ms_quant_component Class Reference

An object of this class represent a single component element in quantitation.xml. More...

#include <ms_quant_component.hpp>

Inherits ms_xml_IValidatable.

Public Member Functions
	ms_quant_component ()
	Default constructor.
	ms_quant_component (const ms_quant_component &src)
	Copying constructor.
virtual	~ms_quant_component ()
	Destructor.
void	appendCorrection (const ms_quant_correction *correction)
	Adds a new correction element at the end of the list.
void	appendFileIndex (const ms_quant_file_index *file_index)
	Adds a new correction element at the end of the list.
void	appendIsotope (const ms_quant_isotope *isotope)
	Adds a new isotope element at the end of the list.
void	appendModificationGroup (const ms_quant_modgroup *item)
	Adds a new modification group at the end of the list.
void	clearCorrections ()
	Deletes all correction elements from the list.
void	clearFileIndexes ()
	Deletes all file_index elements from the list.
void	clearIsotopes ()
	Deletes all isotope elements from the list.
void	clearModificationGroups ()
	Deletes all modification groups from the list.
void	copyFrom (const ms_quant_component *right)
	Copies all content from another instance.
void	defaultValues ()
	Call this member if you want to start again.
bool	deleteCorrection (const int idx)
	Remove a correction element from the list.
bool	deleteFileIndex (const int idx)
	Remove a single file_index element from the list.
bool	deleteIsotope (const int idx)
	Remove a isotope element from the list.
bool	deleteModificationGroupByName (const char *name)
	Remove a modification group from the list in memory by its unique name.
bool	deleteModificationGroupByNumber (const int idx)
	Remove a modification group from the list in memory by its index.
void	dropFileIndex ()
	Delete the file_index element.
void	dropMoverz ()
	Delete the moverz element.
void	dropName ()
	Delete the name attribute.
void	dropSatellite ()
	Delete the satellite element.
const ms_quant_correction *	getCorrection (const int idx) const
	Returns a correction element object by its number.
std::string	getCorrectionSchemaType () const
	Obtain a symbolic name for the correction element schema type.
int	getFileIndex () const
	Returns the value of the first file_index element.
const ms_quant_file_index *	getFileIndex (const int idx) const
	Returns a file_index element object by its number.
std::string	getFileIndexSchemaType () const
	Obtain a symbolic name for the file_index element schema type.
const ms_quant_isotope *	getIsotope (const int idx) const
	Returns a isotope element object by its number.
std::string	getIsotopeSchemaType () const
	Obtain a symbolic name for the isotope element schema type.
const ms_quant_modgroup *	getModificationGroupByName (const char *name) const
	Returns a modification group object by its name or a null value in case it is not found.
const ms_quant_modgroup *	getModificationGroupByNumber (const int idx) const
	Returns a modification group object by its number.
std::string	getModificationGroupSchemaType () const
	Obtain a symbolic name for the modification_group element schema type.
const ms_quant_moverz *	getMoverz () const
	Returns the value of the moverz element.
std::string	getMoverzSchemaType () const
	Obtain a symbolic name for the moverz element schema type.
std::string	getName () const
	Returns the value of the name attribute.
std::string	getNameSchemaType () const
	Obtain a symbolic name for the name attribute schema type.
int	getNumberOfCorrections () const
	Returns the number of correction elements held.
int	getNumberOfFileIndexes () const
	Returns the number of file_index elements held.
int	getNumberOfIsotopes () const
	Returns the number of isotope elements held.
int	getNumberOfModificationGroups () const
	Returns the number of nested modification groups.
const ms_quant_satellite *	getSatellite () const
	Returns the value of the satellite element.
std::string	getSatelliteSchemaType () const
	Obtain a symbolic name for the satellite element schema type.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
bool	haveFileIndex () const
	Check for presence of one or more file_index element.
bool	haveMoverz () const
	Check for presence of the moverz element.
bool	haveName () const
	Check for presence of the name attribute.
bool	haveSatellite () const
	Check for presence of the satellite element.
ms_quant_component &	operator= (const ms_quant_component &right)
	C++ style assignment operator.
void	setFileIndex (const int file_index)
	Supply a custom content for the first file_index element.
void	setMoverz (const ms_quant_moverz *moverz)
	Supply a custom content for the moverz element.
void	setName (const char *value)
	Set a custom value for the name attribute.
void	setSatellite (const ms_quant_satellite *satellite)
	Supply a custom content for the satellite element.
bool	updateCorrection (const int idx, const ms_quant_correction *isotope)
	Update the information for a specific correction element.
bool	updateFileIndex (const int idx, const ms_quant_file_index *file_index)
	Adds a new correction element at the end of the list.
bool	updateIsotope (const int idx, const ms_quant_isotope *isotope)
	Update the information for a specific isotope element.
bool	updateModificationGroupByName (const char *name, const ms_quant_modgroup *modgroup)
	Update the information for a specific modification group refering to it by its unique name.
bool	updateModificationGroupByNumber (const int idx, const ms_quant_modgroup *modgroup)
	Update the information for a specific modification group refering to it by its index.
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

An object of this class represent a single component element in quantitation.xml.

Identifies a component used to calculate a ratio.

Constructor & Destructor Documentation

ms_quant_component() [1/2]

ms_quant_component

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_component() [2/2]

ms_quant_component

(

const ms_quant_component &

src

)

Copying constructor.

Parameters

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

Member Function Documentation

appendCorrection()

void appendCorrection

(

const ms_quant_correction *

correction

)

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

Parameters

correction

an instance to copy the content into the newly added element from.

appendFileIndex()

void appendFileIndex

(

const ms_quant_file_index *

file_index

)

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

Parameters

file_index

a new content for the element.

appendIsotope()

void appendIsotope

(

const ms_quant_isotope *

isotope

)

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

Parameters

isotope

an instance to copy the content into the newly added element from.

appendModificationGroup()

void appendModificationGroup

(

const ms_quant_modgroup *

item

)

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

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

Parameters

item	an instance of modification group object to copy content from.

clearCorrections()

void clearCorrections

(

)

Deletes all correction elements from the list.

Deletes all nested correction elements.

clearFileIndexes()

void clearFileIndexes

(

)

Deletes all file_index elements from the list.

Deletes all file_index elements from the list.

copyFrom()

void copyFrom

(

const ms_quant_component *

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.

deleteCorrection()

bool deleteCorrection

(

const int

idx

)

Remove a correction element from the list.

Parameters

idx	a zero-based index of the element to delete.

Returns

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

deleteFileIndex()

bool deleteFileIndex

(

const int

idx

)

Remove a single file_index element from the list.

Parameters

idx	is the zero based index for the element and should be >=0 and < getNumberOfFileIndexes()

Returns

true if idx >=0 and < getNumberOfFileIndexes()

deleteIsotope()

bool deleteIsotope

(

const int

idx

)

Remove a isotope element from the list.

Parameters

idx	a zero-based index of the element to delete.

Returns

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

deleteModificationGroupByName()

bool deleteModificationGroupByName

(

const char *

name

)

Remove a modification group from the list in memory by its unique name.

Parameters

name	name of the modification group for deletion.

Returns

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

deleteModificationGroupByNumber()

bool deleteModificationGroupByNumber

(

const int

idx

)

Remove a modification group from the list in memory by its index.

Parameters

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

Returns

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

dropFileIndex()

void dropFileIndex

(

)

Delete the file_index element.

Deprecated:

After version 2.7.2, multiple file indexes are supported per component

Just calls clearFileIndexes()

dropMoverz()

void dropMoverz

(

)

Delete the moverz element.

Deletes the element until it is re-set.

dropName()

void dropName

(

)

Delete the name attribute.

Deletes the attribute until it is re-set.

dropSatellite()

void dropSatellite

(

)

Delete the satellite element.

Deletes the element until it is re-set.

getCorrection()

const ms_quant_correction * getCorrection

(

const int

idx

)

const

Returns a correction element object by its number.

Parameters

idx	a zero-based index of the element to retrieve.

Returns

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

getCorrectionSchemaType()

std::string getCorrectionSchemaType

(

)

const

Obtain a symbolic name for the correction 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.

getFileIndex() [1/2]

int getFileIndex

(

)

const

Returns the value of the first file_index element.

The file_index element is a data file identifier (replicate).

Deprecated:

After version 2.7.2, multiple file indexes are supported per component and this just returns the first one.

Call getNumberOfFileIndexes() and for each one call getFileIndex(const int idx) to return a matrix_science::ms_quant_file_index * and then call ms_quant_file_index::getContent() to retrieve the the file index

Returns

current element content.

getFileIndex() [2/2]

const ms_quant_file_index * getFileIndex

(

const int

idx

)

const

Returns a file_index element object by its number.

Parameters

idx	a zero-based index of the element to retrieve.

Returns

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

getFileIndexSchemaType()

std::string getFileIndexSchemaType

(

)

const

Obtain a symbolic name for the file_index 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.

getIsotope()

const ms_quant_isotope * getIsotope

(

const int

idx

)

const

Returns a isotope element object by its number.

Element for non-SILAC metabolic labelling. Applies to residues only.

Parameters

idx	a zero-based index of the element to retrieve.

Returns

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

getIsotopeSchemaType()

std::string getIsotopeSchemaType

(

)

const

Obtain a symbolic name for the isotope 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.

getModificationGroupByName()

const ms_quant_modgroup * getModificationGroupByName

(

const char *

name

)

const

Returns a modification group object by its name or a null value in case it is not found.

Parameters

name	name of the modification group to find.

Returns

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

getModificationGroupByNumber()

const ms_quant_modgroup * getModificationGroupByNumber

(

const int

idx

)

const

Returns a modification group object by its number.

Parameters

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

Returns

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

getModificationGroupSchemaType()

std::string getModificationGroupSchemaType

(

)

const

Obtain a symbolic name for the modification_group 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.

getMoverz()

const ms_quant_moverz * getMoverz

(

)

const

Returns the value of the moverz element.

Returns

a read-only pointer to an object with the current element content. See Maintaining object references: two rules of thumb.

getMoverzSchemaType()

std::string getMoverzSchemaType

(

)

const

Obtain a symbolic name for the moverz 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.

getName()

std::string getName

(

)

const

Returns the value of the name attribute.

Returns

a descriptive name that will appear in drop down lists, etc.

getNameSchemaType()

std::string getNameSchemaType

(

)

const

Obtain a symbolic name for the 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.

getNumberOfCorrections()

int getNumberOfCorrections

(

)

const

Returns the number of correction elements held.

Returns

total number of correction elements held.

getNumberOfFileIndexes()

int getNumberOfFileIndexes

(

)

const

Returns the number of file_index elements held.

Returns

the number of file index / fraction pairs found

getNumberOfIsotopes()

int getNumberOfIsotopes

(

)

const

Returns the number of isotope elements held.

Returns

total number of isotope elements held.

getNumberOfModificationGroups()

int getNumberOfModificationGroups

(

)

const

Returns the number of nested modification groups.

Returns

total number of nested modification groups.

getSatellite()

const ms_quant_satellite * getSatellite

(

)

const

Returns the value of the satellite element.

Returns

a read-only pointer to an object with the current element content. See Maintaining object references: two rules of thumb.

getSatelliteSchemaType()

std::string getSatelliteSchemaType

(

)

const

Obtain a symbolic name for the satellite 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.

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")

haveFileIndex()

bool haveFileIndex

(

)

const

Check for presence of one or more file_index element.

Deprecated:

After version 2.7.2, multiple file indexes are supported per component

Use getNumberOfFileIndexes()

Returns

TRUE if the element is present and FALSE otherwise.

haveMoverz()

bool haveMoverz

(

)

const

Check for presence of the moverz element.

Returns

TRUE if the element is present and FALSE otherwise.

haveName()

bool haveName

(

)

const

Check for presence of the name attribute.

Returns

TRUE if the attribute is present and FALSE otherwise.

haveSatellite()

bool haveSatellite

(

)

const

Check for presence of the satellite element.

Returns

TRUE if the element is present and FALSE otherwise.

operator=()

ms_quant_component & operator=

(

const ms_quant_component &

right

)

C++ style assignment operator.

Parameters

right

another instance of this class to copy the content from.

Returns

reference to the current object

setFileIndex()

void setFileIndex

(

const int

file_index

)

Supply a custom content for the first file_index element.

Deprecated:

After version 2.7.2, multiple file indexes are supported per component and this just sets the first one.

Call appendFileIndex() or updateFileIndex() to set a file_index

Parameters

file_index

a new content for the element.

setMoverz()

void setMoverz

(

const ms_quant_moverz *

moverz

)

Supply a custom content for the moverz element.

Parameters

moverz

a new content for the element.

setName()

void setName

(

const char *

value

)

Set a custom value for the name attribute.

Parameters

value

a new value for the attribute.

setSatellite()

void setSatellite

(

const ms_quant_satellite *

satellite

)

Supply a custom content for the satellite element.

Parameters

satellite

a new content for the element.

updateCorrection()

bool updateCorrection	(	const int	idx,
		const ms_quant_correction *	correction
	)

Update the information for a specific correction element.

Parameters

idx	a zero-based index of the element to update.
correction	an instance to copy the content from.

Returns

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

updateFileIndex()

bool updateFileIndex	(	const int	idx,
		const ms_quant_file_index *	file_index
	)

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

Parameters

idx	is the zero based index for the element and should be >= 0 and < getNumberOfFileIndexes()
file_index	a new content for the element.

Returns

true if idx >= 0 and < getNumberOfFileIndexes()

updateIsotope()

bool updateIsotope	(	const int	idx,
		const ms_quant_isotope *	isotope
	)

Update the information for a specific isotope element.

Parameters

idx	a zero-based index of the element to update.
isotope	an instance to copy the content from.

Returns

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

updateModificationGroupByName()

bool updateModificationGroupByName	(	const char *	name,
		const ms_quant_modgroup *	modgroup
	)

Update the information for a specific modification group refering to it by its unique name.

Parameters

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

Returns

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

updateModificationGroupByNumber()

bool updateModificationGroupByNumber	(	const int	idx,
		const ms_quant_modgroup *	modgroup
	)

Update the information for a specific modification group refering to it by its index.

Parameters

idx	number of the modification group for updating from 0 to (getNumberOfModificationGroups() - 1).
modgroup	an object to copy the content from.

Returns

TRUE if the modification group 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_quant_component.hpp
• ms_quant_component.cpp