#include <OpenMS/METADATA/MSQuantifications.h>
Classes | |
| struct | AnalysisSummary |
| struct | Assay |
Public Member Functions | |
| MSQuantifications () | |
| Constructor. More... | |
| ~MSQuantifications () | |
| Destructor. More... | |
| MSQuantifications (const MSQuantifications &source) | |
| Copy constructor. More... | |
| MSQuantifications & | operator= (const MSQuantifications &source) |
| Assignment operator. More... | |
| bool | operator== (const MSQuantifications &rhs) const |
| Equality operator. More... | |
| bool | operator!= (const MSQuantifications &rhs) const |
| Equality operator. More... | |
| const std::vector< DataProcessing > | getDataProcessingList () const |
| Loads data from a text file. More... | |
| const std::vector< Assay > & | getAssays () const |
| std::vector< Assay > & | getAssays () |
| const std::vector< ConsensusMap > & | getConsensusMaps () const |
| std::vector< ConsensusMap > & | getConsensusMaps () |
| void | setConsensusMaps (const std::vector< ConsensusMap > &) |
| const std::vector< FeatureMap<> > & | getFeatureMaps () const |
| const AnalysisSummary & | getAnalysisSummary () const |
| AnalysisSummary & | getAnalysisSummary () |
| void | setDataProcessingList (std::vector< DataProcessing > &dpl) |
| void | setAnalysisSummaryQuantType (QUANT_TYPES r) |
| void | addConsensusMap (ConsensusMap &m) |
| void | assignUIDs () |
| void | registerExperiment (MSExperiment< Peak1D > &exp, std::vector< std::vector< std::pair< String, DoubleReal > > > labels) |
Public Member Functions inherited from ExperimentalSettings | |
| ExperimentalSettings () | |
| Constructor. More... | |
| ExperimentalSettings (const ExperimentalSettings &source) | |
| Copy constructor. More... | |
| ~ExperimentalSettings () | |
| Destructor. More... | |
| ExperimentalSettings & | operator= (const ExperimentalSettings &source) |
| Assignment operator. More... | |
| bool | operator== (const ExperimentalSettings &rhs) const |
| Equality operator. More... | |
| bool | operator!= (const ExperimentalSettings &rhs) const |
| Equality operator. More... | |
| const Sample & | getSample () const |
| returns a const reference to the sample description More... | |
| Sample & | getSample () |
| returns a mutable reference to the sample description More... | |
| void | setSample (const Sample &sample) |
| sets the sample description More... | |
| const std::vector< SourceFile > & | getSourceFiles () const |
| returns a const reference to the source data file More... | |
| std::vector< SourceFile > & | getSourceFiles () |
| returns a mutable reference to the source data file More... | |
| void | setSourceFiles (const std::vector< SourceFile > &source_files) |
| sets the source data file More... | |
| const std::vector < ContactPerson > & | getContacts () const |
| returns a const reference to the list of contact persons More... | |
| std::vector< ContactPerson > & | getContacts () |
| returns a mutable reference to the list of contact persons More... | |
| void | setContacts (const std::vector< ContactPerson > &contacts) |
| sets the list of contact persons More... | |
| const Instrument & | getInstrument () const |
| returns a const reference to the MS instrument description More... | |
| Instrument & | getInstrument () |
| returns a mutable reference to the MS instrument description More... | |
| void | setInstrument (const Instrument &instrument) |
| sets the MS instrument description More... | |
| const HPLC & | getHPLC () const |
| returns a const reference to the description of the HPLC run More... | |
| HPLC & | getHPLC () |
| returns a mutable reference to the description of the HPLC run More... | |
| void | setHPLC (const HPLC &hplc) |
| sets the description of the HPLC run More... | |
| const DateTime & | getDateTime () const |
| returns the date the experiment was performed More... | |
| void | setDateTime (const DateTime &date) |
| sets the date the experiment was performed More... | |
| const String & | getComment () const |
| returns the free-text comment More... | |
| void | setComment (const String &comment) |
| sets the free-text comment More... | |
| const std::vector < ProteinIdentification > & | getProteinIdentifications () const |
| returns a const reference to the protein ProteinIdentification vector More... | |
| std::vector < ProteinIdentification > & | getProteinIdentifications () |
| returns a mutable reference to the protein ProteinIdentification vector More... | |
| void | setProteinIdentifications (const std::vector< ProteinIdentification > &protein_identifications) |
| sets the protein ProteinIdentification vector More... | |
| const String & | getFractionIdentifier () const |
| returns fraction identifier More... | |
| void | setFractionIdentifier (const String &fraction_identifier) |
| sets the fraction identifier 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... | |
Public Member Functions inherited from DocumentIdentifier | |
| DocumentIdentifier () | |
| default constructor More... | |
| DocumentIdentifier (const DocumentIdentifier &source) | |
| Copy constructor. More... | |
| DocumentIdentifier & | operator= (const DocumentIdentifier &source) |
| Assignment operator. More... | |
| bool | operator== (const DocumentIdentifier &rhs) const |
| Equality operator. More... | |
| virtual | ~DocumentIdentifier () |
| destructor More... | |
| void | setIdentifier (const String &id) |
| set document identifier (e.g. an LSID) More... | |
| const String & | getIdentifier () const |
| retrieve document identifier (e.g. an LSID) More... | |
| void | swap (DocumentIdentifier &from) |
exchange content with from More... | |
| void | setLoadedFilePath (const String &file_name) |
| set the file_name_ according to absolute path of the file loaded from preferably done whilst loading More... | |
| const String & | getLoadedFilePath () const |
| get the file_name_ which is the absolute path to the file loaded from More... | |
| void | setLoadedFileType (const String &file_name) |
| set the file_type according to the type of the file loaded from (see FileHandler::Type) preferably done whilst loading More... | |
| const FileTypes::Type & | getLoadedFileType () const |
| get the file_type (e.g. featureXML, consensusXML, mzData, mzXML, mzML, ...) of the file loaded from More... | |
Private Attributes | |
| AnalysisSummary | analysis_summary_ |
| std::vector< MetaInfo > | bibliographic_reference_ |
| std::vector< ConsensusMap > | consensus_maps_ |
| std::vector< FeatureMap<> > | feature_maps_ |
| std::vector< Assay > | assays_ |
| std::vector< DataProcessing > | data_processings_ |
Base type definitions | |
| enum | QUANT_TYPES { MS1LABEL = 0, MS2LABEL, LABELFREE, SIZE_OF_QUANT_TYPES } |
| typedef CVTermList | ParamGroupList |
| typedef docu More... | |
| static const std::string | NamesOfQuantTypes [SIZE_OF_QUANT_TYPES] |
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... | |
Protected Attributes inherited from ExperimentalSettings | |
| Sample | sample_ |
| std::vector< SourceFile > | source_files_ |
| std::vector< ContactPerson > | contacts_ |
| Instrument | instrument_ |
| HPLC | hplc_ |
| DateTime | datetime_ |
| String | comment_ |
| std::vector < ProteinIdentification > | protein_identifications_ |
| String | fraction_identifier_ |
Protected Attributes inherited from MetaInfoInterface | |
| MetaInfo * | meta_ |
| pointer to the MetaInfo object. 0 by default More... | |
Protected Attributes inherited from DocumentIdentifier | |
| String | id_ |
| the ID (e.g. LSID) More... | |
| String | file_path_ |
| the path to the loaded file More... | |
| FileTypes::Type | file_type_ |
| the type of the loaded file More... | |
| typedef CVTermList ParamGroupList |
typedef docu
| enum QUANT_TYPES |
Constructor.
| ~MSQuantifications | ( | ) |
Destructor.
| MSQuantifications | ( | const MSQuantifications & | source | ) |
Copy constructor.
| void addConsensusMap | ( | ConsensusMap & | m | ) |
| void assignUIDs | ( | ) |
| const AnalysisSummary& getAnalysisSummary | ( | ) | const |
| AnalysisSummary& getAnalysisSummary | ( | ) |
| const std::vector<Assay>& getAssays | ( | ) | const |
| std::vector<Assay>& getAssays | ( | ) |
| const std::vector<ConsensusMap>& getConsensusMaps | ( | ) | const |
| std::vector<ConsensusMap>& getConsensusMaps | ( | ) |
| const std::vector<DataProcessing> getDataProcessingList | ( | ) | const |
Loads data from a text file.
| filename | The input file name. |
| trim_lines | Whether or not the lines are trimmed when reading them from file. |
| first_n | If set, only first_n lines the lines from the beginning of the file are read. |
| Exception::FileNotFound | is thrown if the file could not be opened. |
TODO : implement
| const std::vector<FeatureMap<> >& getFeatureMaps | ( | ) | const |
| bool operator!= | ( | const MSQuantifications & | rhs | ) | const |
Equality operator.
| MSQuantifications& operator= | ( | const MSQuantifications & | source | ) |
Assignment operator.
| bool operator== | ( | const MSQuantifications & | rhs | ) | const |
Equality operator.
| void registerExperiment | ( | MSExperiment< Peak1D > & | exp, |
| std::vector< std::vector< std::pair< String, DoubleReal > > > | labels | ||
| ) |
| void setAnalysisSummaryQuantType | ( | QUANT_TYPES | r | ) |
| void setConsensusMaps | ( | const std::vector< ConsensusMap > & | ) |
| void setDataProcessingList | ( | std::vector< DataProcessing > & | dpl | ) |
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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 |