ffAli Struct Reference

#include <fuzzyFind.h>

Collaboration diagram for ffAli:

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Data Fields
ffAli *	left
ffAli *	right
char *	nStart
char *	nEnd
char *	hStart
char *	hEnd
int	startGood
int	endGood

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Detailed Description

Definition at line 51 of file fuzzyFind.h.

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Field Documentation

struct ffAli* ffAli::left [read]

Definition at line 56 of file fuzzyFind.h.

Referenced by addExtraHits(), cutAtBigIntrons(), dumpFf(), expandAlis(), expandLeft(), expandRight(), ffCat(), ffCdnaGapPenalty(), ffGapPenalty(), ffIntronOrientation(), ffMakeRightLinks(), ffMergeNeedleAlis(), ffOneIntronOrientation(), ffRemoveEmptyAlis(), ffScoreSomething(), ffShAliPart(), ffShNeedle(), ffSlideOrientedIntrons(), ffUnlink(), hardRefineSplice(), isMonotonic(), jiggleSmallExons(), lumpHits(), reconsiderAlignedGaps(), recursiveWeave(), saveAliToPermanentMem(), slideIntron(), smallMiddleExons(), smoothOneGap(), smoothSmallGaps(), ssFindBestBig(), ssGraphFindBest(), tradeMismatchToCloseSpliceGap(), and trimFlakyEnds().

struct ffAli* ffAli::right [read]

Definition at line 57 of file fuzzyFind.h.

Referenced by canAdd(), cdaAliFromFfAli(), countAlis(), cutAtBigIntrons(), dumpFf(), evalExactAli(), expandAlis(), expandGapless(), expandLeft(), expandRight(), ffAliCount(), ffAliSort(), ffCat(), ffCdnaGapPenalty(), ffCountGoodEnds(), ffFreeAli(), ffGapPenalty(), ffIntronOrientation(), ffMakeRightLinks(), ffMergeClose(), ffMergeHayOverlaps(), ffMergeNeedleAlis(), ffNextBreak(), ffOneIntronOrientation(), ffRemoveEmptyAlis(), ffRightmost(), ffScoreSomeAlis(), ffScoreSomething(), ffShAliPart(), ffShNeedle(), ffSlideOrientedIntrons(), ffUnlink(), findFromSmallerSeeds(), hardRefineSplice(), isMonotonic(), jiggleSmallExons(), lumpHits(), pslFromFakeFfAli(), reconsiderAlignedGaps(), recursiveWeave(), refineSpliceSites(), rwFindTilesBetween(), saveAliToPermanentMem(), saveAxtBundle(), savePslx(), scanForTinyInternal(), scanIndexForSmallExons(), scoreAli(), slideIntron(), smallMiddleExons(), smoothOneGap(), smoothSmallGaps(), ssFindBestBig(), ssGraphFindBest(), ssGraphMake(), tradeMismatchToCloseSpliceGap(), trimAlis(), trimFlakyEnds(), and weaveAli().

char* ffAli::nStart

Definition at line 58 of file fuzzyFind.h.

Referenced by addExtraHits(), bafSetAli(), bandExtBefore(), bandExtFf(), canAdd(), cdaAliFromFfAli(), countGoodEnd(), countGoodStart(), dumpFf(), evalExactAli(), expandAlis(), expandGapless(), expandLeft(), expandThroughNLeft(), ffCdnaGapPenalty(), ffCmpHitsHayFirst(), ffCmpHitsNeedleFirst(), ffExpandExactLeft(), ffGapPenalty(), ffMergeClose(), ffMergeHayOverlaps(), ffMergeNeedleAlis(), ffNextBreak(), ffOneIntronOrientation(), ffRemoveEmptyAlis(), ffScoreSomeAlis(), ffScoreSomething(), ffShAliPart(), ffShNeedle(), findCrossover(), hardRefineSplice(), isMonotonic(), jiggleSmallExons(), leftGood(), leftNextMatch(), lumpHits(), mergeProtoGenes(), pslFromFakeFfAli(), pslToFakeFfAli(), pslToFfAli(), reconsiderAlignedGaps(), refineSpliceSites(), rightGood(), rightNextMatch(), saveAxtBundle(), savePslx(), scanIndexForSmallExons(), scoreAli(), slideIntron(), smallMiddleExons(), smoothOneGap(), ssFindBestBig(), ssGraphFindBest(), ssGraphMake(), tradeMismatchToCloseSpliceGap(), trimAlis(), trimFlakyEnds(), tripleCanFollow(), and weaveAli().

char * ffAli::nEnd

Definition at line 58 of file fuzzyFind.h.

Referenced by addExtraHits(), bandExtAfter(), bandExtFf(), canAdd(), cdaAliFromFfAli(), countGoodEnd(), countGoodStart(), dumpFf(), evalExactAli(), expandAlis(), expandGapless(), expandRight(), expandThroughNRight(), ffAliFromSym(), ffCdnaGapPenalty(), ffExpandExactRight(), ffGapPenalty(), ffMergeClose(), ffMergeHayOverlaps(), ffMergeNeedleAlis(), ffNextBreak(), ffOneIntronOrientation(), ffRemoveEmptyAlis(), ffShAliPart(), ffShNeedle(), hardRefineSplice(), isMonotonic(), jiggleSmallExons(), leftGood(), leftNextMatch(), lumpHits(), mergeProtoGenes(), pslFromFakeFfAli(), reconsiderAlignedGaps(), recursiveWeave(), refineSpliceSites(), rightGood(), rightNextMatch(), saveAxtBundle(), savePslx(), scanIndexForSmallExons(), scoreAli(), slideIntron(), smallMiddleExons(), smoothOneGap(), ssConnectCost(), ssFindBestBig(), ssGraphFindBest(), ssGraphMake(), tradeMismatchToCloseSpliceGap(), trimAlis(), trimFlakyEnds(), tripleCanFollow(), and weaveAli().

char* ffAli::hStart

Definition at line 59 of file fuzzyFind.h.

Referenced by addExtraHits(), bafSetAli(), bandExtBefore(), bandExtFf(), canAdd(), cdaAliFromFfAli(), countGoodStart(), cutAtBigIntrons(), dumpFf(), expandAlis(), expandGapless(), expandLeft(), expandThroughNLeft(), ffCdnaGapPenalty(), ffCmpHitsHayFirst(), ffCmpHitsNeedleFirst(), ffExpandExactLeft(), ffGapPenalty(), ffMergeClose(), ffMergeHayOverlaps(), ffMergeNeedleAlis(), ffNextBreak(), ffOneIntronOrientation(), ffRemoveEmptyAlis(), ffScoreSomeAlis(), ffScoreSomething(), ffShAliPart(), ffShNeedle(), findCrossover(), hardRefineSplice(), isMonotonic(), jiggleSmallExons(), leftGood(), leftNextMatch(), lumpHits(), mergeProtoGenes(), pslFromFakeFfAli(), reconsiderAlignedGaps(), refineSpliceSites(), rightNextMatch(), saveAxtBundle(), savePslx(), scanExactLeft(), scoreAli(), slideIntron(), smallMiddleExons(), smoothOneGap(), ssConnectCost(), ssFindBestBig(), ssGraphFindBest(), ssGraphMake(), tradeMismatchToCloseSpliceGap(), trimAlis(), trimFlakyEnds(), tripleCanFollow(), and weaveAli().

char * ffAli::hEnd

Definition at line 59 of file fuzzyFind.h.

Referenced by addExtraHits(), bandExtAfter(), bandExtFf(), canAdd(), cdaAliFromFfAli(), countGoodEnd(), cutAtBigIntrons(), dumpFf(), expandAlis(), expandGapless(), expandRight(), expandThroughNRight(), ffCdnaGapPenalty(), ffExpandExactRight(), ffGapPenalty(), ffIntronOrientation(), ffMergeClose(), ffMergeHayOverlaps(), ffMergeNeedleAlis(), ffNextBreak(), ffOneIntronOrientation(), ffRemoveEmptyAlis(), ffScoreSomeAlis(), ffScoreSomething(), ffShAliPart(), findCrossover(), hardRefineSplice(), isMonotonic(), jiggleSmallExons(), leftNextMatch(), lumpHits(), mergeProtoGenes(), pslFromFakeFfAli(), reconsiderAlignedGaps(), recursiveWeave(), refineSpliceSites(), rightGood(), rightNextMatch(), saveAxtBundle(), savePslx(), scanExactRight(), scanIndexForSmallExons(), scoreAli(), slideIntron(), smallMiddleExons(), smoothOneGap(), ssConnectCost(), ssFindBestBig(), ssGraphFindBest(), ssGraphMake(), tradeMismatchToCloseSpliceGap(), trimAlis(), trimFlakyEnds(), tripleCanFollow(), and weaveAli().

int ffAli::startGood

Definition at line 60 of file fuzzyFind.h.

Referenced by ffCountGoodEnds().

int ffAli::endGood

Definition at line 60 of file fuzzyFind.h.

Referenced by ffCountGoodEnds().

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

• inc/fuzzyFind.h

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