Represents a modif object in unimod.xml. More...

#include <ms_umod_modification.hpp>

Inherits ms_xml_IValidatable.

Public Member Functions
	ms_umod_modification ()
	Default constructor.

	ms_umod_modification (const ms_quant_localdef &src, const ms_umod_configfile &umodFile)
	Copying constructor that copies the content from a `quantitation.xml` object.

	ms_umod_modification (const ms_quant_unmodified &src)
	Copying constructor that copies the content from a `quantitation.xml` object.

	ms_umod_modification (const ms_umod_modification &src)
	Copying constructor.

virtual	~ms_umod_modification ()
	Destructor.

void	appendAltName (const char *alt_name)
	Adds a new `alt_name` element at the end of the list.

void	appendIgnore (const ms_umod_composition *ignore)
	Adds a new `Ignore` object at the end of the list.

void	appendSpecificity (const ms_umod_specificity *specificity)
	Adds a new specificity at the end of the list.

void	appendXref (const ms_umod_xref *xref)
	Adds a new 'xref' object at the end of the list.

void	clearAltNames ()
	Deletes all `alt_name` elements from the list.

void	clearIgnores ()
	Deletes all `Ignore` elements from the list.

void	clearSpecificities ()
	Deletes all specificities from the list.

void	clearXrefs ()
	Deletes all `xref` elements from the list.

void	copyFrom (const ms_quant_localdef *right, const ms_umod_configfile &umodFile)
	Copies all content from a `quantitation.xml` object.

void	copyFrom (const ms_quant_unmodified *right)
	Copies all content from a `quantitation.xml` object.

void	copyFrom (const ms_umod_modification *right)
	Copies all content from another instance.

void	defaultValues ()
	Call this member if you want to start again.

bool	deleteAltName (const int idx)
	Remove an `alt_name` element from the list in memory.

bool	deleteIgnore (const int idx)
	Remove an `Ignore` element from the list in memory.

bool	deleteSpecificity (const int idx)
	Remove a specificity from the list in memory.

bool	deleteXref (const int idx)
	Remove an `xref` element from the list in memory.

void	dropApproved ()
	Delete the `approved` attribute.

void	dropDateTimeModified ()
	Delete the `date_time_modified` attribute.

void	dropDateTimePosted ()
	Delete the `date_time_posted` attribute.

void	dropDelta ()
	Delete all information about the currently held `delta` element.

void	dropFullName ()
	Delete the `full_name` attribute.

void	dropGroupOfPoster ()
	Delete the `group_of_poster` attribute.

void	dropMiscNotes ()
	Delete the `misc_notes` element.

void	dropRecordID ()
	Delete the `record_id` attribute.

void	dropTitle ()
	Delete the `title` attribute.

void	dropUsernameOfPoster ()
	Delete the `username_of_poster` attribute.

int	findSpecGroup (const char *modFileName) const
	Retrieves specificity group ID for `mod_file`-style modification name.

std::string	getAltName (const int idx) const
	Returns an `alt_name` element by its number.

std::string	getAltNameSchemaType () const
	Obtain a symbolic name for the `alt_name` element schema type.

std::string	getApprovedSchemaType () const
	Obtain a symbolic name for the `approved` attribute schema type.

std::string	getDateTimeModified () const
	Returns the value of the `date_time_modified` attribute.

std::string	getDateTimeModifiedSchemaType () const
	Obtain a symbolic name for the `date_time_modified` attribute schema type.

std::string	getDateTimePosted () const
	Returns the value of the `date_time_posted` attribute.

std::string	getDateTimePostedSchemaType () const
	Obtain a symbolic name for the `date_time_posted` attribute schema type.

const ms_umod_composition *	getDelta () const
	Returns a read-only pointer to the object representing `delta` element.

std::string	getDeltaSchemaType () const
	Obtain a symbolic name for the `delta` element schema type.

std::string	getFullName () const
	Returns the value of the `full_name` attribute.

std::string	getFullNameSchemaType () const
	Obtain a symbolic name for the `full_name` attribute schema type.

std::string	getGroupOfPoster () const
	Returns the value of the `group_of_poster` attribute.

std::string	getGroupOfPosterSchemaType () const
	Obtain a symbolic name for the `group_of_poster` attribute schema type.

const ms_umod_composition *	getIgnore (const int idx) const
	Returns an `Ignore` object by its number.

std::string	getIgnoreSchemaType () const
	Obtain a symbolic name for the `Ignore` element schema type.

std::string	getMiscNotes () const
	Returns the `misc_notes` element or an empty string if not set.

std::string	getMiscNotesSchemaType () const
	Obtain a symbolic name for the `misc_notes` element schema type.

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

int	getNumberOfAltNames () const
	Returns the number of `alt_name` elements currently held in memory.

int	getNumberOfIgnores () const
	Returns the number of `Ignore` objects currently held in memory.

int	getNumberOfSpecificities () const
	Returns the number of specificities currently held in memory.

int	getNumberOfXrefs () const
	Returns the number of `xref` elements currently held in memory.

std::string	getRecordID () const
	Returns the value of the `record_id` attribute.

std::string	getRecordIDSchemaType () const
	Obtain a symbolic name for the `record_id` attribute schema type.

virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.

const ms_umod_specificity *	getSpecificity (const int idx) const
	Returns a specificity object by its number.

const ms_umod_specificity *	getSpecificityBySite (const char *site) const
	Returns a specificity object by its site name.

const ms_umod_specificity *	getSpecificityBySiteAndPosition (const char site, const char position) const
	Returns a specificity object by its site name and position.

std::string	getSpecificitySchemaType () const
	Obtain a symbolic name for the `specificity` element schema type.

std::string	getTitle () const
	Returns the value of the `title` attribute.

std::string	getTitleSchemaType () const
	Obtain a symbolic name for the `title` attribute schema type.

std::string	getUsernameOfPoster () const
	Returns the value of the `username_of_poster` attribute.

std::string	getUsernameOfPosterSchemaType () const
	Obtain a symbolic name for the `username_of_poster` attribute schema type.

const ms_umod_xref *	getXref (const int idx) const
	Returns a read-only pointer to `xref` element by its number.

std::string	getXrefSchemaType () const
	Obtain a symbolic name for the `xref` element schema type.

bool	haveApproved () const
	Indicates presence of the `approved` attribute.

bool	haveDateTimeModified () const
	Indicates presence of the `date_time_modified` attribute.

bool	haveDateTimePosted () const
	Indicates presence of the `date_time_posted` attribute.

bool	haveDelta () const
	Indicates presence of the `delta` element.

bool	haveFullName () const
	Indicates presence of the `full_name` attribute.

bool	haveGroupOfPoster () const
	Indicates presence of the `group_of_poster` attribute.

bool	haveMiscNotes () const
	Indicates presence of the `misc_notes` element.

bool	haveRecordID () const
	Indicates presence of the `record_id` attribute.

bool	haveTitle () const
	Indicates presence of the `title` attribute.

bool	haveUsernameOfPoster () const
	Indicates presence of the `username_of_poster` attribute.

bool	isApproved () const
	Returns the value of the `approved` attribute.

bool	isPrivacyEnabled () const
	Indicates whether privacy settings are enabled for this modification.

bool	isPrivate () const
	Indicates whether this modification is private and so cannot be viewed or used. Only valid if privacy is enabled.

bool	isSameAs (const ms_umod_modification &right_mod) const
	Returns true if instances contain the same information.

ms_umod_modification &	operator= (const ms_umod_modification &right)
	C++ style assignment operator.

void	setApproved (const bool value)
	Set a custom value for the `approved` attribute.

void	setDateTimeModified (const char *value)
	Set a custom value for the `date_time_modified` attribute.

void	setDateTimePosted (const char *value)
	Set a custom value for the `date_time_posted` attribute.

void	setDelta (const ms_umod_composition *delta)
	Supply new content for the `delta` element.

void	setFullName (const char *value)
	Set a custom value for the `full_name` attribute.

void	setGroupOfPoster (const char *value)
	Set a custom value for the `group_of_poster` attribute.

void	setMiscNotes (const char *value)
	Set a custom value for the `misc_notes` element.

void	setPrivacyEnabled (bool b)
	Sets whether privacy settings are enabled for this modification.

void	setPrivate (bool b)
	Sets whether this modification is private.

void	setRecordID (const char *value)
	Set a custom value for the `record_id` attribute.

void	setTitle (const char *value)
	Set a custom value for the `title` attribute.

void	setUsernameOfPoster (const char *value)
	Set a custom value for the `username_of_poster` attribute.

bool	updateAltName (const int idx, const char *alt_name)
	Update the string for a particular `alt_name` element.

bool	updateIgnore (const int idx, const ms_umod_composition *ignore)
	Update the information for a particular `Ignore` element.

void	updateMasses (const ms_umod_configfile &umodFile, const ms_quant_component &quantComp)
	Recalculates all deltas with isotope-substitution according to selected component in `quantification.xml`.

bool	updateSpecificity (const int idx, const ms_umod_specificity *specificity)
	Update the information for a particular specificity.

bool	updateXref (const int idx, const ms_umod_xref *xref)
	Update the information for a particular `xref` element.

virtual std::string	validateDeep (const ms_xml_schema *pSchemaFileObj) const
	Performs validation of all child elements in addition to 'shallow' validation.

virtual std::string	validateShallow (const ms_xml_schema *pSchemaFileObj) const
	Performs simple validation of the top-level elements only.

Detailed Description

Represents a modif object in unimod.xml.

Constructor & Destructor Documentation

◆ ms_umod_modification() [1/4]

ms_umod_modification ( )

Default constructor.

Assigns reasonable default values to all internal members.

◆ ms_umod_modification() [2/4]

ms_umod_modification ( const ms_umod_modification & src )

Copying constructor.

Parameters

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

◆ ms_umod_modification() [3/4]

ms_umod_modification	(	const ms_quant_localdef &	src,
		const ms_umod_configfile &	umodFile
	)

Copying constructor that copies the content from a quantitation.xml object.

Parameters

src	a `quantitation.xml` object to copy the content from.
umodFile	an instance of a Unimod file object to extract element masses.

◆ ms_umod_modification() [4/4]

ms_umod_modification ( const ms_quant_unmodified & src )

Copying constructor that copies the content from a quantitation.xml object.

Parameters

src	a `quantitation.xml` object to copy the content from.

Member Function Documentation

◆ appendAltName()

void appendAltName ( const char * alt_name )

Adds a new alt_name element at the end of the list.

Creates a new alt_name element, sets it to the supplied string value and adds it at the end of the alt_name elements list.

Parameters

alt_name a string value for the new element.

◆ appendIgnore()

void appendIgnore ( const ms_umod_composition * ignore )

Adds a new Ignore object at the end of the list.

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

Parameters

ignore an Ignore object to copy the content from.

◆ appendSpecificity()

void appendSpecificity ( const ms_umod_specificity * specificity )

Adds a new specificity at the end of the list.

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

Parameters

specificity an instance of specificity object to copy the content from.

◆ appendXref()

void appendXref ( const ms_umod_xref * xref )

Adds a new 'xref' object at the end of the list.

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

Parameters

xref	an `xref` object to copy the content from.

◆ copyFrom() [1/3]

void copyFrom	(	const ms_quant_localdef *	right,
		const ms_umod_configfile &	umodFile
	)

Copies all content from a quantitation.xml object.

Parameters

right	a quantitation object to copy the content from.
umodFile	a Unimod file object to extract element masses from.

◆ copyFrom() [2/3]

void copyFrom ( const ms_quant_unmodified * right )

Copies all content from a quantitation.xml object.

Parameters

right a quantitation object to copy the content from.

◆ copyFrom() [3/3]

void copyFrom ( const ms_umod_modification * right )

Copies all content from another instance.

Parameters

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

◆ defaultValues()

void defaultValues ( )

Call this member if you want to start again.

All internal values are reset to their defaults, as if the object had been freshly created with the default constructor.

◆ deleteAltName()

bool deleteAltName ( const int idx )

Remove an alt_name element from the list in memory.

Parameters

idx	number of the `alt_name` element for deletion from 0 to (getNumberOfAltNames() - 1).

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

◆ deleteIgnore()

bool deleteIgnore ( const int idx )

Remove an Ignore element from the list in memory.

Parameters

idx	number of the `Ignore` element for deletion from 0 to (getNumberOfIgnores() - 1).

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

◆ deleteSpecificity()

bool deleteSpecificity ( const int idx )

Remove a specificity from the list in memory.

Parameters

idx	number of the specificity for deletion from 0 to (getNumberOfSpecificities() - 1).

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

◆ deleteXref()

bool deleteXref ( const int idx )

Remove an xref element from the list in memory.

Parameters

idx	number of the `xref` element for deletion from 0 to (getNumberOfXrefs() - 1).

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

◆ dropApproved()

void dropApproved ( )

Delete the approved attribute.

Deletes the attribute until it is re-set.

◆ dropDateTimeModified()

void dropDateTimeModified ( )

Delete the date_time_modified attribute.

Deletes the attribute until it is re-set.

◆ dropDateTimePosted()

void dropDateTimePosted ( )

Delete the date_time_posted attribute.

Deletes the attribute until it is re-set.

◆ dropDelta()

void dropDelta ( )

Delete all information about the currently held delta element.

Deletes the element until it is re-set.

◆ dropFullName()

void dropFullName ( )

Delete the full_name attribute.

Deletes the attribute until it is re-set.

◆ dropGroupOfPoster()

void dropGroupOfPoster ( )

Delete the group_of_poster attribute.

Deletes the attribute until it is re-set.

◆ dropMiscNotes()

void dropMiscNotes ( )

Delete the misc_notes element.

Deletes the element until it is re-set.

◆ dropRecordID()

void dropRecordID ( )

Delete the record_id attribute.

Deletes the attribute until it is re-set.

◆ dropTitle()

void dropTitle ( )

Delete the title attribute.

Deletes the attribute until it is re-set.

◆ dropUsernameOfPoster()

void dropUsernameOfPoster ( )

Delete the username_of_poster attribute.

Deletes the attribute until it is re-set.

◆ findSpecGroup()

int findSpecGroup ( const char * modFileName ) const

Retrieves specificity group ID for mod_file-style modification name.

As each modification from unimod.xml can be converted into several mod_file-style modifications, we have to be able to find the right specificity group for a given mod_file-style name.

Parameters

modFileName mod_file-style modification name (like 'Acetyl (K)').

Returns: specificity group ID which can be used to extract just a single mod_file-style modification from a Unimod-style modification. If the specificity not found -1 will be returned.

◆ getAltName()

std::string getAltName ( const int idx ) const

Returns an alt_name element by its number.

Retrieves an alt_name element from the list by its number.

Parameters

idx	number of the `alt_name` element from 0 to (getNumberOfAltNames() - 1).

Returns: the retrieved string value.

◆ getAltNameSchemaType()

std::string getAltNameSchemaType ( ) const

Obtain a symbolic name for the alt_name element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getApprovedSchemaType()

std::string getApprovedSchemaType ( ) const

Obtain a symbolic name for the approved attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getDateTimeModified()

std::string getDateTimeModified ( ) const

Returns the value of the date_time_modified attribute.

Returns: current value of the attribute.

◆ getDateTimeModifiedSchemaType()

std::string getDateTimeModifiedSchemaType ( ) const

Obtain a symbolic name for the date_time_modified attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getDateTimePosted()

std::string getDateTimePosted ( ) const

Returns the value of the date_time_posted attribute.

Returns: current value of the attribute.

◆ getDateTimePostedSchemaType()

std::string getDateTimePostedSchemaType ( ) const

Obtain a symbolic name for the date_time_posted attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getDelta()

const ms_umod_composition * getDelta ( ) const

Returns a read-only pointer to the object representing delta element.

Modification delta which is represented as a composition of chemical elements.

Returns: read-only pointer to the 'delta' object. See Maintaining object references: two rules of thumb.

◆ getDeltaSchemaType()

std::string getDeltaSchemaType ( ) const

Obtain a symbolic name for the delta element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getFullName()

std::string getFullName ( ) const

Returns the value of the full_name attribute.

A full name for the modification.

Returns: current value of the attribute.

◆ getFullNameSchemaType()

std::string getFullNameSchemaType ( ) const

Obtain a symbolic name for the full_name attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getGroupOfPoster()

std::string getGroupOfPoster ( ) const

Returns the value of the group_of_poster attribute.

Returns: current value of the attribute.

◆ getGroupOfPosterSchemaType()

std::string getGroupOfPosterSchemaType ( ) const

Obtain a symbolic name for the group_of_poster attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getIgnore()

const ms_umod_composition * getIgnore ( const int idx ) const

Returns an Ignore object by its number.

Parameters

idx	number of the `Ignore` element from 0 to (getNumberOfIgnores() - 1).

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

◆ getIgnoreSchemaType()

std::string getIgnoreSchemaType ( ) const

Obtain a symbolic name for the Ignore element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getMiscNotes()

std::string getMiscNotes ( ) const

Returns the misc_notes element or an empty string if not set.

Returns: current string value of the element.

◆ getMiscNotesSchemaType()

std::string getMiscNotesSchemaType ( ) const

Obtain a symbolic name for the misc_notes element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getNumberOfSpecificities()

int getNumberOfSpecificities ( ) const

Returns the number of specificities currently held in memory.

Returns: total number of specificities in the modification object.

◆ getRecordID()

std::string getRecordID ( ) const

Returns the value of the record_id attribute.

The unique and stable record ID for the unimod record. Added in Mascot Parser version 2.3.01.

Note that in previous versions of parser, this attribute was not loaded or saved from files. This means that files created by the Mascot Server 2.2 configuration editor strip out the record ID. It also means that the Unimod fragments contained in the Mascot results files from version 2.2 do not contain the record ID.

Returns: current value of the attribute.

◆ getRecordIDSchemaType()

std::string getRecordIDSchemaType ( ) const

Obtain a symbolic name for the record_id attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getSchemaType()

std::string getSchemaType ( ) const

virtual

Returns name of the schema type that can be used to validate this element.

Additional information about the current object can be retrieved from the associated XML schema file. Every element in an XML document is defined with a named type, which you can use to find out what kind of limits (numerical or otherwise) are defined for values of that type.

See also: validateShallow(), validateDeep()

Returns: a symbolic fully qualified type name (for example, "umod:nameType")

◆ getSpecificity()

const ms_umod_specificity * getSpecificity ( const int idx ) const

Returns a specificity object by its number.

Parameters

idx	number of the specificity from 0 to (getNumberOfSpecificities() - 1).

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

◆ getSpecificityBySite()

const ms_umod_specificity * getSpecificityBySite ( const char * site ) const

Returns a specificity object by its site name.

Multiple specificities may exist for a given site with differing position definitions. This method returns the first specificity found with the same site definition. Use ms_umod_modification::getSpecificityBySiteAndPosition to obtain a specificity by bot site and position.

Parameters

site	Name of the specificity to return. String that should be one of the Type mqm:siteType values.

Returns: a read-only pointer to the retrieved object, can be NULL if specificity for the site is not yet defined. See Maintaining object references: two rules of thumb.

◆ getSpecificityBySiteAndPosition()

const ms_umod_specificity * getSpecificityBySiteAndPosition	(	const char *	site,
		const char *	position
	)		const

Returns a specificity object by its site name and position.

Multiple specificities may exist for a given site with differing position definitions.

Parameters

site	Name of the specificity to return. String that should be one of the Type mqm:siteType values.
position	Position of the specificity to return. String that should be one of the Type mqm:positionType values.

Returns: a read-only pointer to the retrieved object, can be NULL if specificity for the site is not yet defined. See Maintaining object references: two rules of thumb.

◆ getSpecificitySchemaType()

std::string getSpecificitySchemaType ( ) const

Obtain a symbolic name for the specificity element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getTitle()

std::string getTitle ( ) const

Returns the value of the title attribute.

A unique name for the modification object.

Returns: current value of the attribute.

◆ getTitleSchemaType()

std::string getTitleSchemaType ( ) const

Obtain a symbolic name for the title attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getUsernameOfPoster()

std::string getUsernameOfPoster ( ) const

Returns the value of the username_of_poster attribute.

Returns: current value of the attribute.

◆ getUsernameOfPosterSchemaType()

std::string getUsernameOfPosterSchemaType ( ) const

Obtain a symbolic name for the username_of_poster attribute schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ getXref()

const ms_umod_xref * getXref ( const int idx ) const

Returns a read-only pointer to xref element by its number.

Parameters

idx	number of the 'xref' element from 0 to (getNumberOfXrefs() - 1).

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

◆ getXrefSchemaType()

std::string getXrefSchemaType ( ) const

Obtain a symbolic name for the xref element schema type.

The obtained type name can be used to get a corresponding type description object from ms_xml_schema.

Returns: symbolic type name for the element.

◆ haveApproved()

bool haveApproved ( ) const

Indicates presence of the approved attribute.

Returns: TRUE if the attribute is present and FALSE otherwise.

◆ haveDateTimeModified()

bool haveDateTimeModified ( ) const

Indicates presence of the date_time_modified attribute.

Returns: TRUE if the attribute is present and FALSE otherwise.

◆ haveDateTimePosted()

bool haveDateTimePosted ( ) const

Indicates presence of the date_time_posted attribute.

Returns: TRUE if the attribute is present and FALSE otherwise.

◆ haveDelta()

bool haveDelta ( ) const

Indicates presence of the delta element.

Returns: TRUE if the element 'delta' is present and FALSE otherwise.

◆ haveFullName()

bool haveFullName ( ) const

Indicates presence of the full_name attribute.

Returns: TRUE if the attribute is present and FALSE otherwise.

◆ haveGroupOfPoster()

bool haveGroupOfPoster ( ) const

Indicates presence of the group_of_poster attribute.

Returns: TRUE if the attribute is present and FALSE otherwise.

◆ haveMiscNotes()

bool haveMiscNotes ( ) const

Indicates presence of the misc_notes element.

Returns: TRUE if the element is present and FALSE otherwise.

◆ haveRecordID()

bool haveRecordID ( ) const

Indicates presence of the record_id attribute.

Returns: TRUE if the attribute is present and FALSE otherwise.

◆ haveTitle()

bool haveTitle ( ) const

Indicates presence of the title attribute.

Returns: TRUE if the attribute is present and FALSE otherwise.

◆ haveUsernameOfPoster()

bool haveUsernameOfPoster ( ) const

Indicates presence of the username_of_poster attribute.

Returns: TRUE if the attribute is present and FALSE otherwise.

◆ isApproved()

bool isApproved ( ) const

Returns the value of the approved attribute.

Returns: current value of the attribute.

◆ isPrivacyEnabled()

bool isPrivacyEnabled ( ) const

Indicates whether privacy settings are enabled for this modification.

Returns: true if this modification has privacy enabled. Note: Not part of the Unimod schema file.

◆ isPrivate()

bool isPrivate ( ) const

Indicates whether this modification is private and so cannot be viewed or used. Only valid if privacy is enabled.

Returns: true if this modification is private and so cannot be viewed or used. Only valid if privacy is enabled. Note: Not part of the Unimod schema file.

◆ isSameAs()

bool isSameAs ( const ms_umod_modification & right_mod ) const

Returns true if instances contain the same information.

Compares all data members except modified date, posted date and user.

Parameters

right_mod another instance of this class to compare.

Returns: true if objects contain same information.

◆ operator=()

ms_umod_modification & operator= ( const ms_umod_modification & right )

C++ style assignment operator.

Parameters

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

Returns: reference to the current object

◆ setApproved()

void setApproved ( const bool value )

Set a custom value for the approved attribute.

Parameters

value a new value for the attribute.

◆ setDateTimeModified()

void setDateTimeModified ( const char * value )

Set a custom value for the date_time_modified attribute.

Parameters

value a new value for the attribute.

◆ setDateTimePosted()

void setDateTimePosted ( const char * value )

Set a custom value for the date_time_posted attribute.

Parameters

value a new value for the attribute.

◆ setDelta()

void setDelta ( const ms_umod_composition * delta )

Supply new content for the delta element.

Parameters

delta new content for the 'delta' object. If a NULL pointer is supplied instead of an object, the current content will be deleted and the 'delta' element will be dropped.

◆ setFullName()

void setFullName ( const char * value )

Set a custom value for the full_name attribute.

Parameters

value a new value for the attribute.

◆ setGroupOfPoster()

void setGroupOfPoster ( const char * value )

Set a custom value for the group_of_poster attribute.

Parameters

value a new value for the attribute.

◆ setMiscNotes()

void setMiscNotes ( const char * value )

Set a custom value for the misc_notes element.

Parameters

value a new value for the element.

◆ setPrivacyEnabled()

void setPrivacyEnabled ( bool b )

Sets whether privacy settings are enabled for this modification.

Parameters

b	sets if this modification has privacy enabled.

◆ setPrivate()

void setPrivate ( bool b )

Sets whether this modification is private.

Parameters

b	sets if this modification is private.

◆ setRecordID()

void setRecordID ( const char * value )

Set a custom value for the record_id attribute.

Parameters

value a new value for the attribute.

◆ setTitle()

void setTitle ( const char * value )

Set a custom value for the title attribute.

Parameters

value a new value for the attribute.

◆ setUsernameOfPoster()

void setUsernameOfPoster ( const char * value )

Set a custom value for the username_of_poster attribute.

Parameters

value a new value for the attribute.

◆ updateAltName()

bool updateAltName	(	const int	idx,
		const char *	alt_name
	)

Update the string for a particular alt_name element.

Parameters

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

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

◆ updateIgnore()

bool updateIgnore	(	const int	idx,
		const ms_umod_composition *	ignore
	)

Update the information for a particular Ignore element.

Parameters

idx	number of the `Ignore` element for updating from 0 to (getNumberOfIgnores() - 1).
ignore	an object to copy the content from.

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

◆ updateMasses()

void updateMasses	(	const ms_umod_configfile &	umodFile,
		const ms_quant_component &	quantComp
	)

Recalculates all deltas with isotope-substitution according to selected component in quantification.xml.

The method updates all deltas, neutral losses and ignore masses according to the selected isotope substitution. Masses are recalculated only in the current modification object, not in the whole Unimod file object umodFile. The Unimod file object is used only to retrieve masses of elements and their isotopes.

Parameters

umodFile	a Unimod file object.
quantComp	a component object from the `quantitation.xml` file.

◆ updateSpecificity()

bool updateSpecificity	(	const int	idx,
		const ms_umod_specificity *	specificity
	)

Update the information for a particular specificity.

Parameters

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

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

◆ updateXref()

bool updateXref	(	const int	idx,
		const ms_umod_xref *	xref
	)

Update the information for a particular xref element.

Parameters

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

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

◆ validateDeep()

std::string validateDeep ( const ms_xml_schema * pSchemaFileObj ) const

virtual

Performs validation of all child elements in addition to 'shallow' validation.

The current object can be checked against an XML schema. When using this method all possible checks are performed. However, this is not a substitute for the schema: some schema-defined constraint are not applied (unique fields, foreign keys etc.).

In order to make sure that current object is free from all syntax errors validate it as a part of the whole document.

See also: validateShallow(), getSchemaType()

Parameters

pSchemaFileObj a valid schema object instance to validate against.

Returns: user-friendly description of any errors found during validation or an empty string if no errors detected.

◆ validateShallow()

std::string validateShallow ( const ms_xml_schema * pSchemaFileObj ) const

virtual

Performs simple validation of the top-level elements only.

The current object can be checked against some basic constraints in a schema without looking at children element types. When using this method only the current object and children derived from standard types (for example, restrictions with enumerations) are checked. For more thorough validation, use validateDeep().

See also: getSchemaType()

Parameters

pSchemaFileObj a valid schema object instance to validate against.

Returns: user-friendly description of any errors found during validation or an empty string if no errors detected.

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

ms_umod_modification.hpp
ms_umod_modification.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ms_umod_modification() [1/4]

◆ ms_umod_modification() [2/4]

◆ ms_umod_modification() [3/4]

◆ ms_umod_modification() [4/4]

Member Function Documentation

◆ appendAltName()

◆ appendIgnore()

◆ appendSpecificity()

◆ appendXref()

◆ copyFrom() [1/3]

◆ copyFrom() [2/3]

◆ copyFrom() [3/3]

◆ defaultValues()

◆ deleteAltName()

◆ deleteIgnore()

◆ deleteSpecificity()

◆ deleteXref()

◆ dropApproved()

◆ dropDateTimeModified()

◆ dropDateTimePosted()

◆ dropDelta()

◆ dropFullName()

◆ dropGroupOfPoster()

◆ dropMiscNotes()

◆ dropRecordID()

◆ dropTitle()

◆ dropUsernameOfPoster()

◆ findSpecGroup()

◆ getAltName()

◆ getAltNameSchemaType()

◆ getApprovedSchemaType()

◆ getDateTimeModified()

◆ getDateTimeModifiedSchemaType()

◆ getDateTimePosted()

◆ getDateTimePostedSchemaType()

◆ getDelta()

◆ getDeltaSchemaType()

◆ getFullName()

◆ getFullNameSchemaType()

◆ getGroupOfPoster()

◆ getGroupOfPosterSchemaType()

◆ getIgnore()

◆ getIgnoreSchemaType()

◆ getMiscNotes()

◆ getMiscNotesSchemaType()

◆ getNumberOfSpecificities()

◆ getRecordID()

◆ getRecordIDSchemaType()

◆ getSchemaType()

◆ getSpecificity()

◆ getSpecificityBySite()

◆ getSpecificityBySiteAndPosition()

◆ getSpecificitySchemaType()

◆ getTitle()

◆ getTitleSchemaType()

◆ getUsernameOfPoster()

◆ getUsernameOfPosterSchemaType()

◆ getXref()

◆ getXrefSchemaType()

◆ haveApproved()

◆ haveDateTimeModified()

◆ haveDateTimePosted()

◆ haveDelta()

◆ haveFullName()

◆ haveGroupOfPoster()

◆ haveMiscNotes()

◆ haveRecordID()

◆ haveTitle()

◆ haveUsernameOfPoster()

◆ isApproved()

◆ isPrivacyEnabled()

◆ isPrivate()

◆ isSameAs()

◆ operator=()

◆ setApproved()

◆ setDateTimeModified()

◆ setDateTimePosted()