Represents NeutralLoss and PepNeutralLoss objects in unimod.xml. More...

#include <ms_umod_neutralloss.hpp>

Inheritance diagram for ms_umod_neutralloss:

Collaboration diagram for ms_umod_neutralloss:

Public Member Functions
	ms_umod_neutralloss ()
	Default constructor.
	ms_umod_neutralloss (const ms_umod_neutralloss &src)
	Copying constructor.
	ms_umod_neutralloss (const ms_quant_pepneutralloss &src, const ms_umod_configfile &umodFile)
	Copying constructor.
	ms_umod_neutralloss (const ms_quant_neutralloss &src, const ms_umod_configfile &umodFile)
	Copying constructor.
virtual	~ms_umod_neutralloss ()
	Destructor.
void	appendElemRef (const ms_umod_elemref *elemref)
	Adds a new element reference object at the end of the list.
void	clearElemRefs ()
	Deletes all element reference objects from the list.
void	copyFrom (const ms_quant_neutralloss *right, const ms_umod_configfile &umodFile)
	Copies all content from another object.
void	copyFrom (const ms_umod_composition *right)
	Copies all content from another instance.
void	copyFrom (const ms_quant_composition *right, const ms_umod_configfile &umodFile)
	Copies all content from another object.
void	copyFrom (const ms_quant_pepneutralloss *right, const ms_umod_configfile &umodFile)
	Copies all content from another object.
void	copyFrom (const ms_umod_neutralloss *right)
	Copies all content from another instance.
void	defaultValues ()
	Call this member if you want to start again.
bool	deleteElemRef (const int idx)
	Remove an element reference object from the list in memory.
void	dropAvgeMass ()
	Delete the `avge_mass` attribute.
void	dropCode ()
	Delete the `code` attribute.
void	dropCompositionString ()
	Delete the `composition` attribute.
void	dropDescription ()
	Delete the `description` attribute.
void	dropFlag ()
	Delete the `flag` attribute.
void	dropMonoMass ()
	Delete the `mono_mass` attribute.
void	dropPairsWith ()
	Delete the `pairs_with` attribute.
double	getAvgeMass () const
	Returns the value of the `avge_mass` attribute.
std::string	getAvgeMassSchemaType () const
	Obtain a symbolic name for the `avge_mass` attribute schema type.
std::string	getCode () const
	Returns the value of the `code` attribute.
std::string	getCodeSchemaType () const
	Obtain a symbolic name for the `code` attribute schema type.
std::string	getCompositionString () const
	Returns the value of the `composition` attribute.
std::string	getCompositionStringSchemaType () const
	Obtain a symbolic name for the `composition` attribute schema type.
std::string	getDescription () const
	Returns the value of the `description` attribute.
std::string	getDescriptionSchemaType () const
	Obtain a symbolic name for the `description` attribute schema type.
const ms_umod_elemref *	getElemRef (const int idx) const
	Returns a read-only pointer to an element reference object by its number.
std::string	getElemRefSchemaType () const
	Obtain a symbolic name for the element's schema type.
std::string	getFlagSchemaType () const
	Obtain a symbolic name for the `flag` attribute schema type.
double	getMonoMass () const
	Returns the value of the `mono_mass` attribute.
std::string	getMonoMassSchemaType () const
	Obtain a symbolic name for the `mono_mass` attribute schema type.
int	getNumberOfElemRefs () const
	Returns the number of element reference objects currently held in memory.
std::string	getPairsWith () const
	Returns the value of the `pairs_with` attribute.
std::string	getPairsWithSchemaType () const
	Obtain a symbolic name for the `pairs_with` attribute schema type.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
bool	haveAvgeMass () const
	Indicates presence of the `avge_mass` attribute.
bool	haveCode () const
	Indicates presence of the `code` attribute.
bool	haveCompositionString () const
	Indicates presence of the `composition` attribute.
bool	haveDescription () const
	Indicates presence of the `description` attribute.
bool	haveFlag () const
	Indicates presence of the `flag` attribute.
bool	haveMonoMass () const
	Indicates presence of the `mono_mass` attribute.
bool	havePairsWith () const
	Indicates presence of the `pairs_with` attribute.
bool	isFlag () const
	Returns the value of the `flag` attribute.
bool	isSameAs (const ms_umod_composition &right) const
	Returns true if instances contain the same information.
ms_umod_neutralloss &	operator= (const ms_umod_neutralloss &right)
	C++ style assignment operator.
void	setAvgeMass (const double value)
	Set a custom value for the `avge_mass` attribute.
void	setCode (const char *value)
	Set a custom value for the `code` attribute.
void	setCompositionString (const char *value)
	Set a custom value for the `composition` attribute.
void	setDescription (const char *value)
	Set a custom value for the `description` attribute.
void	setFlag (const bool value)
	Set a custom value for the `flag` attribute.
void	setMonoMass (const double value)
	Set a custom value for the `mono_mass` attribute.
void	setPairsWith (const char *value)
	Set a custom value for the `pairs_with` attribute.
bool	updateElemRef (const int idx, const ms_umod_elemref *elemref)
	Update the information for a particular element reference object.
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`.
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 NeutralLoss and PepNeutralLoss objects in unimod.xml.

The only difference between a composition object and this object is the attribute 'flag' (which can be the required attribute for the PepNeutralLoss element).

Constructor & Destructor Documentation

ms_umod_neutralloss ( )

Default constructor.

Assigns reasonable default values to all internal members.

ms_umod_neutralloss ( const ms_umod_neutralloss & src )

Copying constructor.

Parameters:

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

ms_umod_neutralloss	(	const ms_quant_neutralloss &	src,
		const ms_umod_configfile &	umodFile
	)

Copying constructor.

Parameters:

src	another object to copy the content from.
umodFile	a Unimod file object to extract element masses from.

ms_umod_neutralloss	(	const ms_quant_pepneutralloss &	src,
		const ms_umod_configfile &	umodFile
	)

Copying constructor.

Parameters:

src	another object to copy the content from.
umodFile	a Unimod file object to extract element masses from.

Member Function Documentation

void appendElemRef ( const ms_umod_elemref * elemref ) [inherited]

Adds a new element reference object at the end of the list.

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

Parameters:

elemref an instance of element reference object to copy the content from.

void copyFrom ( const ms_umod_neutralloss * right )

Copies all content from another instance.

Parameters:

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

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

Copies all content from another object.

Parameters:

right	another object to copy the content from.
umodFile	a Unimod file object to obtain chemical element masses from.

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

Copies all content from another object.

Parameters:

right	another object to copy the content from.
umodFile	a Unimod file object to obtain chemical element masses from.

void copyFrom ( const ms_umod_composition * right ) [inherited]

Copies all content from another instance.

Parameters:

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

void copyFrom	(	const ms_quant_composition *	right,
		const ms_umod_configfile &	umodFile
	)		`[inherited]`

Copies all content from another object.

Parameters:

right	another object to copy the content from.
umodFile	a Unimod file object to obtain element masses from.

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.

Reimplemented from ms_umod_composition.

bool deleteElemRef ( const int idx ) [inherited]

Remove an element reference object from the list in memory.

Parameters:

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

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

void dropAvgeMass ( ) [inherited]

Delete the avge_mass attribute.

Deletes the attribute until is re-set.

void dropCode ( )

Delete the code attribute.

Deletes the attribute until it is re-set.

void dropCompositionString ( ) [inherited]

Delete the composition attribute.

Deletes the attribute until it is re-set.

void dropDescription ( )

Delete the description attribute.

Deletes the attribute until it is re-set.

void dropFlag ( )

Delete the flag attribute.

Deletes the attribute until it is re-set.

void dropMonoMass ( ) [inherited]

Delete the mono_mass attribute.

Deletes the attribute until is re-set.

void dropPairsWith ( )

Delete the pairs_with attribute.

Deletes the attribute until it is re-set.

double getAvgeMass ( ) const [inherited]

Returns the value of the avge_mass attribute.

Average mass for the object.

Returns:: current value of the attribute.

std::string getAvgeMassSchemaType ( ) const [inherited]

Obtain a symbolic name for the avge_mass 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.

std::string getCode ( ) const

Returns the value of the code attribute.

The single-letter code for the fragment of the monolink.

Returns:: current value of the attribute.

std::string getCodeSchemaType ( ) const

Obtain a symbolic name for the code 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.

std::string getCompositionString ( ) const [inherited]

Returns the value of the composition attribute.

A composition string for the object.

Returns:: current value of the attribute.

std::string getCompositionStringSchemaType ( ) const [inherited]

Obtain a symbolic name for the composition 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.

std::string getDescription ( ) const

Returns the value of the description attribute.

The partner codes for the monolink.

Returns:: current value of the attribute.

std::string getDescriptionSchemaType ( ) const

Obtain a symbolic name for the description 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.

const ms_umod_elemref * getElemRef ( const int idx ) const [inherited]

Returns a read-only pointer to an element reference object by its number.

Retrieves an element reference object from the list by its number.

Parameters:

idx	number of the reference from 0 to (getNumberOfElemRefs() - 1).

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

std::string getElemRefSchemaType ( ) const [inherited]

Obtain a symbolic name for the element's 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.

std::string getFlagSchemaType ( ) const

Obtain a symbolic name for the flag 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.

double getMonoMass ( ) const [inherited]

Returns the value of the mono_mass attribute.

Monoisotopic mass for the object.

Returns:: current value of the attribute.

std::string getMonoMassSchemaType ( ) const [inherited]

Obtain a symbolic name for the mono_mass 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.

int getNumberOfElemRefs ( ) const [inherited]

Returns the number of element reference objects currently held in memory.

Returns:: total number of chemical element references in the composition object.

std::string getPairsWith ( ) const

Returns the value of the pairs_with attribute.

The partner codes for the monolink.

Returns:: current value of the attribute.

std::string getPairsWithSchemaType ( ) const

Obtain a symbolic name for the pairs_with 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.

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")

Reimplemented from ms_umod_composition.

bool haveAvgeMass ( ) const [inherited]

Indicates presence of the avge_mass attribute.

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

bool haveCode ( ) const

Indicates presence of the code attribute.

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

bool haveCompositionString ( ) const [inherited]

Indicates presence of the composition attribute.

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

bool haveDescription ( ) const

Indicates presence of the description attribute.

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

bool haveFlag ( ) const

Indicates presence of the flag attribute.

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

bool haveMonoMass ( ) const [inherited]

Indicates presence of the mono_mass attribute.

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

bool havePairsWith ( ) const

Indicates presence of the pairs_with attribute.

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

bool isFlag ( ) const

Returns the value of the flag attribute.

Returns:: current value of the attribute.

bool isSameAs ( const ms_umod_composition & right ) const [inherited]

Returns true if instances contain the same information.

Compares the element symbols and number of symbols that make up the composition regardless of storage order. Element symbols may be specified in the composition but have a count of zero and so do not affect the total mass values.

Parameters:

right another instance of this class to compare.

Returns:: true if the two compositions are equivalent.

ms_umod_neutralloss & operator= ( const ms_umod_neutralloss & right )

C++ style assignment operator.

Parameters:

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

Returns:: reference to the current object

void setAvgeMass ( const double value ) [inherited]

Set a custom value for the avge_mass attribute.

Parameters:

value a new value for the attribute.

void setCode ( const char * value )

Set a custom value for the code attribute.

Parameters:

value a new value for the attribute.

void setCompositionString ( const char * value ) [inherited]

Set a custom value for the composition attribute.

Parameters:

value a new value for the attribute.

void setDescription ( const char * value )

Set a custom value for the description attribute.

Parameters:

value a new value for the attribute.

void setFlag ( const bool value )

Set a custom value for the flag attribute.

Parameters:

value a new value for the attribute.

void setMonoMass ( const double value ) [inherited]

Set a custom value for the mono_mass attribute.

Parameters:

value a new value for the attribute.

void setPairsWith ( const char * value )

Set a custom value for the pairs_with attribute.

Parameters:

value a new value for the attribute.

bool updateElemRef	(	const int	idx,
		const ms_umod_elemref *	elemref
	)		`[inherited]`

Update the information for a particular element reference object.

Parameters:

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

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

void updateMasses	(	const ms_umod_configfile &	umodFile,
		const ms_quant_component &	quantComp
	)		`[inherited]`

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

The method updates 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	Unimod file object.
quantComp	component object from `quantitation.xml`.

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.

Reimplemented from ms_umod_composition.

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.

Reimplemented from ms_umod_composition.

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

ms_umod_neutralloss.hpp
ms_umod_neutralloss.cpp

ms_umod_neutralloss Class Reference [Mascot configuration files module]

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

ms_umod_neutralloss Class Reference
[Mascot configuration files module]