#include "GDE_proto.h"
#include <aw_msg.hxx>
#include <climits>
#include <algorithm>

Include dependency graph for GDE_FileIO.cxx:

Functions
static void	Regroup (NA_Alignment &alignment)

static void	NormalizeOffset (NA_Alignment &aln)

static void	ReadNA_Flat (char *filename, NA_Alignment &data)

static GB_ERROR	LoadFile (char *filename, NA_Alignment &dataset, int type, int format)

static int	FindType (char name, int dtype, int *ftype)

void	LoadData (char *filen, NA_Alignment &dataset)

void	AppendNA (NA_Base buffer, int len, NA_Sequence seq)

void	Ascii2NA (char *buffer, int len, int matrix[16])

int	WriteNA_Flat (NA_Alignment &aln, char *filename, int method)

void	Warning (const char *s)

void	InitNASeq (NA_Sequence *seq, int type)

Function Documentation

static void Regroup ( NA_Alignment & alignment )

static

Definition at line 8 of file GDE_FileIO.cxx.

References NA_Alignment::element, group, NA_Sequence::groupb, NA_Sequence::groupf, NA_Sequence::groupid, NULp, NA_Alignment::numelements, and NA_Alignment::numgroups.

Referenced by ReadNA_Flat().

static void NormalizeOffset ( NA_Alignment & aln )

static

Definition at line 31 of file GDE_FileIO.cxx.

References NA_Alignment::element, gde_assert, max, NA_Alignment::maxlen, min, NA_Alignment::numelements, offset, NA_Sequence::offset, NA_Alignment::rel_offset, and NA_Sequence::seqlen.

Referenced by ReadNA_Flat().

static void ReadNA_Flat	(	char *	filename,
		NA_Alignment &	data
	)

static

Definition at line 52 of file GDE_FileIO.cxx.

References AppendNA(), Arbdb_get_curelem(), Ascii2NA(), buffer, DNA, NA_Alignment::element, GBUFSIZ, InitNASeq(), MASK, max, NA_Alignment::maxlen, NormalizeOffset(), NA_Alignment::numelements, offset, NA_Sequence::offset, PROTEIN, Regroup(), NA_Sequence::rmatrix, NA_Sequence::seqlen, NA_Sequence::short_name, SIZE_SHORT_NAME, strcpy_truncate(), and TEXT.

Referenced by LoadFile().

static GB_ERROR LoadFile	(	char *	filename,
		NA_Alignment &	dataset,
		int	type,
		int	format
	)

static

Definition at line 132 of file GDE_FileIO.cxx.

References DataType, error(), NA_Alignment::format, GDE, gde_assert, GENBANK, NA_FLAT, NULp, ReadGen(), and ReadNA_Flat().

Referenced by LoadData().

static int FindType	(	char *	name,
		int *	dtype,
		int *	ftype
	)

static

Definition at line 160 of file GDE_FileIO.cxx.

References Find(), GBUFSIZ, GDE, GENBANK, NA_FLAT, NASEQ_ALIGN, and result.

Referenced by LoadData().

void LoadData	(	char *	filen,
		NA_Alignment &	dataset
	)

Definition at line 211 of file GDE_FileIO.cxx.

References aw_message(), DataType, error(), FileFormat, FileName, Find2(), FindType(), GBS_global_string(), LoadFile(), and NASEQ_ALIGN.

Referenced by GDE_startaction_cb().

void AppendNA	(	NA_Base *	buffer,
		int	len,
		NA_Sequence *	seq
	)

Definition at line 244 of file GDE_FileIO.cxx.

References ARB_realloc(), GBUFSIZ, NA_Sequence::offset, putelem(), NA_Sequence::seqlen, NA_Sequence::seqmaxlen, and NA_Sequence::sequence.

Referenced by AppendNA_and_free(), ReadGen(), and ReadNA_Flat().

void Ascii2NA	(	char *	buffer,
		int	len,
		int	matrix[16]
	)

Definition at line 259 of file GDE_FileIO.cxx.

Referenced by ReadGen(), and ReadNA_Flat().

int WriteNA_Flat	(	NA_Alignment &	aln,
		char *	filename,
		int	method
	)

Definition at line 268 of file GDE_FileIO.cxx.

References ALL, DNA, NA_Alignment::element, fputs(), getelem(), MASK, NA_Alignment::numelements, offset, NA_Sequence::offset, PROTEIN, NA_Alignment::rel_offset, RNA, NA_Sequence::seqlen, TEXT, and Warning().

Referenced by GDE_startaction_cb().

void Warning ( const char * s )

Definition at line 334 of file GDE_FileIO.cxx.

References aw_message().

Referenced by putelem(), WriteGDE(), WriteGen(), and WriteNA_Flat().

void InitNASeq	(	NA_Sequence *	seq,
		int	type
	)

Definition at line 339 of file GDE_FileIO.cxx.

References NA_Sequence::attr, NA_Sequence::authority, NA_Sequence::baggage, NA_Sequence::baggage_len, NA_Sequence::baggage_maxlen, NA_Sequence::barcode, NA_Sequence::col_lut, NA_Sequence::comments, NA_Sequence::comments_len, NA_Sequence::comments_maxlen, NA_Sequence::contig, Default_DNA_Trans, Default_NA_RTrans, Default_NAColor_LKUP, Default_PROColor_LKUP, Default_RNA_Trans, NA_Sequence::description, DNA, NA_Sequence::elementtype, NA_Sequence::groupb, NA_Sequence::groupf, NA_Sequence::groupid, NA_Sequence::id, IS_5_TO_3, IS_PRIMARY, MASK, NA_Sequence::membrane, TimeStamp::modify, NULp, NA_Sequence::offset, TimeStamp::origin, PROTEIN, NA_Sequence::rmatrix, RNA, NA_Sequence::seq_name, NA_Sequence::seqlen, NA_Sequence::seqmaxlen, NA_Sequence::sequence, SetTime(), NA_Sequence::short_name, SIZE_ID, strcpy_truncate(), NA_Sequence::t_stamp, TEXT, NA_Sequence::tmatrix, type, and uniqueID().

Referenced by InsertDatainGDE(), ReadGen(), and ReadNA_Flat().

Functions

Function Documentation