lib/mafFromAxt.c File Reference

#include "common.h"
#include "axt.h"
#include "maf.h"

Include dependency graph for mafFromAxt.c:

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Functions
void	mafFromAxtTemp (struct axt *axt, int tSize, int qSize, struct mafAli *temp)
mafAli *	mafFromAxt (struct axt *axt, int tSize, char *tPrefix, int qSize, char *qPrefix)
Variables
static char const	rcsid [] = "$Id: mafFromAxt.c,v 1.4 2003/05/17 23:47:15 kent Exp $"

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Function Documentation

struct mafAli* mafFromAxt	(	struct axt *	axt,
		int	tSize,
		char *	tPrefix,
		int	qSize,
		char *	qPrefix
	)			[read]

Definition at line 38 of file mafFromAxt.c.

References AllocVar, cloneString(), cloneStringZ(), mafAli::components, name, axt::qEnd, axt::qName, axt::qStart, axt::qStrand, axt::qSym, safef(), axt::score, mafAli::score, mafComp::size, slAddHead, mafComp::src, mafComp::srcSize, mafComp::start, mafComp::strand, axt::symCount, axt::tEnd, mafComp::text, mafAli::textSize, axt::tName, axt::tStart, axt::tStrand, and axt::tSym.

{
struct mafAli *maf;
struct mafComp *mc;
char name[256];
AllocVar(maf);
maf->score = axt->score;
maf->textSize = axt->symCount;
AllocVar(mc);
if (qPrefix == NULL)
    mc->src = cloneString(axt->qName);
else
    {
    safef(name, sizeof(name), "%s.%s", qPrefix, axt->qName);
    mc->src = cloneString(name);
    }
mc->srcSize = qSize;
mc->strand = axt->qStrand;
mc->start = axt->qStart;
mc->size = axt->qEnd - axt->qStart;
mc->text = cloneStringZ(axt->qSym, axt->symCount);
slAddHead(&maf->components, mc);
AllocVar(mc);
if (tPrefix == NULL)
    mc->src = cloneString(axt->tName);
else
    {
    safef(name, sizeof(name), "%s.%s", tPrefix, axt->tName);
    mc->src = cloneString(name);
    }
mc->srcSize = tSize;
mc->strand = axt->tStrand;
mc->start = axt->tStart;
mc->size = axt->tEnd - axt->tStart;
mc->text = cloneStringZ(axt->tSym, axt->symCount);
slAddHead(&maf->components, mc);
return maf;
}

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void mafFromAxtTemp	(	struct axt *	axt,
		int	tSize,
		int	qSize,
		struct mafAli *	temp
	)

Definition at line 8 of file mafFromAxt.c.

References mafAli::components, axt::qEnd, axt::qName, axt::qStart, axt::qStrand, axt::qSym, axt::score, mafAli::score, mafComp::size, slAddHead, mafComp::src, mafComp::srcSize, mafComp::start, mafComp::strand, axt::symCount, axt::tEnd, mafComp::text, mafAli::textSize, axt::tName, axt::tStart, axt::tStrand, axt::tSym, and ZeroVar.

Referenced by mafQueryOut().

{
static struct mafComp qComp, tComp;
ZeroVar(temp);
ZeroVar(&qComp);
ZeroVar(&tComp);
temp->score = axt->score;
temp->textSize = axt->symCount;
qComp.src = axt->qName;
qComp.srcSize = qSize;
qComp.strand = axt->qStrand;
qComp.start = axt->qStart;
qComp.size = axt->qEnd - axt->qStart;
qComp.text = axt->qSym;
slAddHead(&temp->components, &qComp);
tComp.src = axt->tName;
tComp.srcSize = tSize;
tComp.strand = axt->tStrand;
tComp.start = axt->tStart;
tComp.size = axt->tEnd - axt->tStart;
tComp.text = axt->tSym;
slAddHead(&temp->components, &tComp);
}

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Variable Documentation

char const rcsid[] = "$Id: mafFromAxt.c,v 1.4 2003/05/17 23:47:15 kent Exp $" [static]

Definition at line 6 of file mafFromAxt.c.

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