Meta information about the sample. More...
#include <OpenMS/METADATA/Sample.h>
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... | |
| Sample & | operator= (const Sample &source) |
| assignment operator More... | |
| bool | operator== (const Sample &rhs) const |
| Equality operator. More... | |
| const String & | getName () const |
| retuns the sample name (default: "") More... | |
| void | setName (const String &name) |
| sets the sample name More... | |
| const String & | getOrganism () const |
| retuns 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... | |
| 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... | |
| 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 More... | |
| const DataValue & | getMetaValue (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< 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 () |
| 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... | |
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.
| enum SampleState |
| Sample | ( | ) |
default constructor
| ~Sample | ( | ) |
desctuctor
| 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.
| 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 >::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
| 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
| Exception::IndexOverflow | is 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().
| bool operator== | ( | const Sample & | rhs | ) | const |
Equality operator.
| void removeTreatment | ( | UInt | position | ) |
removes the sample treatment at the given position
| 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)
|
protected |
|
protected |
|
protected |
|
protected |
|
static |
Names of sample states.
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
|
protected |
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |