILE *f = netFileFromSocket(sd);
struct chain *chainList = blatzAlign(&lbzp, indexList, seq);
blatzWriteChains(&lbzp, &chainList, seq, 0, seq->size, seq->size, indexList, f);
bzpTime("sent result - %d chains", slCount(chainList));
carefulClose(&f);
}
dnaSeqFree(&seq);
freez(&out);
freez(&mafQ);
freez(&mafT);
}
