ms_quant_file_index Class Reference

Represents a file_index element. More...

#include <ms_quant_file_index.hpp>

Inherits ms_xml_IValidatable.

Public Member Functions
	ms_quant_file_index ()
	Default constructor.
	ms_quant_file_index (const ms_quant_file_index &src)
	Copying constructor.
virtual	~ms_quant_file_index ()
	Destructor.
void	copyFrom (const ms_quant_file_index *right)
	Copies all content from another instance.
void	defaultValues ()
	Call this member if you want to start again.
void	dropFraction ()
	Delete the fraction attribute.
int	getContent () const
	Returns integer value of the element (the actual index).
std::string	getContentSchemaType () const
	Obtain a symbolic name for the element's schema type.
int	getFraction () const
	Returns the value of the fraction attribute.
std::string	getFractionSchemaType () const
	Obtain a symbolic name for the fraction attribute schema type.
virtual std::string	getSchemaType () const
	Returns name of the schema type that can be used to validate this element.
bool	haveFraction () const
	Indicates presence of the fraction attribute.
ms_quant_file_index &	operator= (const ms_quant_file_index &right)
	C++ style assignment operator.
void	setContent (const int fileIndex)
	Set a custom file index as element content.
void	setFraction (const int value)
	Set a custom value for the fraction attribute.
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.

Static Public Attributes
static const int	file_index_value_not_set = -1
	A file_index value is a 1 based number. In cases where file_index values are not used (e.g. precursor), this is the 'default' value.

Detailed Description

Represents a file_index element.

Currently just used for the replicate protocol (label free)

Typically, there is one file for each file sample, so each component is just one raw file. A list of files is submitted for quantitation, and each one is mapped to the component using the file_index

However, if the samples have been prefractionated, either at the protein level or after digestion at the peptide level, then, there will be one file for each fraction, for each component. This class enables the mapping of an individual file to its fraction.

Constructor & Destructor Documentation

ms_quant_file_index() [1/2]

ms_quant_file_index

(

)

Default constructor.

Assigns reasonable default values to all internal members.

ms_quant_file_index() [2/2]

ms_quant_file_index

(

const ms_quant_file_index &

src

)

Copying constructor.

Parameters

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

Member Function Documentation

copyFrom()

void copyFrom

(

const ms_quant_file_index *

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.

dropFraction()

void dropFraction

(

)

Delete the fraction attribute.

Deletes the attribute until is re-set.

getContent()

int getContent

(

)

const

Returns integer value of the element (the actual index).

The default value is ms_quant_file_index::file_index_value_not_set

Returns

the file_index value, which is the element content.

getContentSchemaType()

std::string getContentSchemaType

(

)

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.

getFraction()

int getFraction

(

)

const

Returns the value of the fraction attribute.

There is no requirement for fraction numbers to be sequential. Files with the same fraction number will be 'time aligned' by Distiller to enable prediction of retention times for peptides.

The default value if not set, is -1

Returns

for example, -1.

getFractionSchemaType()

std::string getFractionSchemaType

(

)

const

Obtain a symbolic name for the fraction 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, "mqm:nameType").

haveFraction()

bool haveFraction

(

)

const

Indicates presence of the fraction attribute.

Returns

TRUE if the attribute is present and FALSE otherwise.

operator=()

ms_quant_file_index & operator=

(

const ms_quant_file_index &

right

)

C++ style assignment operator.

Parameters

right

another instance of this class to copy the content from.

Returns

reference to the current object

setContent()

void setContent

(

const int

value

)

Set a custom file index as element content.

Parameters

value

a new value for the content.

setFraction()

void setFraction

(

const int

value

)

Set a custom value for the fraction attribute.

There is no requirement for fraction numbers to be sequential. Files with the same fraction number will be 'time aligned' by Distiller to enable prediction of retention times for peptides.

The default value if not set, is -1

Parameters

value

a new value for the attribute.

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_quant_file_index.hpp
• ms_quant_file_index.cpp