aln Class Reference

#include <aln.h>

List of all members.

Public Member Functions
	dyaln ()
	~dyaln ()
int	align (const char s1n[], const char s1str[], const char s2n[], const char s2str[])
void	setup ()
void	outputTab (ostream &os)
void	freeTrace ()
void	outputAln (FILE *ou=stdout)
void	setMatrix (char m[])
void	setGapCost (int alpha, int beta)
void	setcsub (int cs)
bool	isSimple () const
void	setNaligns (int n)
Private Member Functions
void	allocateMem ()
void	initParameter ()
Private Attributes
struct SEQALN_SEQUENCE *	seq1
struct SEQALN_SEQUENCE *	seq2
struct SEQALN_CONSTANTS *	scoring
struct SEQALN_RESULTS *	results
struct SEQALN_IO *	io
char	distrib_file1 [51]
char	distrib_file2 [51]
pair< float, char >	sortedFreq1 [20]
pair< float, char >	sortedFreq2 [20]

---

Constructor & Destructor Documentation

aln::~dyaln

(

)

---

Member Function Documentation

void aln::allocateMem

(

)

[private]

void aln::initParameter

(

)

[private]

aln::dyaln

(

)

int aln::align	(	const char	s1n[],
		const char	s1str[],
		const char	s2n[],
		const char	s2str[]
	)

void aln::setup

(

)

void aln::outputTab

(

ostream &

os

)

void aln::freeTrace

(

)

[inline]

References freeTraceList(), and results.

void aln::outputAln

(

FILE *

ou = stdout

)

void aln::setMatrix

(

char

m[]

)

[inline]

References io, load_mat(), and scoring.

void aln::setGapCost	(	int	alpha,
		int	beta
	)

void aln::setcsub

(

int

cs

)

[inline]

References SEQALN_CONSTANTS::csub, and scoring.

bool aln::isSimple

(

)

const

void aln::setNaligns

(

int

n

)

[inline]

References SEQALN_CONSTANTS::naligns, and scoring.

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Member Data Documentation

struct SEQALN_SEQUENCE* aln::seq1 [read, private]

struct SEQALN_SEQUENCE * aln::seq2 [read, private]

struct SEQALN_CONSTANTS* aln::scoring [read, private]

Referenced by setcsub(), setMatrix(), and setNaligns().

struct SEQALN_RESULTS* aln::results [read, private]

Referenced by freeTrace().

struct SEQALN_IO* aln::io [read, private]

Referenced by setMatrix().

char aln::distrib_file1[51] [private]

char aln::distrib_file2[51] [private]

pair<float, char> aln::sortedFreq1[20] [private]

pair<float, char> aln::sortedFreq2[20] [private]

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

• seqaln/seqaln/kzaln/aln.h