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

#include <ms_umod_configfile.hpp>

Inheritance diagram for ms_umod_configfile:

Collaboration diagram for ms_umod_configfile:

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Public Types
enum	MODFILE_FLAGS { MODFILE_FLAGS_EMPTY = 0x00000000 , MODFILE_FLAGS_REGULAR = 0x00000001 , MODFILE_FLAGS_HIDDEN = 0x00000002 , MODFILE_FLAGS_AASUBST = 0x00000004 , MODFILE_FLAGS_ALL = 0x7FFFFFFF }
	Flags for the type of modifications to retrieve. More...

Public Member Functions
	ms_umod_configfile ()
	Default constructor.

	ms_umod_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_umod_configfile (const ms_umod_configfile &right)
	Copying constructor.

virtual	~ms_umod_configfile ()
	Desctructor.

void	appendAminoAcid (const ms_umod_aminoacid *aa)
	Adds a new amino acid at the end of the list.

void	appendElement (const ms_umod_element *elem)
	Adds a new element 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	appendModBrick (const ms_umod_modbrick *brick)
	Adds a new modification brick at the end of the list.

void	appendModification (const ms_umod_modification *mod)
	Adds a new modification at the end of the list.

void	applyVisibility (const ms_session *session)
	If visibility settings are present for this file and session then apply to the currently loaded list of modifications.

void	applyVisibility (const std::vector< int > &groupIds)
	If visibility settings are present for this file and these group ids, then apply to the currently loaded list of modifications.

void	clearAllErrors ()
	Remove all errors from the current list of errors.

void	clearAminoAcids ()
	Deletes all amino acids from the list.

void	clearElements ()
	Deletes all elements from the list.

void	clearModBricks ()
	Deletes all modification bricks from the list.

void	clearModifications ()
	Deletes all modifications from the list.

void	copyFrom (const ms_errors *right)
	Use this member to make a copy of another instance.

void	copyFrom (const ms_umod_configfile *right)
	Copies all the information from another instance.

virtual void	defaultValues ()
	Re-initialises the instance.

bool	deleteAminoAcidByName (const char *name)
	Remove an amino acid from the list in memory.

bool	deleteAminoAcidByNumber (const int idx)
	Remove an amino acid from the list in memory.

bool	deleteElementByName (const char *name)
	Remove an element from the list in memory.

bool	deleteElementByNumber (const int idx)
	Remove an element from the list in memory.

bool	deleteModBrickByName (const char *name)
	Remove a modification brick from the list in memory.

bool	deleteModBrickByNumber (const int idx)
	Remove a modification brick from the list in memory.

bool	deleteModificationByName (const char *name)
	Remove a modification from the list in memory.

bool	deleteModificationByNumber (const int idx)
	Remove a modification from the list in memory.

int	findModFileName (const char *modFileName) const
	Returns modification index by its `mod_file`-style name (like "Acetyl (K)").

int	findModification (const char *modName) const
	Retrieves modification index by its plain name.

const ms_umod_aminoacid *	getAminoAcidByName (const char *name) const
	Returns an amino acid object by its name or NULL in case of not found.

const ms_umod_aminoacid *	getAminoAcidByNumber (const int idx) const
	Returns an amino acid object by its number.

ms_connection_settings	getConnectionSettings () const
	Returns the sessionID and proxy server for use with an HTTP transfer.

const ms_umod_element *	getElementByName (const char *name) const
	Returns an element object by its name or NULL in case of not found.

const ms_umod_element *	getElementByNumber (const int idx) const
	Returns an element object by its number.

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.

std::string	getMinorVersion () const
	Returns minor document schema version as read from the file, otherwise the latest.

const ms_umod_modbrick *	getModBrickByName (const char *name) const
	Returns a modification brick object by its name or NULL in case of not found.

const ms_umod_modbrick *	getModBrickByNumber (const int idx) const
	Returns an modification brick object by its number.

std::vector< std::string >	getModFileList (const unsigned int flags=MODFILE_FLAGS_ALL) const
	Returns an ordered list of modification names in mod_file-style, i.e. "Acetyl (K)" instead of "Acetyl".

const ms_umod_modification *	getModificationByName (const char *name) const
	Returns a modification object by its name or NULL in case of not found.

const ms_umod_modification *	getModificationByNumber (const int idx) const
	Returns a modification object by its number.

int	getNumberOfAminoAcids () const
	Returns a number of amino acids currently held in memory.

int	getNumberOfElements () const
	Returns a number of elements currently held in memory.

int	getNumberOfModBricks () const
	Returns a number of modification bricks currently held in memory.

int	getNumberOfModifications () const
	Returns a number of modifications 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_umod_configfile &	operator= (const ms_umod_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 (do not use it for saving in a `mod_file`!).

void	setMajorVersion (const std::string &version)
	Update the major document schema version.

void	setMinorVersion (const std::string &version)
	Update the minor document schema version.

void	setSchemaFileName (const char *name)
	Call this member to specify a custom schema file name for validating the XML file.

bool	updateAminoAcidByName (const char name, const ms_umod_aminoacid aa)
	Update the information for a specific amino acid.

bool	updateAminoAcidByNumber (const int idx, const ms_umod_aminoacid *aa)
	Update the information for a specific amino acid.

bool	updateElementByName (const char name, const ms_umod_element element)
	Update the information for a specific element.

bool	updateElementByNumber (const int idx, const ms_umod_element *element)
	Update the information for a specific element.

void	updateMasses ()
	Recalculates all masses derived from elements (brick masses, modification deltas etc.).

bool	updateModBrickByName (const char name, const ms_umod_modbrick brick)
	Update the information for a specific modification brick.

bool	updateModBrickByNumber (const int idx, const ms_umod_modbrick *brick)
	Update the information for a specific modification brick.

bool	updateModificationByName (const char name, const ms_umod_modification mod)
	Update the information for a specific modification.

bool	updateModificationByNumber (const int idx, const ms_umod_modification *mod)
	Update the information for a specific modification.

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 unimod.xml.

The Unimod file comprises chemical elements, amino-acids and modifications. The file can be created from scratch, read from a disk file or retrieved from a remote location (HTTP) and then saved as a mod_file or another unimod.xml.

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.

Member Enumeration Documentation

◆ MODFILE_FLAGS

enum MODFILE_FLAGS

Flags for the type of modifications to retrieve.

See Using enumerated values and static const ints in Perl, Java, Python and C#.

The result of combining these flags is a union of modifications sets.

Enumerator
MODFILE_FLAGS_EMPTY	Default behaviour (regular modifications only).
MODFILE_FLAGS_REGULAR	Non-hidden modifications which are not AA-substitutions.
MODFILE_FLAGS_HIDDEN	Hidden modifications which are not AA-substitutions.
MODFILE_FLAGS_AASUBST	AA substitutions.
MODFILE_FLAGS_ALL	Get all modifications.

Constructor & Destructor Documentation

◆ ms_umod_configfile() [1/2]

ms_umod_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:/unimod.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:/unimod_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_umod_configfile() [2/2]

ms_umod_configfile ( const ms_umod_configfile & src )

Copying constructor.

Parameters

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

Member Function Documentation

◆ appendAminoAcid()

void appendAminoAcid ( const ms_umod_aminoacid * aa )

Adds a new amino acid at the end of the list.

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

Parameters

aa	an instance of the amino acid object to copy content from.

◆ appendElement()

void appendElement ( const ms_umod_element * elem )

Adds a new element at the end of the list.

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

Parameters

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

◆ 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.

◆ appendModBrick()

void appendModBrick ( const ms_umod_modbrick * brick )

Adds a new modification brick at the end of the list.

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

Parameters

brick an instance of the modification brick object to copy content from.

◆ appendModification()

void appendModification ( const ms_umod_modification * mod )

Adds a new modification at the end of the list.

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

Parameters

mod	an instance of the modification object to copy content from.

◆ applyVisibility() [1/2]

void applyVisibility ( const ms_session * session )

If visibility settings are present for this file and session then apply to the currently loaded list of modifications.

Parameters

session Optional session object used to apply user security restrictions. Can be NULL or not supplied.

◆ applyVisibility() [2/2]

void applyVisibility ( const std::vector< int > & groupIds )

If visibility settings are present for this file and these group ids, then apply to the currently loaded list of modifications.

If visibility settings are present for this file and group ids then apply to the currently loaded list of modifications.

Parameters

groupIds vector of group ids to apply visibility for

◆ 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_errors * right )

inherited

Use this member to make a copy of another instance.

Parameters

right is the source to initialise from

◆ copyFrom() [2/2]

void copyFrom ( const ms_umod_configfile * right )

Copies all the information from another instance.

Parameters

right another instance of this class to copy the content 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:

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

◆ deleteAminoAcidByName()

bool deleteAminoAcidByName ( const char * name )

Remove an amino acid from the list in memory.

Parameters

name	name of the amino acid for deletion.

Returns: TRUE if the amino acid has been found and successfully deleted and FALSE otherwise.

◆ deleteAminoAcidByNumber()

bool deleteAminoAcidByNumber ( const int idx )

Remove an amino acid from the list in memory.

Parameters

idx	number of the amino acid for deletion from 0 to (getNumberOfAminoAcids() - 1).

Returns: TRUE if the amino acid has been found and successfully deleted and FALSE otherwise.

◆ deleteElementByName()

bool deleteElementByName ( const char * name )

Remove an element from the list in memory.

Parameters

name	name of the element for deletion.

Returns: TRUE if the element has been found and successfully deleted and FALSE otherwise.

◆ deleteElementByNumber()

bool deleteElementByNumber ( const int idx )

Remove an element from the list in memory.

Parameters

idx	number of the element for deletion from 0 to (getNumberOfElements() - 1).

Returns: TRUE if the element has been found and successfully deleted and FALSE otherwise.

◆ deleteModBrickByName()

bool deleteModBrickByName ( const char * name )

Remove a modification brick from the list in memory.

Parameters

name	name of the modification brick for deletion.

Returns: TRUE if the modification brick has been found and successfully deleted and FALSE otherwise.

◆ deleteModBrickByNumber()

bool deleteModBrickByNumber ( const int idx )

Remove a modification brick from the list in memory.

Parameters

idx	number of the modification brick for deletion from 0 to (getNumberOfModBricks() - 1).

Returns: TRUE if the modification brick has been found and successfully deleted and FALSE otherwise.

◆ deleteModificationByName()

bool deleteModificationByName ( const char * name )

Remove a modification from the list in memory.

Parameters

name	name of the modification for deletion.

Returns: TRUE if the modification has been found and successfully deleted and FALSE otherwise.

◆ deleteModificationByNumber()

bool deleteModificationByNumber ( const int idx )

Remove a modification from the list in memory.

Parameters

idx	number of the modification for deletion from 0 to (getNumberOfModifications() - 1).

Returns: TRUE if the modification has been found and successfully deleted and FALSE otherwise.

◆ findModFileName()

int findModFileName ( const char * modFileName ) const

Returns modification index by its mod_file-style name (like "Acetyl (K)").

Parameters

modFileName modification string name.

Returns: modification zero-based index or -1 (if not found).

◆ findModification()

int findModification ( const char * modName ) const

Retrieves modification index by its plain name.

Tries to find modification by its name (not mod_file-style name).

Parameters

modName modification string name.

Returns: modification zero-based index if the modification is found and -1 otherwise.

◆ getAminoAcidByName()

const ms_umod_aminoacid * getAminoAcidByName ( const char * name ) const

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

Parameters

name	a unique name of the amino acid.

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

◆ getAminoAcidByNumber()

const ms_umod_aminoacid * getAminoAcidByNumber ( const int idx ) const

Returns an amino acid object by its number.

Parameters

idx	number of the amino acid from 0 to (getNumberOfAminoAcids() - 1).

Returns: a read-only pointer to an amino acid object.

◆ 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 "unimod_2.xsd" (at version 2.6.1)

◆ getElementByName()

const ms_umod_element * getElementByName ( const char * name ) const

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

Parameters

name	a unique name of the element.

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

◆ getElementByNumber()

const ms_umod_element * getElementByNumber ( const int idx ) const

Returns an element object by its number.

Parameters

idx	number of the element from 0 to (getNumberOfElements() - 1).

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

◆ 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.

◆ getModBrickByName()

const ms_umod_modbrick * getModBrickByName ( const char * name ) const

Returns a modification brick object by its name or NULL in case of not found.

Parameters

name	a unique name of the modification brick.

Returns: a read-only pointer to a modification brick object. See Maintaining object references: two rules of thumb.

◆ getModBrickByNumber()

const ms_umod_modbrick * getModBrickByNumber ( const int idx ) const

Returns an modification brick object by its number.

Parameters

idx	number of the modification brick from 0 to (getNumberOfModBricks() - 1).

Returns: a read-only pointer to a modification brick object.

◆ getModFileList()

std::vector< std::string > getModFileList ( const unsigned int flags = MODFILE_FLAGS_ALL ) const

Returns an ordered list of modification names in mod_file-style, i.e. "Acetyl (K)" instead of "Acetyl".

Parameters

flags can be one or more of the ms_umod_configfile::MODFILE_FLAGS values OR'ed together.

Returns: an ordered modification names list.

◆ getModificationByName()

const ms_umod_modification * getModificationByName ( const char * name ) const

Returns a modification object by its name or NULL in case of not found.

Parameters

name	a unique name of the modification.

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

◆ getModificationByNumber()

const ms_umod_modification * getModificationByNumber ( const int idx ) const

Returns a modification object by its number.

Parameters

idx	number of the modification from 0 to (getNumberOfModifications() - 1).

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

◆ getNumberOfAminoAcids()

int getNumberOfAminoAcids ( ) const

Returns a number of amino acids currently held in memory.

Returns: total number of amino acids in the configuration file.

◆ getNumberOfElements()

int getNumberOfElements ( ) const

Returns a number of elements currently held in memory.

Returns: total number of elements in the configuration file.

◆ getNumberOfModBricks()

int getNumberOfModBricks ( ) const

Returns a number of modification bricks currently held in memory.

Returns: total number of modification bricks in the configuration file.

◆ getNumberOfModifications()

int getNumberOfModifications ( ) const

Returns a number of modifications currently held in memory.

Returns: total number of modifications 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_umod_configfile & operator= ( const ms_umod_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 Unimod 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 (do not use it for saving in a mod_file!).

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).

◆ updateAminoAcidByName()

bool updateAminoAcidByName	(	const char *	name,
		const ms_umod_aminoacid *	aa
	)

Update the information for a specific amino acid.

Parameters

name	name of the amino acid for updating.
aa	an object to copy the content from.

Returns: TRUE if the amino acid has been found and successfully updated and FALSE otherwise.

◆ updateAminoAcidByNumber()

bool updateAminoAcidByNumber	(	const int	idx,
		const ms_umod_aminoacid *	aa
	)

Update the information for a specific amino acid.

Parameters

idx	number of the amino acid for updating from 0 to (getNumberOfAminoAcids() - 1).
aa	an object to copy the content from.

Returns: TRUE if the amino acid has been found and successfully updated and FALSE otherwise.

◆ updateElementByName()

bool updateElementByName	(	const char *	name,
		const ms_umod_element *	element
	)

Update the information for a specific element.

Parameters

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

Returns: TRUE if the element has been found and successfully updated and FALSE otherwise.

◆ updateElementByNumber()

bool updateElementByNumber	(	const int	idx,
		const ms_umod_element *	element
	)

Update the information for a specific element.

Parameters

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

Returns: TRUE if the element has been found and successfully updated and FALSE otherwise.

◆ updateModBrickByName()

bool updateModBrickByName	(	const char *	name,
		const ms_umod_modbrick *	brick
	)

Update the information for a specific modification brick.

Parameters

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

Returns: TRUE if the modification brick has been found and successfully updated and FALSE otherwise.

◆ updateModBrickByNumber()

bool updateModBrickByNumber	(	const int	idx,
		const ms_umod_modbrick *	brick
	)

Update the information for a specific modification brick.

Parameters

idx	number of the modification brick for updating from 0 to (getNumberOfModBricks() - 1).
brick	an object to copy the content from.

Returns: TRUE if the modification brick has been found and successfully updated and FALSE otherwise.

◆ updateModificationByName()

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

Update the information for a specific modification.

Parameters

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

Returns: TRUE if the modification has been found and successfully updated and FALSE otherwise.

◆ updateModificationByNumber()

bool updateModificationByNumber	(	const int	idx,
		const ms_umod_modification *	mod
	)

Update the information for a specific modification.

Parameters

idx	number of the modification for updating from 0 to (getNumberOfModifications() - 1).
mod	an object to copy the content from.

Returns: TRUE if the modification 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_umod_configfile.hpp
ms_umod_configfile.cpp

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ MODFILE_FLAGS

Constructor & Destructor Documentation

◆ ms_umod_configfile() [1/2]

◆ ms_umod_configfile() [2/2]

Member Function Documentation

◆ appendAminoAcid()

◆ appendElement()

◆ appendErrors()

◆ appendModBrick()

◆ appendModification()

◆ applyVisibility() [1/2]

◆ applyVisibility() [2/2]

◆ clearAllErrors()

◆ copyFrom() [1/2]

◆ copyFrom() [2/2]

◆ defaultValues()

◆ deleteAminoAcidByName()

◆ deleteAminoAcidByNumber()

◆ deleteElementByName()

◆ deleteElementByNumber()

◆ deleteModBrickByName()

◆ deleteModBrickByNumber()

◆ deleteModificationByName()

◆ deleteModificationByNumber()

◆ findModFileName()

◆ findModification()

◆ getAminoAcidByName()

◆ getAminoAcidByNumber()

◆ getDefaultSchemaFileName()

◆ getElementByName()

◆ getElementByNumber()

◆ getErrorHandler()

◆ getFileName()

◆ getLastError()

◆ getLastErrorString()

◆ getModBrickByName()

◆ getModBrickByNumber()

◆ getModFileList()

◆ getModificationByName()

◆ getModificationByNumber()

◆ getNumberOfAminoAcids()

◆ getNumberOfElements()

◆ getNumberOfModBricks()

◆ getNumberOfModifications()

◆ getSchemaFileName()

◆ isValid()

◆ operator=()

◆ read_buffer()

◆ read_file()

◆ save_buffer()

◆ save_file()

◆ setConnectionSettings()

◆ setFileName()

◆ setSchemaFileName()

◆ updateAminoAcidByName()

◆ updateAminoAcidByNumber()

◆ updateElementByName()

◆ updateElementByNumber()

◆ updateModBrickByName()

◆ updateModBrickByNumber()

◆ updateModificationByName()

◆ updateModificationByNumber()

◆ validateDocument()