A container for features. More...
#include <OpenMS/KERNEL/FeatureMap.h>
Public Types | |
Type definitions | |
typedef std::vector< FeatureT > | privvec |
typedef FeatureT | FeatureType |
typedef RangeManager< 2 > | RangeManagerType |
typedef std::vector< FeatureType > | Base |
typedef Base::iterator | Iterator |
typedef Base::const_iterator | ConstIterator |
typedef Base::reverse_iterator | ReverseIterator |
typedef Base::const_reverse_iterator | ConstReverseIterator |
typedef FeatureType & | Reference |
typedef const FeatureType & | ConstReference |
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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... | |
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enum | { INVALID = 0 } |
This is the invalid unique id (cast it to a UInt64 if you like) More... | |
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typedef boost::unordered_map < UInt64, Size > | UniqueIdMap |
Public Member Functions | |
FeatureMap & | operator= (const FeatureMap &rhs) |
Assignment operator. More... | |
bool | operator== (const FeatureMap &rhs) const |
Equality operator. More... | |
bool | operator!= (const FeatureMap &rhs) const |
Equality operator. More... | |
FeatureMap | operator+ (const FeatureMap &rhs) const |
Joins two feature maps. More... | |
FeatureMap & | operator+= (const FeatureMap &rhs) |
Add one feature map to another. More... | |
void | updateRanges () |
Updates minimum and maximum position/intensity. More... | |
void | swapFeaturesOnly (FeatureMap &from) |
Swaps the feature content (plus its range information) of this map with the content of from . More... | |
void | swap (FeatureMap &from) |
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... | |
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 | clear (bool clear_meta_data=true) |
Clears all data and meta data. More... | |
template<typename Type > | |
Size | applyMemberFunction (Size(Type::*member_function)()) |
Applies a member function of Type to the container itself and all features (including subordinates). The returned values are accumulated. More... | |
template<typename Type > | |
Size | applyMemberFunction (Size(Type::*member_function)() const) const |
The "const" variant. More... | |
AnnotationStatistics | getAnnotationStatistics () const |
Constructors and Destructor | |
FeatureMap () | |
Default constructor. More... | |
FeatureMap (const FeatureMap &source) | |
Copy constructor. More... | |
virtual | ~FeatureMap () |
Destructor. More... | |
Sorting. | |
These simplified sorting methods are supported in addition to the standard sorting methods of std::vector. | |
void | sortByIntensity (bool reverse=false) |
Sorts the peaks according to ascending intensity. More... | |
void | sortByPosition () |
Sort features by position. Lexicographical comparison (first RT then m/z) is done. More... | |
void | sortByRT () |
Sort features by RT position. More... | |
void | sortByMZ () |
Sort features by m/z position. More... | |
void | sortByOverallQuality (bool reverse=false) |
Sort features by ascending overall quality. More... | |
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RangeManager () | |
Default constructor. More... | |
RangeManager (const RangeManager &rhs) | |
Copy 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... | |
DoubleReal | getMinInt () const |
Returns the minimum intensity. More... | |
DoubleReal | getMaxInt () const |
Returns the maximum intensity. More... | |
void | clearRanges () |
Resets the ranges. 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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UniqueIdInterface () | |
Default constructor - the unique id will be invalid More... | |
UniqueIdInterface (const UniqueIdInterface &rhs) | |
Copy constructor - copies the unique id. More... | |
UniqueIdInterface & | operator= (UniqueIdInterface const &rhs) |
Assignment operator - copies the unique id. More... | |
~UniqueIdInterface () | |
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... | |
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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 | |
std::vector < ProteinIdentification > | protein_identifications_ |
protein identifications More... | |
std::vector < PeptideIdentification > | unassigned_peptide_identifications_ |
peptide identifications not matched to a specific feature More... | |
std::vector< DataProcessing > | data_processing_ |
applied data processing More... | |
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IntensityRangeType | int_range_ |
Intensity range (1-dimensional) More... | |
PositionRangeType | pos_range_ |
Position range (D-dimensional) 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... | |
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UInt64 | unique_id_ |
the unique id More... | |
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UniqueIdMap | uniqueid_to_index_ |
hash map from unique id to index of features More... | |
Additional Inherited Members | |
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static bool | isValid (UInt64 unique_id) |
Returns true if the unique_id is valid, false otherwise. More... | |
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void | updateRanges_ (const PeakIteratorType &begin, const PeakIteratorType &end) |
Updates the range using data points in the iterator range. More... | |
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const FeatureMap< FeatureT > & | getBase_ () const |
A little helper to get access to the base (!) class RandomAccessContainer. More... | |
FeatureMap< FeatureT > & | getBase_ () |
A little helper to get access to the base (!) class RandomAccessContainer. More... | |
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T | elements |
STL member. More... | |
A container for features.
A map is a container holding 2-dimensional features, which in turn represent chemical entities (peptides, proteins, etc.) found in a 2-dimensional experiment.
Maps are implemented as vectors of features and have basically the same interface as an STL vector has (model of Random Access Container and Back Insertion Sequence).
Feature maps are typically created from peak data of 2D runs through the FeatureFinder.
typedef std::vector<FeatureType> Base |
typedef Base::const_iterator ConstIterator |
typedef const FeatureType& ConstReference |
typedef Base::const_reverse_iterator ConstReverseIterator |
typedef FeatureT FeatureType |
typedef Base::iterator Iterator |
typedef RangeManager<2> RangeManagerType |
typedef FeatureType& Reference |
typedef Base::reverse_iterator ReverseIterator |
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Default constructor.
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Copy constructor.
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inlinevirtual |
Destructor.
Applies a member function of Type to the container itself and all features (including subordinates). 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):
See e.g. UniqueIdInterface for what else can be done this way.
Referenced by SILACAnalyzer::writeFeatures().
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Clears all data and meta data.
clear_meta_data | If true, all meta data is cleared in addition to the data. |
Referenced by ConsensusMap::convert(), and FeatureFinder::run().
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Referenced by IDMapper::annotate().
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returns a const reference to the description of the applied data processing
Referenced by TOPPBase::addDataProcessing_(), and IDMapper::annotate().
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returns a mutable reference to the description of the applied data processing
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non-mutable access to the protein identifications
Referenced by MetaDataBrowser::add(), IDMapper::annotate(), ConsensusMap::convert(), and MRMFeatureFinderScoring::pickExperiment().
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mutable access to the protein identifications
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non-mutable access to the unassigned peptide identifications
Referenced by MetaDataBrowser::add(), IDMapper::annotate(), and ConsensusMap::convert().
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mutable access to the unassigned peptide identifications
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Equality operator.
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Joins two feature maps.
Features are merged into one container (see operator+= for details).
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Add one feature map to another.
Features are merged into one container, simply by appending. UnassignedPeptides and ProteinIdentifications are appended. Information on DocumentIdentifier, UniqueIdInterface (of container only) are reset to default.
For conflicting UID's, new UID's will be assigned.
rhs | The feature to add to this one. |
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Assignment operator.
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Equality operator.
Referenced by FeatureMap< OpenMS::Feature >::operator!=().
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sets the description of the applied data processing
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sets the protein identifications
Referenced by ConsensusMap::convert().
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sets the unassigned peptide identifications
Referenced by ConsensusMap::convert().
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Sorts the peaks according to ascending intensity.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Sort features by m/z position.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().
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Sort features by ascending overall quality.
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inline |
Sort features by position. Lexicographical comparison (first RT then m/z) is done.
Referenced by SILACAnalyzer::writeFeatures().
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Sort features by RT position.
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Referenced by FeatureMap< OpenMS::Feature >::swap().
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Swaps the feature content (plus its range information) of this map with the content of from
.
Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureMap< OpenMS::Feature >::swap().
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Updates minimum and maximum position/intensity.
This method is usually implemented by calling clearRanges() and updateRanges_().
Implements RangeManager< 2 >.
Referenced by ConsensusMap::convert().
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applied data processing
Referenced by FeatureMap< OpenMS::Feature >::clear(), FeatureMap< OpenMS::Feature >::getDataProcessing(), FeatureMap< OpenMS::Feature >::operator+=(), FeatureMap< OpenMS::Feature >::operator=(), FeatureMap< OpenMS::Feature >::operator==(), FeatureMap< OpenMS::Feature >::setDataProcessing(), and FeatureMap< OpenMS::Feature >::swap().
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protein identifications
Referenced by FeatureMap< OpenMS::Feature >::clear(), FeatureMap< OpenMS::Feature >::getProteinIdentifications(), FeatureMap< OpenMS::Feature >::operator+=(), FeatureMap< OpenMS::Feature >::operator=(), FeatureMap< OpenMS::Feature >::operator==(), FeatureMap< OpenMS::Feature >::setProteinIdentifications(), and FeatureMap< OpenMS::Feature >::swap().
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peptide identifications not matched to a specific feature
Referenced by FeatureMap< OpenMS::Feature >::clear(), FeatureMap< OpenMS::Feature >::getUnassignedPeptideIdentifications(), FeatureMap< OpenMS::Feature >::operator+=(), FeatureMap< OpenMS::Feature >::operator=(), FeatureMap< OpenMS::Feature >::operator==(), FeatureMap< OpenMS::Feature >::setUnassignedPeptideIdentifications(), and FeatureMap< OpenMS::Feature >::swap().
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:32 using doxygen 1.8.5 |