Base class for all map-alignment algorithms. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithm.h>
 
  
 | Public Member Functions | |
| MapAlignmentAlgorithm () | |
| Default constructor.  More... | |
| virtual | ~MapAlignmentAlgorithm () | 
| Destructor.  More... | |
| virtual void | alignPeakMaps (std::vector< MSExperiment<> > &, std::vector< TransformationDescription > &) | 
| Aligns peak maps.  More... | |
| virtual void | alignCompactFeatureMaps (std::vector< std::vector< Peak2D > > &, std::vector< TransformationDescription > &) | 
| Aligns vectors of 2D peaks (memory efficient version of FeatureMap)  More... | |
| virtual void | alignFeatureMaps (std::vector< FeatureMap<> > &, std::vector< TransformationDescription > &) | 
| Aligns feature maps.  More... | |
| virtual void | alignConsensusMaps (std::vector< ConsensusMap > &, std::vector< TransformationDescription > &) | 
| Aligns consensus maps.  More... | |
| virtual void | alignPeptideIdentifications (std::vector< std::vector< PeptideIdentification > > &, std::vector< TransformationDescription > &) | 
| Aligns peptide identifications.  More... | |
| virtual void | setReference (Size reference_index=0, const String &reference_file="") | 
| Defines a reference for the alignment.  More... | |
|  Public Member Functions inherited from DefaultParamHandler | |
| DefaultParamHandler (const String &name) | |
| Constructor with name that is displayed in error messages.  More... | |
| DefaultParamHandler (const DefaultParamHandler &rhs) | |
| Copy constructor.  More... | |
| virtual | ~DefaultParamHandler () | 
| Destructor.  More... | |
| virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) | 
| Assignment operator.  More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const | 
| Equality operator.  More... | |
| void | setParameters (const Param ¶m) | 
| Sets the parameters.  More... | |
| const Param & | getParameters () const | 
| Non-mutable access to the parameters.  More... | |
| const Param & | getDefaults () const | 
| Non-mutable access to the default parameters.  More... | |
| const String & | getName () const | 
| Non-mutable access to the name.  More... | |
| void | setName (const String &name) | 
| Mutable access to the name.  More... | |
| const std::vector< String > & | getSubsections () const | 
| Non-mutable access to the registered subsections.  More... | |
|  Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor.  More... | |
| ~ProgressLogger () | |
| Destructor.  More... | |
| void | setLogType (LogType type) const | 
| Sets the progress log that should be used. The default type is NONE!  More... | |
| LogType | getLogType () const | 
| Returns the type of progress log being used.  More... | |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const | 
| Initializes the progress display.  More... | |
| void | setProgress (SignedSize value) const | 
| Sets the current progress.  More... | |
| void | endProgress () const | 
| Ends the progress display.  More... | |
| Static Public Member Functions | |
| static void | fitModel (const String &model_type, const Param ¶ms, std::vector< TransformationDescription > &trafos) | 
| Fits a model with given parameters to the transformations.  More... | |
| static void | registerChildren () | 
| Register all derived classes in this method.  More... | |
| Private Member Functions | |
| MapAlignmentAlgorithm (const MapAlignmentAlgorithm &) | |
| Copy constructor is not implemented -> private.  More... | |
| MapAlignmentAlgorithm & | operator= (const MapAlignmentAlgorithm &) | 
| Assignment operator is not implemented -> private.  More... | |
| Additional Inherited Members | |
|  Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } | 
| Possible log types.  More... | |
|  Protected Member Functions inherited from DefaultParamHandler | |
| virtual void | updateMembers_ () | 
| This method is used to update extra member variables at the end of the setParameters() method.  More... | |
| void | defaultsToParam_ () | 
| Updates the parameters after the defaults have been set in the constructor.  More... | |
|  Protected Attributes inherited from DefaultParamHandler | |
| Param | param_ | 
| Container for current parameters.  More... | |
| Param | defaults_ | 
| Container for default parameters. This member should be filled in the constructor of derived classes!  More... | |
| std::vector< String > | subsections_ | 
| Container for registered subsections. This member should be filled in the constructor of derived classes!  More... | |
| String | error_name_ | 
| Name that is displayed in error messages during the parameter checking.  More... | |
| bool | check_defaults_ | 
| If this member is set to false no checking if parameters in done;.  More... | |
| bool | warn_empty_defaults_ | 
| If this member is set to false no warning is emitted when defaults are empty;.  More... | |
|  Protected Attributes inherited from ProgressLogger | |
| LogType | type_ | 
| SignedSize | begin_ | 
| SignedSize | end_ | 
| SignedSize | value_ | 
| QProgressDialog * | dlg_ | 
| StopWatch | stop_watch_ | 
| time_t | last_invoke_ | 
|  Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ | 
Base class for all map-alignment algorithms.
It takes two or more maps and corrects for retention time distortions.
The input maps are transformed and the transformation description is returned.
Default constructor.
| 
 | virtual | 
Destructor.
| 
 | private | 
Copy constructor is not implemented -> private.
| 
 | virtual | 
Aligns vectors of 2D peaks (memory efficient version of FeatureMap)
| Exception::NotImplemented | is thrown if an algorithm cannot align feature maps | 
| 
 | virtual | 
Aligns consensus maps.
| Exception::NotImplemented | is thrown if an algorithm cannot align consensus maps | 
Reimplemented in MapAlignmentAlgorithmIdentification.
| 
 | virtual | 
Aligns feature maps.
| Exception::NotImplemented | is thrown if an algorithm cannot align feature maps | 
Reimplemented in MapAlignmentAlgorithmIdentification.
| 
 | virtual | 
Aligns peak maps.
| Exception::NotImplemented | is thrown if an algorithm cannot align peak maps | 
Reimplemented in MapAlignmentAlgorithmIdentification, and MapAlignmentAlgorithmSpectrumAlignment.
| 
 | virtual | 
Aligns peptide identifications.
| Exception::NotImplemented | is thrown if an algorithm cannot align peptide identifications | 
Reimplemented in MapAlignmentAlgorithmIdentification.
| 
 | static | 
Fits a model with given parameters to the transformations.
This will not alter transformations of reference files (transformation type "identity").
| 
 | private | 
Assignment operator is not implemented -> private.
| 
 | static | 
Register all derived classes in this method.
Defines a reference for the alignment.
| reference_index | Index of input file to use as reference (1-based!) | 
| reference_file | Path to external reference file | 
| Exception::InvalidParameter | is thrown if the algorithm does not support references | 
Reimplemented in MapAlignmentAlgorithmIdentification.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |