Sample Class Reference

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 More...
	Sample (const Sample &source)
	copy constructor More...
	~Sample ()
	destructor More...
Sample &	operator= (const Sample &source)
	assignment operator More...
bool	operator== (const Sample &rhs) const
	Equality operator. More...
const String &	getName () const
	returns the sample name (default: "") More...
void	setName (const String &name)
	sets the sample name More...
const String &	getOrganism () const
	returns the sample name (default: "") More...
void	setOrganism (const String &organism)
	sets the sample name More...
const String &	getNumber () const
	returns the sample number (default: "") More...
void	setNumber (const String &number)
	sets the sample number (e.g. sample ID) More...
const String &	getComment () const
	returns the comment (default: "") More...
void	setComment (const String &comment)
	sets the comment (may contain newline characters) More...
SampleState	getState () const
	returns the state of aggregation (default: SAMPLENULL) More...
void	setState (SampleState state)
	sets the state of aggregation More...
double	getMass () const
	returns the mass (in gram) (default: 0.0) More...
void	setMass (double mass)
	sets the mass (in gram) More...
double	getVolume () const
	returns the volume (in ml) (default: 0.0) More...
void	setVolume (double volume)
	sets the volume (in ml) More...
double	getConcentration () const
	returns the concentration (in g/l) (default: 0.0) More...
void	setConcentration (double concentration)
	sets the concentration (in g/l) More...
std::vector< Sample > &	getSubsamples ()
	returns a mutable reference to the vector of subsamples that were combined to create this sample More...
const std::vector< Sample > &	getSubsamples () const
	returns a const reference to the vector of subsamples that were combined to create this sample More...
void	setSubsamples (const std::vector< Sample > &subsamples)
	sets the vector of subsamples that were combined to create this sample More...
void	addTreatment (const SampleTreatment &treatment, Int before_position=-1)
	adds a sample treatment before the given position (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. More...
SampleTreatment &	getTreatment (UInt position)
	returns a mutable reference to the sample treatment at the given position More...
const SampleTreatment &	getTreatment (UInt position) const
	returns a const reference to the sample treatment at the given position More...
void	removeTreatment (UInt position)
	removes the sample treatment at the given position More...
Int	countTreatments () const
	returns the number of sample treatments More...
Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()
	Constructor. More...
	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor. More...
	~MetaInfoInterface ()
	Destructor. More...
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...
bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator. More...
bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator. More...
const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string (or DataValue::EMPTY if not found) More...
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to an index (or DataValue::EMPTY if not found) More...
bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists. More...
bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists. More...
void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name. More...
void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index. More...
void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to name if it exists. More...
void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to index if it exists. More...
void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...
void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...
bool	isMetaEmpty () const
	Returns if the MetaInfo is empty. More...
void	clearMetaInfo ()
	Removes all meta values. More...

Static Public Attributes
static const std::string	NamesOfSampleState [SIZE_OF_SAMPLESTATE]
	Names of sample states. More...

Protected Attributes
String	name_
String	number_
String	comment_
String	organism_
SampleState	state_
double	mass_
double	volume_
double	concentration_
std::vector< Sample >	subsamples_
std::list< SampleTreatment * >	treatments_
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...

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

SampleState

enum SampleState

state of aggregation of the sample

Enumerator
SAMPLENULL
SOLID
LIQUID
GAS
SOLUTION
EMULSION
SUSPENSION
SIZE_OF_SAMPLESTATE

Constructor & Destructor Documentation

Sample() [1/2]

Sample

(

)

default constructor

Sample() [2/2]

Sample

(

const Sample &

source

)

copy constructor

~Sample()

~Sample

(

)

destructor

Member Function Documentation

addTreatment()

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

adds a sample treatment before the given position (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.

countTreatments()

Int countTreatments

(

)

const

returns the number of sample treatments

getComment()

const String& getComment

(

)

const

returns the comment (default: "")

getConcentration()

double getConcentration

(

)

const

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

getMass()

double getMass

(

)

const

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

getName()

const String& getName

(

)

const

returns the sample name (default: "")

getNumber()

const String& getNumber

(

)

const

returns the sample number (default: "")

getOrganism()

const String& getOrganism

(

)

const

returns the sample name (default: "")

getState()

SampleState getState

(

)

const

returns the state of aggregation (default: SAMPLENULL)

getSubsamples() [1/2]

std::vector<Sample>& getSubsamples

(

)

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

getSubsamples() [2/2]

const std::vector<Sample>& getSubsamples

(

)

const

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

getTreatment() [1/2]

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.

getTreatment() [2/2]

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.

getVolume()

double getVolume

(

)

const

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

operator=()

Sample& operator=

(

const Sample &

source

)

assignment operator

operator==()

bool operator==

(

const Sample &

rhs

)

const

Equality operator.

removeTreatment()

void removeTreatment

(

UInt

position

)

removes the sample treatment at the given position

Exceptions

Exception::IndexOverflow

is thrown if the position is invalid.

setComment()

void setComment

(

const String &

comment

)

sets the comment (may contain newline characters)

setConcentration()

void setConcentration

(

double

concentration

)

sets the concentration (in g/l)

setMass()

void setMass

(

double

mass

)

sets the mass (in gram)

setName()

void setName

(

const String &

name

)

sets the sample name

setNumber()

void setNumber

(

const String &

number

)

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

setOrganism()

void setOrganism

(

const String &

organism

)

sets the sample name

setState()

void setState

(

SampleState

state

)

sets the state of aggregation

setSubsamples()

void setSubsamples

(

const std::vector< Sample > &

subsamples

)

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

setVolume()

void setVolume

(

double

volume

)

sets the volume (in ml)

Member Data Documentation

comment_

String comment_

protected

concentration_

double concentration_

protected

mass_

double mass_

protected

name_

String name_

protected

NamesOfSampleState

const std::string NamesOfSampleState[SIZE_OF_SAMPLESTATE]

static

Names of sample states.

number_

String number_

protected

organism_

String organism_

protected

state_

SampleState state_

protected

subsamples_

std::vector<Sample> subsamples_

protected

treatments_

std::list<SampleTreatment *> treatments_

protected

volume_

double volume_

protected