global multiple sequence alignment in (standard) string representation More...

#include <alignment.hh>

Public Member Functions
	StringAlignment (size_t numrows)

void	insert (std::list< MsaInsertion > &insList, int maxInsertLen=INT_MAX)

size_t	removeGapOnlyCols ()

bool	isGapOnlyCol (size_t col)

void	computeLen ()

Friends
ostream &	operator<< (ostream &strm, const StringAlignment &msa)

Detailed Description

global multiple sequence alignment in (standard) string representation

Member Function Documentation

void StringAlignment::computeLen ( )

inline

Ensure all rows have the same length and compute and set this length.

void StringAlignment::insert	(	std::list< MsaInsertion > &	insList,
		int	maxInsertLen = `INT_MAX`
	)

Insert unaligned sequences into an alignment. The insertion positions all refer to the MSA before insertions. Example:

a-tt-g insert((0, 0, "ggg"), (2, 4, "gaga"), ggga-tt--—g –ctgg (1, 4, "ttt")) --—ctttt-gg a-ttgc ===================================> —a-ttgagagc

Parameters

[in] insList a list of inserts at certain positions

size_t StringAlignment::removeGapOnlyCols ( )

Remove all columns which in which each row that is present has a gap. Example

ggga-tt--—g gggatt--—g --—ctttt-gg ====> -—ctttt-gg —a-ttgagagc —attgagagc

Parameters

[in] insList a list of inserts at certain positions

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