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Sample Class Reference

Meta information about the sample. More...

#include <OpenMS/METADATA/Sample.h>

Inheritance diagram for Sample:
MetaInfoInterface

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 ()
 desctuctor More...
 
Sampleoperator= (const Sample &source)
 assignment operator More...
 
bool operator== (const Sample &rhs) const
 Equality operator. More...
 
const StringgetName () const
 retuns the sample name (default: "") More...
 
void setName (const String &name)
 sets the sample name More...
 
const StringgetOrganism () const
 retuns the sample name (default: "") More...
 
void setOrganism (const String &organism)
 sets the sample name More...
 
const StringgetNumber () const
 returns the sample number (default: "") More...
 
void setNumber (const String &number)
 sets the sample number (e.g. sample ID) More...
 
const StringgetComment () 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...
 
DoubleReal getMass () const
 returns the mass (in gram) (default: 0.0) More...
 
void setMass (DoubleReal mass)
 sets the mass (in gram) More...
 
DoubleReal getVolume () const
 returns the volume (in ml) (default: 0.0) More...
 
void setVolume (DoubleReal volume)
 sets the volume (in ml) More...
 
DoubleReal getConcentration () const
 returns the concentration (in g/l) (default: 0.0) More...
 
void setConcentration (DoubleReal 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 referenct 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 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. More...
 
SampleTreatmentgetTreatment (UInt position)
 returns a mutable reference to the sample treatment at the given position More...
 
const SampleTreatmentgetTreatment (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...
 
MetaInfoInterfaceoperator= (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 DataValuegetMetaValue (const String &name) const
 returns the value corresponding to a string More...
 
const DataValuegetMetaValue (UInt index) const
 returns the value corresponding to an index More...
 
bool metaValueExists (const String &name) const
 returns if this MetaInfo is set More...
 
bool metaValueExists (UInt index) const
 returns if this MetaInfo is set 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_
 
DoubleReal mass_
 
DoubleReal volume_
 
DoubleReal concentration_
 
std::vector< Samplesubsamples_
 
std::list< SampleTreatment * > treatments_
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 pointer to the MetaInfo object. 0 by default More...
 

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 retuns 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

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::IndexOverflowis 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 >::writeHeader_().

DoubleReal getConcentration ( ) const

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

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

DoubleReal getMass ( ) const

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

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

const String& getName ( ) const

retuns the sample name (default: "")

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

const String& getNumber ( ) const

returns the sample number (default: "")

Referenced by MzMLHandler< MapType >::writeHeader_(), 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 >::writeHeader_(), 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::IndexOverflowis 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::IndexOverflowis thrown if the position is invalid.
DoubleReal getVolume ( ) const

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

Referenced by MzMLHandler< MapType >::writeHeader_(), 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::IndexOverflowis 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 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5