ungappedExtension Struct Reference

#include <global.h>

Collaboration diagram for ungappedExtension:

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Data Fields
coordinate	start
coordinate	end
coordinate	seed
int4	nominalScore
char	status
ungappedExtension *	next

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Detailed Description

Definition at line 42 of file global.h.

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Field Documentation

struct coordinate ungappedExtension::start [read]

Definition at line 44 of file global.h.

Referenced by alignments_checkForJoin(), alignments_contains(), alignments_pruneRegion(), bytepackGappedScoring_score(), fasterGappedExtension_build(), fasterGappedExtension_prune(), gappedExtension_build(), gappedExtension_prune(), gappedScoring_score(), nuGappedScoring_score(), oldGappedScoring_score(), oldSemiGappedScoring_score(), semiGappedScoring_score(), tableGappedScoring_score(), ungappedExtension_extend(), ungappedExtension_nucleotideExtend(), ungappedExtension_oneHitExtend(), ungappedExtension_print(), ungappedExtension_simpleScoring(), and unpack_getRegions().

struct coordinate ungappedExtension::end [read]

Definition at line 45 of file global.h.

Referenced by alignments_checkForJoin(), alignments_contains(), alignments_pruneRegion(), bytepackGappedScoring_score(), fasterGappedExtension_build(), fasterGappedExtension_prune(), gappedExtension_build(), gappedExtension_prune(), gappedScoring_score(), nuGappedScoring_score(), oldGappedScoring_score(), oldSemiGappedScoring_score(), semiGappedScoring_score(), tableGappedScoring_score(), ungappedExtension_extend(), ungappedExtension_nucleotideExtend(), ungappedExtension_oneHitExtend(), ungappedExtension_print(), and unpack_getRegions().

struct coordinate ungappedExtension::seed [read]

Definition at line 46 of file global.h.

Referenced by alignments_getTracebacks(), alignments_selectRegion(), bytepackGappedScoring_score(), fasterGappedExtension_build(), gappedExtension_build(), gappedScoring_score(), nuGappedScoring_score(), oldGappedScoring_score(), oldSemiGappedScoring_score(), semiGappedScoring_score(), tableGappedScoring_score(), ungappedExtension_extend(), ungappedExtension_findSeed(), ungappedExtension_nucleotideExtend(), ungappedExtension_oneHitExtend(), ungappedExtension_print(), and unpack_getRegions().

int4 ungappedExtension::nominalScore

Definition at line 47 of file global.h.

Referenced by alignments_addUngappedExtension(), alignments_checkForJoin(), alignments_contains(), alignments_findFinalAlignments(), alignments_findTopFinalAlignments(), alignments_getTracebacks(), alignments_pruneRegion(), alignments_regularGappedAlignment(), bytepackGappedScoring_score(), fasterGappedExtension_build(), gappedExtension_build(), tableGappedScoring_score(), ungappedExtension_extend(), ungappedExtension_nucleotideExtend(), ungappedExtension_oneHitExtend(), and ungappedExtension_print().

char ungappedExtension::status

Definition at line 48 of file global.h.

Referenced by alignments_checkForJoin(), alignments_findFinalAlignments(), alignments_findGoodAlignments(), alignments_findTopFinalAlignments(), alignments_getTracebacks(), alignments_pruneRegion(), alignments_regularGappedAlignment(), alignments_unpruneRegion(), ungappedExtension_extend(), ungappedExtension_nucleotideExtend(), ungappedExtension_oneHitExtend(), ungappedExtension_print(), and unpack_getRegions().

struct ungappedExtension* ungappedExtension::next [read]

Definition at line 49 of file global.h.

Referenced by alignments_addUngappedExtension(), alignments_addUngappedExtensionAtEnd(), alignments_checkForJoin(), alignments_findFinalAlignments(), alignments_findGoodAlignments(), alignments_findTopFinalAlignments(), alignments_getTracebacks(), alignments_pruneRegion(), alignments_unpruneRegion(), fasterGappedExtension_prune(), gappedExtension_prune(), ungappedExtension_extend(), ungappedExtension_nucleotideExtend(), ungappedExtension_oneHitExtend(), and unpack_getRegions().

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

• include/global.h

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