dnaSeq Struct Reference

#include <dnaseq.h>

Collaboration diagram for dnaSeq:

[legend]

Data Fields
dnaSeq *	next
char *	name
DNA *	dna
int	size
Bits *	mask

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Detailed Description

Definition at line 17 of file dnaseq.h.

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Field Documentation

struct dnaSeq* dnaSeq::next [read]

Definition at line 20 of file dnaseq.h.

Referenced by bigBlat(), blat(), dnaMark0(), dnaMark1(), dnaMarkTriple(), dnaSeqHash(), doBlat(), faReadAllIntoHash(), faWriteAll(), freeDnaSeqList(), gfClientSeqList(), gfClientUnmask(), gfLargeIndexSeq(), gfMakeOoc(), gfSmallIndexSeq(), makePatSpace(), maskFromOut(), maskNucSeqList(), and seqListToTrans3List().

char* dnaSeq::name

Definition at line 21 of file dnaseq.h.

Referenced by addToBigBundleList(), axtAffine(), axtAffine2Level(), blat(), cloneDnaSeq(), clumpTargetName(), clumpToExactRange(), clumpToHspRange(), dnaLoadSingle(), dnaSeqHash(), doBlat(), faReadAllIntoHash(), faWriteAll(), freeDnaSeq(), genoFindDirect(), gfAlignSomeClumps(), gfClient(), gfFindAlignAaTrans(), gfFindNamedSource(), gfServerWarn(), loadHashT3Ranges(), maskFromOut(), maskQuerySeq(), nextSeqFromMem(), nibInput(), refineBundle(), saveAlignments(), saveAxtBundle(), savePslx(), searchOneIndex(), ssFindBestBig(), ssFindBundles(), startServer(), trans3New(), translateSeqN(), twoBitFromDnaSeq(), twoBitReadSeqFragExt(), and untranslateRangeList().

DNA* dnaSeq::dna

Definition at line 22 of file dnaseq.h.

Referenced by addExtraHits(), addToPatSpace(), alignComponents(), axtAffine(), axtAffine2Level(), axtFromBlocks(), bandedExtend(), bigBlat(), cBlockFindCrossover(), chainCalcScore(), chainCalcScoreSubChain(), cloneDnaSeq(), clumpToExactRange(), clumpToHspRange(), countPatSpace(), dnaLoadNextFromStack(), dnaMark0(), dnaMark1(), dnaMarkTriple(), doBlat(), dumpBuns(), expandGapless(), faReadAllMixableInLf(), faWriteAll(), fillInMatchEtc(), freeDnaSeq(), genoFindDirect(), gfAddLargeSeq(), gfAddSeq(), gfClient(), gfClientUnmask(), gfCountSeq(), gfFastFindDnaHits(), gfiExpandAndLoadCached(), gfMakeOoc(), gfRangesToFfItem(), gfSegmentedFindHits(), gfSegmentedFindNearHits(), gfStraightFindHits(), gfStraightFindNearHits(), maskFromOut(), maskFromUpperCaseSeq(), maskNucSeqList(), maskQuerySeq(), nextSeqFromMem(), nibInput(), nibOutput(), pcrLocalStrand(), pslHasIntron(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslToFfAli(), pslWeightedIntronOrientation(), queryServer(), rangeScore(), readMaskedNib(), readMaskedTwoBit(), saveAxtBundle(), savePslx(), scanForSmallerExons(), scanIndexForSmallExons(), searchOne(), searchOneIndex(), seqIsDna(), seqIsLower(), ssFindBestBig(), ssFindBundles(), ssStitch(), startSeqQuery(), startServer(), trans3GenoPos(), trans3Offset(), trans3Offsets(), transCountBothStrands(), transIndexBothStrands(), translateSeqN(), transTripleSearch(), trimSeq(), twoBitFromDnaSeq(), twoBitReadSeqFragExt(), and whichSeqIn().

int dnaSeq::size

Definition at line 23 of file dnaseq.h.

Referenced by addExtraHits(), addToPatSpace(), axtAffine(), axtAffine2Level(), bandedExtend(), bigBlat(), blat(), cBlockFindCrossover(), cloneDnaSeq(), clumpToExactRange(), clumpToHspRange(), countPatSpace(), dnaLoadNextFromStack(), dnaLoadSingle(), dnaMark0(), dnaMark1(), dnaMarkTriple(), dnaQuery(), doBlat(), doDetailLine(), expandGapless(), faReadAllMixableInLf(), faSomeSpeedReadNext(), faWriteAll(), fixBlockSize(), genoFindDirect(), gfAddLargeSeq(), gfAddSeq(), gfAlignSomeClumps(), gfAlignStrand(), gfAlignTrans(), gfAlignTransTrans(), gfClient(), gfClientUnmask(), gfClumpsToBundles(), gfCountSeq(), gfFastFindDnaHits(), gfFindAlignAaTrans(), gfFindClumpsWithQmask(), gfiExpandAndLoadCached(), gfIndexNibsAndTwoBits(), gfIndexTransNibsAndTwoBits(), gfLongDnaInMem(), gfLongTransTransInMem(), gfMakeOoc(), gfSegmentedFindHits(), gfSegmentedFindNearHits(), gfStraightFindHits(), gfStraightFindNearHits(), makePatSpace(), maskFromOut(), maskFromUpperCaseSeq(), maskNucSeqList(), maskQuerySeq(), newClump(), nextSeqFromMem(), nibInput(), nibOutput(), pcrLocalStrand(), pslShowAlignmentStranded(), pslShowAlignmentStranded2(), pslToFfAli(), queryServer(), readMaskedNib(), readMaskedTwoBit(), saveAlignments(), saveAxtBundle(), savePslx(), scanForSmallerExons(), scanIndexForSmallExons(), searchOne(), searchOneIndex(), searchOneMaskTrim(), seqIsDna(), seqIsLower(), ssFindBestBig(), ssFindBundles(), startSeqQuery(), startServer(), trans3New(), trans3Offset(), trans3Offsets(), transCountBothStrands(), transIndexBothStrands(), translateSeqN(), transTripleSearch(), trimSeq(), twoBitFromDnaSeq(), twoBitReadSeqFragExt(), and whichSeqIn().

Bits* dnaSeq::mask

Definition at line 24 of file dnaseq.h.

Referenced by cloneDnaSeq(), freeDnaSeq(), nibInput(), and nibOutput().

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

• inc/dnaseq.h

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