gfOutput Struct Reference

#include <genoFind.h>

Collaboration diagram for gfOutput:

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Data Fields
gfOutput *	next
void *	data
void(*	out )(char *chromName, int chromSize, int chromOffset, struct ffAli *ali, bioSeq *tSeq, struct hash *t3Hash, bioSeq *qSeq, boolean qIsRc, boolean tIsRc, enum ffStringency stringency, int minMatch, struct gfOutput *out)
void(*	queryOut )(struct gfOutput *out, FILE *f)
void(*	fileHead )(struct gfOutput *out, FILE *f)
boolean	reportTargetStrand
hash *	maskHash
int	minGood
boolean	qIsProt
boolean	tIsProt
int	queryIx
boolean	includeTargetFile

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Detailed Description

Definition at line 130 of file genoFind.h.

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Field Documentation

struct gfOutput* gfOutput::next [read]

Definition at line 133 of file genoFind.h.

void* gfOutput::data

Definition at line 134 of file genoFind.h.

Referenced by axtQueryOut(), blastQueryOut(), gfOutputAxtMem(), gfOutputBlast(), gfOutputPsl(), gfOutputSim4(), mafQueryOut(), pslOut(), saveAxtBundle(), and sim4QueryOut().

void(* gfOutput::out)(char *chromName, int chromSize, int chromOffset, struct ffAli *ali, bioSeq *tSeq, struct hash *t3Hash, bioSeq *qSeq, boolean qIsRc, boolean tIsRc, enum ffStringency stringency, int minMatch, struct gfOutput *out)

Referenced by gfOutputAny(), gfOutputAxt(), gfOutputAxtMem(), gfOutputBlast(), gfOutputFree(), gfOutputHead(), gfOutputInit(), gfOutputMaf(), gfOutputPsl(), gfOutputQuery(), gfOutputSim4(), and saveAlignments().

void(* gfOutput::queryOut)(struct gfOutput *out, FILE *f)

Referenced by gfOutputBlast(), and gfOutputSim4().

void(* gfOutput::fileHead)(struct gfOutput *out, FILE *f)

Referenced by bigBlat(), and gfOutputPsl().

boolean gfOutput::reportTargetStrand

Definition at line 169 of file genoFind.h.

Referenced by doBlat(), gfClient(), pslOut(), transTripleSearch(), and tripleSearch().

struct hash* gfOutput::maskHash [read]

Definition at line 170 of file genoFind.h.

Referenced by pslOut(), and searchOne().

int gfOutput::minGood

Definition at line 171 of file genoFind.h.

Referenced by pslOut().

boolean gfOutput::qIsProt

Definition at line 172 of file genoFind.h.

Referenced by blastQueryOut(), pslOut(), and saveAxtBundle().

boolean gfOutput::tIsProt

Definition at line 173 of file genoFind.h.

Referenced by pslOut().

int gfOutput::queryIx

Definition at line 174 of file genoFind.h.

Referenced by blastQueryOut().

boolean gfOutput::includeTargetFile

Definition at line 175 of file genoFind.h.

Referenced by doBlat(), gfAlignStrand(), gfAlignTrans(), and gfAlignTransTrans().

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The documentation for this struct was generated from the following file:

• inc/genoFind.h

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