global multiple sequence alignment More...

#include <alignment.hh>

Public Member Functions
	AlignmentRow (string seqID, int chrPos, Strand strand, string rowbuffer)

int	chrStart () const

int	chrEnd () const

int	aliEnd () const

int	getSeqLen () const

int	getCumFragLen () const

void	setCumFragLen (int len)

int	gapLenAfterFrag (size_t i) const

void	addFragment (int chrPos, int aliPos, int len)

void	addFragment (fragment &f)

string	getSignature () const

void	pack ()

int	getAliPos (int chrPos, vector< fragment >::const_iterator from)

int	getAliPos (int chrPos, vector< fragment >::const_iterator *from)

int	getAliPos (int chrPos)

int	getChrPos (int aliPos, vector< fragment >::const_iterator from)

int	getChrPos (int aliPos)

Public Attributes
string	seqID

Strand	strand

vector< fragment >	frags

Friends
ostream &	operator<< (ostream &strm, const AlignmentRow &row)

void	appendRow (AlignmentRow *r1, const AlignmentRow r2, int aliLen1, string sigstr)

Detailed Description

global multiple sequence alignment

alignment does not contain the sequence itself, but the info, where gaps are.
Generation of exon candidates.

Author: Mario Stanke

Member Function Documentation

◆ getAliPos()

int AlignmentRow::getAliPos	(	int	chrPos,
		vector< fragment >::const_iterator	from
	)

convert from chromosomal to alignment position start search from the fragment 'from' on, i.e. assume that aliPos is not to the left of fragment *from return -1, if chrPos is outside the range of these fragments return -2, if position is otherwise not mappable: no fragment contains the chrPos, i.e. chrPos is in a gap

Friends And Related Symbol Documentation

◆ appendRow

void appendRow	(	AlignmentRow **	r1,
		const AlignmentRow *	r2,
		int	aliLen1,
		string	sigstr
	)

friend

append row r2 to r1, thereby shifting all alignment coordinates of r2 by aliLen1 if signature string (chr and strand) is not empty, treat everything else as missing

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

include/alignment.hh
src/alignment.cc

Public Member Functions

Public Attributes

Friends

Detailed Description

Member Function Documentation

◆ getAliPos()

Friends And Related Symbol Documentation

◆ appendRow