ms_enzymefile Class Reference [Mascot configuration files module]

Reads and parses the enzymes file that contains multiple enzyme definitions. More...

#include <ms_enzyme.hpp>

Inheritance diagram for ms_enzymefile:

Collaboration diagram for ms_enzymefile:

List of all members.

Public Member Functions
	ms_enzymefile ()
	Default constructor.
	ms_enzymefile (const ms_enzymefile &src)
	Copying constructor.
	ms_enzymefile (const char *filename, const matrix_science::ms_connection_settings *cs=0)
	This constructor may be used in order to read the given file immediately on construction.
	~ms_enzymefile ()
	Destructor.
void	appendEnzyme (const ms_enzyme *item)
	Adds a copy of given enzyme at the end of the list.
void	appendErrors (const ms_errors &src)
	Copies all errors from another instance and appends them at the end of own list.
void	clearAllErrors ()
	Remove all errors from the current list of errors.
void	clearEnzymes ()
	Deletes all enzymes from the list.
void	copyFrom (const ms_errors *right)
	Use this member to make a copy of another instance.
void	copyFrom (const ms_enzymefile *right)
	Call this member to copy all the information from another instance.
void	defaultValues ()
	Use this member to re-initialise the instance.
bool	deleteEnzymeByName (const char *name)
	Remove an enzyme from the list in memory.
bool	deleteEnzymeByNumber (const int num)
	Remove an enzyme from the list in memory.
matrix_science::ms_connection_settings	getConnectionSettings () const
	Returns the sessionID and proxy server for use with an HTTP transfer.
const ms_enzyme *	getEnzymeByName (const char *name) const
	Finds an enzyme with the specified name (case insensitive).
const ms_enzyme *	getEnzymeByNumber (const int num) const
	Returns a pointer to an internally stored enzyme.
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 previously set or a default one used to read the file.
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.
int	getNumberOfEnzymes () const
	Returns a number of enzymes successfully read from the file.
bool	isNoneFound () const
	Returns TRUE if an entry with name "NONE" has been found in the file.
bool	isValid () const
	Call this function to determine if there have been any errors.
ms_enzymefile &	operator= (const ms_enzymefile &right)
	C++ style assignment operator.
void	read_buffer (const char *buffer)
	Reads and parses an in-memory null-terminated buffer instead of a disk file.
void	read_file ()
	Reads and parses the file.
void	save_file ()
	Stores enzyme definitions in a file.
void	setConnectionSettings (const matrix_science::ms_connection_settings &cs)
	Sets the sessionID and proxy server for use with an HTTP transfer.
void	setFileName (const char *filename)
	Call this member before reading the file if you want to specify a non-default name.
bool	updateEnzymeByName (const char *name, const ms_enzyme enzyme)
	Update the information for a specific enzyme.
bool	updateEnzymeByNumber (const int num, const ms_enzyme enzyme)
	Update the information for a specific enzyme.

---

Detailed Description

Reads and parses the enzymes file that contains multiple enzyme definitions.

Proteolytic enzymes and specific chemical cleavage agents are defined in ../config/enzymes .

Usage is simple:

• Create an instance of this class.
• Set a file name if needed, otherwise a default name will be used.
• Call read_file().
• Check for errors with isValid().
• Iterate thourgh enzyme list using getNumberOfEnzymes() and getEnzymeByNumber().
• Alternatively, one can find an enzyme by name (if known) with getEnzymeByName().

Examples:

config_enzymes.cpp, and tools_aahelper.cpp.

---

Constructor & Destructor Documentation

ms_enzymefile

(

)

Default constructor.

Creates an empty list of enzymes in memory. A file is not created.

ms_enzymefile

(

const ms_enzymefile &

src )

Copying constructor.

Note:

This constructor can only be used from C++.

Parameters:

src	is the ms_enzymefile to make a copy of.

ms_enzymefile	(	const char *	filename,
		const matrix_science::ms_connection_settings *	cs = 0
	)

This constructor may be used in order to read the given file immediately on construction.

Equivalent to the following call sequence:

• default contructor ms_enzymefile();
• setFileName();
• setConnectionSettings();
• read_file().

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 .
cs	is a an optional pointer to the connection settings. This should contain a sessionID and optionally the proxy server settings.

~ms_enzymefile

(

)

Destructor.

Called automatically from C++ and other languages.

---

Member Function Documentation

void appendEnzyme

(

const ms_enzyme *

item )

Adds a copy of given enzyme at the end of the list.

Parameters:

item	is the new item to add to the end of the list of enzymes.

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 clearEnzymes

(

)

Deletes all enzymes from the list.

Similar to calling defaultValues() except that this function doesn't clear all the comments from the file.

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

void copyFrom

(

const ms_enzymefile *

right )

Call this member to copy all the information from another instance.

Simply create an instance of the class using the default constructor and call this method.

Parameters:

right

Pointer to another instance to copy from.

void defaultValues

(

)

Use this member to re-initialise the instance.

Note that this member doesn't clear the file name; that has to be re-set explicitly if needed.

bool deleteEnzymeByName

(

const char *

name )

Remove an enzyme from the list in memory.

Parameters:

name	must be a valid enzyme name.

Returns:

True if the enyzme name is valid.

Examples:

config_enzymes.cpp.

bool deleteEnzymeByNumber

(

const int

num )

Remove an enzyme from the list in memory.

Parameters:

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

Returns:

True if the enyzme 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_enzyme * getEnzymeByName

(

const char *

name )

const

Finds an enzyme with the specified name (case insensitive).

The special entry "NONE" being found also generates NULL as an outcome. For more information on this see isNoneFound().

Parameters:

name	name of the enzyme to look for

Returns:

a pointer to the found one or NULL otherwise. See Maintaining object references: two rules of thumb.

const ms_enzyme * getEnzymeByNumber

(

const int

num )

const

Returns a pointer to an internally stored enzyme.

Parameters:

num	Must be in the range 0..getNumberOfEnzymes()-1.

Returns:

A pointer to an ms_enzyme object. If num is out of range, then the return value is a null object.

Examples:

config_enzymes.cpp.

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.

std::string getFileName

(

)

const

Returns a file name previously set or a default one used to read the file.

Returns:

The filename (if any) as set in a previous call to setFileName() or as specified in the constructor.

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.

int getNumberOfEnzymes

(

)

const

Returns a number of enzymes successfully read from the file.

Returns:

The current number of enzymes in the list.

Examples:

config_enzymes.cpp.

bool isNoneFound

(

)

const

Returns TRUE if an entry with name "NONE" has been found in the file.

The standard enzymes files has an entry "None" which is used to specify a no enzyme search. This special entry never represents a real enzyme and therefore all properties of the entry are meaningless. Therefore, calling getEnzymeByName() with "None" as a parameter will always return NULL.

Returns:

True if there is an entry for "None" in the file.

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.

ms_enzymefile & operator=

(

const ms_enzymefile &

right )

C++ style assignment operator.

Note:

This operator can only be used in C++.

Acts identically to copyFrom() member.

Parameters:

right

is the enzymefile definition to copy from.

Returns:

reference to the current object

void read_buffer

(

const char *

buffer )

Reads and parses an in-memory null-terminated buffer instead of a disk file.

Check for possible errors after calling this functions with isValid(). In case of any errors it keeps all of the already read entries that can still be accessed in a usual way.

Parameters:

buffer

a null-terminated string with enzymes definitions.

void read_file

(

)

Reads and parses the file.

Check for possible errors after calling this functions with isValid(). In case of any errors it keeps all of the already read entries that can still be accessed in a usual way.

void save_file

(

)

Stores enzyme definitions in a file.

Don't forget to check for errors after this function call. The filename used to save the file is specified by setFileName().

Examples:

config_enzymes.cpp.

void setConnectionSettings

(

const matrix_science::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 *

filename )

Call this member before reading the file if you want to specify a non-default name.

Parameters:

filename

is the name of the file to be saved using save_file() or read using read_file().

Examples:

config_enzymes.cpp.

bool updateEnzymeByName	(	const char *	name,
		const ms_enzyme	enzyme
	)

Update the information for a specific enzyme.

Parameters:

name	title of the enzyme to retrieve.
enzyme	is a pointer to the new definition of the enzyme.

Returns:

true if the name can be found, false otherwise

bool updateEnzymeByNumber	(	const int	num,
		const ms_enzyme	enzyme
	)

Update the information for a specific enzyme.

Parameters:

num	must be in the range 0..getNumberOfEnzymes()-1.
enzyme	Is a pointer to the new definition of the enzyme.

Returns:

true if num param is in range, false otherwise

Examples:

config_enzymes.cpp.

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

• ms_enzyme.hpp
• ms_enzyme.cpp