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OpenMS
2.4.0
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#include <OpenMS/METADATA/MSQuantifications.h>
Classes | |
struct | AnalysisSummary |
struct | Assay |
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] |
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_ |
MSQuantifications () | |
Constructor. More... | |
MSQuantifications (FeatureMap fm, ExperimentalSettings &es, std::vector< DataProcessing > &dps, std::vector< std::vector< std::pair< String, double > > > labels=(std::vector< std::vector< std::pair< String, double > > >())) | |
Detailed Constructor. More... | |
~MSQuantifications () override | |
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 (PeakMap &exp, std::vector< std::vector< std::pair< String, double > > > labels) |
void | registerExperiment (ExperimentalSettings &es, std::vector< DataProcessing > &dp, std::vector< std::vector< std::pair< String, double > > > labels=(std::vector< std::vector< std::pair< String, double > > >())) |
Additional Inherited Members | |
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ExperimentalSettings () | |
Constructor. More... | |
ExperimentalSettings (const ExperimentalSettings &source) | |
Copy constructor. More... | |
~ExperimentalSettings () override | |
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... | |
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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 (or DataValue::EMPTY if not found) More... | |
const DataValue & | getMetaValue (UInt index) const |
Returns the value corresponding to an index (or 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... | |
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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... | |
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static MetaInfoRegistry & | metaRegistry () |
Returns a reference to the MetaInfoRegistry. More... | |
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void | createIfNotExists_ () |
Creates the MetaInfo object if it does not exist. More... | |
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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_ |
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MetaInfo * | meta_ |
Pointer to the MetaInfo object (0 by default) More... | |
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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 | ( | FeatureMap | fm, |
ExperimentalSettings & | es, | ||
std::vector< DataProcessing > & | dps, | ||
std::vector< std::vector< std::pair< String, double > > > | labels = (std::vector< std::vector< std::pair< String, double > > >()) |
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Detailed Constructor.
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override |
Destructor.
MSQuantifications | ( | const MSQuantifications & | source | ) |
Copy constructor.
void addConsensusMap | ( | ConsensusMap & | m | ) |
void assignUIDs | ( | ) |
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 |
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 | ( | ExperimentalSettings & | es, |
std::vector< DataProcessing > & | dp, | ||
std::vector< std::vector< std::pair< String, double > > > | labels = (std::vector< std::vector< std::pair< String, double > > >()) |
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void registerExperiment | ( | PeakMap & | exp, |
std::vector< std::vector< std::pair< String, double > > > | labels | ||
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void setAnalysisSummaryQuantType | ( | QUANT_TYPES | r | ) |
void setConsensusMaps | ( | const std::vector< ConsensusMap > & | ) |
void setDataProcessingList | ( | std::vector< DataProcessing > & | dpl | ) |
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