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 nameif it exists.  More... | |
| void | removeMetaValue (UInt index) | 
| Removes the DataValue corresponding to indexif 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)
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Names of sample states.
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |