static struct gfRange *gfQuerySeq(int conn, struct dnaSeq *seq)
/* Ask server for places sequence hits. */
{
struct gfRange *rangeList = NULL, *range;
char buf[256], *row[6];
int rowSize;
startSeqQuery(conn, seq, "query");
/* Read results line by line and save in list, and return. */
for (;;)
{
netRecieveString(conn, buf);
if (sameString(buf, "end"))
{
break;
}
else if (startsWith("Error:", buf))
{
gfServerWarn(seq, buf);
break;
}
else
{
rowSize = chopLine(buf, row);
if (rowSize < 6)
errAbort("Expecting 6 words from server got %d", rowSize);
range = gfRangeLoad(row);
slAddHead(&rangeList, range);
}
}
slReverse(&rangeList);
return rangeList;
}
int botDelayTime(char *host, int port, char *botCheckString)
/* Figure out suggested delay time for ip address in
* milliseconds. */
{
int sd = netMustConnect(host, port);
char buf[256];
netSendString(sd, botCheckString);
netRecieveString(sd, buf);
close(sd);
return atoi(buf);
}
static void gfQuerySeqTransTrans(int conn, struct dnaSeq *seq,
struct gfClump *clumps[2][3][3],
struct lm *lm, struct gfSeqSource **retSsList, int *retTileSize)
/* Query server for clumps where translated DNA sequence hits translated
* index. */
{
int qFrame, tFrame, isRc, rowSize;
struct gfClump *clump;
int tileSize = 0;
char *line;
char buf[256], *row[12];
struct gfSeqSource *ssList = NULL, *ss;
for (isRc = 0; isRc <= 1; ++isRc)
for (qFrame = 0; qFrame<3; ++qFrame)
for (tFrame = 0; tFrame<3; ++tFrame)
clumps[isRc][qFrame][tFrame] = NULL;
/* Send sequence to server. */
startSeqQuery(conn, seq, "transQuery");
line = netRecieveString(conn, buf);
if (!startsWith("Error:", line))
{
tileSize = findTileSize(line);
/* Read results line by line and save in memory. */
for (;;)
{
/* Read and parse first line that describes clump overall. */
netRecieveString(conn, buf);
if (sameString(buf, "end"))
{
break;
}
else if (startsWith("Error:", buf))
{
gfServerWarn(seq, buf);
break;
}
rowSize = chopLine(buf, row);
if (rowSize < 9)
errAbort("Expecting 9 words from server got %d", rowSize);
AllocVar(clump);
clump->qStart = sqlUnsigned(row[0]);
clump->qEnd = sqlUnsigned(row[1]);
AllocVar(ss);
ss->fileName = cloneString(row[2]);
slAddHead(&ssList, ss);
clump->target = ss;
clump->tStart = sqlUnsigned(row[3]);
clump->tEnd = sqlUnsigned(row[4]);
clump->hitCount = sqlUnsigned(row[5]);
isRc = ((row[6][0] == '-') ? 1 : 0);
qFrame = sqlUnsigned(row[7]);
tFrame = sqlUnsigned(row[8]);
slAddHead(&clumps[isRc][qFrame][tFrame], clump);
/* Read and parse next (long) line that describes hits. */
clump->hitList = getHitsFromServer(conn, lm);
assert(slCount(clump->hitList) == clump->hitCount);
}
for (isRc = 0; isRc <= 1; ++isRc)
for (qFrame = 0; qFrame<3; ++qFrame)
for (tFrame = 0; tFrame<3; ++tFrame)
slReverse(&clumps[isRc][qFrame][tFrame]);
}
else
{
gfServerWarn(seq, buf);
}
*retSsList = ssList;
*retTileSize = tileSize;
}
