file_util.h File Reference

Header file for file checking functions. More...

#include "Bstring.h"
#include <fstream>

Macros
#define	_filetype_

Enumerations
enum	FileType {   Unknown_FileType = 0 , Image = 1 , Micrograph = 2 , Molecule = 3 ,   Model = 4 , MgRelion = 11 }
	File type enumeration. More...

Functions
int	fread_large (unsigned char *aptr, size_t pagesize, size_t offset, ifstream *fimg)
	Reads blocks of memeory no larger than 1Gb. More...
int	fread_large (unsigned char *aptr, size_t pagesize, size_t offset, ifstream &fimg)
Bstring	find_file (Bstring filename, Bstring path, int flag=0)
	Searches for a file within or without the given path. More...
string	find_file (string filename, string path, int flag=0)
vector< string >	file_list (string path)
	Returns a list of files in the requested directory. More...
vector< string >	file_list (string path, string ext)
	Returns a list of files in the requested directory. More...
FileType	file_type (const char *filename)
	Checks the file type using the extension and contents. More...
FileType	file_type (Bstring &filename)
int	detect_and_fix_carriage_return (const char *filename)
	Detects carriage returns in text files and converts them to new-lines. More...

Detailed Description

Header file for file checking functions.

Author

Bernard Heymann

Date

Created: 20010601

Modified: 20210413

Macro Definition Documentation

_filetype_

#define _filetype_

Enumeration Type Documentation

FileType

enum FileType

File type enumeration.

The types are mostly based on Bsoft objects. Additional types enumerated above 10 are for other packages.

Enumerator
Unknown_FileType
Image
Micrograph
Molecule
Model
MgRelion

Function Documentation

detect_and_fix_carriage_return()

int detect_and_fix_carriage_return

(

const char *

filename

)

Detects carriage returns in text files and converts them to new-lines.

Parameters

*filename

file name.

Returns

int 0, <0 if error.

The first line is read and if any carriage returns are found, the whole
file is scanned and carriage returns converted to new-lines.

file_list() [1/2]

vector< string > file_list

(

string

path

)

Returns a list of files in the requested directory.

Parameters

&path

directory path.

Returns

vector<string> list of file names.

file_list() [2/2]

vector< string > file_list	(	string	path,
		string	ext
	)

Returns a list of files in the requested directory.

Parameters

&path	directory path.
&ext	file name extension.

Returns

vector<string> list of file names.

file_type() [1/2]

FileType file_type

(

Bstring &

filename

)

file_type() [2/2]

FileType file_type

(

const char *

filename

)

Checks the file type using the extension and contents.

Parameters

*filename

file name.

Returns

FileType enumerated file type.

The file extension is the main determinant of the file type.
File formats with multiple types (such as the STAR and PDB formats)
are distinguished based on content.

find_file() [1/2]

Bstring find_file	(	Bstring	filename,
		Bstring	path,
		int	flag
	)

Searches for a file within or without the given path.

Parameters

filename	file name to search for.
path	path to search in.
flag	if not found: bit 4 = warn; bit 5 = delete file name.

Returns

Bstring found file, empty if not found and delete_flag set.

The input filename is first tested for access.
If not found, the filename without its original path is tested.
If not found, the filename with the given path is tested.
If not found, an error is reported and the original filename returned 
unless the delete flag is set.

find_file() [2/2]

string find_file	(	string	filename,
		string	path,
		int	flag = 0
	)

fread_large() [1/2]

int fread_large	(	unsigned char *	aptr,
		size_t	pagesize,
		size_t	offset,
		ifstream &	fimg
	)

fread_large() [2/2]

int fread_large	(	unsigned char *	aptr,
		size_t	pagesize,
		size_t	offset,
		ifstream *	fimg
	)

Reads blocks of memeory no larger than 1Gb.

Parameters

*aptr	pointer to pre-allocated memory.
pagesize	size of pre-allocated memory.
offset	offset in file.
*fimg	file pointer.

Returns

int 0, <0 if error.

Each block is packed in sequence into the pre-allocated memory provided.