inc/gfPcrLib.h File Reference

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Data Structures
struct	gfPcrInput
struct	gfPcrOutput
Functions
void	gfPcrInputStaticLoad (char **row, struct gfPcrInput *ret)
gfPcrInput *	gfPcrInputLoad (char **row)
gfPcrInput *	gfPcrInputLoadAll (char *fileName)
void	gfPcrInputFree (struct gfPcrInput **pEl)
void	gfPcrInputFreeList (struct gfPcrInput **pList)
void	gfPcrOutputFree (struct gfPcrOutput **pOut)
void	gfPcrOutputFreeList (struct gfPcrOutput **pList)
void	gfPcrLocal (char *pcrName, struct dnaSeq *seq, int seqOffset, char *seqName, int seqSize, int maxSize, char *fPrimer, int fPrimerSize, char *rPrimer, int rPrimerSize, int minPerfect, int minGood, char strand, struct gfPcrOutput **pOutList)
gfRange *	gfPcrGetRanges (char *host, char *port, char *fPrimer, char *rPrimer, int maxSize)
gfPcrOutput *	gfPcrViaNet (char *host, char *port, char *seqDir, struct gfPcrInput *inList, int maxSize, int minPerfect, int minGood)
void	gfPcrOutputWriteList (struct gfPcrOutput *outList, char *outType, char *url, FILE *f)
void	gfPcrOutputWriteAll (struct gfPcrOutput *outList, char *outType, char *url, char *fileName)
char *	gfPcrMakePrimer (char *s)

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Function Documentation

struct gfRange* gfPcrGetRanges	(	char *	host,
		char *	port,
		char *	fPrimer,
		char *	rPrimer,
		int	maxSize
	)			[read]

Definition at line 380 of file gfPcrLib.c.

References AllocVar, cloneString(), errAbort(), gfConnect(), gfSignature(), name, netGetString(), nextWord(), rangeList, safef(), sameString, slAddHead, slReverse(), and startsWith().

Referenced by gfPcrOneViaNet().

{
char buf[256];
int conn = gfConnect(host, port);
struct gfRange *rangeList = NULL, *range;

/* Query server and put results into rangeList. */
safef(buf, sizeof(buf), "%spcr %s %s %d", gfSignature(), fPrimer, rPrimer, maxSize);
write(conn, buf, strlen(buf));
for (;;)
    {
    if (netGetString(conn, buf) == NULL)
        break;
    if (sameString(buf, "end"))
        break;
    else if (startsWith("Error:", buf))
        errAbort(buf);
    else
        {
        char *s = buf;
        char *name, *start, *end, *strand;
        name = nextWord(&s);
        start = nextWord(&s);
        end = nextWord(&s);
        strand = nextWord(&s);
        if (strand == NULL)
            errAbort("Truncated gfServer response");
        AllocVar(range);
        range->tName = cloneString(name);
        range->tStart = atoi(start);
        range->tEnd = atoi(end);
        range->tStrand = strand[0];
        slAddHead(&rangeList, range);
        }
    }
close(conn);
slReverse(&rangeList);
return rangeList;
}

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void gfPcrInputFree

(

struct gfPcrInput **

pEl

)

Definition at line 89 of file gfPcrLib.c.

References gfPcrInput::fPrimer, freeMem(), freez(), gfPcrInput::name, and gfPcrInput::rPrimer.

Referenced by gfPcrInputFreeList().

{
struct gfPcrInput *el;

if ((el = *pEl) == NULL) return;
freeMem(el->name);
freeMem(el->fPrimer);
freeMem(el->rPrimer);
freez(pEl);
}

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void gfPcrInputFreeList

(

struct gfPcrInput **

pList

)

Definition at line 102 of file gfPcrLib.c.

References gfPcrInputFree(), and gfPcrInput::next.

{
struct gfPcrInput *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    gfPcrInputFree(&el);
    }
*pList = NULL;
}

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struct gfPcrInput* gfPcrInputLoad

(

char **

row

)

[read]

Definition at line 57 of file gfPcrLib.c.

References AllocVar, cloneString(), gfPcrInput::fPrimer, gfPcrInput::name, and gfPcrInput::rPrimer.

Referenced by gfPcrInputLoadAll().

{
struct gfPcrInput *ret;

AllocVar(ret);
ret->name = cloneString(row[0]);
ret->fPrimer = cloneString(row[1]);
ret->rPrimer = cloneString(row[2]);
return ret;
}

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struct gfPcrInput* gfPcrInputLoadAll

(

char *

fileName

)

[read]

Definition at line 70 of file gfPcrLib.c.

References gfPcrInputLoad(), lineFileClose(), lineFileOpen(), lineFileRow, slAddHead, slReverse(), and TRUE.

{
struct gfPcrInput *list = NULL, *el;
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *row[3];

while (lineFileRow(lf, row))
    {
    el = gfPcrInputLoad(row);
    slAddHead(&list, el);
    }
lineFileClose(&lf);
slReverse(&list);
return list;
}

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void gfPcrInputStaticLoad	(	char **	row,
		struct gfPcrInput *	ret
	)

Definition at line 48 of file gfPcrLib.c.

References gfPcrInput::fPrimer, gfPcrInput::name, and gfPcrInput::rPrimer.

{
ret->name = row[0];
ret->fPrimer = row[1];
ret->rPrimer = row[2];
}

void gfPcrLocal	(	char *	pcrName,
		struct dnaSeq *	seq,
		int	seqOffset,
		char *	seqName,
		int	seqSize,
		int	maxSize,
		char *	fPrimer,
		int	fPrimerSize,
		char *	rPrimer,
		int	rPrimerSize,
		int	minPerfect,
		int	minGood,
		char	strand,
		struct gfPcrOutput **	pOutList
	)

Definition at line 361 of file gfPcrLib.c.

References pcrLocalStrand().

Referenced by gfPcrOneViaNet().

{
/* For PCR primers reversing search strand just means switching
 * order of primers. */
if (strand == '-')
    pcrLocalStrand(pcrName, seq, seqOffset, seqName, seqSize, maxSize, 
        rPrimer, rPrimerSize, fPrimer, fPrimerSize, 
        minPerfect, minGood, strand, pOutList);
else
    pcrLocalStrand(pcrName, seq, seqOffset, seqName, seqSize, maxSize, 
        fPrimer, fPrimerSize, rPrimer, rPrimerSize, 
        minPerfect, minGood, strand, pOutList);
}

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char* gfPcrMakePrimer

(

char *

s

)

Definition at line 482 of file gfPcrLib.c.

References countChars(), dnaFilter(), dnaFilteredSize(), errAbort(), and needMem().

{
int size = dnaFilteredSize(s);
int realSize;
char *primer = needMem(size+1);
dnaFilter(s, primer);
realSize = size - countChars(primer, 'n');
if (realSize < 10 || realSize < size/2)
   errAbort("%s does not seem to be a good primer", s);
return primer;
}

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void gfPcrOutputFree

(

struct gfPcrOutput **

pOut

)

Definition at line 20 of file gfPcrLib.c.

References gfPcrOutput::dna, gfPcrOutput::fPrimer, freeMem(), freez(), gfPcrOutput::name, gfPcrOutput::rPrimer, and gfPcrOutput::seqName.

Referenced by gfPcrOutputFreeList().

{
struct gfPcrOutput *out = *pOut;
if (pOut != NULL)
    {
    freeMem(out->name);
    freeMem(out->fPrimer);
    freeMem(out->rPrimer);
    freeMem(out->seqName);
    freeMem(out->dna);
    freez(pOut);
    }
}

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void gfPcrOutputFreeList

(

struct gfPcrOutput **

pList

)

Definition at line 35 of file gfPcrLib.c.

References gfPcrOutputFree(), and gfPcrOutput::next.

{
struct gfPcrOutput *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    gfPcrOutputFree(&el);
    }
*pList = NULL;
}

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void gfPcrOutputWriteAll	(	struct gfPcrOutput *	outList,
		char *	outType,
		char *	url,
		char *	fileName
	)

Definition at line 275 of file gfPcrLib.c.

References carefulClose(), gfPcrOutputWriteList(), and mustOpen().

{
FILE *f = mustOpen(fileName, "w");
gfPcrOutputWriteList(outList, outType, url, f);
carefulClose(&f);
}

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void gfPcrOutputWriteList	(	struct gfPcrOutput *	outList,
		char *	outType,
		char *	url,
		FILE *	f
	)

Definition at line 255 of file gfPcrLib.c.

References errAbort(), gfPcrOutput::next, outputBed(), outputFa(), outputPsl(), and sameWord.

Referenced by gfPcrOutputWriteAll().

{
struct gfPcrOutput *out;
void (*output)(struct gfPcrOutput *out, FILE *f, char *url) = NULL;
if (sameWord(outType, "fa"))
    output = outputFa;
else if (sameWord(outType, "bed"))
    output = outputBed;
else if (sameWord(outType, "psl"))
    output = outputPsl;
else
    errAbort("Unrecognized pcr output type %s", outType);
for (out = outList; out != NULL; out = out->next)
    output(out, f, url);
}

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struct gfPcrOutput* gfPcrViaNet	(	char *	host,
		char *	port,
		char *	seqDir,
		struct gfPcrInput *	inList,
		int	maxSize,
		int	minPerfect,
		int	minGood
	)			[read]

Definition at line 462 of file gfPcrLib.c.

References gfPcrInput::fPrimer, gfFileCacheFree(), gfFileCacheNew(), gfPcrOneViaNet(), gfPcrInput::name, gfPcrInput::next, gfPcrInput::rPrimer, and slReverse().

{
struct hash *tFileCache = gfFileCacheNew();
struct gfPcrInput *in;
struct gfPcrOutput *outList = NULL;

for (in = inList; in != NULL; in = in->next)
    {
    gfPcrOneViaNet(host, port, seqDir,
        in->name, in->fPrimer, in->rPrimer, maxSize,
        minPerfect, minGood,
        tFileCache, &outList);
    }
gfFileCacheFree(&tFileCache);
slReverse(&outList);
return outList;
}

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