35 #ifndef OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMSPECTRUMALIGNMENT_H
36 #define OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMSPECTRUMALIGNMENT_H
65 virtual void alignPeakMaps(std::vector<
MSExperiment<> > &, std::vector<TransformationDescription> &);
76 return "spectrum_alignment";
107 inline bool operator()(
const std::pair<std::pair<Int, float>,
float> & c1,
const std::pair<std::pair<Int, float>,
float> & c2)
111 return c1.second > c2.second;
115 return (c1.first).first < (c2.first).first;
120 inline bool operator()(
const std::pair<float, float> & c1,
const std::pair<float, float> & c2)
124 return c1.first > c2.first;
128 return c1.first < c2.first;
148 void prepareAlign_(
const std::vector<
MSSpectrum<> *> & pattern,
MSExperiment<> & aligned, std::vector<TransformationDescription> & transformation);
209 float scoreCalculation_(
Size i,
Size j,
Size patternbegin,
Size alignbegin,
const std::vector<
MSSpectrum<> *> & pattern, std::vector<
MSSpectrum<> *> & aligned, std::map<
Size, std::map<Size, float> > & buffer,
bool column_row_orientation);
238 void affineGapalign_(
Size xbegin,
Size ybegin,
Size xend,
Size yend,
const std::vector<
MSSpectrum<> *> & pattern, std::vector<
MSSpectrum<> *> & aligned, std::vector<int> & xcoordinate, std::vector<float> & ycoordinate, std::vector<int> & xcoordinatepattern);
253 void bucketFilter_(
const std::vector<
MSSpectrum<> *> & pattern, std::vector<
MSSpectrum<> *> & aligned, std::vector<Int> & xcoordinate, std::vector<float> & ycoordinate, std::vector<Int> & xcoordinatepattern);
270 void debugscoreDistributionCalculation_(
float score);
298 void updateMembers_();
303 #endif // OPENMS_ANALYSIS_MAPMATCHING_MAPALIGNMENTALGORITHMSPECTRUMALIGNMENT_H
std::vector< std::vector< float > > debugmatrix_
Container holding the score of the matchmatrix and also the insertmatrix.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:290
A more convenient string class.
Definition: String.h:57
float mismatchscore_
Represent the cost of a mismatch in the alignment.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:286
Size anchorPoints_
Defines the amount of anchor points which are selected within one bucket.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:282
bool debug_
Debug mode flag default: False.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:284
Base class for all map-alignment algorithms.
Definition: MapAlignmentAlgorithm.h:58
PeakSpectrumCompareFunctor * c1_
Pointer holds the scoring function, which can be selected.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:276
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::vector< float > scoredistribution_
Container holding the score of each cell(matchmatrix,insertmatrix, traceback)
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:296
bool flag
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:96
Size bucketsize_
Defines the size of one bucket.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:280
float e_
Extension cost after a gap is open.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:274
Compare(bool b=false)
Default constructor with an order flag.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:101
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
innerclass necessary for using the sort algo.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:93
A map alignment algorithm based on spectrum similarity (dynamic programming).
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:54
bool operator()(const std::pair< float, float > &c1, const std::pair< float, float > &c2)
overloaded operator() for comparing pairs of float, float std::pair. If the order flag i...
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:120
static String getProductName()
Returns the product name (for the Factory)
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:74
bool operator()(const std::pair< std::pair< Int, float >, float > &c1, const std::pair< std::pair< Int, float >, float > &c2)
overloaded operator() for comparing maps of maps std::pair,float>. If flag is false the second argument of the outer map is selected. The output is an ascending order. If the order flag is true, the first argument of the inner class is selected to get a descending order.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:107
std::vector< std::pair< float, float > > debugtraceback_
Container holding the path of the traceback.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:294
float cutoffScore_
This is the minimal score to be count as a mismatch(range 0.0 - 1.0)
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:278
static MapAlignmentAlgorithm * create()
Creates a new instance of this class (for Factory)
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:68
std::vector< std::vector< float > > debugscorematrix_
Container holding the only the score of Spectra.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:292
Base class for compare functors of spectra, that return a similarity value for two spectra...
Definition: PeakSpectrumCompareFunctor.h:53
float gap_
Represent the gap cost for opening or closing a gap in the alignment.
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:272
float threshold_
This is the minimum score for counting as a match(1-cutoffScore_)
Definition: MapAlignmentAlgorithmSpectrumAlignment.h:288
int Int
Signed integer type.
Definition: Types.h:96