ms_crosslinking_configfile Class Reference

This class represents the file crosslinking.xml. More...

#include <ms_crosslinking_configfile.hpp>

Inheritance diagram for ms_crosslinking_configfile:

Collaboration diagram for ms_crosslinking_configfile:

Public Member Functions
	ms_crosslinking_configfile ()
	Default constructor.
	ms_crosslinking_configfile (const char *fileName, const char *schemaFileName, const ms_connection_settings *cs=0, bool useSchema=true)
	Immediate action constructor that reads the XML file with the given name.
	ms_crosslinking_configfile (const ms_crosslinking_configfile &right)
	Copying constructor.
virtual	~ms_crosslinking_configfile ()
	Desctructor.
void	appendErrors (const ms_errors &src)
	Copies all errors from another instance and appends them at the end of own list.
void	appendMethod (const ms_crosslinking_method *elem)
	Adds a new method at the end of the list.
void	clearAllErrors ()
	Remove all errors from the current list of errors.
void	clearMethods ()
	Deletes all methods from the list.
void	copyFrom (const ms_crosslinking_configfile *right)
	Copies all the information from another instance.
void	copyFrom (const ms_errors *right)
	Use this member to make a copy of another instance.
virtual void	defaultValues ()
	Re-initialises the instance.
bool	deleteMethodByName (const char *name)
	Remove an method from the list in memory.
bool	deleteMethodByNumber (const int idx)
	Remove an method 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 the current file name.
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.
std::string	getMajorVersion () const
	Returns major document schema version as read from the file, otherwise the latest.
const ms_crosslinking_method *	getMethodByName (const char *name) const
	Returns an method object by its name or NULL in case of not found.
const ms_crosslinking_method *	getMethodByNumber (const int idx) const
	Returns an method object by its number.
std::string	getMinorVersion () const
	Returns minor document schema version as read from the file, otherwise the latest.
int	getNumberOfMethods () const
	Returns a number of methods currently held in memory.
std::string	getSchemaFileName () const
	Returns the current schema file name that is used to validate the XML file.
bool	isValid () const
	Call this function to determine if there have been any errors.
ms_crosslinking_configfile &	operator= (const ms_crosslinking_configfile &right)
	Assignment operator for C++ applications.
void	read_buffer (const char *buffer)
	Reads configuration information from a string buffer.
void	read_file ()
	Reads configuration information from the XML file.
std::string	save_buffer (bool validateAgainstSchema=true)
	Creates a string representation of the XML document with all the content of the object.
void	save_file ()
	Saves configuration information in the XML file (not mod_file).
void	setConnectionSettings (const ms_connection_settings &cs)
	Sets the sessionID and proxy server for use with an HTTP transfer.
void	setFileName (const char *filename)
	Changes the file name for subsequent read/write operations.
void	setSchemaFileName (const char *name)
	Call this member to specify a custom schema file name for validating the XML file.
bool	updateMethodByName (const char *name, const ms_crosslinking_method *method)
	Update the information for a specific method.
bool	updateMethodByNumber (const int idx, const ms_crosslinking_method *method)
	Update the information for a specific method.
std::string	validateDocument () const
	Validates the whole document against schema and returns errors as a string.

Static Public Member Functions
static std::string	getDefaultSchemaFileName ()
	Returns the default schema filename (no path)

Detailed Description

This class represents the file crosslinking.xml.

The crosslinking configuration file contains definitions for crosslinking methods. The method comprises settings such as intact vs cleavable linker, which protein accessions to intralink or interlink and various method-specific filters and settings. The file can be created from scratch, read from a disk file or retrieved from a remote location (HTTP).

After reading a file and before using the object check validity by calling isValid() and retrieve error descriptions with getLastErrorString() if not valid. Similarly, after writing out the file, isValid() can be used to check if the file has been created correctly and is valid for further use.

Constructor & Destructor Documentation

ms_crosslinking_configfile() [1/2]

ms_crosslinking_configfile	(	const char *	fileName,
		const char *	schemaFileName,
		const ms_connection_settings *	cs = 0,
		bool	useSchema = true
	)

Immediate action constructor that reads the XML file with the given name.

An instance of this class is normally created using this form of the constructor.

Parameters

fileName	represents either local file name (for example, "C:/crosslinking.xml") or a fully formed URL such as http://www.matrixscience.com/cgi . The filename may use backslashes or forward slashes on Windows and spaces in file or directory names are allowed.
schemaFileName	is a local file name for the schema (for example, "C:/crosslinking_2.xsd"). The schema must be a local file – it cannot be accessed using HTTP. The schema filename may use backslashes or forward slashes on Windows and spaces in file or directory names are allowed.
cs	a connection settings object for downloading the file from a Mascot server. This should contain a sessionID and optionally the proxy server settings. For a local file cs is not required and will be ignored.
useSchema	specify whether it should use a xsd schema validator, true by default

ms_crosslinking_configfile() [2/2]

ms_crosslinking_configfile

(

const ms_crosslinking_configfile &

src

)

Copying constructor.

Parameters

src	another instance of this class to copy the content from.

Member Function Documentation

appendErrors()

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.

appendMethod()

void appendMethod

(

const ms_crosslinking_method *

elem

)

Adds a new method at the end of the list.

Creates a new method object, copies all content from the object supplied as a parameter and adds it at the end of the methods list.

Parameters

elem	an instance of the method object to copy content from.

clearAllErrors()

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.

copyFrom() [1/2]

void copyFrom

(

const ms_crosslinking_configfile *

right

)

Copies all the information from another instance.

Parameters

right

another instance of this class to copy the content from.

copyFrom() [2/2]

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

defaultValues()

void defaultValues ( )

virtual

Re-initialises the instance.

After calling this method, all internal values will be reset to their defaults, as if the object had been freshly created with the default constructor.

This method, however, doesn't change file name, schema location and connection settings. If a complete cleanup is required, you need to do three additional calls:

   crosslinking_configfile.setFileName(""); 
   crosslinking_configfile.setSchemaFileName("");
   crosslinking_configfile.setConnectionSetting(ms_connection_settings());

deleteMethodByName()

bool deleteMethodByName

(

const char *

name

)

Remove an method from the list in memory.

Parameters

name	name of the method for deletion.

Returns

TRUE if the method has been found and successfully deleted and FALSE otherwise.

deleteMethodByNumber()

bool deleteMethodByNumber

(

const int

idx

)

Remove an method from the list in memory.

Parameters

idx	number of the method for deletion from 0 to (getNumberOfMethods() - 1).

Returns

TRUE if the method has been found and successfully deleted and FALSE otherwise.

getDefaultSchemaFileName()

std::string getDefaultSchemaFileName ( )

static

Returns the default schema filename (no path)

Static method to return the filename of the currently used schema

Returns

Returns "crosslinking_2.xsd" (at version 2.6.1)

getErrorHandler()

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.

getFileName()

std::string getFileName

(

)

const

Returns the current file name.

Returns

currently set file location (not necessarily the location from which the current content has been read).

getLastError()

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.

getLastErrorString()

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()

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.

getMethodByName()

const ms_crosslinking_method * getMethodByName

(

const char *

name

)

const

Returns an method object by its name or NULL in case of not found.

Parameters

name	a unique name of the method.

Returns

a read-only pointer to an method object. See Maintaining object references: two rules of thumb.

getMethodByNumber()

const ms_crosslinking_method * getMethodByNumber

(

const int

idx

)

const

Returns an method object by its number.

Parameters

idx	number of the method from 0 to (getNumberOfMethods() - 1).

Returns

a read-only pointer to an method object. See Maintaining object references: two rules of thumb.

getNumberOfMethods()

int getNumberOfMethods

(

)

const

Returns a number of methods currently held in memory.

Returns

total number of methods in the configuration file.

getSchemaFileName()

std::string getSchemaFileName

(

)

const

Returns the current schema file name that is used to validate the XML file.

Returns

currently set file location (not necessarily the location from which the current content has been read).

isValid()

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, repeat_search.cpp, resfile_error.cpp, resfile_info.cpp, resfile_input.cpp, resfile_params.cpp, resfile_summary.cpp, and tools_aahelper.cpp.

operator=()

ms_crosslinking_configfile & operator=

(

const ms_crosslinking_configfile &

right

)

Assignment operator for C++ applications.

Parameters

right

another instance of this class to copy the content from.

Returns

reference to the current object

read_buffer()

void read_buffer

(

const char *

buffer

)

Reads configuration information from a string buffer.

This method is useful when reading configuration information from a mascor result file. Old content of the object will be removed and substituted with the information read from the buffer.

Parameters

buffer

string buffer that contains a valid xml-document. It can be a document with just one modification in it, or only with amino acid masses.

read_file()

void read_file

(

)

Reads configuration information from the XML file.

Downloads the file if necessary from the Crosslinking web site and parses it. Check for errors before using any other methods for retrieving content.

save_buffer()

std::string save_buffer

(

bool

validateAgainstSchema = true

)

Creates a string representation of the XML document with all the content of the object.

Creates a valid XML document and returns it as a string which can be used, for example, for writing out configuration information to mascot result file.

To produce a 'file' that validates against the schema, it is not sufficient to add, for example, just a modification because this will be missing keyrefs to elements and termini building 'bricks'.

If you choose not to validate against the schema, then it is sufficient to just output, say, a single modification.

Parameters

validateAgainstSchema

specifies whether to validate against the schema. If true and the schema file exists and the resulting XML fails to validate, then an empty string will be returned and the errors will indicate why it failed to validate.

Returns

XML document with the object content.

save_file()

void save_file

(

)

Saves configuration information in the XML file (not mod_file).

Check for errors after calling this method to see if the operation has been successful or to get any schema validation errors. If the document is not valid it is going to be saved anyway unless there are other problems.

If you want to validate document without actually saving it use validateDocument().

setConnectionSettings()

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.

setFileName()

void setFileName

(

const char *

name

)

Changes the file name for subsequent read/write operations.

Calling this method does not mean an immediate update on disk. Use either read_file() or save_file() for that.

Parameters

name	a new file location.

setSchemaFileName()

void setSchemaFileName

(

const char *

name

)

Call this member to specify a custom schema file name for validating the XML file.

Parameters

name	a new file location (if empty default value will be assigned).

updateMethodByName()

bool updateMethodByName	(	const char *	name,
		const ms_crosslinking_method *	method
	)

Update the information for a specific method.

Parameters

name	name of the method for updating.
method	an object to copy the content from.

Returns

TRUE if the method has been found and successfully updated and FALSE otherwise.

updateMethodByNumber()

bool updateMethodByNumber	(	const int	idx,
		const ms_crosslinking_method *	method
	)

Update the information for a specific method.

Parameters

idx	number of the method for updating from 0 to (getNumberOfMethods() - 1).
method	an object to copy the content from.

Returns

TRUE if the method has been found and successfully updated and FALSE otherwise.

validateDocument()

std::string validateDocument

(

)

const

Validates the whole document against schema and returns errors as a string.

This method doesn't attempt to store the document anywhere and doesn't make the object invalid. Also, no errors are stored. Therefore, this method can be called as many times as necessary without any consequences.

All validation errors will be returned back as a string. However, the XML parser will describe errors in terms of row and column numbers as if the document was actually saved in a file.

Returns

validation errors as a string or an empty string if there are no errors detected.

---

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

• ms_crosslinking_configfile.hpp
• ms_crosslinking_configfile.cpp