mgsaln Class Reference

#include <mgaln.h>

List of all members.

Public Member Functions
	mgsaln (char *seq2name, char *seq1str, char *seq2name, char *seq2str)
char *	newmem ()
	if (argc< 7)
	parseargs (seq1, seq2, scoring, results, io, argc, argv)
	results_init (seq1, seq2, scoring, results, io)
	while (seq1status > 0)
	exit (0)
Public Attributes
int	i
int	j
int	seq1status
	seq1 = (struct SEQALN_SEQUENCE *)newmem(1, sizeof(struct SEQALN_SEQUENCE))
	seq2 = (struct SEQALN_SEQUENCE *)newmem(1, sizeof(struct SEQALN_SEQUENCE))
	scoring = (struct SEQALN_CONSTANTS *)newmem(1, sizeof(struct SEQALN_CONSTANTS))
	results = (struct SEQALN_RESULTS *)newmem(1, sizeof(struct SEQALN_RESULTS))
	io = (struct SEQALN_IO *)newmem(1, sizeof(struct SEQALN_IO))
io	STDIN = stdin
io	STDOUT = stdout
io	STDERR = stderr
scoring	ptype = GLOBAL
scoring	stype = MATRIX
scoring	mtype = SIMILARITY
scoring	btype = FULL
scoring	memuse = SQUARE
	seq1status = seq1->len
Private Attributes
struct SEQALN_SEQUENCE *	seq1
struct SEQALN_SEQUENCE *	seq2
struct SEQALN_CONSTANTS *	scoring
struct SEQALN_RESULTS *	results
struct SEQALN_IO *	io

---

Constructor & Destructor Documentation

mgsaln::mgsaln	(	char *	seq2name,
		char *	seq1str,
		char *	seq2name,
		char *	seq2str
	)

---

Member Function Documentation

char* mgsaln::newmem

(

)

mgsaln::if

(

)

[inline]

References argv, io, and SEQALN_IO::STDOUT.

mgsaln::parseargs	(	seq1	,
		seq2	,
		scoring	,
		results	,
		io	,
		argc	,
		argv
	)

mgsaln::results_init	(	seq1	,
		seq2	,
		scoring	,
		results	,
		io
	)

Referenced by while().

mgsaln::while	(	seq1status	,
		0
	)			[inline]

References gen_align(), globalS(), i, io, LINEAR, load_seq(), SEQALN_CONSTANTS::memuse, print_trace(), results, results_init(), rpt_align(), SEQALN_CONSTANTS::rptalign, SEQALN_CONSTANTS::rptboth, SEQALN_CONSTANTS::rptscore, SEQALN_CONSTANTS::rpttrace, scoring, seq1, seq1status, seq2, SEQALN_IO::STDOUT, trace(), and SEQALN_CONSTANTS::traceupper.

mgsaln::exit

(

0

)

---

Member Data Documentation

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

Referenced by while().

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

Referenced by while().

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

Referenced by while().

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

Referenced by while().

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

Referenced by if(), and while().

int mgsaln::i

Referenced by while().

int mgsaln::j

int mgsaln::seq1status

Referenced by while().

mgsaln::seq1 = (struct SEQALN_SEQUENCE *)newmem(1, sizeof(struct SEQALN_SEQUENCE))

mgsaln::seq2 = (struct SEQALN_SEQUENCE *)newmem(1, sizeof(struct SEQALN_SEQUENCE))

mgsaln::scoring = (struct SEQALN_CONSTANTS *)newmem(1, sizeof(struct SEQALN_CONSTANTS))

mgsaln::results = (struct SEQALN_RESULTS *)newmem(1, sizeof(struct SEQALN_RESULTS))

mgsaln::io = (struct SEQALN_IO *)newmem(1, sizeof(struct SEQALN_IO))

io mgsaln::STDIN = stdin

io mgsaln::STDOUT = stdout

io mgsaln::STDERR = stderr

scoring mgsaln::ptype = GLOBAL

scoring mgsaln::stype = MATRIX

scoring mgsaln::mtype = SIMILARITY

scoring mgsaln::btype = FULL

scoring mgsaln::memuse = SQUARE

mgsaln::seq1status = seq1->len

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

• seqaln/seqaln/kzaln/mgaln.h