gfServer/gfServer.c File Reference

#include "common.h"
#include <signal.h>
#include <sys/socket.h>
#include <netinet/in.h>
#include <netdb.h>
#include "portable.h"
#include "net.h"
#include "dnautil.h"
#include "dnaseq.h"
#include "nib.h"
#include "twoBit.h"
#include "fa.h"
#include "dystring.h"
#include "errabort.h"
#include "memalloc.h"
#include "genoFind.h"
#include "options.h"
#include "trans3.h"
#include "log.h"

Include dependency graph for gfServer.c:

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Functions
void	usage ()
void	genoFindDirect (char *probeName, int fileCount, char *seqFiles[])
void	genoPcrDirect (char *fPrimer, char *rPrimer, int fileCount, char *seqFiles[])
int	getPortIx (char *portName)
void	dnaQuery (struct genoFind *gf, struct dnaSeq *seq, int connectionHandle, char buf[256])
void	transQuery (struct genoFind *transGf[2][3], aaSeq *seq, int connectionHandle, char buf[256])
void	transTransQuery (struct genoFind *transGf[2][3], struct dnaSeq *seq, int connectionHandle, char buf[256])
static void	pcrQuery (struct genoFind *gf, char *fPrimer, char *rPrimer, int maxDistance, int connectionHandle)
static void	gfAbort ()
static void	errorSafeSetup ()
static void	errorSafeCleanupMess (int connectionHandle, char *message)
static void	errorSafeQuery (boolean doTrans, boolean queryIsProt, struct dnaSeq *seq, struct genoFind *gf, struct genoFind *transGf[2][3], int connectionHandle, char *buf)
static void	errorSafePcr (struct genoFind *gf, char *fPrimer, char *rPrimer, int maxDistance, int connectionHandle)
boolean	badPcrPrimerSeq (char *s)
void	startServer (char *hostName, char *portName, int fileCount, char *seqFiles[])
void	stopServer (char *hostName, char *portName)
int	statusServer (char *hostName, char *portName)
void	queryServer (char *type, char *hostName, char *portName, char *faName, boolean complex, boolean isProt)
void	pcrServer (char *hostName, char *portName, char *fPrimer, char *rPrimer, int maxSize)
void	getFileList (char *hostName, char *portName)
int	main (int argc, char *argv[])
Variables
static char const	rcsid [] = "$Id: gfServer.c,v 1.54 2007/03/31 19:38:13 markd Exp $"
static struct optionSpec	optionSpecs []
int	maxNtSize = 40000
int	maxAaSize = 8000
int	minMatch = gfMinMatch
int	tileSize = gfTileSize
int	stepSize = 0
boolean	doTrans = FALSE
boolean	allowOneMismatch = FALSE
int	repMatch = 1024
int	maxDnaHits = 100
int	maxTransHits = 200
int	maxGap = gfMaxGap
boolean	seqLog = FALSE
boolean	doMask = FALSE
boolean	canStop = FALSE
sockaddr_in	sai
long	baseCount = 0
long	blatCount = 0
long	aaCount = 0
long	pcrCount = 0
int	warnCount = 0
int	noSigCount = 0
int	missCount = 0
int	trimCount = 0
static jmp_buf	gfRecover
static char *	ripCord = NULL

---

Function Documentation

boolean badPcrPrimerSeq

(

char *

s

)

Definition at line 469 of file gfServer.c.

References FALSE, ntVal, and TRUE.

Referenced by startServer().

{
unsigned char c;
while ((c = *s++) != 0)
    {
    if (ntVal[c] < 0)
        return TRUE;
    }
return FALSE;
}

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void dnaQuery	(	struct genoFind *	gf,
		struct dnaSeq *	seq,
		int	connectionHandle,
		char	buf[256]
	)

Definition at line 218 of file gfServer.c.

References clock1000(), gfClumpFreeList(), gfFindClumps(), gfClump::hitCount, lm, lmCleanup(), lmInit(), logDebug(), maxDnaHits, missCount, netSendString(), gfClump::next, dnaSeq::size, ss, genoFind::stepSize, and genoFind::tileSize.

Referenced by errorSafeQuery().

{
struct gfClump *clumpList = NULL, *clump;
int limit = 1000;
int clumpCount = 0, hitCount = -1;
struct lm *lm = lmInit(0);

if (seq->size > gf->tileSize + gf->stepSize + gf->stepSize)
     limit = maxDnaHits;
clumpList = gfFindClumps(gf, seq, lm, &hitCount);
if (clumpList == NULL)
    ++missCount;
for (clump = clumpList; clump != NULL; clump = clump->next)
    {
    struct gfSeqSource *ss = clump->target;
    sprintf(buf, "%d\t%d\t%s\t%d\t%d\t%d", 
        clump->qStart, clump->qEnd, ss->fileName,
        clump->tStart-ss->start, clump->tEnd-ss->start, clump->hitCount);
    netSendString(connectionHandle, buf);
    ++clumpCount;
    if (--limit < 0)
        break;
    }
gfClumpFreeList(&clumpList);
lmCleanup(&lm);
logDebug("%lu %d clumps, %d hits", clock1000(), clumpCount, hitCount);
}

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static void errorSafeCleanupMess	(	int	connectionHandle,
		char *	message
	)			[static]

Definition at line 411 of file gfServer.c.

References logError(), netSendString(), and popAbortHandler().

Referenced by errorSafePcr(), and errorSafeQuery().

{
popAbortHandler();
logError("Recovering from error via longjmp");
netSendString(connectionHandle, message);
}

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static void errorSafePcr	(	struct genoFind *	gf,
		char *	fPrimer,
		char *	rPrimer,
		int	maxDistance,
		int	connectionHandle
	)			[static]

Definition at line 449 of file gfServer.c.

References errorSafeCleanupMess(), errorSafeSetup(), gfRecover, memTrackerEnd(), pcrQuery(), and popAbortHandler().

Referenced by startServer().

{
int status;
errorSafeSetup();
status = setjmp(gfRecover);
if (status == 0)    /* Always true except after long jump. */
    {
    pcrQuery(gf, fPrimer, rPrimer, maxDistance, connectionHandle);
    popAbortHandler();
    }
else    /* They long jumped here because of an error. */
    {
    errorSafeCleanupMess(connectionHandle, 
        "Error: gfServer out of memory."); 
    }
memTrackerEnd();
}

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static void errorSafeQuery	(	boolean	doTrans,
		boolean	queryIsProt,
		struct dnaSeq *	seq,
		struct genoFind *	gf,
		struct genoFind *	transGf[2][3],
		int	connectionHandle,
		char *	buf
	)			[static]

Definition at line 419 of file gfServer.c.

References dnaQuery(), errorSafeCleanupMess(), errorSafeSetup(), gfRecover, memTrackerEnd(), popAbortHandler(), transQuery(), and transTransQuery().

Referenced by startServer().

{
int status;
errorSafeSetup();
status = setjmp(gfRecover);
if (status == 0)    /* Always true except after long jump. */
    {
    if (doTrans)
       {
       if (queryIsProt)
            transQuery(transGf, seq, connectionHandle, buf);
       else
            transTransQuery(transGf, seq, 
                connectionHandle, buf);
       }
    else
        dnaQuery(gf, seq, connectionHandle, buf);
    popAbortHandler();
    }
else    /* They long jumped here because of an error. */
    {
    errorSafeCleanupMess(connectionHandle, 
        "Error: gfServer out of memory. Try reducing size of query.");
    }
memTrackerEnd();
}

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static void errorSafeSetup

(

)

[static]

Definition at line 403 of file gfServer.c.

References gfAbort(), memTrackerStart(), needMem(), pushAbortHandler(), and ripCord.

Referenced by errorSafePcr(), and errorSafeQuery().

{
memTrackerStart();
pushAbortHandler(gfAbort);
ripCord = needMem(64*1024); /* Memory for error recovery. memTrackerEnd frees */
}

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void genoFindDirect	(	char *	probeName,
		int	fileCount,
		char *	seqFiles[]
	)

Definition at line 121 of file gfServer.c.

References allowOneMismatch, dnaSeq::dna, doTrans, errAbort(), FALSE, faSpeedReadNext(), genoFindFree(), gfClumpDump(), gfClumpFreeList(), gfFindClumps(), gfIndexNibsAndTwoBits(), lineFileClose(), lineFileOpen(), lm, lmCleanup(), lmInit(), maxGap, minMatch, dnaSeq::name, gfClump::next, repMatch, dnaSeq::size, stepSize, tileSize, TRUE, and ZeroVar.

Referenced by main().

{
struct genoFind *gf = NULL;
struct lineFile *lf = lineFileOpen(probeName, TRUE);
struct dnaSeq seq;
int hitCount = 0, clumpCount = 0, oneHit;
ZeroVar(&seq);

if (doTrans)
    errAbort("Don't support translated direct stuff currently, sorry");

gf = gfIndexNibsAndTwoBits(fileCount, seqFiles, minMatch, maxGap, 
        tileSize, repMatch, FALSE,
        allowOneMismatch, stepSize);

while (faSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
    {
    struct lm *lm = lmInit(0);
    struct gfClump *clumpList = gfFindClumps(gf, &seq, lm, &oneHit), *clump;
    hitCount += oneHit;
    for (clump = clumpList; clump != NULL; clump = clump->next)
        {
        ++clumpCount;
        printf("%s ", seq.name);
        gfClumpDump(gf, clump, stdout);
        }
    gfClumpFreeList(&clumpList);
    lmCleanup(&lm);
    }
lineFileClose(&lf);
genoFindFree(&gf);
}

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void genoPcrDirect	(	char *	fPrimer,
		char *	rPrimer,
		int	fileCount,
		char *	seqFiles[]
	)

Definition at line 155 of file gfServer.c.

References allowOneMismatch, clock1000(), FALSE, genoFindFree(), gfClumpDump(), gfIndexNibsAndTwoBits(), gfPcrClumps(), maxGap, minMatch, gfClump::next, repMatch, gfSeqSource::start, stepSize, gfClump::target, gfClump::tEnd, tileSize, and gfClump::tStart.

Referenced by main().

{
struct genoFind *gf = NULL;
int fPrimerSize = strlen(fPrimer);
int rPrimerSize = strlen(rPrimer);
struct gfClump *clumpList, *clump;
time_t startTime, endTime;

startTime = clock1000();
gf = gfIndexNibsAndTwoBits(fileCount, seqFiles, minMatch, maxGap, 
        tileSize, repMatch, FALSE,
        allowOneMismatch, stepSize);
endTime = clock1000();
printf("Index built in %4.3f seconds\n", 0.001 * (endTime - startTime));

printf("plus strand:\n");
startTime = clock1000();
clumpList = gfPcrClumps(gf, fPrimer, fPrimerSize, rPrimer, rPrimerSize, 0, 4*1024);
endTime = clock1000();
printf("Index searched in %4.3f seconds\n", 0.001 * (endTime - startTime));
for (clump = clumpList; clump != NULL; clump = clump->next)
    {
    /* Clumps from gfPcrClumps have already had target->start subtracted out 
     * of their coords, but gfClumpDump assumes they have not and does the 
     * subtraction; rather than write a new gfClumpDump, tweak here: */
    clump->tStart += clump->target->start;
    clump->tEnd += clump->target->start;
    gfClumpDump(gf, clump, stdout);
    }
printf("minus strand:\n");
startTime = clock1000();
clumpList = gfPcrClumps(gf, rPrimer, rPrimerSize, fPrimer, fPrimerSize, 0, 4*1024);
endTime = clock1000();
printf("Index searched in %4.3f seconds\n", 0.001 * (endTime - startTime));
for (clump = clumpList; clump != NULL; clump = clump->next)
    {
    /* Same as above, tweak before gfClumpDump: */
    clump->tStart += clump->target->start;
    clump->tEnd += clump->target->start;
    gfClumpDump(gf, clump, stdout);
    }

genoFindFree(&gf);
}

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void getFileList	(	char *	hostName,
		char *	portName
	)

Definition at line 863 of file gfServer.c.

References gfSignature(), netGetString(), netMustConnectTo(), and netRecieveString().

Referenced by main().

{
char buf[256];
int sd = 0;
int fileCount;
int i;

/* Put together command. */
sd = netMustConnectTo(hostName, portName);
sprintf(buf, "%sfiles", gfSignature());
write(sd, buf, strlen(buf));

/* Get count of files, and then each file name. */
if (netGetString(sd, buf) != NULL)
    {
    fileCount = atoi(buf);
    for (i=0; i<fileCount; ++i)
        {
        printf("%s\n", netRecieveString(sd, buf));
        }
    }
close(sd);
}

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int getPortIx

(

char *

portName

)

Definition at line 201 of file gfServer.c.

References errAbort().

{
if (!isdigit(portName[0]))
    errAbort("Expecting a port number got %s", portName);
return atoi(portName);
}

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static void gfAbort

(

)

[static]

Definition at line 396 of file gfServer.c.

References freez(), gfRecover, and ripCord.

Referenced by errorSafeSetup().

{
freez(&ripCord);
longjmp(gfRecover, -1);
}

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int main	(	int	argc,
		char *	argv[]
	)

Definition at line 888 of file gfServer.c.

References canStop, dnaUtilOpen(), doMask, doTrans, FALSE, genoFindDirect(), genoPcrDirect(), getFileList(), gfCatchPipes(), gfPepMaxTileUse, logOpenFile(), logOpenSyslog(), maxAaSize, maxDnaHits, maxGap, maxNtSize, maxTransHits, minMatch, optionExists(), optionInit(), optionInt(), optionSpecs, optionVal(), pcrServer(), queryServer(), repMatch, round, sameWord, seqLog, startServer(), statusServer(), stepSize, stopServer(), tileSize, TRUE, and usage().

{
char *command;

gfCatchPipes();
dnaUtilOpen();
optionInit(&argc, argv, optionSpecs);
command = argv[1];
if (optionExists("trans"))
    {
    doTrans = TRUE;
    tileSize = 4;
    minMatch = 3;
    maxGap = 0;
    repMatch = gfPepMaxTileUse;
    }
tileSize = optionInt("tileSize", tileSize);
stepSize = optionInt("stepSize", stepSize);
if (stepSize == 0)
    stepSize = tileSize;
repMatch = round( (double)tileSize/(double)stepSize * repMatch);
minMatch = optionInt("minMatch", minMatch);
repMatch = optionInt("repMatch", repMatch);
maxDnaHits = optionInt("maxDnaHits", maxDnaHits);
maxTransHits = optionInt("maxTransHits", maxTransHits);
maxNtSize = optionInt("maxNtSize", maxNtSize);
maxAaSize = optionInt("maxAaSize", maxAaSize);
seqLog = optionExists("seqLog");
doMask = optionExists("mask");
canStop = optionExists("canStop");
if (argc < 2)
    usage();
if (optionExists("log"))
    logOpenFile(argv[0], optionVal("log", NULL));
if (optionExists("syslog"))
    logOpenSyslog(argv[0], optionVal("logFacility", NULL));

if (sameWord(command, "direct"))
    {
    if (argc < 4)
        usage();
    genoFindDirect(argv[2], argc-3, argv+3);
    }
else if (sameWord(command, "pcrDirect"))
    {
    if (argc < 5)
        usage();
    genoPcrDirect(argv[2], argv[3], argc-4, argv+4);
    }
else if (sameWord(command, "start"))
    {
    if (argc < 5)
        usage();
    startServer(argv[2], argv[3], argc-4, argv+4);
    }
else if (sameWord(command, "stop"))
    {
    if (argc != 4)
        usage();
    stopServer(argv[2], argv[3]);
    }
else if (sameWord(command, "query"))
    {
    if (argc != 5)
        usage();
    queryServer(command, argv[2], argv[3], argv[4], FALSE, FALSE);
    }
else if (sameWord(command, "protQuery"))
    {
    if (argc != 5)
        usage();
    queryServer(command, argv[2], argv[3], argv[4], TRUE, TRUE);
    }
else if (sameWord(command, "transQuery"))
    {
    if (argc != 5)
        usage();
    queryServer(command, argv[2], argv[3], argv[4], TRUE, FALSE);
    }
else if (sameWord(command, "pcr"))
    {
    if (argc != 7)
        usage();
    pcrServer(argv[2], argv[3], argv[4], argv[5], atoi(argv[6]));
    }
else if (sameWord(command, "status"))
    {
    if (argc != 4)
        usage();
    if (statusServer(argv[2], argv[3]))
        {
        exit(-1);
        }
    }
else if (sameWord(command, "files"))
    {
    if (argc != 4)
        usage();
    getFileList(argv[2], argv[3]);
    }
else
    {
    usage();
    }
return 0;
}

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static void pcrQuery	(	struct genoFind *	gf,
		char *	fPrimer,
		char *	rPrimer,
		int	maxDistance,
		int	connectionHandle
	)			[static]

Definition at line 355 of file gfServer.c.

References clock1000(), gfClumpFreeList(), gfPcrClumps(), logDebug(), netSendString(), gfClump::next, safef(), ss, gfClump::target, gfClump::tEnd, and gfClump::tStart.

Referenced by errorSafePcr().

{
int fPrimerSize = strlen(fPrimer);
int rPrimerSize = strlen(rPrimer);
struct gfClump *clumpList, *clump;
int clumpCount = 0;
char buf[256];

clumpList = gfPcrClumps(gf, fPrimer, fPrimerSize, rPrimer, rPrimerSize, 0, maxDistance);
for (clump = clumpList; clump != NULL; clump = clump->next)
    {
    struct gfSeqSource *ss = clump->target;
    safef(buf, sizeof(buf), "%s\t%d\t%d\t+", ss->fileName, 
        clump->tStart, clump->tEnd);
    netSendString(connectionHandle, buf);
    ++clumpCount;
    }
gfClumpFreeList(&clumpList);

clumpList = gfPcrClumps(gf, rPrimer, rPrimerSize, fPrimer, fPrimerSize, 0, maxDistance);

for (clump = clumpList; clump != NULL; clump = clump->next)
    {
    struct gfSeqSource *ss = clump->target;
    safef(buf, sizeof(buf), "%s\t%d\t%d\t-", ss->fileName, 
        clump->tStart, clump->tEnd);
    netSendString(connectionHandle, buf);
    ++clumpCount;
    }
gfClumpFreeList(&clumpList);
netSendString(connectionHandle, "end");
logDebug("%lu PCR %s %s %d clumps\n", clock1000(), fPrimer, rPrimer, clumpCount);
}

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void pcrServer	(	char *	hostName,
		char *	portName,
		char *	fPrimer,
		char *	rPrimer,
		int	maxSize
	)

Definition at line 831 of file gfServer.c.

References errAbort(), gfSignature(), netGetString(), netMustConnectTo(), sameString, and startsWith().

Referenced by main().

{
char buf[256];
int sd = 0;

/* Put together query command and send. */
sd = netMustConnectTo(hostName, portName);
sprintf(buf, "%spcr %s %s %d", gfSignature(), fPrimer, rPrimer, maxSize);
write(sd, buf, strlen(buf));

/* Fetch and display results. */
for (;;)
    {
    if (netGetString(sd, buf) == NULL)
        break;
    if (sameString(buf, "end"))
        break;
    else if (startsWith("Error:", buf))
        {
        errAbort(buf);
        break;
        }
    else
        {
        printf("%s\n", buf);
        }
    }
close(sd);
}

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void queryServer	(	char *	type,
		char *	hostName,
		char *	portName,
		char *	faName,
		boolean	complex,
		boolean	isProt
	)

Definition at line 775 of file gfServer.c.

References dnaSeq::dna, errAbort(), faReadSeq(), freeMem(), gfSignature(), netGetLongString(), netGetString(), netMustConnectTo(), netRecieveString(), sameString, dnaSeq::size, and startsWith().

Referenced by main().

{
char buf[256];
int sd = 0;
bioSeq *seq = faReadSeq(faName, !isProt);
int matchCount = 0;

/* Put together query command. */
sd = netMustConnectTo(hostName, portName);
sprintf(buf, "%s%s %d", gfSignature(), type, seq->size);
write(sd, buf, strlen(buf));

read(sd, buf, 1);
if (buf[0] != 'Y')
    errAbort("Expecting 'Y' from server, got %c", buf[0]);
write(sd, seq->dna, seq->size);

if (complex)
    {
    char *s = netRecieveString(sd, buf);
    printf("%s\n", s);
    }

for (;;)
    {
    if (netGetString(sd, buf) == NULL)
        break;
    if (sameString(buf, "end"))
        {
        printf("%d matches\n", matchCount);
        break;
        }
    else if (startsWith("Error:", buf))
       {
       errAbort(buf);
       break;
       }
    else
        {
        printf("%s\n", buf);
        if (complex)
            {
            char *s = netGetLongString(sd);
            if (s == NULL)
                break;
            printf("%s\n", s);
            freeMem(s);
            }
        }
    ++matchCount;
    }
close(sd);
}

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void startServer	(	char *	hostName,
		char *	portName,
		int	fileCount,
		char *	seqFiles[]
	)

Definition at line 481 of file gfServer.c.

References aaCount, aaFilter(), aaFilteredSize(), allowOneMismatch, badPcrPrimerSeq(), baseCount, blatCount, canStop, dnaSeq::dna, dnaFilter(), dnaFilteredSize(), doMask, doTrans, errno, errorSafePcr(), errorSafeQuery(), FALSE, faWriteNext(), freez(), gfIndexNibsAndTwoBits(), gfIndexTransNibsAndTwoBits(), gfReadMulti(), gfSignature(), gfVersion, logDebug(), logError(), logGetFile(), logInfo(), maxAaSize, maxGap, maxNtSize, minMatch, missCount, dnaSeq::name, needLargeMem(), netAcceptingSocket(), netBlockBrokenPipes(), netSendString(), nextWord(), noSigCount, pcrCount, repMatch, sameString, seqLog, dnaSeq::size, startsWith(), stepSize, tileSize, trimCount, uglyf, warn(), warnCount, and ZeroVar.

Referenced by main().

{
struct genoFind *gf = NULL;
static struct genoFind *transGf[2][3];
char buf[256];
char *line, *command;
socklen_t fromLen;
int readSize;
int socketHandle = 0, connectionHandle = 0;
int port = atoi(portName);
time_t curtime;
struct tm *loctime;
char timestr[256];

netBlockBrokenPipes();

curtime = time (NULL);           /* Get the current time. */
loctime = localtime (&curtime);  /* Convert it to local time representation. */
strftime (timestr, sizeof(timestr), "%Y-%m-%d %H:%M", loctime); /* formate datetime as string */
                                                                
logInfo("gfServer version %s on host %s, port %s  (%s)", gfVersion, 
        hostName, portName, timestr);
if (doTrans)
    {
    uglyf("starting translated server...\n");
    logInfo("setting up translated index");
    gfIndexTransNibsAndTwoBits(transGf, fileCount, seqFiles, 
        minMatch, maxGap, tileSize, repMatch, NULL, allowOneMismatch, 
        doMask, stepSize);
    }
else
    {
    uglyf("starting untranslated server...\n");
    logInfo("setting up untranslated index");
    gf = gfIndexNibsAndTwoBits(fileCount, seqFiles, minMatch, 
        maxGap, tileSize, repMatch, NULL, allowOneMismatch, stepSize);
    }
logInfo("indexing complete");

/* Set up socket.  Get ready to listen to it. */
socketHandle = netAcceptingSocket(port, 100);

logInfo("Server ready for queries!");
printf("Server ready for queries!\n");
for (;;)
    {
    connectionHandle = accept(socketHandle, NULL, &fromLen);
    if (connectionHandle < 0)
        {
        warn("Error accepting the connection");
        ++warnCount;
        continue;
        }
    readSize = read(connectionHandle, buf, sizeof(buf)-1);
    if (readSize < 0)
        {
        warn("Error reading from socket: %s", strerror(errno));
        ++warnCount;
        close(connectionHandle);
        continue;
        }
    if (readSize == 0)
        {
        warn("Zero sized query");
        ++warnCount;
        close(connectionHandle);
        continue;
        }
    buf[readSize] = 0;
    logDebug("%s", buf);
    if (!startsWith(gfSignature(), buf))
        {
        ++noSigCount;
        close(connectionHandle);
        continue;
        }
    line = buf + strlen(gfSignature());
    command = nextWord(&line);
    if (sameString("quit", command))
        {
        if (canStop)
            break;
        else
            logError("Ignoring quit message");
        }
    else if (sameString("status", command))
        {
        sprintf(buf, "version %s", gfVersion);
        netSendString(connectionHandle, buf);
        sprintf(buf, "type %s", (doTrans ? "translated" : "nucleotide"));
        netSendString(connectionHandle, buf);
        sprintf(buf, "host %s", hostName);
        netSendString(connectionHandle, buf);
        sprintf(buf, "port %s", portName);
        netSendString(connectionHandle, buf);
        sprintf(buf, "tileSize %d", tileSize);
        netSendString(connectionHandle, buf);
        sprintf(buf, "stepSize %d", stepSize);
        netSendString(connectionHandle, buf);
        sprintf(buf, "minMatch %d", minMatch);
        netSendString(connectionHandle, buf);
        sprintf(buf, "pcr requests %ld", pcrCount);
        netSendString(connectionHandle, buf);
        sprintf(buf, "blat requests %ld", blatCount);
        netSendString(connectionHandle, buf);
        sprintf(buf, "bases %ld", baseCount);
        netSendString(connectionHandle, buf);
        if (doTrans)
            {
            sprintf(buf, "aa %ld", aaCount);
            netSendString(connectionHandle, buf);
            }
        sprintf(buf, "misses %d", missCount);
        netSendString(connectionHandle, buf);
        sprintf(buf, "noSig %d", noSigCount);
        netSendString(connectionHandle, buf);
        sprintf(buf, "trimmed %d", trimCount);
        netSendString(connectionHandle, buf);
        sprintf(buf, "warnings %d", warnCount);
        netSendString(connectionHandle, buf);
        netSendString(connectionHandle, "end");
        }
    else if (sameString("query", command) || 
        sameString("protQuery", command) || sameString("transQuery", command))
        {
        boolean queryIsProt = sameString(command, "protQuery");
        char *s = nextWord(&line);
        if (s == NULL || !isdigit(s[0]))
            {
            warn("Expecting query size after query command");
            ++warnCount;
            }
        else
            {
            struct dnaSeq seq;
            ZeroVar(&seq);

            if (queryIsProt && !doTrans)
                {
                warn("protein query sent to nucleotide server");
                ++warnCount;
                queryIsProt = FALSE;
                }
            else
                {
                buf[0] = 'Y';
                if (write(connectionHandle, buf, 1) == 1)
                    {
                    seq.size = atoi(s);
                    seq.name = NULL;
                    if (seq.size > 0)
                        {
                        ++blatCount;
                        seq.dna = needLargeMem(seq.size+1);
                        if (gfReadMulti(connectionHandle, seq.dna, seq.size) != seq.size)
                            {
                            warn("Didn't sockRecieveString all %d bytes of query sequence", seq.size);
                            ++warnCount;
                            }
                        else
                            {
                            int maxSize = (doTrans ? maxAaSize : maxNtSize);

                            seq.dna[seq.size] = 0;
                            if (queryIsProt)
                                {
                                seq.size = aaFilteredSize(seq.dna);
                                aaFilter(seq.dna, seq.dna);
                                }
                            else
                                {
                                seq.size = dnaFilteredSize(seq.dna);
                                dnaFilter(seq.dna, seq.dna);
                                }
                            if (seq.size > maxSize)
                                {
                                ++trimCount;
                                seq.size = maxSize;
                                seq.dna[maxSize] = 0;
                                }
                            if (queryIsProt)
                                aaCount += seq.size;
                            else
                                baseCount += seq.size;
                            if (seqLog && (logGetFile() != NULL))
                                {
                                FILE *lf = logGetFile();
                                faWriteNext(lf, "query", seq.dna, seq.size);
                                fflush(lf);
                                }
                            errorSafeQuery(doTrans, queryIsProt, &seq, gf, 
                                    transGf, connectionHandle, buf);
                            }
                        freez(&seq.dna);
                        }
                    netSendString(connectionHandle, "end");
                    }
                }
            }
        }
    else if (sameString("pcr", command))
        {
        char *f = nextWord(&line);
        char *r = nextWord(&line);
        char *s = nextWord(&line);
        int maxDistance;
        ++pcrCount;
        if (s == NULL || !isdigit(s[0]))
            {
            warn("Badly formatted pcr command");
            ++warnCount;
            }
        else if (doTrans)
            {
            warn("Can't pcr on translated server");
            ++warnCount;
            }
        else if (badPcrPrimerSeq(f) || badPcrPrimerSeq(r))
            {
            warn("Can only handle ACGT in primer sequences.");
            ++warnCount;
            }
        else
            {
            maxDistance = atoi(s);
            errorSafePcr(gf, f, r, maxDistance, connectionHandle);
            }
        }
    else if (sameString("files", command))
        {
        int i;
        sprintf(buf, "%d", fileCount);
        netSendString(connectionHandle, buf);
        for (i=0; i<fileCount; ++i)
            {
            sprintf(buf, "%s", seqFiles[i]);
            netSendString(connectionHandle, buf);
            }
        }
    else
        {
        warn("Unknown command %s", command);
        ++warnCount;
        }
    close(connectionHandle);
    connectionHandle = 0;
    }
close(socketHandle);
}

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int statusServer	(	char *	hostName,
		char *	portName
	)

Definition at line 746 of file gfServer.c.

References gfSignature(), netGetString(), netMustConnectTo(), sameString, and warn().

Referenced by main().

{
char buf[256];
int sd = 0;
int ret = 0;

/* Put together command. */
sd = netMustConnectTo(hostName, portName);
sprintf(buf, "%sstatus", gfSignature());
write(sd, buf, strlen(buf));

for (;;)
    {
    if (netGetString(sd, buf) == NULL)
        {
        warn("Error reading status information from %s:%s",hostName,portName);
        ret = -1;
        break;
        }
    if (sameString(buf, "end"))
        break;
    else
        printf("%s\n", buf);
    }
close(sd);
return(ret); 
}

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void stopServer	(	char *	hostName,
		char *	portName
	)

Definition at line 733 of file gfServer.c.

References gfSignature(), and netMustConnectTo().

Referenced by main().

{
char buf[256];
int sd = 0;

sd = netMustConnectTo(hostName, portName);
sprintf(buf, "%squit", gfSignature());
write(sd, buf, strlen(buf));
close(sd);
printf("sent stop message to server\n");
}

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void transQuery	(	struct genoFind *	transGf[2][3],
		aaSeq *	seq,
		int	connectionHandle,
		char	buf[256]
	)

Definition at line 248 of file gfServer.c.

References clock1000(), dyStringClear, dyStringPrintf(), freeDyString(), gfClumpFreeList(), gfTransFindClumps(), gfClump::hitCount, gfClump::hitList, lm, lmCleanup(), lmInit(), logDebug(), maxTransHits, missCount, netSendLongString(), netSendString(), newDyString(), gfHit::next, gfClump::next, gfClump::qEnd, gfHit::qStart, gfClump::qStart, ss, gfClump::target, gfClump::tEnd, tileSize, gfHit::tStart, and gfClump::tStart.

Referenced by errorSafeQuery().

{
struct gfClump *clumps[3], *clump;
int isRc, frame;
char strand;
struct dyString *dy  = newDyString(1024);
struct gfHit *hit;
int clumpCount = 0, hitCount = 0, oneHit;
struct lm *lm = lmInit(0);

sprintf(buf, "tileSize %d", tileSize);
netSendString(connectionHandle, buf);
for (frame = 0; frame < 3; ++frame)
    clumps[frame] = NULL;
for (isRc = 0; isRc <= 1; ++isRc)
    {
    strand = (isRc ? '-' : '+');
    gfTransFindClumps(transGf[isRc], seq, clumps, lm, &oneHit);
    hitCount += oneHit;
    for (frame = 0; frame < 3; ++frame)
        {
        int limit = maxTransHits;
        for (clump = clumps[frame]; clump != NULL; clump = clump->next)
            {
            struct gfSeqSource *ss = clump->target;
            sprintf(buf, "%d\t%d\t%s\t%d\t%d\t%d\t%c\t%d", 
                clump->qStart, clump->qEnd, ss->fileName,
                clump->tStart-ss->start, clump->tEnd-ss->start, clump->hitCount,
                strand, frame);
            netSendString(connectionHandle, buf);
            dyStringClear(dy);
            for (hit = clump->hitList; hit != NULL; hit = hit->next)
                dyStringPrintf(dy, " %d %d", hit->qStart, hit->tStart - ss->start);
            netSendLongString(connectionHandle, dy->string);
            ++clumpCount;
            if (--limit < 0)
                break;
            }
        gfClumpFreeList(&clumps[frame]);
        }
    }
if (clumpCount == 0)
    ++missCount;
freeDyString(&dy);
lmCleanup(&lm);
logDebug("%lu %d clumps, %d hits", clock1000(), clumpCount, hitCount);
}

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void transTransQuery	(	struct genoFind *	transGf[2][3],
		struct dnaSeq *	seq,
		int	connectionHandle,
		char	buf[256]
	)

Definition at line 298 of file gfServer.c.

References clock1000(), dyStringClear, dyStringPrintf(), gfClumpFreeList(), gfTransTransFindClumps(), gfClump::hitCount, gfClump::hitList, lmCleanup(), lmInit(), logDebug(), maxTransHits, missCount, netSendLongString(), netSendString(), newDyString(), gfHit::next, gfClump::next, gfClump::qEnd, gfHit::qStart, gfClump::qStart, trans3::seq, ss, gfClump::target, gfClump::tEnd, tileSize, trans3::trans, trans3Free(), trans3New(), gfHit::tStart, and gfClump::tStart.

Referenced by errorSafeQuery().

{
struct gfClump *clumps[3][3], *clump;
int isRc, qFrame, tFrame;
char strand;
struct trans3 *t3 = trans3New(seq);
struct dyString *dy  = newDyString(1024);
struct gfHit *hit;
int clumpCount = 0, hitCount = 0, oneCount;

sprintf(buf, "tileSize %d", tileSize);
netSendString(connectionHandle, buf);
for (qFrame = 0; qFrame<3; ++qFrame)
    for (tFrame=0; tFrame<3; ++tFrame)
        clumps[qFrame][tFrame] = NULL;
for (isRc = 0; isRc <= 1; ++isRc)
    {
    struct lm *lm = lmInit(0);
    strand = (isRc ? '-' : '+');
    gfTransTransFindClumps(transGf[isRc], t3->trans, clumps, lm, &oneCount);
    hitCount += oneCount;
    for (qFrame = 0; qFrame<3; ++qFrame)
        {
        for (tFrame=0; tFrame<3; ++tFrame)
            {
            int limit = maxTransHits;
            for (clump = clumps[qFrame][tFrame]; clump != NULL; clump = clump->next)
                {
                struct gfSeqSource *ss = clump->target;
                sprintf(buf, "%d\t%d\t%s\t%d\t%d\t%d\t%c\t%d\t%d", 
                    clump->qStart, clump->qEnd, ss->fileName,
                    clump->tStart-ss->start, clump->tEnd-ss->start, clump->hitCount,
                    strand, qFrame, tFrame);
                netSendString(connectionHandle, buf);
                dyStringClear(dy);
                for (hit = clump->hitList; hit != NULL; hit = hit->next)
                    {
                    dyStringPrintf(dy, " %d %d", hit->qStart, hit->tStart - ss->start);
                    }
                netSendLongString(connectionHandle, dy->string);
                ++clumpCount;
                if (--limit < 0)
                    break;
                }
            gfClumpFreeList(&clumps[qFrame][tFrame]);
            }
        }
    lmCleanup(&lm);
    }
trans3Free(&t3);
if (clumpCount == 0)
    ++missCount;
logDebug("%lu %d clumps, %d hits", clock1000(), clumpCount, hitCount);
}

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void usage

(

)

Definition at line 63 of file gfServer.c.

References errAbort(), gfVersion, maxAaSize, maxDnaHits, maxNtSize, maxTransHits, and repMatch.

{
errAbort(
  "gfServer v %s - Make a server to quickly find where DNA occurs in genome.\n"
  "To set up a server:\n"
  "   gfServer start host port file(s)\n"
  "   Where the files are in .nib or .2bit format\n"
  "To remove a server:\n"
  "   gfServer stop host port\n"
  "To query a server with DNA sequence:\n"
  "   gfServer query host port probe.fa\n"
  "To query a server with protein sequence:\n"
  "   gfServer protQuery host port probe.fa\n"
  "To query a server with translated dna sequence:\n"
  "   gfServer transQuery host port probe.fa\n"
  "To query server with PCR primers\n"
  "   gfServer pcr host port fPrimer rPrimer maxDistance\n"
  "To process one probe fa file against a .nib format genome (not starting server):\n"
  "   gfServer direct probe.fa file(s).nib\n"
  "To test pcr without starting server:\n"
  "   gfServer pcrDirect fPrimer rPrimer file(s).nib\n"
  "To figure out usage level\n"
  "   gfServer status host port\n"
  "To get input file list\n"
  "   gfServer files host port\n"
  "Options:\n"
  "   -tileSize=N size of n-mers to index.  Default is 11 for nucleotides, 4 for\n"
  "               proteins (or translated nucleotides).\n"
  "   -stepSize=N spacing between tiles. Default is tileSize.\n"
  "   -minMatch=N Number of n-mer matches that trigger detailed alignment\n"
  "               Default is 2 for nucleotides, 3 for protiens.\n"
  "   -maxGap=N   Number of insertions or deletions allowed between n-mers.\n"
  "               Default is 2 for nucleotides, 0 for protiens.\n"
  "   -trans  Translate database to protein in 6 frames.  Note: it is best\n"
  "           to run this on RepeatMasked data in this case.\n"
  "   -log=logFile keep a log file that records server requests.\n"
  "   -seqLog    Include sequences in log file (not logged with -syslog)\n"
  "   -syslog    Log to syslog\n"
  "   -logFacility=facility log to the specified syslog facility - default local0.\n"
  "   -mask      Use masking from nib file.\n"
  "   -repMatch=N Number of occurrences of a tile (nmer) that trigger repeat masking the tile.\n"
  "               Default is %d.\n"
  "   -maxDnaHits=N Maximum number of hits for a dna query that are sent from the server.\n"
  "               Default is %d.\n"
  "   -maxTransHits=N Maximum number of hits for a translated query that are sent from the server.\n"
  "               Default is %d.\n"
  "   -maxNtSize=N Maximum size of untranslated DNA query sequence\n"
  "               Default is %d\n"
  "   -maxAsSize=N Maximum size of protein or translated DNA queries\n"
  "               Default is %d\n"
  "   -canStop If set then a quit message will actually take down the\n"
  "            server\n"
  ,     gfVersion, repMatch, maxDnaHits, maxTransHits, maxNtSize, maxAaSize
  );

}

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---

Variable Documentation

long aaCount = 0

Definition at line 212 of file gfServer.c.

Referenced by startServer().

boolean allowOneMismatch = FALSE

Definition at line 54 of file gfServer.c.

Referenced by genoFindDirect(), genoPcrDirect(), and startServer().

long baseCount = 0

Definition at line 212 of file gfServer.c.

Referenced by gfCountTilesInTwoBit(), gfIndexNibsAndTwoBits(), and startServer().

long blatCount = 0

Definition at line 212 of file gfServer.c.

Referenced by startServer().

boolean canStop = FALSE

Definition at line 61 of file gfServer.c.

Referenced by main(), and startServer().

boolean doMask = FALSE

Definition at line 60 of file gfServer.c.

Referenced by gfClientSeqList(), main(), and startServer().

boolean doTrans = FALSE

Definition at line 53 of file gfServer.c.

Referenced by genoFindDirect(), main(), and startServer().

jmp_buf gfRecover [static]

Definition at line 392 of file gfServer.c.

Referenced by errorSafePcr(), errorSafeQuery(), and gfAbort().

int maxAaSize = 8000

Definition at line 48 of file gfServer.c.

Referenced by main(), startServer(), and usage().

int maxDnaHits = 100

Definition at line 56 of file gfServer.c.

Referenced by dnaQuery(), main(), and usage().

int maxGap = gfMaxGap

Definition at line 58 of file gfServer.c.

int maxNtSize = 40000

Definition at line 47 of file gfServer.c.

Referenced by main(), startServer(), and usage().

int maxTransHits = 200

Definition at line 57 of file gfServer.c.

Referenced by main(), transQuery(), transTransQuery(), and usage().

int minMatch = gfMinMatch

Definition at line 50 of file gfServer.c.

int missCount = 0

Definition at line 215 of file gfServer.c.

Referenced by dnaQuery(), startServer(), transQuery(), and transTransQuery().

int noSigCount = 0

Definition at line 214 of file gfServer.c.

Referenced by startServer().

struct optionSpec optionSpecs[] [static]

Initial value:

 {
    {"canStop", OPTION_BOOLEAN},
    {"log", OPTION_STRING},
    {"logFacility", OPTION_STRING},
    {"mask", OPTION_BOOLEAN},
    {"maxAaSize", OPTION_INT},
    {"maxDnaHits", OPTION_INT},
    {"maxGap", OPTION_INT},
    {"maxNtSize", OPTION_INT},
    {"maxTransHits", OPTION_INT},
    {"minMatch", OPTION_INT},
    {"repMatch", OPTION_INT},
    {"seqLog", OPTION_BOOLEAN},
    {"stepSize", OPTION_INT},
    {"tileSize", OPTION_INT},
    {"trans", OPTION_BOOLEAN},
    {"syslog", OPTION_BOOLEAN},
    {NULL, 0}
}

Definition at line 26 of file gfServer.c.

long pcrCount = 0

Definition at line 212 of file gfServer.c.

Referenced by startServer().

char const rcsid[] = "$Id: gfServer.c,v 1.54 2007/03/31 19:38:13 markd Exp $" [static]

Definition at line 24 of file gfServer.c.

int repMatch = 1024

Definition at line 55 of file gfServer.c.

char* ripCord = NULL [static]

Definition at line 393 of file gfServer.c.

Referenced by errorSafeSetup(), and gfAbort().

struct sockaddr_in sai

Definition at line 209 of file gfServer.c.

boolean seqLog = FALSE

Definition at line 59 of file gfServer.c.

Referenced by main(), and startServer().

int stepSize = 0

Definition at line 52 of file gfServer.c.

int tileSize = gfTileSize

Definition at line 51 of file gfServer.c.

int trimCount = 0

Definition at line 216 of file gfServer.c.

Referenced by startServer(), and trimAlis().

int warnCount = 0

Definition at line 213 of file gfServer.c.

Referenced by startServer().

---