gfClump Struct Reference

#include <genoFind.h>

Collaboration diagram for gfClump:

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Data Fields
gfClump *	next
bits32	qStart
bits32	qEnd
gfSeqSource *	target
bits32	tStart
bits32	tEnd
int	hitCount
gfHit *	hitList
int	queryCoverage

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Detailed Description

Definition at line 65 of file genoFind.h.

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Field Documentation

struct gfClump* gfClump::next [read]

Definition at line 73 of file genoFind.h.

Referenced by clumpHits(), dnaQuery(), fastMapClumpsToBundles(), ffSeedExtInMem(), genoFindDirect(), genoPcrDirect(), gfAlignSomeClumps(), gfAlignTrans(), gfAlignTransTrans(), gfClumpComputeQueryCoverage(), gfClumpFreeList(), gfFindAlignAaTrans(), gfTransTransFindBundles(), pcrQuery(), seqClumpToRangeList(), transQuery(), and transTransQuery().

bits32 gfClump::qStart

Definition at line 74 of file genoFind.h.

Referenced by findClumpBounds(), gfClumpDump(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), seqClumpToRangeList(), transQuery(), and transTransQuery().

bits32 gfClump::qEnd

Definition at line 74 of file genoFind.h.

Referenced by findClumpBounds(), gfClumpDump(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), seqClumpToRangeList(), transQuery(), and transTransQuery().

struct gfSeqSource* gfClump::target [read]

Definition at line 75 of file genoFind.h.

Referenced by clumpTargetName(), clumpToExactRange(), clumpToHspRange(), genoPcrDirect(), gfAlignTrans(), gfAlignTransTrans(), gfClumpDump(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), pcrQuery(), seqClumpToRangeList(), targetClump(), transQuery(), and transTransQuery().

bits32 gfClump::tStart

Definition at line 76 of file genoFind.h.

Referenced by findClumpBounds(), genoPcrDirect(), gfAlignTrans(), gfAlignTransTrans(), gfClumpDump(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), pcrQuery(), seqClumpToRangeList(), targetClump(), transQuery(), and transTransQuery().

bits32 gfClump::tEnd

Definition at line 76 of file genoFind.h.

Referenced by findClumpBounds(), genoPcrDirect(), gfAlignTrans(), gfAlignTransTrans(), gfClumpDump(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), pcrQuery(), seqClumpToRangeList(), targetClump(), transQuery(), and transTransQuery().

int gfClump::hitCount

Definition at line 77 of file genoFind.h.

Referenced by dnaQuery(), gfClumpDump(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), gfTransFindClumps(), gfTransTransFindClumps(), transQuery(), and transTransQuery().

struct gfHit* gfClump::hitList [read]

Definition at line 78 of file genoFind.h.

Referenced by clumpToExactRange(), clumpToHspRange(), findClumpBounds(), gfClumpComputeQueryCoverage(), gfClumpDump(), gfQuerySeqTrans(), gfQuerySeqTransTrans(), targetClump(), transQuery(), and transTransQuery().

int gfClump::queryCoverage

Definition at line 79 of file genoFind.h.

Referenced by gfClumpCmpQueryCoverage(), and gfClumpComputeQueryCoverage().

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

• inc/genoFind.h

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