ms_umod_composition Class Reference

Represents the composition type in unimod.xml. More...

#include <ms_umod_composition.hpp>

Inheritance diagram for ms_umod_composition:

Public Member Functions
	ms_umod_composition ()
	Default constructor.
	ms_umod_composition (const ms_quant_composition &src, const ms_umod_configfile &umodFile)
	Copying constructor.
	ms_umod_composition (const ms_umod_composition &src)
	Copying constructor.
virtual	~ms_umod_composition ()
	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_composition *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	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	dropCompositionString ()
	Delete the composition attribute.
void	dropMonoMass ()
	Delete the mono_mass 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	getCompositionString () const
	Returns the value of the composition attribute.
std::string	getCompositionStringSchemaType () const
	Obtain a symbolic name for the composition 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.
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.
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	haveCompositionString () const
	Indicates presence of the composition attribute.
bool	haveMonoMass () const
	Indicates presence of the mono_mass attribute.
bool	isSameAs (const ms_umod_composition &right) const
	Returns true if instances contain the same information.
ms_umod_composition &	operator= (const ms_umod_composition &right)
	C++ style assignment operator.
void	setAvgeMass (const double value)
	Set a custom value for the avge_mass attribute.
void	setCompositionString (const char *value)
	Set a custom value for the composition attribute.
void	setMonoMass (const double value)
	Set a custom value for the mono_mass 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 the composition type in unimod.xml.

This type is used for modification delta and ignore elements in unimod.xml.

Constructor & Destructor Documentation

ms_umod_composition() [1/3]

ms_umod_composition

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_umod_composition() [2/3]

ms_umod_composition

(

const ms_umod_composition &

src

)

Copying constructor.

Parameters

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

ms_umod_composition() [3/3]

ms_umod_composition	(	const ms_quant_composition &	src,
		const ms_umod_configfile &	umodFile
	)

Copying constructor.

Parameters

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

Member Function Documentation

appendElemRef()

void appendElemRef

(

const ms_umod_elemref *

elemref

)

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.

copyFrom() [1/2]

void copyFrom	(	const ms_quant_composition *	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 element masses from.

copyFrom() [2/2]

void copyFrom

(

const ms_umod_composition *

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.

This will reset all internal values to their defaults, as if the object had been freshly created with the default constructor.

deleteElemRef()

bool deleteElemRef

(

const int

idx

)

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.

dropAvgeMass()

void dropAvgeMass

(

)

Delete the avge_mass attribute.

Deletes the attribute until is re-set.

dropCompositionString()

void dropCompositionString

(

)

Delete the composition attribute.

Deletes the attribute until it is re-set.

dropMonoMass()

void dropMonoMass

(

)

Delete the mono_mass attribute.

Deletes the attribute until is re-set.

getAvgeMass()

double getAvgeMass

(

)

const

Returns the value of the avge_mass attribute.

Average mass for the object.

Returns

current value of the attribute.

getAvgeMassSchemaType()

std::string getAvgeMassSchemaType

(

)

const

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.

getCompositionString()

std::string getCompositionString

(

)

const

Returns the value of the composition attribute.

A composition string for the object.

Returns

current value of the attribute.

getCompositionStringSchemaType()

std::string getCompositionStringSchemaType

(

)

const

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.

getElemRef()

const ms_umod_elemref * getElemRef

(

const int

idx

)

const

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.

getElemRefSchemaType()

std::string getElemRefSchemaType

(

)

const

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.

getMonoMass()

double getMonoMass

(

)

const

Returns the value of the mono_mass attribute.

Monoisotopic mass for the object.

Returns

current value of the attribute.

getMonoMassSchemaType()

std::string getMonoMassSchemaType

(

)

const

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.

getNumberOfElemRefs()

int getNumberOfElemRefs

(

)

const

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

Returns

total number of chemical element references in the composition object.

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").

Reimplemented in ms_umod_neutralloss.

haveAvgeMass()

bool haveAvgeMass

(

)

const

Indicates presence of the avge_mass attribute.

Returns

TRUE if the attribute is present and FALSE otherwise.

haveCompositionString()

bool haveCompositionString

(

)

const

Indicates presence of the composition attribute.

Returns

TRUE if the attribute is present and FALSE otherwise.

haveMonoMass()

bool haveMonoMass

(

)

const

Indicates presence of the mono_mass attribute.

Returns

TRUE if the attribute is present and FALSE otherwise.

isSameAs()

bool isSameAs

(

const ms_umod_composition &

right

)

const

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.

operator=()

ms_umod_composition & operator=

(

const ms_umod_composition &

right

)

C++ style assignment operator.

Parameters

right

another instance of this class to copy the content from.

Returns

reference to the current object

setAvgeMass()

void setAvgeMass

(

const double

value

)

Set a custom value for the avge_mass attribute.

Parameters

value

a new value for the attribute.

setCompositionString()

void setCompositionString

(

const char *

value

)

Set a custom value for the composition attribute.

Parameters

value

a new value for the attribute.

setMonoMass()

void setMonoMass

(

const double

value

)

Set a custom value for the mono_mass attribute.

Parameters

value

a new value for the attribute.

updateElemRef()

bool updateElemRef	(	const int	idx,
		const ms_umod_elemref *	elemref
	)

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.

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 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.

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.

Reimplemented in ms_umod_neutralloss.

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.

Reimplemented in ms_umod_neutralloss.

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

• ms_umod_composition.hpp
• ms_umod_composition.cpp