IsotopeWaveletTransform< PeakType > Class Template Reference

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 double min_mz, const double max_mz, const UInt max_charge, const Size max_scan_size=0, const bool hr_data=false, const String intenstype="ref")
	Constructor. More...
virtual	~IsotopeWaveletTransform ()
	Destructor. More...
virtual void	getTransform (MSSpectrum &c_trans, const MSSpectrum &c_ref, const UInt c)
	Computes the isotope wavelet transform of charge state c. More...
virtual void	getTransformHighRes (MSSpectrum &c_trans, const MSSpectrum &c_ref, const UInt c)
	Computes the isotope wavelet transform of charge state c. More...
virtual void	identifyCharge (const MSSpectrum &candidates, const MSSpectrum &ref, const UInt scan_index, const UInt c, const double 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 &c_ref, const UInt c=0)
void	updateBoxStates (const PeakMap &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	mapSeeds2Features (const PeakMap &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< double, Box >	getClosedBoxes ()
	Returns the closed boxes. More...
double	getLinearInterpolation (const typename MSSpectrum::const_iterator &left_iter, const double mz_pos, const typename MSSpectrum::const_iterator &right_iter)
	Computes a linear (intensity) interpolation. More...
double	getLinearInterpolation (const double mz_a, const double intens_a, const double mz_pos, const double mz_b, const double intens_b)
	Computes a linear (intensity) interpolation. More...
double	getSigma () const
void	setSigma (const double sigma)
virtual void	computeMinSpacing (const MSSpectrum &c_ref)
double	getMinSpacing () const
Size	getMaxScanSize () const

Protected Member Functions
	IsotopeWaveletTransform ()
	Default Constructor. More...
void	sampleTheCMarrWavelet_ (const MSSpectrum &scan, const Int wavelet_length, const Int mz_index, const UInt charge)
virtual double	scoreThis_ (const TransSpectrum &candidate, const UInt peak_cutoff, const double seed_mz, const UInt c, const double ampl_cutoff)
	Given a candidate for an isotopic pattern, this function computes the corresponding score. More...
virtual double	scoreThis_ (const MSSpectrum &candidate, const UInt peak_cutoff, const double seed_mz, const UInt c, const double ampl_cutoff)
	Given a candidate for an isotopic pattern, this function computes the corresponding score. More...
virtual bool	checkPositionForPlausibility_ (const TransSpectrum &candidate, const MSSpectrum &ref, const double seed_mz, const UInt c, const UInt scan_index, const bool check_PPMs, const double transintens, const double 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 &candidate, const MSSpectrum &ref, const double seed_mz, const UInt c, const UInt scan_index, const bool check_PPMs, const double transintens, const double 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< double, double >	checkPPMTheoModel_ (const MSSpectrum &ref, const double c_mz, const UInt c)
double	getAvIntens_ (const TransSpectrum &scan)
	Computes the average (transformed) intensity (neglecting negative values) of scan. More...
double	getAvIntens_ (const MSSpectrum &scan)
	Computes the average intensity (neglecting negative values) of scan. More...
double	getSdIntens_ (const TransSpectrum &scan, const double mean)
	Computes the standard deviation (neglecting negative values) of the (transformed) intensities of scan. More...
double	getSdIntens_ (const MSSpectrum &scan, const double mean)
	Computes the standard deviation (neglecting negative values) of the intensities of scan. More...
virtual void	push2Box_ (const double mz, const UInt scan, UInt c, const double score, const double intens, const double rt, const UInt MZ_begin, const UInt MZ_end, const double 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 double mz, const UInt scan, UInt charge, const double score, const double intens, const double rt, const UInt MZ_begin, const UInt MZ_end)
	Essentially the same function as. More...
double	getAvMZSpacing_ (const MSSpectrum &scan)
	Computes the average MZ spacing of scan. More...
void	clusterSeeds_ (const TransSpectrum &candidates, const MSSpectrum &ref, const UInt scan_index, const UInt c, const bool check_PPMs)
	Clusters the seeds stored by push2TmpBox_. More...
virtual void	clusterSeeds_ (const MSSpectrum &candidates, const MSSpectrum &ref, const UInt scan_index, const UInt c, const bool check_PPMs)
	Clusters the seeds stored by push2TmpBox_. More...
void	extendBox_ (const PeakMap &map, const Box box)
	A currently still necessary function that extends the box box in order to capture also signals whose isotopic pattern is nearly diminishing. More...
double	peptideMassRule_ (const double c_mass) const
	Returns the monoisotopic mass (with corresponding decimal values) we would expect at c_mass. More...
double	getPPMs_ (const double mass_a, const double mass_b) const
	Returns the parts-per-million deviation of the masses. More...

Protected Attributes
std::multimap< double, Box >	open_boxes_
std::multimap< double, Box >	closed_boxes_
std::multimap< double, Box >	end_boxes_
std::multimap< double, Box >	front_boxes_
std::vector< std::multimap< double, Box > > *	tmp_boxes_
double	av_MZ_spacing_
double	sigma_
std::vector< double >	c_mzs_
std::vector< double >	c_spacings_
std::vector< double >	psi_
std::vector< double >	prod_
std::vector< double >	xs_
std::vector< double >	interpol_xs_
std::vector< double >	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_
double	min_spacing_
double	max_mz_cutoff_
std::vector< float >	scores_
std::vector< float >	zeros_

Detailed Description

template<typename PeakType>
class OpenMS::IsotopeWaveletTransform< PeakType >

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.

Member Typedef Documentation

Box

typedef std::multimap<UInt, BoxElement> Box

Key: RT index, value: BoxElement.

Constructor & Destructor Documentation

IsotopeWaveletTransform() [1/2]

IsotopeWaveletTransform	(	const double	min_mz,
		const double	max_mz,
		const UInt	max_charge,
		const Size	max_scan_size = 0,
		const bool	hr_data = false,
		const String	intenstype = "ref"
	)

Constructor.

Parameters

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 IsotopeWaveletTransform< PeakType >::av_MZ_spacing_, OpenMS::Constants::DEFAULT_NUM_OF_INTERPOLATION_POINTS, IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getNumPeakCutOff(), IsotopeWaveletTransform< PeakType >::hr_data_, IsotopeWavelet::init(), IsotopeWaveletTransform< PeakType >::intenstype_, IsotopeWaveletTransform< PeakType >::interpol_xs_, IsotopeWaveletTransform< PeakType >::interpol_ys_, OpenMS::Constants::IW_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::max_charge_, IsotopeWaveletTransform< PeakType >::max_mz_cutoff_, IsotopeWaveletTransform< PeakType >::max_num_peaks_per_pattern_, IsotopeWaveletTransform< PeakType >::max_scan_size_, IsotopeWaveletTransform< PeakType >::prod_, IsotopeWaveletTransform< PeakType >::psi_, IsotopeWaveletTransform< PeakType >::tmp_boxes_, and IsotopeWaveletTransform< PeakType >::xs_.

~IsotopeWaveletTransform()

~IsotopeWaveletTransform ( )

virtual

Destructor.

References IsotopeWaveletTransform< PeakType >::tmp_boxes_.

IsotopeWaveletTransform() [2/2]

IsotopeWaveletTransform ( )

protected

Default Constructor.

Note

Provided just for inheritance reasons. You should always use the other constructor.

References IsotopeWaveletTransform< PeakType >::av_MZ_spacing_, IsotopeWaveletTransform< PeakType >::hr_data_, IsotopeWaveletTransform< PeakType >::intenstype_, IsotopeWaveletTransform< PeakType >::max_mz_cutoff_, IsotopeWaveletTransform< PeakType >::max_num_peaks_per_pattern_, IsotopeWaveletTransform< PeakType >::max_scan_size_, and IsotopeWaveletTransform< PeakType >::tmp_boxes_.

Referenced by IsotopeWaveletTransform< PeakType >::getMaxScanSize().

Member Function Documentation

checkPositionForPlausibility_() [1/2]

bool checkPositionForPlausibility_ ( const TransSpectrum &  candidate, const MSSpectrum &  ref, const double  seed_mz, const UInt  c, const UInt  scan_index, const bool  check_PPMs, const double  transintens, const double  prev_score  )

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)

Parameters

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(), IsotopeWaveletTransform< PeakType >::BoxElement::c, IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_(), IsotopeWaveletTransform< PeakType >::TransSpectrum::end(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getNumPeakCutOff(), MSSpectrum::getRT(), OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::TransSpectrum::MZBegin(), MSSpectrum::MZBegin(), IsotopeWaveletTransform< PeakType >::push2Box_(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

Referenced by IsotopeWaveletTransform< PeakType >::clusterSeeds_(), and IsotopeWaveletTransform< PeakType >::getMaxScanSize().

checkPositionForPlausibility_() [2/2]

bool checkPositionForPlausibility_ ( const MSSpectrum &  candidate, const MSSpectrum &  ref, const double  seed_mz, const UInt  c, const UInt  scan_index, const bool  check_PPMs, const double  transintens, const double  prev_score  )

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)

Parameters

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 >::BoxElement::c, IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getNumPeakCutOff(), MSSpectrum::getRT(), OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, MSSpectrum::MZBegin(), IsotopeWaveletTransform< PeakType >::push2Box_(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

checkPPMTheoModel_()

std::pair< double, double > checkPPMTheoModel_ ( const MSSpectrum &  ref, const double  c_mz, const UInt  c  )

protectedvirtual

References IsotopeWaveletTransform< PeakType >::getPPMs_(), OpenMS::Constants::IW_PROTON_MASS, MSSpectrum::MZBegin(), OpenMS::Constants::PEPTIDE_MASS_RULE_THEO_PPM_BOUND, and IsotopeWaveletTransform< PeakType >::peptideMassRule_().

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), and IsotopeWaveletTransform< PeakType >::getMaxScanSize().

clusterSeeds_() [1/2]

void clusterSeeds_ ( const TransSpectrum &  candidates, const MSSpectrum &  ref, const UInt  scan_index, const UInt  c, const bool  check_PPMs  )

protected

Clusters the seeds stored by push2TmpBox_.

Parameters

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, IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::BoxElement::intens, IsotopeWaveletTransform< PeakType >::BoxElement::mz, IsotopeWaveletTransform< PeakType >::BoxElement::RT, IsotopeWaveletTransform< PeakType >::BoxElement::score, and IsotopeWaveletTransform< PeakType >::tmp_boxes_.

Referenced by IsotopeWaveletTransform< PeakType >::getMaxScanSize(), and IsotopeWaveletTransform< PeakType >::identifyCharge().

clusterSeeds_() [2/2]

void clusterSeeds_ ( const MSSpectrum &  candidates, const MSSpectrum &  ref, const UInt  scan_index, const UInt  c, const bool  check_PPMs  )

protectedvirtual

Clusters the seeds stored by push2TmpBox_.

Parameters

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, IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::BoxElement::intens, IsotopeWaveletTransform< PeakType >::BoxElement::mz, IsotopeWaveletTransform< PeakType >::BoxElement::RT, IsotopeWaveletTransform< PeakType >::BoxElement::score, and IsotopeWaveletTransform< PeakType >::tmp_boxes_.

computeMinSpacing()

void computeMinSpacing ( const MSSpectrum &  c_ref )

virtual

References IsotopeWaveletTransform< PeakType >::min_spacing_.

Referenced by IsotopeWaveletTransform< PeakType >::initializeScan(), and IsotopeWaveletTransform< PeakType >::setSigma().

extendBox_()

void extendBox_ ( const PeakMap &  map, const Box  box  )

protected

A currently still necessary function that extends the box box in order to capture also signals whose isotopic pattern is nearly diminishing.

Parameters

map	The experimental map.
box	The box to be extended.

References MSExperiment::begin(), and IsotopeWaveletTransform< PeakType >::push2Box_().

Referenced by IsotopeWaveletTransform< PeakType >::getMaxScanSize().

getAvIntens_() [1/2]

double getAvIntens_ ( const TransSpectrum &  scan )

inlineprotected

Computes the average (transformed) intensity (neglecting negative values) of scan.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::getTransIntensity(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::size().

Referenced by IsotopeWaveletTransform< PeakType >::getMaxScanSize(), and IsotopeWaveletTransform< PeakType >::identifyCharge().

getAvIntens_() [2/2]

double getAvIntens_ ( const MSSpectrum &  scan )

inlineprotected

Computes the average intensity (neglecting negative values) of scan.

getAvMZSpacing_()

double getAvMZSpacing_ ( const MSSpectrum &  scan )

inlineprotected

Computes the average MZ spacing of scan.

Parameters

scan	The scan we are interested in.

Referenced by IsotopeWaveletTransform< PeakType >::getMaxScanSize().

getClosedBoxes()

virtual std::multimap<double, Box> getClosedBoxes ( )

inlinevirtual

Returns the closed boxes.

References IsotopeWaveletTransform< PeakType >::closed_boxes_.

getLinearInterpolation() [1/2]

double getLinearInterpolation ( const typename MSSpectrum::const_iterator &  left_iter, const double  mz_pos, const typename MSSpectrum::const_iterator &  right_iter  )

inline

Computes a linear (intensity) interpolation.

Parameters

left_iter	The point left to the query.
mz_pos	The query point.
right_iter	The point right to the query.

Referenced by IsotopeWaveletTransform< PeakType >::identifyCharge().

getLinearInterpolation() [2/2]

double getLinearInterpolation ( const double  mz_a, const double  intens_a, const double  mz_pos, const double  mz_b, const double  intens_b  )

inline

Computes a linear (intensity) interpolation.

Parameters

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.

getMaxScanSize()

Size getMaxScanSize ( ) const

inline

References IsotopeWaveletTransform< PeakType >::BoxElement::c, IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_(), IsotopeWaveletTransform< PeakType >::clusterSeeds_(), IsotopeWaveletTransform< PeakType >::extendBox_(), IsotopeWaveletTransform< PeakType >::getAvIntens_(), IsotopeWaveletTransform< PeakType >::getAvMZSpacing_(), IsotopeWaveletTransform< PeakType >::getSdIntens_(), IsotopeWaveletTransform< PeakType >::BoxElement::intens, IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform(), IsotopeWaveletTransform< PeakType >::max_scan_size_, OpenMS::Math::mean(), IsotopeWaveletTransform< PeakType >::BoxElement::mz, IsotopeWaveletTransform< PeakType >::BoxElement::MZ_begin, IsotopeWaveletTransform< PeakType >::BoxElement::MZ_end, IsotopeWaveletTransform< PeakType >::push2Box_(), IsotopeWaveletTransform< PeakType >::push2TmpBox_(), IsotopeWaveletTransform< PeakType >::BoxElement::ref_intens, IsotopeWaveletTransform< PeakType >::sampleTheCMarrWavelet_(), IsotopeWaveletTransform< PeakType >::BoxElement::score, and IsotopeWaveletTransform< PeakType >::scoreThis_().

getMinSpacing()

double getMinSpacing ( ) const

inline

References IsotopeWaveletTransform< PeakType >::min_spacing_.

getPPMs_()

double getPPMs_ ( const double  mass_a, const double  mass_b  ) const

inlineprotected

Returns the parts-per-million deviation of the masses.

Parameters

mass_a	The first mass.
mass_b	The second mass.

Referenced by IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_().

getSdIntens_() [1/2]

double getSdIntens_ ( const TransSpectrum &  scan, const double  mean  )

inlineprotected

Computes the standard deviation (neglecting negative values) of the (transformed) intensities of scan.

References IsotopeWaveletTransform< PeakType >::TransSpectrum::getTransIntensity(), IsotopeWaveletTransform< PeakType >::BoxElement::intens, OpenMS::Math::mean(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::size().

Referenced by IsotopeWaveletTransform< PeakType >::getMaxScanSize(), and IsotopeWaveletTransform< PeakType >::identifyCharge().

getSdIntens_() [2/2]

double getSdIntens_ ( const MSSpectrum &  scan, const double  mean  )

inlineprotected

Computes the standard deviation (neglecting negative values) of the intensities of scan.

References IsotopeWaveletTransform< PeakType >::BoxElement::intens, and OpenMS::Math::mean().

getSigma()

double getSigma ( ) const

inline

References IsotopeWaveletTransform< PeakType >::sigma_.

getTransform()

void getTransform ( MSSpectrum &  c_trans, const MSSpectrum &  c_ref, const UInt  c  )

virtual

Computes the isotope wavelet transform of charge state c.

Parameters

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 IsotopeWaveletTransform< PeakType >::from_max_to_left_, IsotopeWavelet::getLambdaL(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getValueByLambda(), OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, and IsotopeWaveletTransform< PeakType >::min_spacing_.

getTransformHighRes()

void getTransformHighRes ( MSSpectrum &  c_trans, const MSSpectrum &  c_ref, const UInt  c  )

virtual

Computes the isotope wavelet transform of charge state c.

Parameters

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 IsotopeWaveletTransform< PeakType >::from_max_to_left_, IsotopeWavelet::getLambdaL(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getValueByLambda(), and OpenMS::Constants::IW_QUARTER_NEUTRON_MASS.

identifyCharge()

void identifyCharge ( const MSSpectrum &  candidates, const MSSpectrum &  ref, const UInt  scan_index, const UInt  c, const double  ampl_cutoff, const bool  check_PPMs  )

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.

Parameters

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

See also

getTransforms.)

Parameters

ref	The reference scan (the untransformed raw data) corresponding to candidates.
c	The corresponding 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_cutoff the 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 start ampl_cutoff=0 or even ampl_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 IsotopeWaveletTransform< PeakType >::BoxElement::c, IsotopeWaveletTransform< PeakType >::clusterSeeds_(), IsotopeWaveletTransform< PeakType >::getAvIntens_(), IsotopeWaveletTransform< PeakType >::getLinearInterpolation(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWavelet::getNumPeakCutOff(), MSSpectrum::getRT(), IsotopeWaveletTransform< PeakType >::getSdIntens_(), IsotopeWaveletTransform< PeakType >::hr_data_, OpenMS::Constants::IW_NEUTRON_MASS, OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::BoxElement::MZ_end, MSSpectrum::MZBegin(), MSSpectrum::MZEnd(), IsotopeWaveletTransform< PeakType >::push2TmpBox_(), IsotopeWaveletTransform< PeakType >::scoreThis_(), and ConstRefVector< ContainerT >::sortByIntensity().

initializeScan()

void initializeScan ( const MSSpectrum &  c_ref, const UInt  c = 0  )

virtual

References IsotopeWaveletTransform< PeakType >::computeMinSpacing(), IsotopeWaveletTransform< PeakType >::data_length_, IsotopeWaveletTransform< PeakType >::from_max_to_left_, IsotopeWaveletTransform< PeakType >::from_max_to_right_, IsotopeWavelet::getMzPeakCutOffAtMonoPos(), MSSpectrum::getRT(), IsotopeWaveletTransform< PeakType >::hr_data_, OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::max_charge_, IsotopeWaveletTransform< PeakType >::max_mz_cutoff_, IsotopeWaveletTransform< PeakType >::min_spacing_, MSSpectrum::MZBegin(), and MSSpectrum::MZEnd().

mapSeeds2Features()

FeatureMap mapSeeds2Features	(	const PeakMap &	map,
		const UInt	RT_votes_cutoff
	)

Filters the candidates further more and maps the internally used data structures to the OpenMS framework.

Parameters

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(), IsotopeWaveletTransform< PeakType >::closed_boxes_, IsotopeWavelet::getLambdaL(), IsotopeWavelet::getMzPeakCutOffAtMonoPos(), IsotopeWaveletTransform< PeakType >::intenstype_, OpenMS::Constants::IW_NEUTRON_MASS, OpenMS::Constants::IW_QUARTER_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::max_charge_, MSSpectrum::MZBegin(), BaseFeature::setCharge(), Feature::setConvexHulls(), Peak2D::setIntensity(), Peak2D::setMZ(), Feature::setOverallQuality(), Peak2D::setRT(), and MSExperiment::size().

mergeFeatures()

void mergeFeatures	(	IsotopeWaveletTransform< PeakType > *	later_iwt,
		const UInt	RT_interleave,
		const UInt	RT_votes_cutoff
	)

peptideMassRule_()

double peptideMassRule_ ( const double  c_mass ) const

inlineprotected

Returns the monoisotopic mass (with corresponding decimal values) we would expect at c_mass.

Parameters

c_mass

The mass for which we would like to know the averagine decimal places.

References OpenMS::Constants::PEPTIDE_MASS_RULE_BOUND, and OpenMS::Constants::PEPTIDE_MASS_RULE_FACTOR.

Referenced by IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_().

push2Box_()

void push2Box_ ( const double  mz, const UInt  scan, UInt  c, const double  score, const double  intens, const double  rt, const UInt  MZ_begin, const UInt  MZ_end, const double  ref_intens  )

protectedvirtual

Inserts a potential isotopic pattern into an open box or - if no such box exists - creates a new one.

Parameters

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, IsotopeWaveletTransform< PeakType >::BoxElement::intens, OpenMS::Constants::IW_HALF_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::max_charge_, IsotopeWaveletTransform< PeakType >::BoxElement::mz, IsotopeWaveletTransform< PeakType >::BoxElement::MZ_begin, IsotopeWaveletTransform< PeakType >::BoxElement::MZ_end, IsotopeWaveletTransform< PeakType >::open_boxes_, IsotopeWaveletTransform< PeakType >::BoxElement::ref_intens, IsotopeWaveletTransform< PeakType >::BoxElement::RT, IsotopeWaveletTransform< PeakType >::BoxElement::RT_index, and IsotopeWaveletTransform< PeakType >::BoxElement::score.

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::extendBox_(), and IsotopeWaveletTransform< PeakType >::getMaxScanSize().

push2TmpBox_()

void push2TmpBox_ ( const double  mz, const UInt  scan, UInt  charge, const double  score, const double  intens, const double  rt, const UInt  MZ_begin, const UInt  MZ_end  )

protectedvirtual

Essentially the same function as.

See also

push2Box_. In contrast to

push2Box this function stores its candidates only temporarily. In particular, this function is only used within a single scan transform. After the wavelet transform is computed on that scan, all candidates are pushed by this function and finally clustered together by

clusterSeeds_. Afterwards, a final push by

push2Box_ is performed storing the clustered candidates.

Parameters

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, IsotopeWaveletTransform< PeakType >::BoxElement::intens, OpenMS::Constants::IW_HALF_NEUTRON_MASS, IsotopeWaveletTransform< PeakType >::max_charge_, 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, IsotopeWaveletTransform< PeakType >::BoxElement::score, and IsotopeWaveletTransform< PeakType >::tmp_boxes_.

Referenced by IsotopeWaveletTransform< PeakType >::getMaxScanSize(), and IsotopeWaveletTransform< PeakType >::identifyCharge().

sampleTheCMarrWavelet_()

void sampleTheCMarrWavelet_ ( const MSSpectrum &  scan, const Int  wavelet_length, const Int  mz_index, const UInt  charge  )

inlineprotected

Referenced by IsotopeWaveletTransform< PeakType >::getMaxScanSize().

scoreThis_() [1/2]

double scoreThis_ ( const TransSpectrum &  candidate, const UInt  peak_cutoff, const double  seed_mz, const UInt  c, const double  ampl_cutoff  )

protectedvirtual

Given a candidate for an isotopic pattern, this function computes the corresponding score.

Parameters

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().

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::getMaxScanSize(), and IsotopeWaveletTransform< PeakType >::identifyCharge().

scoreThis_() [2/2]

double scoreThis_ ( const MSSpectrum &  candidate, const UInt  peak_cutoff, const double  seed_mz, const UInt  c, const double  ampl_cutoff  )

protectedvirtual

Given a candidate for an isotopic pattern, this function computes the corresponding score.

Parameters

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::MZBegin().

setSigma()

void setSigma ( const double  sigma )

inline

References IsotopeWaveletTransform< PeakType >::computeMinSpacing(), and IsotopeWaveletTransform< PeakType >::sigma_.

updateBoxStates()

void updateBoxStates	(	const PeakMap &	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.

Parameters

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 IsotopeWaveletTransform< PeakType >::closed_boxes_, IsotopeWaveletTransform< PeakType >::end_boxes_, IsotopeWaveletTransform< PeakType >::front_boxes_, IsotopeWaveletTransform< PeakType >::open_boxes_, and MSExperiment::size().

Member Data Documentation

av_MZ_spacing_

double av_MZ_spacing_

protected

Referenced by IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

c_mzs_

std::vector<double> c_mzs_

protected

c_spacings_

std::vector<double> c_spacings_

protected

closed_boxes_

std::multimap<double, Box> closed_boxes_

protected

Referenced by IsotopeWaveletTransform< PeakType >::getClosedBoxes(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), and IsotopeWaveletTransform< PeakType >::updateBoxStates().

data_length_

UInt data_length_

protected

Referenced by IsotopeWaveletTransform< PeakType >::initializeScan().

end_boxes_

std::multimap<double, Box> end_boxes_

protected

Referenced by IsotopeWaveletTransform< PeakType >::updateBoxStates().

from_max_to_left_

Int from_max_to_left_

protected

Referenced by IsotopeWaveletTransform< PeakType >::getTransform(), IsotopeWaveletTransform< PeakType >::getTransformHighRes(), and IsotopeWaveletTransform< PeakType >::initializeScan().

from_max_to_right_

Int from_max_to_right_

protected

Referenced by IsotopeWaveletTransform< PeakType >::initializeScan().

front_boxes_

std::multimap<double, Box> front_boxes_

protected

Referenced by IsotopeWaveletTransform< PeakType >::updateBoxStates().

hr_data_

bool hr_data_

protected

Referenced by IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), and IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

indices_

std::vector<int> indices_

protected

intenstype_

String intenstype_

protected

Referenced by IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform(), and IsotopeWaveletTransform< PeakType >::mapSeeds2Features().

interpol_xs_

std::vector<double> interpol_xs_

protected

Referenced by IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

interpol_ys_

std::vector<double> interpol_ys_

protected

Referenced by IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

max_charge_

UInt max_charge_

protected

Referenced by IsotopeWaveletTransform< PeakType >::initializeScan(), IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), IsotopeWaveletTransform< PeakType >::push2Box_(), and IsotopeWaveletTransform< PeakType >::push2TmpBox_().

max_mz_cutoff_

double max_mz_cutoff_

protected

Referenced by IsotopeWaveletTransform< PeakType >::initializeScan(), and IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

max_num_peaks_per_pattern_

UInt max_num_peaks_per_pattern_

protected

Referenced by IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

max_scan_size_

Size max_scan_size_

protected

Referenced by IsotopeWaveletTransform< PeakType >::getMaxScanSize(), and IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

min_spacing_

double min_spacing_

protected

Referenced by IsotopeWaveletTransform< PeakType >::computeMinSpacing(), IsotopeWaveletTransform< PeakType >::getMinSpacing(), IsotopeWaveletTransform< PeakType >::getTransform(), and IsotopeWaveletTransform< PeakType >::initializeScan().

open_boxes_

std::multimap<double, Box> open_boxes_

protected

Referenced by IsotopeWaveletTransform< PeakType >::push2Box_(), and IsotopeWaveletTransform< PeakType >::updateBoxStates().

prod_

std::vector<double> prod_

protected

Referenced by IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

psi_

std::vector<double> psi_

protected

Referenced by IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

scores_

std::vector<float> scores_

protected

sigma_

double sigma_

protected

Referenced by IsotopeWaveletTransform< PeakType >::getSigma(), and IsotopeWaveletTransform< PeakType >::setSigma().

tmp_boxes_

std::vector<std::multimap<double, Box> >* tmp_boxes_

protected

Referenced by IsotopeWaveletTransform< PeakType >::clusterSeeds_(), IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform(), IsotopeWaveletTransform< PeakType >::push2TmpBox_(), and IsotopeWaveletTransform< PeakType >::~IsotopeWaveletTransform().

xs_

std::vector<double> xs_

protected

Referenced by IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().

zeros_

std::vector<float> zeros_

protected