ms_umod_aminoacid Class Reference

Represents an "amino acid" object in unimod.xml. More...

#include <ms_umod_aminoacid.hpp>

Inherits ms_xml_IValidatable.

Public Member Functions
	ms_umod_aminoacid ()
	Default constructor.
	ms_umod_aminoacid (const ms_umod_aminoacid &src)
	Copying constructor.
virtual	~ms_umod_aminoacid ()
	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_umod_aminoacid *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	dropFullName ()
	Delete the full_name attribute.
void	dropMonoMass ()
	Delete the mono_mass attribute.
void	dropThreeLetter ()
	Delete the three_letter attribute.
void	dropTitle ()
	Delete the title 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.
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	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.
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 a 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.
std::string	getThreeLetter () const
	Returns the value of the three_letter attribute.
std::string	getThreeLetterSchemaType () const
	Obtain a symbolic name for the three_letter attribute 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.
bool	haveAvgeMass () const
	Indicates presence of the avge_mass attribute.
bool	haveFullName () const
	Indicates presence of the full_name attribute.
bool	haveMonoMass () const
	Indicates presence of the mono_mass attribute.
bool	haveThreeLetter () const
	Indicates presence of the three_letter attribute.
bool	haveTitle () const
	Indicates presence of the title attribute.
ms_umod_aminoacid &	operator= (const ms_umod_aminoacid &right)
	C++ style assignment operator.
void	setAvgeMass (const double value)
	Set a custom value for the avge_mass attribute.
void	setFullName (const char *value)
	Set a custom value for the full_name attribute.
void	setMonoMass (const double value)
	Set a custom value for the mono_mass attribute.
void	setThreeLetter (const char *value)
	Set a custom value for the three_letter attribute.
void	setTitle (const char *value)
	Set a custom value for the title attribute.
bool	updateElemRef (const int idx, const ms_umod_elemref *elemref)
	Update the information for a particular element reference object.
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 an "amino acid" object in unimod.xml.

Constructor & Destructor Documentation

ms_umod_aminoacid() [1/2]

ms_umod_aminoacid

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_umod_aminoacid() [2/2]

ms_umod_aminoacid

(

const ms_umod_aminoacid &

src

)

Copying constructor.

Parameters

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

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.

clearElemRefs()

void clearElemRefs

(

)

Deletes all element reference objects from the list.

Deletes all element references from the list

copyFrom()

void copyFrom

(

const ms_umod_aminoacid *

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.

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.

dropFullName()

void dropFullName

(

)

Delete the full_name attribute.

Deletes the attribute until it is re-set.

dropMonoMass()

void dropMonoMass

(

)

Delete the mono_mass attribute.

Deletes the attribute until is re-set.

dropThreeLetter()

void dropThreeLetter

(

)

Delete the three_letter attribute.

Deletes the attribute until it is re-set.

dropTitle()

void dropTitle

(

)

Delete the title attribute.

Deletes the attribute until it is re-set.

getAvgeMass()

double getAvgeMass

(

)

const

Returns the value of the avge_mass attribute.

Average mass for the amino acid.

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.

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.

getFullName()

std::string getFullName

(

)

const

Returns the value of the full_name attribute.

A full name for the amino acid.

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.

getMonoMass()

double getMonoMass

(

)

const

Returns the value of the mono_mass attribute.

Monoisotopic mass for the amino acid.

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 a number of element reference objects currently held in memory.

Returns

total number of chemical element references in the modification 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").

getThreeLetter()

std::string getThreeLetter

(

)

const

Returns the value of the three_letter attribute.

A three-letter name for the amino acid.

Returns

current value of the attribute.

getThreeLetterSchemaType()

std::string getThreeLetterSchemaType

(

)

const

Obtain a symbolic name for the three_letter 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.

getTitle()

std::string getTitle

(

)

const

Returns the value of the title attribute.

A unique name for the amino acid.

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.

haveAvgeMass()

bool haveAvgeMass

(

)

const

Indicates presence of the avge_mass attribute.

Returns

TRUE if the attribute 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.

haveMonoMass()

bool haveMonoMass

(

)

const

Indicates presence of the mono_mass attribute.

Returns

TRUE if the attribute is present and FALSE otherwise.

haveThreeLetter()

bool haveThreeLetter

(

)

const

Indicates presence of the three_letter 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.

operator=()

ms_umod_aminoacid & operator=

(

const ms_umod_aminoacid &

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.

setFullName()

void setFullName

(

const char *

value

)

Set a custom value for the full_name 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.

setThreeLetter()

void setThreeLetter

(

const char *

value

)

Set a custom value for the three_letter 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.

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.

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.

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

• ms_umod_aminoacid.hpp
• ms_umod_aminoacid.cpp