| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Attributes | Protected Attributes | List of all members
Sample Class Reference
Metadata

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 (Sample &&)=default
| Move constructor. More...
| ~Sample ()
| Destructor. More...
Sample & | operator= (const Sample &source)
| Assignment operator. More...
Sample & | operator= (Sample &&) &=default
| Move 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 (MetaInfoInterface &&) noexcept
| Move constructor. More...
| ~MetaInfoInterface ()
| Destructor. More...
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs)
| Assignment operator. More...
MetaInfoInterface & | operator= (MetaInfoInterface &&) noexcept
| Move 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 DataValue &default_value=DataValue::EMPTY) const
| Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...
const DataValue & | getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
| Returns the value corresponding to an index, or a default value (default: 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() [1/3]

Sample | ( |  | ) |

Default constructor.

## ◆ Sample() [2/3]

Sample | ( | const Sample & | source | ) |

Copy constructor.

## ◆ Sample() [3/3]

Sample | ( | Sample && |  | ) |

default

Move 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=() [1/2]

Sample& operator= | ( | const Sample & | source | ) |

Assignment operator.

## ◆ operator=() [2/2]

Sample& operator= | ( | Sample && |  | ) | &

default

Move 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