| OpenMS 2.5.0

Classes | Public Types | Public Member Functions | Protected Attributes | Private Member Functions | List of all members
ConsensusMap Class Reference
Kernel

A container for consensus elements. More...

`#include <OpenMS/KERNEL/ConsensusMap.h>`

Inheritance diagram for ConsensusMap:

## Classes

struct | ColumnHeader
| Description of the columns in a consensus map. More...

## Public Types

typedef std::vector< ConsensusFeature > | privvec
Type definitions
typedef std::vector< ConsensusFeature > | Base
typedef RangeManager< 2 > | RangeManagerType
typedef std::map< UInt64, ColumnHeader > | ColumnHeaders
typedef std::vector< ConsensusFeature >::iterator | Iterator
| Mutable iterator. More...
typedef std::vector< ConsensusFeature >::const_iterator | ConstIterator
| Non-mutable iterator. More...
typedef std::vector< ConsensusFeature >::reverse_iterator | ReverseIterator
| Mutable reverse iterator. More...
typedef std::vector< ConsensusFeature >::const_reverse_iterator | ConstReverseIterator
| Non-mutable reverse iterator. More...
Public Types inherited from RangeManager< 2 >
enum |
| Dimension of the position range. More...
typedef DRange< D > | PositionRangeType
| Position range type. More...
typedef DPosition< D > | PositionType
| Position Type. More...
typedef DRange< 1 > | IntensityRangeType
| Intensity range type. More...
Public Types inherited from UniqueIdInterface
enum | { INVALID = 0 }
| This is the invalid unique id (cast it to a UInt64 if you like) More...
Public Types inherited from UniqueIdIndexer< ConsensusMap >
typedef boost::unordered_map< UInt64, Size > | UniqueIdMap

## Public Member Functions

| ConsensusMap ()
| Default constructor. More...
| ConsensusMap (const ConsensusMap &source)
| Copy constructor. More...
| ~ConsensusMap () override
| Destructor. More...
| ConsensusMap (Base::size_type n)
| Creates a ConsensusMap with n elements. More...
ConsensusMap & | operator= (const ConsensusMap &source)
| Assignment operator. More...
ConsensusMap & | appendRows (const ConsensusMap &rhs)
| Add consensus map entries as new rows. More...
ConsensusMap & | appendColumns (const ConsensusMap &rhs)
| Add consensus map entries as new columns. More...
void | clear (bool clear_meta_data=true)
| Clears all data and meta data. More...
const ColumnHeaders & | getColumnHeaders () const
| Non-mutable access to the file descriptions. More...
ColumnHeaders & | getColumnHeaders ()
| Mutable access to the file descriptions. More...
void | setColumnHeaders (const ColumnHeaders &column_description)
| Mutable access to the file descriptions. More...
const String & | getExperimentType () const
| Non-mutable access to the experiment type. More...
void | setExperimentType (const String &experiment_type)
| Mutable access to the experiment type. More...
void | updateRanges () override
| Updates minimum and maximum position/intensity. More...
void | swap (ConsensusMap &from)
| Swaps the content of this map with the content of `from`. More...
const std::vector< ProteinIdentification > & | getProteinIdentifications () const
| non-mutable access to the protein identifications More...
std::vector< ProteinIdentification > & | getProteinIdentifications ()
| mutable access to the protein identifications More...
void | setProteinIdentifications (const std::vector< ProteinIdentification > &protein_identifications)
| sets the protein identifications More...
void | setProteinIdentifications (std::vector< ProteinIdentification > &&protein_identifications)
| sets the protein identifications by moving More...
const std::vector< PeptideIdentification > & | getUnassignedPeptideIdentifications () const
| non-mutable access to the unassigned peptide identifications More...
std::vector< PeptideIdentification > & | getUnassignedPeptideIdentifications ()
| mutable access to the unassigned peptide identifications More...
void | setUnassignedPeptideIdentifications (const std::vector< PeptideIdentification > &unassigned_peptide_identifications)
| sets the unassigned peptide identifications More...
const std::vector< DataProcessing > & | getDataProcessing () const
| returns a const reference to the description of the applied data processing More...
std::vector< DataProcessing > & | getDataProcessing ()
| returns a mutable reference to the description of the applied data processing More...
void | setDataProcessing (const std::vector< DataProcessing > &processing_method)
| sets the description of the applied data processing More...
void | setPrimaryMSRunPath (const StringList &s)
| set the file paths to the primary MS run (stored in ColumnHeaders) More...
void | setPrimaryMSRunPath (const StringList &s, MSExperiment &e)
void | getPrimaryMSRunPath (StringList &toFill) const
| returns the MS run path (stored in ColumnHeaders) More...
void | applyFunctionOnPeptideHits (std::function< void(PeptideHit &)> &f, bool include_unassigned=true)
| applies a function on all PeptideHits or only assigned ones More...
void | applyFunctionOnPeptideIDs (std::function< void(PeptideIdentification &)> &f, bool include_unassigned=true)
| applies a function on all PeptideIDs or only assigned ones More...
void | applyFunctionOnPeptideHits (std::function< void(const PeptideHit &)> &, bool include_unassigned=true) const
| applies a const function on all PeptideHits or only assigned ones More...
void | applyFunctionOnPeptideIDs (std::function< void(const PeptideIdentification &)> &f, bool include_unassigned=true) const
| applies a const function on all PeptideIDs or only assigned ones More...
bool | operator== (const ConsensusMap &rhs) const
| Equality operator. More...
bool | operator!= (const ConsensusMap &rhs) const
| Equality operator. More...
template<typename Type >
Size | applyMemberFunction (Size(Type::*member_function)())
| Applies a member function of Type to the container itself and all consensus features. The returned values are accumulated. More...
template<typename Type >
Size | applyMemberFunction (Size(Type::*member_function)() const) const
| The "const" variant. More...
bool | isMapConsistent (Logger::LogStream *stream=nullptr) const
| checks if the given maps are unique and all FeatureHandles actually refer to a registered map More...
Sorting.
These specialized sorting methods are supported in addition to the standard sorting methods of std::vector. All use stable sorting.
void | sortByIntensity (bool reverse=false)
| Sorts the peaks according to ascending intensity. More...
void | sortByRT ()
| Sorts the peaks to RT position. More...
void | sortByMZ ()
| Sorts the peaks to m/z position. More...
void | sortByPosition ()
| Lexicographically sorts the peaks by their position (First RT then m/z). More...
void | sortByQuality (bool reverse=false)
| Sorts the peaks according to ascending quality. More...
void | sortBySize ()
| Sorts with respect to the size (number of elements) More...
void | sortByMaps ()
| Sorts with respect to the sets of maps covered by the consensus features (lexicographically). More...
void | sortPeptideIdentificationsByMapIndex ()
| Sorts PeptideIdentifications of consensus features with respect to their map index. 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...
Public Member Functions inherited from RangeManager< 2 >
| RangeManager ()
| Default constructor. More...
| RangeManager (const RangeManager &rhs)
| Copy constructor. More...
| RangeManager (RangeManager &&) noexcept=default
| Move constructor. More...
virtual | ~RangeManager ()
| Destructor. More...
RangeManager & | operator= (const RangeManager &rhs)
| Assignment operator. More...
bool | operator== (const RangeManager &rhs) const
| Equality operator. More...
bool | operator!= (const RangeManager &rhs) const
| Equality operator. More...
const PositionType & | getMin () const
| Returns the minimum position. More...
const PositionType & | getMax () const
| Returns the maximum position. More...
double | getMinInt () const
| Returns the minimum intensity. More...
double | getMaxInt () const
| Returns the maximum intensity. More...
void | clearRanges ()
| Resets the ranges. More...
Public Member Functions inherited from DocumentIdentifier
| DocumentIdentifier ()
| Default constructor. More...
| DocumentIdentifier (const DocumentIdentifier &)=default
| Copy constructor. More...
| DocumentIdentifier (DocumentIdentifier &&)=default
| Move constructor. More...
virtual | ~DocumentIdentifier ()
| Destructor. More...
DocumentIdentifier & | operator= (const DocumentIdentifier &)=default
| Assignment operator. More...
DocumentIdentifier & | operator= (DocumentIdentifier &&) &=default
| Move assignment operator. More...
bool | operator== (const DocumentIdentifier &rhs) const
| Equality operator. 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...
Public Member Functions inherited from UniqueIdInterface
| UniqueIdInterface ()
| Default constructor - the unique id will be invalid More...
| UniqueIdInterface (const UniqueIdInterface &rhs)=default
| Copy constructor - copies the unique id. More...
| UniqueIdInterface (UniqueIdInterface &&rhs)=default
| Move constructor. More...
UniqueIdInterface & | operator= (UniqueIdInterface const &rhs)=default
| Assignment operator - copies the unique id. More...
UniqueIdInterface & | operator= (UniqueIdInterface &&) &=default
| Move Assignment operator - copies the unique id. More...
virtual | ~UniqueIdInterface ()=default
| Destructor. More...
bool | operator== (UniqueIdInterface const &rhs) const
| Equality comparison operator - the unique ids must be equal (!) More...
UInt64 | getUniqueId () const
| Non-mutable access to unique id - returns the unique id. More...
Size | clearUniqueId ()
| Clear the unique id. The new unique id will be invalid. Returns 1 if the unique id was changed, 0 otherwise. More...
void | swap (UniqueIdInterface &from)
Size | hasValidUniqueId () const
| Returns whether the unique id is valid. Returns 1 if the unique id is valid, 0 otherwise. More...
Size | hasInvalidUniqueId () const
| Returns whether the unique id is invalid. Returns 1 if the unique id is invalid, 0 otherwise. More...
Size | setUniqueId ()
| Assigns a new, valid unique id. Always returns 1. More...
Size | ensureUniqueId ()
| Assigns a valid unique id, but only if the present one is invalid. Returns 1 if the unique id was changed, 0 otherwise. More...
void | setUniqueId (UInt64 rhs)
| Assigns the given unique id. More...
void | setUniqueId (const String &rhs)
| Mutable access to unique id. More...
Public Member Functions inherited from UniqueIdIndexer< ConsensusMap >
Size | uniqueIdToIndex (UInt64 unique_id) const
| Returns the index of the feature with the given unique id, or Size(-1) if none exists in this random access container. More...
void | updateUniqueIdToIndex () const
| Updates the hash map from unique id to index. More...
Size | resolveUniqueIdConflicts ()
| Assign new UID's to doubly occurring UID's. More...
void | swap (UniqueIdIndexer &rhs)
| Swap. More...

## Protected Attributes

ColumnHeaders | column_description_
| Map from index to file description. More...
String | experiment_type_ = "label-free"
| type of experiment (label-free, labeled_MS1, labeled_MS2) More...
std::vector< ProteinIdentification > | protein_identifications_
| protein identifications More...
std::vector< PeptideIdentification > | unassigned_peptide_identifications_
| unassigned peptide identifications (without feature) More...
std::vector< DataProcessing > | data_processing_
| applied data processing More...
Protected Attributes inherited from MetaInfoInterface
MetaInfo * | meta_
| Pointer to the MetaInfo object (0 by default) More...
Protected Attributes inherited from RangeManager< 2 >
IntensityRangeType | int_range_
| Intensity range (1-dimensional) More...
PositionRangeType | pos_range_
| Position range (D-dimensional) 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...
Protected Attributes inherited from UniqueIdInterface
UInt64 | unique_id_
| the unique id More...
Protected Attributes inherited from UniqueIdIndexer< ConsensusMap >
UniqueIdMap | uniqueid_to_index_
| hash map from unique id to index of features More...

## Private Member Functions

void | applyFunctionOnPeptideIDs_ (const std::vector< PeptideIdentification > &idvec, std::function< void(const PeptideIdentification &)> &f) const
void | applyFunctionOnPeptideHits_ (const std::vector< PeptideIdentification > &idvec, std::function< void(const PeptideHit &)> &f) const
void | applyFunctionOnPeptideIDs_ (std::vector< PeptideIdentification > &idvec, std::function< void(PeptideIdentification &)> &f)
void | applyFunctionOnPeptideHits_ (std::vector< PeptideIdentification > &idvec, std::function< void(PeptideHit &)> &f)

## Additional Inherited Members

Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry & | metaRegistry ()
| Returns a reference to the MetaInfoRegistry. More...
Static Public Member Functions inherited from UniqueIdInterface
static bool | isValid (UInt64 unique_id)
| Returns true if the unique_id is valid, false otherwise. More...
Protected Member Functions inherited from MetaInfoInterface
void | createIfNotExists_ ()
| Creates the MetaInfo object if it does not exist. More...
Protected Member Functions inherited from RangeManager< 2 >
void | updateRanges_ (const PeakIteratorType &begin, const PeakIteratorType &end)
| Updates the range using data points in the iterator range. More...
Protected Member Functions inherited from UniqueIdIndexer< ConsensusMap >
const ConsensusMap & | getBase_ () const
| A little helper to get access to the base (!) class RandomAccessContainer. More...
ConsensusMap & | getBase_ ()
| A little helper to get access to the base (!) class RandomAccessContainer. More...

## Detailed Description

A container for consensus elements.

A ConsensusMap is a container holding 2-dimensional consensus elements (ConsensusFeature) which in turn represent analytes that have been quantified across multiple LC-MS/MS experiments. Each analyte in a ConsensusFeature is linked to its original LC-MS/MS run, the links are maintained by the ConsensusMap class. The map is implemented as a vector of elements of type ConsensusFeature.

To be consistent, all maps who are referenced by ConsensusFeature objects (through a unique id) need to be registered in this class.

## Member Typedef Documentation

## ◆ Base

typedef std::vector<ConsensusFeature> Base

## ◆ ColumnHeaders

typedef std::map<UInt64, ColumnHeader> ColumnHeaders

## ◆ ConstIterator

typedef std::vector<ConsensusFeature>::const_iterator ConstIterator

Non-mutable iterator.

## ◆ ConstReverseIterator

typedef std::vector<ConsensusFeature>::const_reverse_iterator ConstReverseIterator

Non-mutable reverse iterator.

## ◆ Iterator

typedef std::vector<ConsensusFeature>::iterator Iterator

Mutable iterator.

## ◆ privvec

typedef std::vector<ConsensusFeature> privvec

## ◆ RangeManagerType

typedef RangeManager<2> RangeManagerType

## ◆ ReverseIterator

typedef std::vector<ConsensusFeature>::reverse_iterator ReverseIterator

Mutable reverse iterator.

## Constructor & Destructor Documentation

## ◆ ConsensusMap() [1/3]

ConsensusMap | ( |  | ) |

Default constructor.

## ◆ ConsensusMap() [2/3]

ConsensusMap | ( | const ConsensusMap & | source | ) |

Copy constructor.

## ◆ ~ConsensusMap()

~ConsensusMap | ( |  | ) |

override

Destructor.

## ◆ ConsensusMap() [3/3]

ConsensusMap | ( | Base::size_type | n | ) |

explicit

Creates a ConsensusMap with n elements.

## Member Function Documentation

## ◆ appendColumns()

ConsensusMap& appendColumns | ( | const ConsensusMap & | rhs | ) |

Add consensus map entries as new columns.

The number of columns (maximum map index) is the sum of both maps.

Parameters

  rhs | The consensus map to be merged.

Referenced by UTILProteomicsLFQ::main_().

## ◆ appendRows()

ConsensusMap& appendRows | ( | const ConsensusMap & | rhs | ) |

Add consensus map entries as new rows.

Consensus elements are merged into one container, simply by appending.

The number of columns (maximum map index) stays the same.

Parameters

  rhs | The consensus map to be merged.

## ◆ applyFunctionOnPeptideHits() [1/2]

void applyFunctionOnPeptideHits | ( | std::function< void(PeptideHit &)> & | f,
|  | bool | include_unassigned = `true`
| ) |  |

applies a function on all PeptideHits or only assigned ones

## ◆ applyFunctionOnPeptideHits() [2/2]

void applyFunctionOnPeptideHits | ( | std::function< void(const PeptideHit &)> & | ,
|  | bool | include_unassigned = `true`
| ) |  | const

applies a const function on all PeptideHits or only assigned ones

## ◆ applyFunctionOnPeptideHits_() [1/2]

void applyFunctionOnPeptideHits_ | ( | const std::vector< PeptideIdentification > & | idvec,
|  | std::function< void(const PeptideHit &)> & | f
| ) |  | const

private

## ◆ applyFunctionOnPeptideHits_() [2/2]

void applyFunctionOnPeptideHits_ | ( | std::vector< PeptideIdentification > & | idvec,
|  | std::function< void(PeptideHit &)> & | f
| ) |  |

private

## ◆ applyFunctionOnPeptideIDs() [1/2]

void applyFunctionOnPeptideIDs | ( | std::function< void(PeptideIdentification &)> & | f,
|  | bool | include_unassigned = `true`
| ) |  |

applies a function on all PeptideIDs or only assigned ones

Referenced by IDScoreGetterSetter::getPeptideScoresFromMap_(), and IDScoreGetterSetter::setPeptideScoresForMap_().

## ◆ applyFunctionOnPeptideIDs() [2/2]

void applyFunctionOnPeptideIDs | ( | std::function< void(const PeptideIdentification &)> & | f,
|  | bool | include_unassigned = `true`
| ) |  | const

applies a const function on all PeptideIDs or only assigned ones

## ◆ applyFunctionOnPeptideIDs_() [1/2]

void applyFunctionOnPeptideIDs_ | ( | const std::vector< PeptideIdentification > & | idvec,
|  | std::function< void(const PeptideIdentification &)> & | f
| ) |  | const

private

## ◆ applyFunctionOnPeptideIDs_() [2/2]

void applyFunctionOnPeptideIDs_ | ( | std::vector< PeptideIdentification > & | idvec,
|  | std::function< void(PeptideIdentification &)> & | f
| ) |  |

private

## ◆ applyMemberFunction() [1/2]

Size applyMemberFunction | ( | Size(Type::*)() | member_function | ) |

inline

Applies a member function of Type to the container itself and all consensus features. The returned values are accumulated.

Example: The following will print the number of features with invalid unique ids (plus 1 if the container has an invalid UID as well):

ConsensusMap cm;
(...)
std::cout << cm.applyMemberFunction(&UniqueIdInterface::hasInvalidUniqueId) << std::endl;

See e.g. UniqueIdInterface for what else can be done this way.

Referenced by UTILProteomicsLFQ::quantifyFraction_().

## ◆ applyMemberFunction() [2/2]

Size applyMemberFunction | ( | Size(Type::*)() const | member_function | ) | const

inline

The "const" variant.

## ◆ clear()

void clear | ( | bool | clear_meta_data = `true` | ) |

Clears all data and meta data.

Parameters

  clear_meta_data | If true, all meta data is cleared in addition to the data.

Referenced by UTILProteomicsLFQ::main_().

## ◆ getColumnHeaders() [1/2]

const ColumnHeaders& getColumnHeaders | ( |  | ) | const

Non-mutable access to the file descriptions.

Referenced by UTILProteomicsLFQ::getPeptideOccurrence_(), and UTILProteomicsLFQ::quantifyFraction_().

## ◆ getColumnHeaders() [2/2]

ColumnHeaders& getColumnHeaders | ( |  | ) |

Mutable access to the file descriptions.

## ◆ getDataProcessing() [1/2]

const std::vector<DataProcessing>& getDataProcessing | ( |  | ) | const

returns a const reference to the description of the applied data processing

## ◆ getDataProcessing() [2/2]

std::vector<DataProcessing>& getDataProcessing | ( |  | ) |

returns a mutable reference to the description of the applied data processing

## ◆ getExperimentType()

const String& getExperimentType | ( |  | ) | const

Non-mutable access to the experiment type.

## ◆ getPrimaryMSRunPath()

void getPrimaryMSRunPath | ( | StringList & | toFill | ) | const

returns the MS run path (stored in ColumnHeaders)

## ◆ getProteinIdentifications() [1/2]

const std::vector<ProteinIdentification>& getProteinIdentifications | ( |  | ) | const

non-mutable access to the protein identifications

Referenced by UTILProteomicsLFQ::main_(), and FeatureGroupingAlgorithm::postprocess_().

## ◆ getProteinIdentifications() [2/2]

std::vector<ProteinIdentification>& getProteinIdentifications | ( |  | ) |

mutable access to the protein identifications

## ◆ getUnassignedPeptideIdentifications() [1/2]

const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications | ( |  | ) | const

non-mutable access to the unassigned peptide identifications

Referenced by FeatureGroupingAlgorithm::postprocess_().

## ◆ getUnassignedPeptideIdentifications() [2/2]

std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications | ( |  | ) |

mutable access to the unassigned peptide identifications

## ◆ isMapConsistent()

bool isMapConsistent | ( | Logger::LogStream * | stream = `nullptr` | ) | const

checks if the given maps are unique and all FeatureHandles actually refer to a registered map

To avoid inconsistencies in map IDs and make sure the maps are unique in terms of name+label

If you want some verbose output, provide a stream.

: alternative to this method we could check the features while they are added to the map directly, but

- currently we can't because the interface is not designed for this (derived from std::vector, no encapsulation)
- we should restrict the user to first fill the list of maps, before any datapoints can be inserted

## ◆ operator!=()

bool operator!= | ( | const ConsensusMap & | rhs | ) | const

Equality operator.

## ◆ operator=()

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

Assignment operator.

## ◆ operator==()

bool operator== | ( | const ConsensusMap & | rhs | ) | const

Equality operator.

## ◆ setColumnHeaders()

void setColumnHeaders | ( | const ColumnHeaders & | column_description | ) |

Mutable access to the file descriptions.

## ◆ setDataProcessing()

void setDataProcessing | ( | const std::vector< DataProcessing > & | processing_method | ) |

sets the description of the applied data processing

## ◆ setExperimentType()

void setExperimentType | ( | const String & | experiment_type | ) |

Mutable access to the experiment type.

## ◆ setPrimaryMSRunPath() [1/2]

void setPrimaryMSRunPath | ( | const StringList & | s | ) |

set the file paths to the primary MS run (stored in ColumnHeaders)

## ◆ setPrimaryMSRunPath() [2/2]

void setPrimaryMSRunPath | ( | const StringList & | s,
|  | MSExperiment & | e
| ) |  |

set the file path to the primary MS run using the mzML annotated in the MSExperiment

Parameters

  e. | If it doesn't exist, fallback to
  s. |

## ◆ setProteinIdentifications() [1/2]

void setProteinIdentifications | ( | const std::vector< ProteinIdentification > & | protein_identifications | ) |

sets the protein identifications

## ◆ setProteinIdentifications() [2/2]

void setProteinIdentifications | ( | std::vector< ProteinIdentification > && | protein_identifications | ) |

sets the protein identifications by moving

## ◆ setUnassignedPeptideIdentifications()

void setUnassignedPeptideIdentifications | ( | const std::vector< PeptideIdentification > & | unassigned_peptide_identifications | ) |

sets the unassigned peptide identifications

## ◆ sortByIntensity()

void sortByIntensity | ( | bool | reverse = `false` | ) |

Sorts the peaks according to ascending intensity.

## ◆ sortByMaps()

void sortByMaps | ( |  | ) |

Sorts with respect to the sets of maps covered by the consensus features (lexicographically).

Referenced by FeatureGroupingAlgorithm::postprocess_().

## ◆ sortByMZ()

void sortByMZ | ( |  | ) |

Sorts the peaks to m/z position.

## ◆ sortByPosition()

void sortByPosition | ( |  | ) |

Lexicographically sorts the peaks by their position (First RT then m/z).

Referenced by UTILProteomicsLFQ::main_().

## ◆ sortByQuality()

void sortByQuality | ( | bool | reverse = `false` | ) |

Sorts the peaks according to ascending quality.

Referenced by FeatureGroupingAlgorithm::postprocess_().

## ◆ sortByRT()

void sortByRT | ( |  | ) |

Sorts the peaks to RT position.

## ◆ sortBySize()

void sortBySize | ( |  | ) |

Sorts with respect to the size (number of elements)

Referenced by FeatureGroupingAlgorithm::postprocess_().

## ◆ sortPeptideIdentificationsByMapIndex()

void sortPeptideIdentificationsByMapIndex | ( |  | ) |

Sorts PeptideIdentifications of consensus features with respect to their map index.

Referenced by UTILProteomicsLFQ::main_(), and UTILProteomicsLFQ::quantifyFraction_().

## ◆ swap()

void swap | ( | ConsensusMap & | from | ) |

Swaps the content of this map with the content of `from`.

## ◆ updateRanges()

void updateRanges | ( |  | ) |

override virtual

Updates minimum and maximum position/intensity.

This method is usually implemented by calling clearRanges() and updateRanges_().

Implements RangeManager< 2 >.

## Member Data Documentation

## ◆ column_description_

ColumnHeaders column_description_

protected

Map from index to file description.

## ◆ data_processing_

std::vector<DataProcessing> data_processing_

protected

applied data processing

## ◆ experiment_type_

String experiment_type_ = "label-free"

protected

type of experiment (label-free, labeled_MS1, labeled_MS2)

## ◆ protein_identifications_

std::vector<ProteinIdentification> protein_identifications_

protected

protein identifications

## ◆ unassigned_peptide_identifications_

std::vector<PeptideIdentification> unassigned_peptide_identifications_

protected

unassigned peptide identifications (without feature)