ms_modfile Class Reference [Mascot configuration files module]

Use this class in order to read in the amino acid modification file. More...

#include <ms_modfile.hpp>

Inheritance diagram for ms_modfile:

Collaboration diagram for ms_modfile:

List of all members.

Public Member Functions
	ms_modfile ()
	Default constructor.
	ms_modfile (const ms_modfile &src)
	Copying constructor.
	ms_modfile (const char *filename, const ms_masses *massFile, const bool fromSubstitutions=false, const ms_connection_settings *cs=0)
	Immediate-action constructor that reads the given file on construction.
	ms_modfile (const ms_umod_configfile &src, const unsigned int flags=ms_umod_configfile::MODFILE_FLAGS_ALL)
	Copying constructor that accepts unimod-file object.
	~ms_modfile ()
	Destructor.
void	appendErrors (const ms_errors &src)
	Copies all errors from another instance and appends them at the end of own list.
void	appendModification (const ms_modification *item)
	Adds a new modification at the end of the list.
void	clearAllErrors ()
	Remove all errors from the current list of errors.
void	clearModifications ()
	Deletes all modifications from the list.
void	copyFrom (const ms_umod_configfile *right, const unsigned int flags=ms_umod_configfile::MODFILE_FLAGS_ALL)
	Copies all content from unimod-file object.
void	copyFrom (const ms_modfile *right)
	Copies all content from another instance.
void	copyFrom (const ms_errors *right)
	Use this member to make a copy of another instance.
void	defaultValues ()
	Call this member if you want to start again.
bool	deleteModificationByName (const char *name)
	Remove a modification from the list in memory.
bool	deleteModificationByNumber (const int num)
	Remove a modification from the list in memory.
ms_connection_settings	getConnectionSettings () const
	Returns the sessionID and proxy server for use with an HTTP transfer.
const ms_errs *	getErrorHandler () const
	Retrive the error object using this function to get access to all errors and error parameters.
std::string	getFileName () const
	Returns a file name that is used to read configuration information.
int	getLastError () const
	Return the error description of the last error that occurred.
std::string	getLastErrorString () const
	Return the error description of the last error that occurred.
const ms_masses *	getMassFile () const
	Returns previously set ms_masses class instance.
const ms_modification *	getModificationByName (const char *nameMod) const
	Returns a modification object by its name or NULL in case of not found.
const ms_modification *	getModificationByNumber (const int numMod) const
	Returns a modification object by its number.
int	getNumberOfModifications () const
	Returns a number of modifications currently held in memory.
bool	isFromSubstitutions () const
	Returns TRUE if reading is done from the substitutions file.
bool	isValid () const
	Call this function to determine if there have been any errors.
ms_modfile &	operator= (const ms_modfile &right)
	C++ style assignment operator.
void	read_file ()
	Reads configuration information from the file.
void	save_file ()
	Stores modification information in the file.
void	saveToString (std::string &modfileAsStr)
	Stores modification information in the string supplied.
void	setConnectionSettings (const ms_connection_settings &cs)
	Sets the sessionID and proxy server for use with an HTTP transfer.
void	setFileName (const char *name)
	Call this member to set a custom file name to read from a different location.
void	setFromSubstitutions (const bool value)
	Sets internal flag telling which file should be used for extracting modifications.
void	setMassFile (const ms_masses *massFile)
	Set the atom masses to use when generating fragmentation mass deltas.
void	sortModifications ()
	Re-orders mods by their names.
bool	updateModificationByName (const char *name, const ms_modification mod)
	Update the information for a specific modification.
bool	updateModificationByNumber (const int num, const ms_modification mod)
	Update the information for a specific modification.

---

Detailed Description

Use this class in order to read in the amino acid modification file.

Amino acid modifications are defined in two files: mod_file and substitutions. An instance of this class can be used to read a file with any other name. Otherwise, the default name ../config/mod_file is used. Just create an instance of the class and call read_file()-member.

Alternatively, you can call setFileName() to supply a custom file name. It is also recommended to read in the atom masses configuration file with ms_masses and call setMassFile() before calling read_file().

After reading a file and before using the object, check its by calling isValid() and retrieve error descriptions with getLastErrorString() if not valid.

Examples:

config_modfile.cpp, and tools_aahelper.cpp.

---

Constructor & Destructor Documentation

ms_modfile	(	const ms_umod_configfile &	src,
		const unsigned int	flags = ms_umod_configfile::MODFILE_FLAGS_ALL
	)

Copying constructor that accepts unimod-file object.

Parameters:

src	a Unimod file object to extract modifications from.
flags	can be one or more of the ms_umod_configfile::MODFILE_FLAGS values OR'ed together.

ms_modfile	(	const char *	filename,
		const ms_masses *	massFile,
		const bool	fromSubstitutions = false,
		const ms_connection_settings *	cs = 0
	)

Immediate-action constructor that reads the given file on construction.

Parameters:

filename	The file name parameter can be either a local file path or a Mascot server URL, it cannot be an empty string or NULL pointer. If it is a URL it should be of the form http://your-server/mascot/cgi .
massFile	In order to use default masses, use a null value.
fromSubstitutions	is an optional parameter is only used when the first parameter is a Mascot Server URL. Use FALSE or (leave the parameter out) to open the mod_file, and use TRUE to open the substitutions file.
cs	connection settings to use when accessing remote files. This should contain a sessionID and optionally the proxy server settings. If security is enabled on the session and visibility control files are present in a unimod subdirectory then private modifications will not be loaded.

---

Member Function Documentation

void appendErrors

(

const ms_errors &

src )

[inherited]

Copies all errors from another instance and appends them at the end of own list.

Parameters:

src	The object to copy the errors across from. See Maintaining object references: two rules of thumb.

void clearAllErrors

(

)

[inherited]

Remove all errors from the current list of errors.

The list of 'errors' can include fatal errors, warning messages, information messages and different levels of debugging messages.

All messages are accumulated into a list in this object, until clearAllErrors() is called.

See Error Handling.

See also:

isValid(), getLastError(), getLastErrorString(), getErrorHandler()

Examples:

common_error.cpp, resfile_error.cpp, and resfile_summary.cpp.

void copyFrom	(	const ms_umod_configfile *	right,
		const unsigned int	flags = ms_umod_configfile::MODFILE_FLAGS_ALL
	)

Copies all content from unimod-file object.

Parameters:

right	unimod file object to extract modifications from.
flags	can be one or more of the ms_umod_configfile::MODFILE_FLAGS values OR'ed together.

void copyFrom

(

const ms_errors *

right )

[inherited]

Use this member to make a copy of another instance.

Parameters:

right

is the source to initialise from

bool deleteModificationByName

(

const char *

name )

Remove a modification from the list in memory.

Parameters:

name	must be a valid modification name.

Returns:

True if the modification name is valid and the modification was removed.

Examples:

config_modfile.cpp.

bool deleteModificationByNumber

(

const int

num )

Remove a modification from the list in memory.

Parameters:

num	must be in the range 0..getNumberOfModifications()-1.

Returns:

True if the modification number is valid.

matrix_science::ms_connection_settings getConnectionSettings

(

)

const

Returns the sessionID and proxy server for use with an HTTP transfer.

See also the constructor documentation and setConnectionSettings().

Returns:

The current connection settings.

const ms_errs * getErrorHandler

(

)

const [inherited]

Retrive the error object using this function to get access to all errors and error parameters.

See Error Handling.

Returns:

Constant pointer to the error handler

See also:

isValid(), getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples:

common_error.cpp, and http_helper_getstring.cpp.

int getLastError

(

)

const [inherited]

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

See Error Handling.

See also:

isValid(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Returns:

the error number of the last error, or 0 if there have been no errors.

Reimplemented in ms_mascotresfile.

std::string getLastErrorString

(

)

const [inherited]

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

Returns:

Most recent error, warning, information or debug message

See Error Handling.

See also:

isValid(), getLastError(), clearAllErrors(), getErrorHandler()

Reimplemented in ms_mascotresfile.

Examples:

common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, and tools_aahelper.cpp.

const ms_modification * getModificationByNumber

(

const int

numMod )

const

Returns a modification object by its number.

Parameters:

numMod

is the modification number greater than or equal to zero and less than getNumberOfModifications().

Returns:

The modification object, or a null value if an invalid numMod value is passed. See Maintaining object references: two rules of thumb.

Examples:

config_modfile.cpp.

bool isFromSubstitutions

(

)

const

Returns TRUE if reading is done from the substitutions file.

This flag is important only when downloading the file from a remote host since the URL doesn't contain the file name -- only the location. See setFromSubstitutions() and read_file().

Returns:

true if the subtitutions file is used to extract modifications, false if the mod file is used

bool isValid

(

)

const [inherited]

Call this function to determine if there have been any errors.

This will return true unless there have been any fatal errors.

See Error Handling.

Returns:

True if no fatal error occured

See also:

getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples:

common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, peptide_list.cpp, resfile_summary.cpp, and tools_aahelper.cpp.

void read_file

(

)

Reads configuration information from the file.

The function uses the file name supplied in setFileName() for reading.

void saveToString

(

std::string &

modfileAsStr )

Stores modification information in the string supplied.

See Multiple return values in Perl, Java, Python and C#.

Parameters:

[out]

modfileAsStr

is the complete file as a string

void setConnectionSettings

(

const ms_connection_settings &

cs )

Sets the sessionID and proxy server for use with an HTTP transfer.

This value would normally be passed in the constructor.

Parameters:

cs	is the new connection settings.

void setFileName

(

const char *

name )

Call this member to set a custom file name to read from a different location.

The file name passed as the parameter can be either full/relative path to a local file or URL of the web-site to download it from. In case of URL, the parameter should specify only web-site address. The file name will be chosen depending on whether the file is substitutions or a regular one. Call setFromSubstitutions() before calling read_file() if you want to obtain substitutions configurations rather than regular modifications.

Parameters:

name	The file name parameter can be either a local file path or a Mascot server URL, it cannot be an empty string or NULL pointer. If it is a URL it should be of the form http://your-server/mascot/cgi .

Examples:

config_modfile.cpp.

void setFromSubstitutions

(

const bool

value )

Sets internal flag telling which file should be used for extracting modifications.

In case of remote URL it is necessary to tell which file (mod_file or substitutions) should be used for extracting modifications. By default all modifications are read from mod_file either locally or remotely.

See read_file() for more information.

Parameters:

value

set whether the mod file or the substutitions file is used to extract modifications

bool updateModificationByName	(	const char *	name,
		const ms_modification	mod
	)

Update the information for a specific modification.

Parameters:

name	must be a valid modification name.
mod	is the new definition of the modification.

Returns:

true if the modification was found and updated.

Examples:

config_modfile.cpp.

bool updateModificationByNumber	(	const int	num,
		const ms_modification	mod
	)

Update the information for a specific modification.

Parameters:

num	must be in the range 0..(getNumberOfModifications() - 1).
mod	is the new definition of the modification.

Returns:

true if the modification was found and updated.

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

• ms_modfile.hpp
• ms_modfile.cpp