alignment.cc File Reference

#include "alignment.h"
#include <fstream>
#include <utility>
#include <list>
#include <cstdlib>
#include <sstream>

Functions
pair< string, string >	split (const string &ln)
void	outputList (list< pair< int, int > > &gl, ostream &os)
void	outputGapList (const list< pair< int, int > > &gl, ostream &os)
int	getSeqStartIdx (const string &ln)
ostream &	operator<< (ostream &ou, const alignment &aln)
list< pair< int, int > >	listgap (const string &s, const char gapChar)
void	outputList (const list< pair< int, int > > &gl, ostream &os)

---

Function Documentation

int getSeqStartIdx

(

const string &

ln

)

list<pair<int, int> > listgap	(	const string &	s,
		const char	gapChar = '-'
	)

helper functons given the aligned sequence string it will return the list of gap position and gap length pair The default gap character is '-'

Referenced by main(), operator<<(), outputgaparray(), and printgaplist().

ostream& operator<<	(	ostream &	ou,
		const alignment &	aln
	)

dump the alignment model as array version

References listgap(), and outputGapList().

void outputGapList	(	const list< pair< int, int > > &	gl,
		ostream &	os
	)

Referenced by operator<<().

void outputList	(	const list< pair< int, int > > &	gl,
		ostream &	os
	)

in the array formatd as in C++ and postgres

void outputList	(	list< pair< int, int > > &	gl,
		ostream &	os
	)

Referenced by main().

pair< string, string > split

(

const string &

ln

)

separate the line into name and sequence parts first=name, second=sequence string with gaps

References name.

Referenced by acronym(), Aceobj::at(), Book::Book(), digestLine(), prt::getAC(), gbseq::getOrgAcronym(), Gsubrecord::Gsubrecord(), hitCount(), feature::loadGeneName(), Ref::loadKey(), Reference::loadKey(), gbseq::loadOrgmap(), main(), feature::makeGeneSymbol(), prt::next(), operator<<(), book::parse(), locseg::parse(), Aceobj::parse(), Patent::parsejl(), Reference::parseJournal(), feature::parseLoc(), ref::process(), prt::processID(), RangeChain::RangeChain(), Reference::read(), gbseq::read(), Gsubreader::read(), readandstoreSam(), readConf(), ref::readkeymap(), Ref::Ref(), refloc::refloc(), feature::RNAdump(), feature::subCDS(), table2map(), feature::wjoinseg(), gbprt::write(), prt::writeAce(), feature::writeGene(), feature::writeProtein(), feature::writeSource(), and gbseq::writeSpecies().