A map alignment algorithm based on pose clustering. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmPoseClustering.h>
Public Member Functions | |
MapAlignmentAlgorithmPoseClustering () | |
Default constructor. More... | |
virtual | ~MapAlignmentAlgorithmPoseClustering () |
Destructor. More... | |
void | align (const FeatureMap &map, TransformationDescription &trafo) |
void | align (const MSExperiment<> &map, TransformationDescription &trafo) |
void | align (const ConsensusMap &map, TransformationDescription &trafo) |
template<typename MapType > | |
void | setReference (const MapType &map) |
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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... | |
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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... | |
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ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (const ProgressLogger &other) |
Assignment Operator. 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 MapAlignmentAlgorithm * | create () |
Creates a new instance of this class (for Factory) More... | |
static String | getProductName () |
Returns the product name (for the Factory) More... | |
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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... | |
Protected Member Functions | |
virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
PoseClusteringAffineSuperimposer | superimposer_ |
StablePairFinder | pairfinder_ |
ConsensusMap | reference_ |
Int | max_num_peaks_considered_ |
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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... | |
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LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
Private Member Functions | |
MapAlignmentAlgorithmPoseClustering (const MapAlignmentAlgorithmPoseClustering &) | |
Copy constructor intentionally not implemented -> private. More... | |
MapAlignmentAlgorithmPoseClustering & | operator= (const MapAlignmentAlgorithmPoseClustering &) |
Assignment operator intentionally not implemented -> private. More... | |
Additional Inherited Members | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
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static int | recursion_depth_ |
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
Name | Type | Default | Restrictions | Description |
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max_num_peaks_considered | int | 1000 | min: -1 | The maximal number of peaks/features to be considered per map. To use all, set to '-1'. |
superimposer:mz_pair_max_distance | float | 0.5 | min: 0 | Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing. |
superimposer:rt_pair_distance_fraction | float | 0.1 | min: 0 max: 1 | Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min). |
superimposer:num_used_points | int | 2000 | min: -1 | Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1. |
superimposer:scaling_bucket_size | float | 0.005 | min: 0 | The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs. |
superimposer:shift_bucket_size | float | 3 | min: 0 | The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans. |
superimposer:max_shift | float | 1000 | min: 0 | Maximal shift which is considered during histogramming. This applies for both directions. |
superimposer:max_scaling | float | 2 | min: 1 | Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this. |
superimposer:dump_buckets | string | [DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically. | ||
superimposer:dump_pairs | string | [DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically. | ||
pairfinder:second_nearest_gap | float | 2 | min: 1 | The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself. |
pairfinder:use_identifications | string | false | true, false | Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account). |
pairfinder:ignore_charge | string | false | true, false | Compare features normally even if their charge states are different |
pairfinder:distance_RT:max_difference | float | 100 | min: 0 | Maximum allowed difference in RT in seconds |
pairfinder:distance_RT:exponent | float | 1 | min: 0 | Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
pairfinder:distance_RT:weight | float | 1 | min: 0 | RT distances are weighted by this factor |
pairfinder:distance_MZ:max_difference | float | 0.3 | min: 0 | Maximum allowed difference in m/z (unit defined by 'unit') |
pairfinder:distance_MZ:unit | string | Da | Da, ppm | Unit of the 'max_difference' parameter |
pairfinder:distance_MZ:exponent | float | 2 | min: 0 | Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
pairfinder:distance_MZ:weight | float | 1 | min: 0 | m/z distances are weighted by this factor |
pairfinder:distance_intensity:exponent | float | 1 | min: 0 | Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow) |
pairfinder:distance_intensity:weight | float | 0 | min: 0 | Distances based on relative intensity are weighted by this factor |
Default constructor.
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virtual |
Destructor.
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private |
Copy constructor intentionally not implemented -> private.
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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inlinestatic |
Creates a new instance of this class (for Factory)
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private |
Assignment operator intentionally not implemented -> private.
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inline |
References MapConversion::convert().
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protectedvirtual |
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
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OpenMS / TOPP release 2.0.0 | Documentation generated on Thu Aug 20 2015 01:44:36 using doxygen 1.8.9.1 |