alignment Class Reference

#include <alignment.h>

List of all members.

Public Member Functions
	alignment ()
void	read (istream &in)
void	readDia (istream &in)
void	readClustal (istream &in)
void	printPolymorphic (ostream &ous) const
alignpos	getPosition () const
string	getalnmodel () const
void	dumpaln ()
bool	highQuality (float cut=0.2)
int	length () const
int	nogapLength () const
float	identity () const
float	similarity () const
int	getIdentityCount () const
int	getSimilarityCount () const
bool	goodSegment ()
float	nogapIdentity () const
float	nogapSimilarity ()
int	seqCount () const
int	size () const
ostream &	dumpQuality (ostream &ou)
float	partialCount (float gapcut=0.51)
bool	partialGood (float base)
quality	getqual (float base=0.08, float top=1.2)
int	read (istream &ins, char ln[], string &bf)
int	begin () const
int	end () const
int	sbjbegin () const
int	sbjend () const
float	score () const
double	eValue () const
int	length () const
int	identical_residue () const
double	calBias (double &efflen, int psw=6) const
string	querySeq () const
string	matchSeq () const
float	identity () const
bool	isup () const
bool	iscompl () const
int	read (istream &ins, char ln[], string &bf)
int	begin () const
int	end () const
int	sbjbegin () const
int	sbjend () const
float	score () const
double	eValue () const
int	length () const
int	identical_residue () const
double	calBias (double &efflen, int psw=6) const
string	querySeq () const
string	matchSeq () const
float	identity () const
bool	isup () const
bool	iscompl () const
Public Attributes
float	idenCut
alnmethod	method
string	clusterid
Static Public Attributes
static const int	nogapcolcut
Protected Member Functions
float	calcut (float top, float n, int iden)
void	count ()
void	countDia ()
Protected Attributes
vector< string >	seqarr
vector< string >	namearr
string	consensus
int	idenCnt
int	simCnt
int	nogapsimCnt
int	nogapCol
int	partiden
int	partcol
float	avgThick
Private Attributes
float	sco
double	exp
int	iden
int	simil
int	len
string	qseq
string	sbjseq
int	qs
int	qe
int	ss
int	se
Friends
class	region
ostream &	operator<< (ostream &ou, const alignment &aln)
void	split (char ln[], int &s, string &seq, int &e)

---

Constructor & Destructor Documentation

alignment::alignment

(

)

[inline]

---

Member Function Documentation

void alignment::read

(

istream &

in

)

void alignment::readDia

(

istream &

in

)

read the dialignment output format

void alignment::readClustal

(

istream &

in

)

read from the clustalw output

void alignment::printPolymorphic

(

ostream &

ous

)

const

prints the polymorphic positions only

alignpos alignment::getPosition

(

)

const

string alignment::getalnmodel

(

)

const

void alignment::dumpaln

(

)

bool alignment::highQuality

(

float

cut = 0.2

)

int alignment::length

(

)

const [inline]

References seqarr.

Referenced by identity(), and similarity().

int alignment::nogapLength

(

)

const [inline]

References nogapCol.

float alignment::identity

(

)

const [inline]

References idenCnt, and length().

float alignment::similarity

(

)

const [inline]

References idenCnt, length(), and simCnt.

int alignment::getIdentityCount

(

)

const [inline]

References idenCnt.

int alignment::getSimilarityCount

(

)

const [inline]

References simCnt.

bool alignment::goodSegment

(

)

float alignment::nogapIdentity

(

)

const [inline]

References idenCnt, and nogapCol.

float alignment::nogapSimilarity

(

)

[inline]

References idenCnt, nogapCol, and nogapsimCnt.

int alignment::seqCount

(

)

const [inline]

References seqarr.

int alignment::size

(

)

const [inline]

References seqarr.

ostream& alignment::dumpQuality

(

ostream &

ou

)

float alignment::partialCount

(

float

gapcut = 0.51

)

bool alignment::partialGood

(

float

base

)

quality alignment::getqual	(	float	base = 0.08,
		float	top = 1.2
	)

float alignment::calcut	(	float	top,
		float	n,
		int	iden
	)			[protected]

void alignment::count

(

)

[protected]

void alignment::countDia

(

)

[protected]

int alignment::read	(	istream &	ins,
		char	ln[],
		string &	bf
	)

int alignment::begin

(

)

const [inline]

References qs.

int alignment::end

(

)

const [inline]

References qe.

int alignment::sbjbegin

(

)

const [inline]

References ss.

int alignment::sbjend

(

)

const [inline]

References se.

float alignment::score

(

)

const [inline]

References sco.

double alignment::eValue

(

)

const [inline]

References exp.

int alignment::length

(

)

const [inline]

References len.

int alignment::identical_residue

(

)

const [inline]

References iden.

double alignment::calBias	(	double &	efflen,
		int	psw = 6
	)			const

string alignment::querySeq

(

)

const [inline]

References qseq.

string alignment::matchSeq

(

)

const [inline]

References sbjseq.

float alignment::identity

(

)

const [inline]

References iden, and len.

bool alignment::isup

(

)

const [inline]

References qe, and qs.

bool alignment::iscompl

(

)

const [inline]

References qe, and qs.

int alignment::read	(	istream &	ins,
		char	ln[],
		string &	bf
	)

int alignment::begin

(

)

const [inline]

References qs.

int alignment::end

(

)

const [inline]

References qe.

int alignment::sbjbegin

(

)

const [inline]

References ss.

int alignment::sbjend

(

)

const [inline]

References se.

float alignment::score

(

)

const [inline]

References sco.

double alignment::eValue

(

)

const [inline]

References exp.

int alignment::length

(

)

const [inline]

References len.

int alignment::identical_residue

(

)

const [inline]

References iden.

double alignment::calBias	(	double &	efflen,
		int	psw = 6
	)			const

string alignment::querySeq

(

)

const [inline]

References qseq.

string alignment::matchSeq

(

)

const [inline]

References sbjseq.

float alignment::identity

(

)

const [inline]

References iden, and len.

bool alignment::isup

(

)

const [inline]

References qe, and qs.

bool alignment::iscompl

(

)

const [inline]

References qe, and qs.

---

Friends And Related Function Documentation

friend class region [friend]

ostream& operator<<	(	ostream &	ou,
		const alignment &	aln
	)			[friend]

dump the alignment model as array version

void split	(	char	ln[],
		int &	s,
		string &	seq,
		int &	e
	)			[friend]

---

Member Data Documentation

const int alignment::nogapcolcut [static]

float alignment::idenCut

alnmethod alignment::method

string alignment::clusterid

vector<string> alignment::seqarr [protected]

Referenced by length(), seqCount(), and size().

vector<string> alignment::namearr [protected]

string alignment::consensus [protected]

the consensus string is the exact output from Clustalw.

int alignment::idenCnt [protected]

Referenced by getIdentityCount(), identity(), nogapIdentity(), nogapSimilarity(), and similarity().

int alignment::simCnt [protected]

Referenced by getSimilarityCount(), and similarity().

int alignment::nogapsimCnt [protected]

Referenced by nogapSimilarity().

int alignment::nogapCol [protected]

Referenced by nogapIdentity(), nogapLength(), and nogapSimilarity().

int alignment::partiden [protected]

int alignment::partcol [protected]

float alignment::avgThick [protected]

float alignment::sco [private]

Referenced by score().

double alignment::exp [private]

Referenced by eValue().

int alignment::iden [private]

Referenced by identical_residue(), and identity().

int alignment::simil [private]

int alignment::len [private]

Referenced by identity(), and length().

string alignment::qseq [private]

Referenced by querySeq().

string alignment::sbjseq [private]

Referenced by matchSeq().

int alignment::qs [private]

Referenced by begin(), iscompl(), and isup().

int alignment::qe [private]

Referenced by end(), iscompl(), and isup().

int alignment::ss [private]

Referenced by sbjbegin().

int alignment::se [private]

Referenced by sbjend().

---

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

• alnmodel/alignment.h
• seqana/blast.h
• seqana/blastio/blast.h