exon Class Reference

#include <sim4.h>

List of all members.

Public Member Functions
	exon ()
bool	isEmpty () const
int	sumLength (int matchCut=90) const
Public Attributes
int	from1
int	from2
int	to1
int	to2
int	min_diag
int	max_diag
int	match
char	ori
int	length
int	flag
int	ematches
int	edist
Msp_ptr	msps
exon *	next_exon
Friends
ostream &	operator<< (ostream &os, const exon &ex)

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Constructor & Destructor Documentation

exon::exon

(

)

References edist, ematches, flag, length, max_diag, and min_diag.

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Member Function Documentation

bool exon::isEmpty

(

)

const [inline]

References length.

int exon::sumLength

(

int

matchCut = 90

)

const

References length, match, and next_exon.

Referenced by writeAlign().

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Friends And Related Function Documentation

ostream& operator<<	(	ostream &	os,
		const exon &	ex
	)			[friend]

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Member Data Documentation

int exon::from1

Referenced by complement_exons(), exon_cores(), IDISPLAY(), merge(), msp2exons(), new_exon(), operator<<(), pluri_align(), print_exons(), print_pipmaker_exons(), relink(), resolve_overlap(), SIM4(), slide_intron(), and sync_slide_intron().

int exon::from2

Referenced by add_offset_exons(), compact_list(), complement_exons(), exon_cores(), get_match_quality(), get_stats(), get_sync_flag(), IDISPLAY(), merge(), msp2exons(), new_exon(), operator<<(), pluri_align(), print_exons(), relink(), resolve_overlap(), SIM4(), slide_intron(), and sync_slide_intron().

int exon::to1

Referenced by add_offset_exons(), check_consistency_intron_ori(), compact_list(), complement_exons(), exon_cores(), get_match_quality(), get_stats(), get_sync_flag(), IDISPLAY(), merge(), msp2exons(), new_exon(), operator<<(), pluri_align(), print_exons(), print_pipmaker_exons(), relink(), resolve_overlap(), SIM4(), slide_intron(), and sync_slide_intron().

int exon::to2

Referenced by add_offset_exons(), compact_list(), complement_exons(), exon_cores(), get_match_quality(), get_stats(), get_sync_flag(), merge(), msp2exons(), new_exon(), operator<<(), print_exons(), relink(), resolve_overlap(), SIM4(), slide_intron(), and sync_slide_intron().

int exon::min_diag

Referenced by exon().

int exon::max_diag

Referenced by exon().

int exon::match

Referenced by operator<<(), print_exons(), and sumLength().

char exon::ori

Referenced by bmatch(), check_consistency_intron_ori(), complement_exons(), fmatch(), IDISPLAY(), operator<<(), print_exons(), SIM4(), slide_intron(), and sync_slide_intron().

int exon::length

Referenced by compact_list(), exon(), exon_cores(), get_stats(), isEmpty(), merge(), new_exon(), relink(), resolve_overlap(), SIM4(), slide_intron(), sumLength(), and sync_slide_intron().

int exon::flag

Referenced by exon(), exon_cores(), merge(), new_exon(), and relink().

int exon::ematches

Referenced by exon().

int exon::edist

Referenced by compact_list(), exon(), get_match_quality(), merge(), msp2exons(), and new_exon().

Msp_ptr exon::msps

exon* exon::next_exon

Referenced by add_offset_exons(), check_consistency_intron_ori(), compact_list(), complement_exons(), exon_cores(), find_previous(), flip_list(), free_list(), get_match_quality(), get_stats(), get_sync_flag(), IDISPLAY(), merge(), new_exon(), operator<<(), pluri_align(), print_exons(), print_pipmaker_exons(), relink(), SIM4(), slide_intron(), sumLength(), and sync_slide_intron().

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The documentation for this class was generated from the following files:

• sim4cpp/sim4.h
• sim4cpp/sim4.cpp