Meta information about the sample. More...

#include <OpenMS/METADATA/Sample.h>

Inheritance diagram for Sample:

Public Types
enum	SampleState { SAMPLENULL, SOLID, LIQUID, GAS, SOLUTION, EMULSION, SUSPENSION, SIZE_OF_SAMPLESTATE }
	state of aggregation of the sample More...
Public Member Functions
	Sample ()
	default constructor
	Sample (const Sample &source)
	copy constructor
	~Sample ()
	desctuctor
Sample &	operator= (const Sample &source)
	assignment operator
bool	operator== (const Sample &rhs) const
	Equality operator.
const String &	getName () const
	retuns the sample name (default: "")
void	setName (const String &name)
	sets the sample name
const String &	getOrganism () const
	retuns the sample name (default: "")
void	setOrganism (const String &organism)
	sets the sample name
const String &	getNumber () const
	returns the sample number (default: "")
void	setNumber (const String &number)
	sets the sample number (e.g. sample ID)
const String &	getComment () const
	returns the comment (default: "")
void	setComment (const String &comment)
	sets the comment (may contain newline characters)
SampleState	getState () const
	returns the state of aggregation (default: SAMPLENULL)
void	setState (SampleState state)
	sets the state of aggregation
DoubleReal	getMass () const
	returns the mass (in gram) (default: 0.0)
void	setMass (DoubleReal mass)
	sets the mass (in gram)
DoubleReal	getVolume () const
	returns the volume (in ml) (default: 0.0)
void	setVolume (DoubleReal volume)
	sets the volume (in ml)
DoubleReal	getConcentration () const
	returns the concentration (in g/l) (default: 0.0)
void	setConcentration (DoubleReal concentration)
	sets the concentration (in g/l)
std::vector< Sample > &	getSubsamples ()
	returns a mutable reference to the vector of subsamples that were combined to create this sample
const std::vector< Sample > &	getSubsamples () const
	returns a const referenct to the vector of subsamples that were combined to create this sample
void	setSubsamples (const std::vector< Sample > &subsamples)
	sets the vector of subsamples that were combined to create this sample
void	addTreatment (const SampleTreatment &treatment, Int before_position=-1)
	adds a sample treatment before the given postion (default is the end of the list). Sample treatments are ordered in the order of application to the sample. If before_position is smaller than 0, the sample treatment is appended to the list.
SampleTreatment &	getTreatment (UInt position)
	returns a mutable reference to the sample treatment at the given position
const SampleTreatment &	getTreatment (UInt position) const
	returns a const reference to the sample treatment at the given position
void	removeTreatment (UInt position)
	removes the sample treatment at the given position
Int	countTreatments () const
	returns the number of sample treatments
Static Public Attributes
static const std::string	NamesOfSampleState [SIZE_OF_SAMPLESTATE]
	Names of sample states.
Protected Attributes
String	name_
String	number_
String	comment_
String	organism_
SampleState	state_
DoubleReal	mass_
DoubleReal	volume_
DoubleReal	concentration_
std::vector< Sample >	subsamples_
std::list< SampleTreatment * >	treatments_

Detailed Description

Meta information about the sample.

It contains basic descriptions like name, number (i.e. order number), mass, volume, concentration, state and a comment.

Additionally sample treatments like Digestion, Modification or Tagging can be added.

A Sample can be composed of other samples.

Member Enumeration Documentation

enum SampleState

state of aggregation of the sample

Enumerator:

SAMPLENULL
SOLID
LIQUID
GAS
SOLUTION
EMULSION
SUSPENSION
SIZE_OF_SAMPLESTATE

Constructor & Destructor Documentation

Sample ( )

default constructor

Sample ( const Sample & source )

copy constructor

~Sample ( )

desctuctor

Member Function Documentation

void addTreatment	(	const SampleTreatment &	treatment,
		Int	before_position = `-1`
	)

adds a sample treatment before the given postion (default is the end of the list). Sample treatments are ordered in the order of application to the sample. If before_position is smaller than 0, the sample treatment is appended to the list.

Exceptions:

Exception::IndexOverflow

is thrown if the position is invalid.

Int countTreatments ( ) const

returns the number of sample treatments

const String& getComment ( ) const

returns the comment (default: "")

Referenced by MzMLHandler< MapType >::writeTo().

DoubleReal getConcentration ( ) const

returns the concentration (in g/l) (default: 0.0)

Referenced by MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

DoubleReal getMass ( ) const

returns the mass (in gram) (default: 0.0)

Referenced by MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

const String& getName ( ) const

retuns the sample name (default: "")

Referenced by MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

const String& getNumber ( ) const

returns the sample number (default: "")

Referenced by MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

const String& getOrganism ( ) const

retuns the sample name (default: "")

SampleState getState ( ) const

returns the state of aggregation (default: SAMPLENULL)

Referenced by MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

std::vector<Sample>& getSubsamples ( )

returns a mutable reference to the vector of subsamples that were combined to create this sample

const std::vector<Sample>& getSubsamples ( ) const

returns a const referenct to the vector of subsamples that were combined to create this sample

SampleTreatment& getTreatment ( UInt position )

returns a mutable reference to the sample treatment at the given position

Exceptions:

Exception::IndexOverflow

is thrown if the position is invalid.

const SampleTreatment& getTreatment ( UInt position ) const

returns a const reference to the sample treatment at the given position

Exceptions:

Exception::IndexOverflow

is thrown if the position is invalid.

DoubleReal getVolume ( ) const

returns the volume (in ml) (default: 0.0)

Referenced by MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

Sample& operator= ( const Sample & source )

assignment operator

bool operator== ( const Sample & rhs ) const

Equality operator.

void removeTreatment ( UInt position )

removes the sample treatment at the given position

Exceptions:

Exception::IndexOverflow

is thrown if the position is invalid.

void setComment ( const String & comment )

sets the comment (may contain newline characters)

void setConcentration ( DoubleReal concentration )

sets the concentration (in g/l)

void setMass ( DoubleReal mass )

sets the mass (in gram)

void setName ( const String & name )

sets the sample name

void setNumber ( const String & number )

sets the sample number (e.g. sample ID)

void setOrganism ( const String & organism )

sets the sample name

void setState ( SampleState state )

sets the state of aggregation

void setSubsamples ( const std::vector< Sample > & subsamples )

sets the vector of subsamples that were combined to create this sample

void setVolume ( DoubleReal volume )

sets the volume (in ml)

Member Data Documentation

String comment_ [protected]

DoubleReal concentration_ [protected]

DoubleReal mass_ [protected]

String name_ [protected]

const std::string NamesOfSampleState[SIZE_OF_SAMPLESTATE] [static]

Names of sample states.

String number_ [protected]

String organism_ [protected]

SampleState state_ [protected]

std::vector<Sample> subsamples_ [protected]

std::list<SampleTreatment *> treatments_ [protected]

DoubleReal volume_ [protected]

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:56 using doxygen 1.7.1

Sample Class Reference [Metadata]

Public Types

Public Member Functions

Static Public Attributes

Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

Sample Class Reference
[Metadata]