AlignmentRow Class Reference

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

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

• include/alignment.hh
• src/alignment.cc