#include <BALL/FORMAT/trajectoryFile.h>

Inheritance diagram for BALL::TrajectoryFile:

Public Member Functions
Constructors and Destructor
	TrajectoryFile ()
	Default constructor. More...

	TrajectoryFile (const String &filename, File::OpenMode open_mode=std::ios::in)

virtual	~TrajectoryFile ()
	Destructor. More...

Assignment
virtual void	clear ()
	Clear method. More...

Predicates
bool	operator== (const TrajectoryFile &file) const
	Equality operator. More...

Accessors
virtual Size	getNumberOfSnapShots ()

Size	getNumberOfAtoms () const

Public methods for file handling
virtual bool	readHeader ()

virtual bool	writeHeader ()

virtual bool	append (const SnapShot &snapshot)

virtual bool	read (SnapShot &snapshot)

virtual bool	flushToDisk (const std::vector< SnapShot > &buffer)

Public Member Functions inherited from BALL::File
	File ()

	File (const String &name, OpenMode open_mode=std::ios::in)

virtual	~File ()

bool	isValid () const

bool	open (const String &name, File::OpenMode open_mode=std::ios::in)

bool	reopen ()

bool	reopen (File::OpenMode open_mode)

void	close ()

const String &	getName () const

void	setName (const String &name)

const String &	getOriginalName () const

Size	getSize ()

File::OpenMode	getOpenMode () const

Type	getType (bool trace_link) const

bool	copyTo (const String &destination_name, Size buffer_size=4096)

bool	moveTo (const String &destination_name)

bool	remove ()

bool	renameTo (const String &new_path)

bool	truncate (Size size=0)

std::fstream &	getFileStream ()

TransformationManager &	getTransformationManager ()

const TransformationManager &	getTransformationManager () const

bool	operator== (const File &file) const

bool	operator!= (const File &file) const

bool	isOpen () const

bool	isClosed () const

bool	isAccessible () const

bool	isCanonized () const

bool	isReadable () const

bool	isWritable () const

bool	isExecutable () const

Protected Attributes

Size	number_of_snapshots_

Size	number_of_atoms_

Protected Attributes inherited from BALL::File
String	name_

String	original_name_

OpenMode	open_mode_

bool	is_open_

bool	is_temporary_

Private Member Functions
const TrajectoryFile &	operator= (const TrajectoryFile &file)

Additional Inherited Members
Public Types inherited from BALL::File
typedef std::ios::openmode	OpenMode

enum	Transformation { TRANSFORMATION__EXEC = 1, TRANSFORMATION__FILTER = 2, TRANSFORMATION__URL = 3 }

enum	Type { TYPE__UNKNOWN = 0, TYPE__DIRECTORY = 1, TYPE__CHAR_SPECIAL_FILE = 2, TYPE__BLOCK_SPECIAL_FILE = 3, TYPE__REGULAR_FILE = 4, TYPE__SYMBOLIC_LINK = 5, TYPE__SOCKET = 6, TYPE__FIFO_SPECIAL_FILE = 7 }

Static Public Member Functions inherited from BALL::File
static Size	getSize (String name)

static Type	getType (String name, bool trace_link)

static bool	copy (String source_name, String destination_name, Size buffer_size=4096)

static bool	move (const String &source_name, const String &destination_name)

static bool	remove (String name)

static bool	rename (String old_path, String new_path)

static bool	truncate (String path, Size size=0)

static bool	createTemporaryFilename (String &temporary, const String &suffix=".TMP")

static void	enableTransformation (Transformation transformation)

static void	disableTransformation (Transformation transformation)

static bool	isTransformationEnabled (Transformation transformation)

static void	registerTransformation (const String &pattern, const String &exec)

static void	unregisterTransformation (const String &pattern)

static bool	isAccessible (String name)

static bool	isReadable (String name)

static bool	isWritable (String name)

static bool	isExecutable (String name)

Static Public Attributes inherited from BALL::File
static const OpenMode	MODE_IN
	Open for input (default) More...

static const OpenMode	MODE_OUT
	Open for output. More...

static const OpenMode	MODE_APP
	Append. Seek to end before each write operation. More...

static const OpenMode	MODE_BINARY
	Binary mode. More...

static const OpenMode	MODE_ATE
	Seek to end directly after opening. More...

static const OpenMode	MODE_TRUNC
	Truncate an existing file. More...

static const String	TRANSFORMATION_EXEC_PREFIX
	Prefix for filenames that are created through the execution of commands "exec:". More...

static const String	TRANSFORMATION_FILE_PREFIX
	Prefix for files (to mimick URL-like behavior) "file:". More...

static const String	TRANSFORMATION_FTP_PREFIX
	Prefix for FTP-transfers "ftp://". More...

static const String	TRANSFORMATION_HTTP_PREFIX
	Prefix for HTTP-transfer "http://". More...

Static Protected Attributes inherited from BALL::File
static HashSet< String >	created_temp_filenames_

static TransformationManager	transformation_manager_

static Size	transformation_methods_

Detailed Description

Trajectory file format for MD simulation. This is more an interface definition than an actual class, because it would not make too much sense to create yet-another-trajectory-format. This class will be specialized by actual formats, like DCD.

Definition at line 28 of file trajectoryFile.h.

Constructor & Destructor Documentation

BALL::TrajectoryFile::TrajectoryFile ( )

Default constructor.

BALL::TrajectoryFile::TrajectoryFile	(	const String &	filename,
		File::OpenMode	open_mode = `std::ios::in`
	)

Detailed constructor requiring a filename and the mode in which this file should be opened.

Parameters

filename	the name of the file
open_mode	the mode in which this file should be opened

Exceptions

Exception::FileNotFound if the file could not be openend

See Also: File

virtual BALL::TrajectoryFile::~TrajectoryFile ( )

virtual

Destructor.

Member Function Documentation

virtual bool BALL::TrajectoryFile::append ( const SnapShot & snapshot )

virtual

Append a SnapShot to an existing file. Note that this method does note update the header.

Parameters

snapshot the SnapShot we want to save

Returns: true, if writing was successful

Reimplemented in BALL::TRRFile, and BALL::DCDFile.

virtual void BALL::TrajectoryFile::clear ( )

virtual

Clear method.

Reimplemented from BALL::File.

Reimplemented in BALL::TRRFile, and BALL::DCDFile.

virtual bool BALL::TrajectoryFile::flushToDisk ( const std::vector< SnapShot > & buffer )

virtual

Write several SnapShots to disk.

Parameters

buffer a vector of snapshots

Returns: true, if flushing was successful, false ow.

Exceptions

File::CannotWrite if writing to the file failed

Reimplemented in BALL::TRRFile, and BALL::DCDFile.

Size BALL::TrajectoryFile::getNumberOfAtoms ( ) const

get the number of atoms coverd by each snapshot.

Returns: the number of atoms

virtual Size BALL::TrajectoryFile::getNumberOfSnapShots ( )

virtual

get the number of snapshots stored in this instance.

Returns: the number of snapshots of this instance

Reimplemented in BALL::TRRFile.

const TrajectoryFile& BALL::TrajectoryFile::operator= ( const TrajectoryFile & file )

private

bool BALL::TrajectoryFile::operator== ( const TrajectoryFile & file ) const

Equality operator.

virtual bool BALL::TrajectoryFile::read ( SnapShot & snapshot )

virtual

Read the next SnapShot from the file.

Parameters

snapshot a buffer for result delivery

Returns: true if a snapshot could be read, false ow.

Reimplemented in BALL::TRRFile, and BALL::DCDFile.

virtual bool BALL::TrajectoryFile::readHeader ( )

virtual

Read the header of an existing file.

Returns: true if the header could be read successfully, false ow.

Reimplemented in BALL::TRRFile, and BALL::DCDFile.

virtual bool BALL::TrajectoryFile::writeHeader ( )

virtual

Write a header.

Returns: true if the header could be written successfully, false ow.

Reimplemented in BALL::DCDFile.

Member Data Documentation

Size BALL::TrajectoryFile::number_of_atoms_

protected

Definition at line 128 of file trajectoryFile.h.

Size BALL::TrajectoryFile::number_of_snapshots_

protected

Definition at line 125 of file trajectoryFile.h.

Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation