A class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the FeatureFinderAlgorithmIsotopeWavelet class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeWaveletTransform.h>
| Classes | |
| struct | BoxElement | 
| Internally used data structure.  More... | |
| class | TransSpectrum | 
| Internally (only by GPUs) used data structure . It allows efficient data exchange between CPU and GPU and avoids unnecessary memory moves. The class is tailored on the isotope wavelet transform and is in general not applicable on similar - but different - situations.  More... | |
| Public Types | |
| typedef std::multimap< UInt, BoxElement > | Box | 
| Key: RT index, value: BoxElement.  More... | |
| Public Member Functions | |
| IsotopeWaveletTransform (const DoubleReal min_mz, const DoubleReal max_mz, const UInt max_charge, const Size max_scan_size=0, const bool use_cuda=false, const bool hr_data=false, const String intenstype="ref") | |
| Constructor.  More... | |
| virtual | ~IsotopeWaveletTransform () | 
| Destructor.  More... | |
| virtual void | getTransform (MSSpectrum< PeakType > &c_trans, const MSSpectrum< PeakType > &c_ref, const UInt c) | 
| Computes the isotope wavelet transform of charge state c.  More... | |
| virtual void | getTransformHighRes (MSSpectrum< PeakType > &c_trans, const MSSpectrum< PeakType > &c_ref, const UInt c) | 
| Computes the isotope wavelet transform of charge state c.  More... | |
| virtual void | identifyCharge (const MSSpectrum< PeakType > &candidates, const MSSpectrum< PeakType > &ref, const UInt scan_index, const UInt c, const DoubleReal ampl_cutoff, const bool check_PPMs) | 
| Given an isotope wavelet transformed spectrum candidates, this function assigns to every significant pattern its corresponding charge state and a score indicating the reliability of the prediction. The result of this process is stored internally. Important: Before calling this function, apply updateRanges() to the original map.  More... | |
| virtual void | initializeScan (const MSSpectrum< PeakType > &c_ref, const UInt c=0) | 
| void | updateBoxStates (const MSExperiment< PeakType > &map, const Size scan_index, const UInt RT_interleave, const UInt RT_votes_cutoff, const Int front_bound=-1, const Int end_bound=-1) | 
| A function keeping track of currently open and closed sweep line boxes. This function is used by the isotope wavelet feature finder and must be called for each processed scan.  More... | |
| void | mergeFeatures (IsotopeWaveletTransform< PeakType > *later_iwt, const UInt RT_interleave, const UInt RT_votes_cutoff) | 
| FeatureMap< Feature > | mapSeeds2Features (const MSExperiment< PeakType > &map, const UInt RT_votes_cutoff) | 
| Filters the candidates further more and maps the internally used data structures to the OpenMS framework.  More... | |
| virtual std::multimap < DoubleReal, Box > | getClosedBoxes () | 
| Returns the closed boxes.  More... | |
| DoubleReal | getLinearInterpolation (const typename MSSpectrum< PeakType >::const_iterator &left_iter, const DoubleReal mz_pos, const typename MSSpectrum< PeakType >::const_iterator &right_iter) | 
| Computes a linear (intensity) interpolation.  More... | |
| DoubleReal | getLinearInterpolation (const DoubleReal mz_a, const DoubleReal intens_a, const DoubleReal mz_pos, const DoubleReal mz_b, const DoubleReal intens_b) | 
| Computes a linear (intensity) interpolation.  More... | |
| DoubleReal | getSigma () const | 
| void | setSigma (const DoubleReal sigma) | 
| virtual void | computeMinSpacing (const MSSpectrum< PeakType > &c_ref) | 
| DoubleReal | getMinSpacing () const | 
| Size | getMaxScanSize () const | 
| Protected Member Functions | |
| IsotopeWaveletTransform () | |
| Default Constructor.  More... | |
| void | sampleTheCMarrWavelet_ (const MSSpectrum< PeakType > &scan, const Int wavelet_length, const Int mz_index, const UInt charge) | 
| virtual DoubleReal | scoreThis_ (const TransSpectrum &candidate, const UInt peak_cutoff, const DoubleReal seed_mz, const UInt c, const DoubleReal ampl_cutoff) | 
| Given a candidate for an isotopic pattern, this function computes the corresponding score.  More... | |
| virtual DoubleReal | scoreThis_ (const MSSpectrum< PeakType > &candidate, const UInt peak_cutoff, const DoubleReal seed_mz, const UInt c, const DoubleReal ampl_cutoff) | 
| Given a candidate for an isotopic pattern, this function computes the corresponding score.  More... | |
| virtual bool | checkPositionForPlausibility_ (const TransSpectrum &candidate, const MSSpectrum< PeakType > &ref, const DoubleReal seed_mz, const UInt c, const UInt scan_index, const bool check_PPMs, const DoubleReal transintens, const DoubleReal prev_score) | 
| A ugly but necessary function to handle "off-by-1-Dalton predictions" due to idiosyncrasies of the data set (in comparison to the averagine model)  More... | |
| virtual bool | checkPositionForPlausibility_ (const MSSpectrum< PeakType > &candidate, const MSSpectrum< PeakType > &ref, const DoubleReal seed_mz, const UInt c, const UInt scan_index, const bool check_PPMs, const DoubleReal transintens, const DoubleReal prev_score) | 
| A ugly but necessary function to handle "off-by-1-Dalton predictions" due to idiosyncrasies of the data set (in comparison to the averagine model)  More... | |
| virtual std::pair< DoubleReal, DoubleReal > | checkPPMTheoModel_ (const MSSpectrum< PeakType > &ref, const DoubleReal c_mz, const UInt c) | 
| DoubleReal | getAvIntens_ (const TransSpectrum &scan) | 
| Computes the average (transformed) intensity (neglecting negative values) of scan.  More... | |
| DoubleReal | getAvIntens_ (const MSSpectrum< PeakType > &scan) | 
| Computes the average intensity (neglecting negative values) of scan.  More... | |
| DoubleReal | getSdIntens_ (const TransSpectrum &scan, const DoubleReal mean) | 
| Computes the standard deviation (neglecting negative values) of the (transformed) intensities of scan.  More... | |
| DoubleReal | getSdIntens_ (const MSSpectrum< PeakType > &scan, const DoubleReal mean) | 
| Computes the standard deviation (neglecting negative values) of the intensities of scan.  More... | |
| virtual void | push2Box_ (const DoubleReal mz, const UInt scan, UInt c, const DoubleReal score, const DoubleReal intens, const DoubleReal rt, const UInt MZ_begin, const UInt MZ_end, const DoubleReal ref_intens) | 
| Inserts a potential isotopic pattern into an open box or - if no such box exists - creates a new one.  More... | |
| virtual void | push2TmpBox_ (const DoubleReal mz, const UInt scan, UInt charge, const DoubleReal score, const DoubleReal intens, const DoubleReal rt, const UInt MZ_begin, const UInt MZ_end) | 
| Essentially the same function as.  More... | |
| DoubleReal | getAvMZSpacing_ (const MSSpectrum< PeakType > &scan) | 
| Computes the average MZ spacing of scan.  More... | |
| void | clusterSeeds_ (const TransSpectrum &candidates, const MSSpectrum< PeakType > &ref, const UInt scan_index, const UInt c, const bool check_PPMs) | 
| Clusters the seeds stored by push2TmpBox_.  More... | |
| virtual void | clusterSeeds_ (const MSSpectrum< PeakType > &candidates, const MSSpectrum< PeakType > &ref, const UInt scan_index, const UInt c, const bool check_PPMs) | 
| Clusters the seeds stored by push2TmpBox_.  More... | |
| void | extendBox_ (const MSExperiment< PeakType > &map, const Box box) | 
| A currently still necessary function that extends the box boxin order to capture also signals whose isotopic pattern is nearly diminishing.  More... | |
| DoubleReal | peptideMassRule_ (const DoubleReal c_mass) const | 
| Returns the monoisotopic mass (with corresponding decimal values) we would expect at c_mass.  More... | |
| DoubleReal | getPPMs_ (const DoubleReal mass_a, const DoubleReal mass_b) const | 
| Returns the parts-per-million deviation of the masses.  More... | |
| Protected Attributes | |
| std::multimap< DoubleReal, Box > | open_boxes_ | 
| std::multimap< DoubleReal, Box > | closed_boxes_ | 
| std::multimap< DoubleReal, Box > | end_boxes_ | 
| std::multimap< DoubleReal, Box > | front_boxes_ | 
| std::vector< std::multimap < DoubleReal, Box > > * | tmp_boxes_ | 
| DoubleReal | av_MZ_spacing_ | 
| DoubleReal | sigma_ | 
| std::vector< DoubleReal > | c_mzs_ | 
| std::vector< DoubleReal > | c_spacings_ | 
| std::vector< DoubleReal > | psi_ | 
| std::vector< DoubleReal > | prod_ | 
| std::vector< DoubleReal > | xs_ | 
| std::vector< DoubleReal > | interpol_xs_ | 
| std::vector< DoubleReal > | interpol_ys_ | 
| Size | max_scan_size_ | 
| UInt | max_num_peaks_per_pattern_ | 
| UInt | max_charge_ | 
| UInt | data_length_ | 
| bool | hr_data_ | 
| String | intenstype_ | 
| Int | from_max_to_left_ | 
| Int | from_max_to_right_ | 
| std::vector< int > | indices_ | 
| MSSpectrum< PeakType > | c_sorted_candidate_ | 
| DoubleReal | min_spacing_ | 
| DoubleReal | max_mz_cutoff_ | 
| std::vector< float > | scores_ | 
| std::vector< float > | zeros_ | 
A class implementing the isotope wavelet transform. If you just want to find features using the isotope wavelet, take a look at the FeatureFinderAlgorithmIsotopeWavelet class. Usually, you only have to consider the class at hand if you plan to change the basic implementation of the transform.
| typedef std::multimap<UInt, BoxElement> Box | 
Key: RT index, value: BoxElement.
| IsotopeWaveletTransform | ( | const DoubleReal | min_mz, | 
| const DoubleReal | max_mz, | ||
| const UInt | max_charge, | ||
| const Size | max_scan_size = 0, | ||
| const bool | use_cuda = false, | ||
| const bool | hr_data = false, | ||
| const String | intenstype = "ref" | ||
| ) | 
Constructor.
| min_mz | The smallest m/z value occurring in your map. | 
| max_mz | The largest m/z value occurring in your map. | 
| max_charge | The highest charge state you would like to consider. | 
References OpenMS::Constants::CUDA_EXTENDED_BLOCK_SIZE_MAX, OpenMS::Constants::DEFAULT_NUM_OF_INTERPOLATION_POINTS, IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getNumPeakCutOff(), IsotopeWavelet::init(), OpenMS::Constants::IW_NEUTRON_MASS, and NULL.
| 
 | virtual | 
Destructor.
References NULL.
| 
 | protected | 
Default Constructor.
References NULL.
| 
 | protectedvirtual | 
A ugly but necessary function to handle "off-by-1-Dalton predictions" due to idiosyncrasies of the data set (in comparison to the averagine model)
| candidate | The wavelet transformed spectrum containing the candidate. | 
| ref | The original spectrum containing the candidate. | 
| seed_mz | The m/z position of the candidate pattern. | 
| c | The predicted charge state minus 1 (e.g. c=2 means charge state 3) of the candidate. | 
| scan_index | The index of the scan under consideration (w.r.t. the original map). | 
References IsotopeWaveletTransform< PeakType >::TransSpectrum::begin(), OpenMS::Constants::c, IsotopeWaveletTransform< PeakType >::TransSpectrum::end(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getNumPeakCutOff(), MSSpectrum< PeakT >::getRT(), OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::TransSpectrum::MZBegin(), and MSSpectrum< PeakT >::MZBegin().
| 
 | protectedvirtual | 
A ugly but necessary function to handle "off-by-1-Dalton predictions" due to idiosyncrasies of the data set (in comparison to the averagine model)
| candidate | The wavelet transformed spectrum containing the candidate. | 
| ref | The original spectrum containing the candidate. | 
| seed_mz | The m/z position of the candidate pattern. | 
| c | The predicted charge state minus 1 (e.g. c=2 means charge state 3) of the candidate. | 
| scan_index | The index of the scan under consideration (w.r.t. the original map). | 
References OpenMS::Constants::c, IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getNumPeakCutOff(), MSSpectrum< PeakT >::getRT(), OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, and MSSpectrum< PeakT >::MZBegin().
| 
 | protectedvirtual | 
| 
 | protected | 
Clusters the seeds stored by push2TmpBox_.
| candidates | A isotope wavelet transformed spectrum. | 
| ref | The corresponding original spectrum (w.r.t. candidates). | 
| scan_index | The index of the scan under consideration (w.r.t. the original map). | 
References IsotopeWaveletTransform< PeakType >::BoxElement::c, OpenMS::Constants::c, IsotopeWaveletTransform< PeakType >::BoxElement::intens, IsotopeWaveletTransform< PeakType >::BoxElement::mz, IsotopeWaveletTransform< PeakType >::BoxElement::RT, and IsotopeWaveletTransform< PeakType >::BoxElement::score.
| 
 | protectedvirtual | 
Clusters the seeds stored by push2TmpBox_.
| candidates | A isotope wavelet transformed spectrum. | 
| ref | The corresponding original spectrum (w.r.t. candidates). | 
| scan_index | The index of the scan under consideration (w.r.t. the original map). | 
References IsotopeWaveletTransform< PeakType >::BoxElement::c, OpenMS::Constants::c, IsotopeWaveletTransform< PeakType >::BoxElement::intens, IsotopeWaveletTransform< PeakType >::BoxElement::mz, IsotopeWaveletTransform< PeakType >::BoxElement::RT, and IsotopeWaveletTransform< PeakType >::BoxElement::score.
| 
 | virtual | 
| 
 | protected | 
A currently still necessary function that extends the box box in order to capture also signals whose isotopic pattern is nearly diminishing. 
| map | The experimental map. | 
| box | The box to be extended. | 
References MSExperiment< PeakT, ChromatogramPeakT >::begin().
| 
 | inlineprotected | 
Computes the average (transformed) intensity (neglecting negative values) of scan. 
References IsotopeWaveletTransform< PeakType >::TransSpectrum::getTransIntensity(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::size().
| 
 | inlineprotected | 
Computes the average intensity (neglecting negative values) of scan. 
| 
 | inlineprotected | 
Computes the average MZ spacing of scan. 
| scan | The scan we are interested in. | 
| 
 | inlinevirtual | 
Returns the closed boxes.
| 
 | inline | 
Computes a linear (intensity) interpolation.
| left_iter | The point left to the query. | 
| mz_pos | The query point. | 
| right_iter | The point right to the query. | 
| 
 | inline | 
Computes a linear (intensity) interpolation.
| mz_a | The m/z value of the point left to the query. | 
| mz_a | The intensity value of the point left to the query. | 
| mz_pos | The query point. | 
| mz_b | The m/z value of the point right to the query. | 
| intens_b | The intensity value of the point left to the query. | 
| 
 | inline | 
| 
 | inline | 
| 
 | inlineprotected | 
Returns the parts-per-million deviation of the masses.
| mass_a | The first mass. | 
| mass_b | The second mass. | 
| 
 | inlineprotected | 
Computes the standard deviation (neglecting negative values) of the (transformed) intensities of scan. 
References IsotopeWaveletTransform< PeakType >::TransSpectrum::getTransIntensity(), OpenMS::Math::mean(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::size().
| 
 | inlineprotected | 
Computes the standard deviation (neglecting negative values) of the intensities of scan. 
References OpenMS::Math::mean().
| 
 | inline | 
| 
 | virtual | 
Computes the isotope wavelet transform of charge state c. 
| c_trans | The transform. | 
| c_ref | The reference spectrum. | 
| c | The charge state minus 1 (e.g. c=2 means charge state 3) at which you want to compute the transform. | 
References IsotopeWavelet::getLambdaL(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getValueByLambda(), and OpenMS::Constants::IW_QUARTER_NEUTRON_MASS.
Referenced by FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run().
| 
 | virtual | 
Computes the isotope wavelet transform of charge state c. 
| c_trans | The transform. | 
| c_ref | The reference spectrum. | 
| c | The charge state minus 1 (e.g. c=2 means charge state 3) at which you want to compute the transform. | 
References IsotopeWavelet::getLambdaL(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getValueByLambda(), and OpenMS::Constants::IW_QUARTER_NEUTRON_MASS.
Referenced by FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run().
| 
 | virtual | 
Given an isotope wavelet transformed spectrum candidates, this function assigns to every significant pattern its corresponding charge state and a score indicating the reliability of the prediction. The result of this process is stored internally. Important: Before calling this function, apply updateRanges() to the original map. 
| candidates | A isotope wavelet transformed spectrum. Entry "number i" in this vector must correspond to the charge-"(i-1)"-transform of its mass signal. (This is exactly the output of the function | 
| ref | The reference scan (the untransformed raw data) corresponding to candidates. | 
| c | The corrsponding charge state minus 1 (e.g. c=2 means charge state 3) | 
| scan_index | The index of the scan (w.r.t. to some map) currently under consideration. | 
| ampl_cutoff | The thresholding parameter. This parameter is the only (and hence a really important) parameter of the isotope wavelet transform. On the basis of ampl_cutoffthe program tries to distinguish between noise and signal. Please note that it is not a "simple" hard thresholding parameter in the sense of drawing a virtual line in the spectrum, which is then used as a guillotine cut. Maybe you should play around a bit with this parameter to get a feeling about its range. For peptide mass fingerprints on small data sets (like single MALDI-scans e.g.), it makes sense to startampl_cutoff=0or evenampl_cutoff=-1, indicating no thresholding at all. Note that also ampl_cutoff=0 triggers (a moderate) thresholding based on the average intensity in the wavelet transform. | 
| check_PPMs | If enabled, the algorithm will check each monoisotopic mass candidate for its plausibility by computing the ppm difference between this mass and the averagine model. | 
References OpenMS::Constants::c, IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getNumPeakCutOff(), MSSpectrum< PeakT >::getRT(), OpenMS::Constants::IW_NEUTRON_MASS, OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, MSSpectrum< PeakT >::MZBegin(), MSSpectrum< PeakT >::MZEnd(), and ConstRefVector< ContainerT >::sortByIntensity().
Referenced by FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run().
| 
 | virtual | 
| FeatureMap< Feature > mapSeeds2Features | ( | const MSExperiment< PeakType > & | map, | 
| const UInt | RT_votes_cutoff | ||
| ) | 
Filters the candidates further more and maps the internally used data structures to the OpenMS framework.
| map | The original map containing the data set to be analyzed. | 
| max_charge | The maximal charge state under consideration. | 
| RT_votes_cutoff | See the IsotopeWaveletFF class. | 
References ConvexHull2D::addPoints(), IsotopeWavelet::getLambdaL(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), OpenMS::Constants::IW_NEUTRON_MASS, OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, MSSpectrum< PeakT >::MZBegin(), BaseFeature::setCharge(), Feature::setConvexHulls(), Peak2D::setIntensity(), Peak2D::setMZ(), Feature::setOverallQuality(), Peak2D::setRT(), and MSExperiment< PeakT, ChromatogramPeakT >::size().
Referenced by FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run().
| void mergeFeatures | ( | IsotopeWaveletTransform< PeakType > * | later_iwt, | 
| const UInt | RT_interleave, | ||
| const UInt | RT_votes_cutoff | ||
| ) | 
| 
 | inlineprotected | 
Returns the monoisotopic mass (with corresponding decimal values) we would expect at c_mass. 
| c_mass | The mass for which we would like to know the averagine decimal places. | 
| 
 | protectedvirtual | 
Inserts a potential isotopic pattern into an open box or - if no such box exists - creates a new one.
| mz | The position of the pattern. | 
| scan | The index of the scan, we are currently analyzing (w.r.t. the data map). This information is necessary for the post-processing (sweep lining). | 
| charge | The estimated charge state minus 1 (e.g. c=2 means charge state 3) of the pattern. | 
| score | The pattern's score. | 
| intens | The intensity at the monoisotopic peak. | 
| rt | The retention time of the scan (similar to scan, but here: no index, but the real value). | 
| MZ_begin | The starting index of the pattern (m/z) w.r.t. the current scan. | 
| MZ_end | The end index (w.r.t. the monoisotopic position!) of the pattern (m/z) w.r.t. the current scan. | 
References IsotopeWaveletTransform< PeakType >::BoxElement::c, OpenMS::Constants::c, IsotopeWaveletTransform< PeakType >::BoxElement::intens, OpenMS::Constants::IW_HALF_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::BoxElement::mz, IsotopeWaveletTransform< PeakType >::BoxElement::MZ_begin, IsotopeWaveletTransform< PeakType >::BoxElement::MZ_end, IsotopeWaveletTransform< PeakType >::BoxElement::ref_intens, IsotopeWaveletTransform< PeakType >::BoxElement::RT, IsotopeWaveletTransform< PeakType >::BoxElement::RT_index, and IsotopeWaveletTransform< PeakType >::BoxElement::score.
| 
 | protectedvirtual | 
Essentially the same function as.
| mz | The position of the pattern. | 
| scan | The index of the scan, we are currently analyzing (w.r.t. the data map). This information is necessary for the post-processing (sweep lining). | 
| charge | The estimated charge state minus 1 (e.g. c=2 means charge state 3) of the pattern. | 
| score | The pattern's score. | 
| intens | The intensity at the monoisotopic peak. | 
| rt | The retention time of the scan (similar to scan, but here: no index, but the real value). | 
| MZ_begin | The starting index of the pattern (m/z) w.r.t. the current scan. | 
| MZ_end | The end index (w.r.t. the monoisotopic position!) of the pattern (m/z) w.r.t. the current scan. | 
References IsotopeWaveletTransform< PeakType >::BoxElement::c, OpenMS::Constants::c, IsotopeWaveletTransform< PeakType >::BoxElement::intens, OpenMS::Constants::IW_HALF_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::BoxElement::mz, IsotopeWaveletTransform< PeakType >::BoxElement::MZ_begin, IsotopeWaveletTransform< PeakType >::BoxElement::MZ_end, IsotopeWaveletTransform< PeakType >::BoxElement::ref_intens, IsotopeWaveletTransform< PeakType >::BoxElement::RT, IsotopeWaveletTransform< PeakType >::BoxElement::RT_index, and IsotopeWaveletTransform< PeakType >::BoxElement::score.
| 
 | inlineprotected | 
| 
 | protectedvirtual | 
Given a candidate for an isotopic pattern, this function computes the corresponding score.
| candidate | A isotope wavelet transformed spectrum. | 
| peak_cutoff | The number of peaks we will consider for the isotopic pattern. | 
| seed_mz | The predicted position of the monoisotopic peak. | 
| c | The charge state minus 1 (e.g. c=2 means charge state 3) for which the score should be determined. | 
| ampl_cutoff | The threshold. | 
References IsotopeWaveletTransform< PeakType >::TransSpectrum::begin(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getMZ(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getTransIntensity(), OpenMS::Constants::IW_HALF_NEUTRON_MASS, OpenMS::Constants::IW_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::TransSpectrum::MZBegin(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::size().
| 
 | protectedvirtual | 
Given a candidate for an isotopic pattern, this function computes the corresponding score.
| candidate | A isotope wavelet transformed spectrum. | 
| peak_cutoff | The number of peaks we will consider for the isotopic pattern. | 
| seed_mz | The predicted position of the monoisotopic peak. | 
| c | The charge state minus 1 (e.g. c=2 means charge state 3) for which the score should be determined. | 
| ampl_cutoff | The threshold. | 
References OpenMS::Constants::IW_HALF_NEUTRON_MASS, OpenMS::Constants::IW_NEUTRON_MASS, and MSSpectrum< PeakT >::MZBegin().
| 
 | inline | 
| void updateBoxStates | ( | const MSExperiment< PeakType > & | map, | 
| const Size | scan_index, | ||
| const UInt | RT_interleave, | ||
| const UInt | RT_votes_cutoff, | ||
| const Int | front_bound = -1, | ||
| const Int | end_bound = -1 | ||
| ) | 
A function keeping track of currently open and closed sweep line boxes. This function is used by the isotope wavelet feature finder and must be called for each processed scan.
| map | The original map containing the data set to be analyzed. | 
| scan_index | The index of the scan currently under consideration w.r.t. its MS map. This information is necessary to sweep across the map after each scan has been evaluated. | 
| RT_votes_cutoff | See the IsotopeWaveletFF class. | 
References MSExperiment< PeakT, ChromatogramPeakT >::clear(), and MSExperiment< PeakT, ChromatogramPeakT >::size().
Referenced by IsotopeWaveletParallelFor< PeakType, FeatureType >::operator()(), and FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::run().
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
Referenced by IsotopeWaveletTransform< OpenMS::Peak2D >::getClosedBoxes().
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
Referenced by IsotopeWaveletTransform< OpenMS::Peak2D >::getMaxScanSize().
| 
 | protected | 
Referenced by IsotopeWaveletTransform< OpenMS::Peak2D >::getMinSpacing().
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| 
 | protected | 
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5 |