genoFind Struct Reference

#include <genoFind.h>

Collaboration diagram for genoFind:

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Data Fields
int	maxPat
int	minMatch
int	maxGap
int	tileSize
int	stepSize
int	tileSpaceSize
int	tileMask
int	sourceCount
gfSeqSource *	sources
bool	isPep
bool	allowOneMismatch
int	segSize
bits32	totalSeqSize
bits32 *	listSizes
void *	allocated
bits32 **	lists
bits16 **	endLists

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Detailed Description

Definition at line 88 of file genoFind.h.

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Field Documentation

int genoFind::maxPat

Definition at line 91 of file genoFind.h.

Referenced by gfAddSeq(), gfAllocLists(), gfCountSeq(), gfNewEmpty(), gfZeroNonOverused(), gfZeroOverused(), and maskSimplePepRepeat().

int genoFind::minMatch

Definition at line 93 of file genoFind.h.

Referenced by gfFindClumpsWithQmask(), gfNewEmpty(), and targetClump().

int genoFind::maxGap

Definition at line 95 of file genoFind.h.

Referenced by clumpHits(), and gfNewEmpty().

int genoFind::tileSize

Definition at line 96 of file genoFind.h.

Referenced by clumpHits(), clumpNear(), dnaQuery(), fastMapClumpsToBundles(), ffSeedExtInMem(), gfAddLargeSeq(), gfAddSeq(), gfAddTilesInNib(), gfAlignSomeClumps(), gfCountSeq(), gfCountTilesInNib(), gfFastFindDnaHits(), gfFindAlignAaTrans(), gfFindClumpsWithQmask(), gfIndexNibsAndTwoBits(), gfNewEmpty(), gfSegmentedFindHits(), gfSegmentedFindNearHits(), gfStraightFindHits(), gfStraightFindNearHits(), gfTransTransFindBundles(), maskSimplePepRepeat(), pcrClumps(), refineBundle(), scanIndexForSmallExons(), and targetClump().

int genoFind::stepSize

Definition at line 97 of file genoFind.h.

Referenced by dnaQuery(), gfAddLargeSeq(), gfAddSeq(), gfCountSeq(), and gfNewEmpty().

int genoFind::tileSpaceSize

Definition at line 98 of file genoFind.h.

Referenced by gfAllocLargeLists(), gfAllocLists(), gfMakeOoc(), gfNewEmpty(), gfZeroNonOverused(), and gfZeroOverused().

int genoFind::tileMask

Definition at line 99 of file genoFind.h.

Referenced by gfFastFindDnaHits(), and gfNewEmpty().

int genoFind::sourceCount

Definition at line 100 of file genoFind.h.

Referenced by findSource(), genoFindFree(), gfFindNamedSource(), and gfIndexNibsAndTwoBits().

struct gfSeqSource* genoFind::sources [read]

Definition at line 101 of file genoFind.h.

Referenced by findSource(), genoFindFree(), gfFindNamedSource(), and gfIndexNibsAndTwoBits().

bool genoFind::isPep

Definition at line 102 of file genoFind.h.

Referenced by clumpHits(), clumpNear(), gfAddLargeSeq(), gfAddSeq(), gfCountSeq(), gfFindHitsWithQmask(), gfNewEmpty(), gfPcrClumps(), gfSegmentedFindHits(), gfSegmentedFindNearHits(), gfStraightFindHits(), and gfStraightFindNearHits().

bool genoFind::allowOneMismatch

Definition at line 103 of file genoFind.h.

Referenced by gfFindHitsWithQmask(), and gfNewEmpty().

int genoFind::segSize

Definition at line 104 of file genoFind.h.

Referenced by gfAddLargeSeq(), gfCountSeq(), gfFindHitsWithQmask(), gfIndexSeq(), gfMakeOoc(), gfNewEmpty(), gfPcrClumps(), gfSegmentedFindHits(), and gfSegmentedFindNearHits().

bits32 genoFind::totalSeqSize

Definition at line 105 of file genoFind.h.

Referenced by clumpHits(), gfIndexNibsAndTwoBits(), and gfIndexTransNibsAndTwoBits().

bits32* genoFind::listSizes

Definition at line 106 of file genoFind.h.

Referenced by genoFindFree(), gfAddLargeSeq(), gfAddSeq(), gfAllocLargeLists(), gfAllocLists(), gfCountSeq(), gfFastFindDnaHits(), gfMakeOoc(), gfNewEmpty(), gfSegmentedFindHits(), gfSegmentedFindNearHits(), gfStraightFindHits(), gfStraightFindNearHits(), gfZeroNonOverused(), gfZeroOverused(), maskSimplePepRepeat(), and pcrClumps().

void* genoFind::allocated

Definition at line 107 of file genoFind.h.

Referenced by genoFindFree(), gfAllocLargeLists(), and gfAllocLists().

bits32** genoFind::lists

Definition at line 108 of file genoFind.h.

Referenced by genoFindFree(), gfAddSeq(), gfAllocLists(), gfFastFindDnaHits(), gfNewEmpty(), gfStraightFindHits(), gfStraightFindNearHits(), and pcrClumps().

bits16** genoFind::endLists

Definition at line 110 of file genoFind.h.

Referenced by gfAddLargeSeq(), gfAllocLargeLists(), gfNewEmpty(), gfSegmentedFindHits(), and gfSegmentedFindNearHits().

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

• inc/genoFind.h

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