Detailed Description

Definition at line 35 of file AlignmentBinaryFile.hpp.

#include <AlignmentBinaryFile.hpp>

Static Public Member Functions
static Alignment *	read (string filename)
static void	write (string filename, Alignment *alignment)
Static Private Member Functions
static void	fwrite_header (FILE *file)
static void	fread_header (FILE *file)
static void	fwrite_sequences (vector< SequenceInfo * > sequences, FILE *file)
static vector< SequenceInfo * >	fread_sequences (FILE *file)
static void	fwrite_alignment_params (AlignmentParams params, FILE file)
static AlignmentParams *	fread_alignment_params (vector< SequenceInfo * > sequences, FILE *file)
static void	fwrite_alignment_result (Alignment alignment, FILE file)
static Alignment *	fread_alignment_result (AlignmentParams params, FILE file)
static void	fwrite_flags (SequenceModifiers modifiers, FILE file)
static SequenceModifiers *	fread_flags (FILE *file)
static void	fwrite_array (const char array, const int len, FILE file)
static void	fread_array (char array, const int len, FILE file)
static void	fwrite_uint4_compressed (const unsigned int i, FILE *file)
static unsigned int	fread_uint4_compressed (FILE *file)
static void	fwrite_int4 (const int i, FILE *file)
static int	fread_int4 (FILE *file)
static void	fwrite_int2 (const short i, FILE *file)
static short	fread_int2 (FILE *file)
static void	fwrite_int1 (const unsigned char i, FILE *file)
static unsigned char	fread_int1 (FILE *file)
static void	fwrite_str (const char str, FILE file)
static string	fread_str (FILE *file)
static void	fwrite_gaps (vector< gap_t > gaps, FILE file)
static void	fread_gaps (vector< gap_t > gaps, FILE file)
static void	fread_dummy (const int len, FILE *file)

Member Function Documentation

AlignmentParams * AlignmentBinaryFile::fread_alignment_params	(	vector< SequenceInfo * >	sequences,
		FILE *	file
	)		`[static, private]`

Definition at line 242 of file AlignmentBinaryFile.cpp.

Alignment * AlignmentBinaryFile::fread_alignment_result	(	AlignmentParams *	params,
		FILE *	file
	)		`[static, private]`

Definition at line 356 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fread_array	(	char *	array,
		const int	len,
		FILE *	file
	)		`[static, private]`

Definition at line 504 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fread_dummy	(	const int	len,
		FILE *	file
	)		`[static, private]`

Definition at line 583 of file AlignmentBinaryFile.cpp.

SequenceModifiers * AlignmentBinaryFile::fread_flags ( FILE * file ) [static, private]

Definition at line 419 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fread_gaps	(	vector< gap_t > *	gaps,
		FILE *	file
	)		`[static, private]`

Definition at line 454 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fread_header ( FILE * file ) [static, private]

Definition at line 109 of file AlignmentBinaryFile.cpp.

unsigned char AlignmentBinaryFile::fread_int1 ( FILE * file ) [static, private]

Definition at line 577 of file AlignmentBinaryFile.cpp.

short AlignmentBinaryFile::fread_int2 ( FILE * file ) [static, private]

Definition at line 567 of file AlignmentBinaryFile.cpp.

int AlignmentBinaryFile::fread_int4 ( FILE * file ) [static, private]

Definition at line 556 of file AlignmentBinaryFile.cpp.

vector< SequenceInfo * > AlignmentBinaryFile::fread_sequences ( FILE * file ) [static, private]

Definition at line 148 of file AlignmentBinaryFile.cpp.

string AlignmentBinaryFile::fread_str ( FILE * file ) [static, private]

Definition at line 479 of file AlignmentBinaryFile.cpp.

unsigned int AlignmentBinaryFile::fread_uint4_compressed ( FILE * file ) [static, private]

Definition at line 540 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_alignment_params	(	AlignmentParams *	params,
		FILE *	file
	)		`[static, private]`

Definition at line 196 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_alignment_result	(	Alignment *	alignment,
		FILE *	file
	)		`[static, private]`

Definition at line 313 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_array	(	const char *	array,
		const int	len,
		FILE *	file
	)		`[static, private]`

Definition at line 500 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_flags	(	SequenceModifiers *	modifiers,
		FILE *	file
	)		`[static, private]`

Definition at line 403 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_gaps	(	vector< gap_t > *	gaps,
		FILE *	file
	)		`[static, private]`

Definition at line 433 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_header ( FILE * file ) [static, private]

Definition at line 103 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_int1	(	const unsigned char	i,
		FILE *	file
	)		`[static, private]`

Definition at line 573 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_int2	(	const short	i,
		FILE *	file
	)		`[static, private]`

Definition at line 562 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_int4	(	const int	i,
		FILE *	file
	)		`[static, private]`

Definition at line 551 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_sequences	(	vector< SequenceInfo * >	sequences,
		FILE *	file
	)		`[static, private]`

Definition at line 128 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_str	(	const char *	str,
		FILE *	file
	)		`[static, private]`

Definition at line 473 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::fwrite_uint4_compressed	(	const unsigned int	i,
		FILE *	file
	)		`[static, private]`

Definition at line 509 of file AlignmentBinaryFile.cpp.

Alignment * AlignmentBinaryFile::read ( string filename ) [static]

Definition at line 90 of file AlignmentBinaryFile.cpp.

void AlignmentBinaryFile::write	(	string	filename,
		Alignment *	alignment
	)		`[static]`

Definition at line 68 of file AlignmentBinaryFile.cpp.

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

Detailed Description

Static Public Member Functions

Static Private Member Functions

Member Function Documentation