kzseq Class Reference

#include <kzseq.h>

List of all members.

Public Member Functions
	kzseq ()
	kzseq (int alloc)
	~kzseq ()
bool	readSeq (ifstream &infs, char ln[])
void	fastRead (caddr_t hstart, caddr_t sstart, size_t seqLen)
const char *	seqchar () const
int	seqlen () const
int	headlen () const
const char *	seqhead () const
const char *	getHeader () const
void	getName (char name[]) const
void	revcomp (char rc[]) const
kzseq &	revcomp ()
void	seq2upper ()
void	polyATsize (int &pA, int &pT) const
bool	isDNA () const
kzseq &	operator= (const kzseq &ks)
void	copyRevcomp (const kzseq &ks)
Private Attributes
char *	seq
char *	header
int	slen
int	maxlen
bool	rc

---

Constructor & Destructor Documentation

kzseq::kzseq

(

)

References header, rc, and slen.

kzseq::kzseq

(

int

alloc

)

References maxlen, rc, and slen.

kzseq::~kzseq

(

)

References header, maxlen, and seq.

---

Member Function Documentation

bool kzseq::readSeq	(	ifstream &	infs,
		char	ln[]
	)

References append(), header, LINE, maxlen, seq, and slen.

Referenced by main().

void kzseq::fastRead	(	caddr_t	hstart,
		caddr_t	sstart,
		size_t	seqLen
	)

References header, seq, and slen.

const char* kzseq::seqchar

(

)

const [inline]

References seq.

Referenced by main(), print_align_blk(), print_align_lat(), and SIM4().

int kzseq::seqlen

(

)

const [inline]

References slen.

Referenced by main(), print_align_blk(), print_align_header_n(), print_align_lat(), and SIM4().

int kzseq::headlen

(

)

const [inline]

References header.

Referenced by main().

const char* kzseq::seqhead

(

)

const [inline]

References header.

Referenced by main(), and writeAlign().

const char* kzseq::getHeader

(

)

const [inline]

References header.

Referenced by print_align_header_n().

void kzseq::getName

(

char

name[]

)

const

References header.

Referenced by print_align_header_n().

void kzseq::revcomp

(

char

rc[]

)

const

References seq, slen, and toupper().

Referenced by main().

kzseq & kzseq::revcomp

(

)

References rc, rcbase(), seq, and slen.

Referenced by copyRevcomp().

void kzseq::seq2upper

(

)

References seq, slen, and toupper().

Referenced by main().

void kzseq::polyATsize	(	int &	pA,
		int &	pT
	)			const

References seq, and slen.

Referenced by main(), and SIM4().

bool kzseq::isDNA

(

)

const

References dchars, seq, and slen.

kzseq & kzseq::operator=

(

const kzseq &

ks

)

References header, maxlen, rc, seq, and slen.

void kzseq::copyRevcomp

(

const kzseq &

ks

)

References revcomp().

Referenced by main().

---

Member Data Documentation

char* kzseq::seq [private]

Referenced by fastRead(), isDNA(), operator=(), polyATsize(), readSeq(), revcomp(), seq2upper(), seqchar(), and ~kzseq().

char* kzseq::header [private]

Referenced by fastRead(), getHeader(), getName(), headlen(), kzseq(), operator=(), readSeq(), seqhead(), and ~kzseq().

int kzseq::slen [private]

Referenced by fastRead(), isDNA(), kzseq(), operator=(), polyATsize(), readSeq(), revcomp(), seq2upper(), and seqlen().

int kzseq::maxlen [private]

Referenced by kzseq(), operator=(), readSeq(), and ~kzseq().

bool kzseq::rc [private]

Referenced by kzseq(), operator=(), and revcomp().

---

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

• sim4cpp/kzseq.h
• sim4cpp/kzseq.cpp