alignment Struct Reference

#include <global.h>

Collaboration diagram for alignment:

[legend]

Data Fields
int4	descriptionLocation
int4	descriptionLength
unsigned char *	subject
int4	subjectLength
ungappedExtension *	ungappedExtensions
gappedExtension *	gappedExtensions
unsigned char *	edits
int4	encodedLength
char	joinChecked
char	inMemorySubject
unpackRegion *	unpackRegions
uint4	numUnpackRegions
uint4	cluster

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Detailed Description

Definition at line 92 of file global.h.

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Field Documentation

int4 alignment::descriptionLocation

Definition at line 94 of file global.h.

Referenced by alignments_checkForJoin(), alignments_compareAlignmentDescriptionLocations(), alignments_createNew(), alignments_expandCluster(), alignments_findFinalAlignments(), alignments_getTracebacks(), alignments_printFinalAlignments(), alignments_printGoodAlignments(), alignments_pruneRegion(), alignments_regularGappedAlignment(), alignments_unpruneRegion(), print_gappedAlignmentsBrief(), print_gappedAlignmentsFull(), unpack_loadSubject(), and unpack_unpackSubject().

int4 alignment::descriptionLength

Definition at line 95 of file global.h.

Referenced by alignments_createNew().

unsigned char* alignment::subject

Definition at line 96 of file global.h.

Referenced by alignment_freeAlignment(), alignments_createNew(), alignments_expandCluster(), alignments_getTracebacks(), alignments_regularGappedAlignment(), alignments_selectRegion(), alignments_unpruneRegion(), print_gappedAlignmentsFull(), unpack_loadSubject(), and unpack_unpackSubject().

int4 alignment::subjectLength

Definition at line 97 of file global.h.

Referenced by alignments_checkForJoin(), alignments_compareFinalAlignments(), alignments_createNew(), alignments_expandCluster(), alignments_getTracebacks(), alignments_regularGappedAlignment(), print_gappedAlignmentsFull(), unpack_entireSubjectUnpacked(), unpack_getRegions(), unpack_loadSubject(), and unpack_unpackSubject().

struct ungappedExtension* alignment::ungappedExtensions [read]

Definition at line 98 of file global.h.

Referenced by alignments_addUngappedExtension(), alignments_addUngappedExtensionAtEnd(), alignments_checkForJoin(), alignments_createNew(), alignments_findFinalAlignments(), alignments_findTopFinalAlignments(), alignments_getTracebacks(), alignments_pruneRegion(), alignments_unpruneRegion(), and unpack_getRegions().

struct gappedExtension* alignment::gappedExtensions [read]

Definition at line 99 of file global.h.

Referenced by alignment_freeAlignment(), alignments_addGappedExtension(), alignments_createNew(), alignments_getTracebacks(), alignments_pruneOverlappingExtensions(), alignments_removeGappedExtension(), print_gappedAlignmentsBrief(), and print_gappedAlignmentsFull().

unsigned char* alignment::edits

Definition at line 100 of file global.h.

Referenced by alignment_freeAlignment(), alignments_createNew(), unpack_loadSubject(), and unpack_unpackSubject().

int4 alignment::encodedLength

Definition at line 101 of file global.h.

Referenced by alignments_createNew(), alignments_expandCluster(), alignments_loadSubjectsIntoMemory(), unpack_loadSubject(), and unpack_unpackSubject().

char alignment::joinChecked

Definition at line 102 of file global.h.

Referenced by alignments_createNew().

char alignment::inMemorySubject

Definition at line 103 of file global.h.

Referenced by alignment_freeAlignment(), alignments_createNew(), alignments_expandCluster(), alignments_loadSubjectsIntoMemory(), and unpack_loadSubject().

struct unpackRegion* alignment::unpackRegions [read]

Definition at line 104 of file global.h.

Referenced by alignments_createNew(), alignments_getTracebacks(), alignments_selectRegion(), print_gappedAlignmentsFull(), unpack_entireSubjectUnpacked(), unpack_loadSubject(), and unpack_unpackSubject().

uint4 alignment::numUnpackRegions

Definition at line 105 of file global.h.

Referenced by alignments_createNew(), alignments_getTracebacks(), alignments_selectRegion(), print_gappedAlignmentsFull(), unpack_loadSubject(), and unpack_unpackSubject().

uint4 alignment::cluster

Definition at line 106 of file global.h.

Referenced by alignments_createNew(), alignments_expandCluster(), and print_gappedAlignmentsFull().

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

• include/global.h

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