#include <BALL/FORMAT/paramFile.h>

Inheritance diagram for BALL::ParamFile:

Classes
struct	ParameterDescription

Public Types
enum	ParameterType { INFILE , OUTFILE , STRING , INT , DOUBLE , INFILELIST , OUTFILELIST , STRINGLIST , INTLIST , DOUBLELIST , GALAXY_OPT_OUTDIR , GALAXY_OPT_OUTID }

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 }

Public Member Functions
	ParamFile (const String &name, File::OpenMode open_mode)

	~ParamFile ()

void	writeSection (String section_name, String section_description, String version, const String &section_helptext, const String &category, const std::list< std::pair< String, ParameterDescription > > &descriptions, const std::map< String, list< String > > &values)

void	readSection (String &tool_name, String &section_description, String &version, String &section_helptext, String &category, std::list< std::pair< String, ParameterDescription > > &descriptions, std::map< String, list< String > > &values, bool overwrite_existing=false)

void	close ()

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

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

virtual	~File ()

virtual void	clear ()

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

Static Public Member Functions
static String	buildNestedParameterName (const String &category, const String &parameter_name)

static Size	parseNestedParameterName (const String &parameter_name, String string_array[])

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)

Protected Attributes
String	filename_

File::OpenMode	open_mode_

bool	mode_read_

QXmlStreamReader *	xmlIn_

QXmlStreamWriter *	xmlOut_

QFile *	file_

Protected Attributes inherited from BALL::File
String	name_

String	original_name_

OpenMode	open_mode_

bool	is_open_

bool	is_temporary_

Additional Inherited Members
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

Class for storing and retrieving parameters (e.g. tool-parameters) to an xml-based file

Definition at line 23 of file paramFile.h.

Member Enumeration Documentation

◆ ParameterType

enum BALL::ParamFile::ParameterType

Enumerator
INFILE
OUTFILE
STRING
INT
DOUBLE
INFILELIST
OUTFILELIST
STRINGLIST
INTLIST
DOUBLELIST
GALAXY_OPT_OUTDIR
GALAXY_OPT_OUTID

Definition at line 27 of file paramFile.h.

Constructor & Destructor Documentation

◆ ParamFile()

BALL::ParamFile::ParamFile	(	const String &	name,
		File::OpenMode	open_mode
	)

◆ ~ParamFile()

BALL::ParamFile::~ParamFile ( )

Member Function Documentation

◆ buildNestedParameterName()

static String BALL::ParamFile::buildNestedParameterName	(	const String &	category,
		const String &	parameter_name
	)

static

From category, parameter_name builds [category]:[parameter_name]

◆ close()

void BALL::ParamFile::close ( )

◆ parseNestedParameterName()

static Size BALL::ParamFile::parseNestedParameterName	(	const String &	parameter_name,
		String	string_array[]
	)

static

Returns [category, parameter] from [category]:[parameter]

◆ readSection()

void BALL::ParamFile::readSection	(	String &	tool_name,
		String &	section_description,
		String &	version,
		String &	section_helptext,
		String &	category,
		std::list< std::pair< String, ParameterDescription > > &	descriptions,
		std::map< String, list< String > > &	values,
		bool	overwrite_existing = `false`
	)

Read a section from input file (e.g. parameters for one tool)

Parameters

descriptions	descriptions of parameters will be stored here
values	values of parameters will be stored here
overwrite_existing	if set to true, entries already existing in 'descriptions' and 'values' will be overwritten.

◆ writeSection()

void BALL::ParamFile::writeSection	(	String	section_name,
		String	section_description,
		String	version,
		const String &	section_helptext,
		const String &	category,
		const std::list< std::pair< String, ParameterDescription > > &	descriptions,
		const std::map< String, list< String > > &	values
	)

Write a section to the output file (e.g. parameters for one tool)

Parameters

section_description	a short description of this section (e.g. the tool), containing only a few words
section_helptext	a longer help-text/detailed description can be specified here
category	the category into which the tool falls (e.g. Docking, QSAR, etc.)
descriptions	description for all parameters to be saved
value	values of all parameters to be saved

Member Data Documentation

◆ file_

QFile* BALL::ParamFile::file_

protected

Definition at line 117 of file paramFile.h.

◆ filename_

String BALL::ParamFile::filename_

protected

Definition at line 112 of file paramFile.h.

◆ mode_read_

bool BALL::ParamFile::mode_read_

protected

Definition at line 114 of file paramFile.h.

◆ open_mode_

File::OpenMode BALL::ParamFile::open_mode_

protected

Definition at line 113 of file paramFile.h.

◆ xmlIn_

QXmlStreamReader* BALL::ParamFile::xmlIn_

protected

Definition at line 115 of file paramFile.h.

◆ xmlOut_

QXmlStreamWriter* BALL::ParamFile::xmlOut_

protected

Definition at line 116 of file paramFile.h.

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ParameterType

Constructor & Destructor Documentation

◆ ParamFile()

◆ ~ParamFile()

Member Function Documentation

◆ buildNestedParameterName()

◆ close()

◆ parseNestedParameterName()

◆ readSection()

◆ writeSection()

Member Data Documentation

◆ file_

◆ filename_

◆ mode_read_

◆ open_mode_

◆ xmlIn_

◆ xmlOut_