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| MapAlignmentAlgorithmPoseClustering () |
| Default constructor. More...
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virtual | ~MapAlignmentAlgorithmPoseClustering () |
| Destructor. More...
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void | align (const FeatureMap &map, TransformationDescription &trafo) |
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void | align (const MSExperiment<> &map, TransformationDescription &trafo) |
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void | align (const ConsensusMap &map, TransformationDescription &trafo) |
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template<typename MapType > |
void | setReference (const MapType &map) |
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| MapAlignmentAlgorithm () |
| Default constructor. More...
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virtual | ~MapAlignmentAlgorithm () |
| Destructor. More...
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virtual void | alignPeakMaps (std::vector< MSExperiment<> > &, std::vector< TransformationDescription > &) |
| Aligns peak maps. More...
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virtual void | alignCompactFeatureMaps (std::vector< std::vector< Peak2D > > &, std::vector< TransformationDescription > &) |
| Aligns vectors of 2D peaks (memory efficient version of FeatureMap) More...
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virtual void | alignFeatureMaps (std::vector< FeatureMap > &, std::vector< TransformationDescription > &) |
| Aligns feature maps. More...
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virtual void | alignConsensusMaps (std::vector< ConsensusMap > &, std::vector< TransformationDescription > &) |
| Aligns consensus maps. More...
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virtual void | alignPeptideIdentifications (std::vector< std::vector< PeptideIdentification > > &, std::vector< TransformationDescription > &) |
| Aligns peptide identifications. More...
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virtual void | setReference (Size reference_index=0, const String &reference_file="") |
| Defines a reference for the alignment. More...
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Public Member Functions inherited from DefaultParamHandler |
| DefaultParamHandler (const String &name) |
| Constructor with name that is displayed in error messages. More...
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| DefaultParamHandler (const DefaultParamHandler &rhs) |
| Copy constructor. More...
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virtual | ~DefaultParamHandler () |
| Destructor. More...
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virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More...
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virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More...
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void | setParameters (const Param ¶m) |
| Sets the parameters. More...
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const Param & | getParameters () const |
| Non-mutable access to the parameters. More...
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const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More...
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const String & | getName () const |
| Non-mutable access to the name. More...
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void | setName (const String &name) |
| Mutable access to the name. More...
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const std::vector< String > & | getSubsections () const |
| Non-mutable access to the registered subsections. More...
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| ProgressLogger () |
| Constructor. More...
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| ~ProgressLogger () |
| Destructor. More...
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| ProgressLogger (const ProgressLogger &other) |
| Copy constructor. More...
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ProgressLogger & | operator= (const ProgressLogger &other) |
| Assignment Operator. More...
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void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More...
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LogType | getLogType () const |
| Returns the type of progress log being used. More...
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void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More...
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void | setProgress (SignedSize value) const |
| Sets the current progress. More...
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void | endProgress () const |
| Ends the progress display. More...
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A map alignment algorithm based on pose clustering.
Pose clustering analyzes pair distances to find the most probable transformation of retention times. The algorithm chooses the x most intensity peaks/features per map. This is modeled via the parameter 'max_num_peaks_considered', which in turn influences the runtime and stability of the results. Bigger values prolong computation, smaller values might lead to no or unstable trafos. Set to -1 to use all features (might take very long for large maps).
For further details see:
Eva Lange et al.
A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data
ISMB/ECCB 2007