OpenMS
2.5.0
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Implements the isotope wavelet function. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeWavelet.h>
Classes | |
union | fi_ |
Internal union for fast computation of the power function. More... | |
Static Public Member Functions | |
static IsotopeWavelet * | init (const double max_m, const UInt max_charge) |
static IsotopeWavelet * | getInstance () |
static void | destroy () |
static double | getValueByMass (const double t, const double m, const UInt z, const Int mode=+1) |
Returns the value of the isotope wavelet at position t . Usually, you do not need to call this function. Please use. More... | |
static double | getValueByLambda (const double lambda, const double tz1) |
Returns the value of the isotope wavelet at position t via a fast table lookup. Usually, you do not need to call this function. Please use. More... | |
static double | getValueByLambdaExtrapol (const double lambda, const double tz1) |
Returns the value of the isotope wavelet at position t . This function is usually significantly slower than the table lookup performed in. More... | |
static double | getValueByLambdaExact (const double lambda, const double tz1) |
static UInt | getMaxCharge () |
Returns the largest charge state we will consider. More... | |
static void | setMaxCharge (const UInt max_charge) |
Sets the max_charge parameter. More... | |
static double | getTableSteps () |
Returns the table_steps_ parameter. More... | |
static double | getInvTableSteps () |
Returns the inv_table_steps_ parameter. More... | |
static void | setTableSteps (const double table_steps) |
Sets the table_steps parameter. More... | |
static double | getLambdaL (const double m) |
Returns the mass-parameter lambda (linear fit). More... | |
static const IsotopeDistribution::ContainerType & | getAveragine (const double m, UInt *size=nullptr) |
Computes the averagine isotopic distribution we would expect at the de-convoluted mass. More... | |
static Size | getGammaTableMaxIndex () |
Returns the largest possible index for the pre-sampled gamma table. More... | |
static Size | getExpTableMaxIndex () |
Returns the largest possible index for the pre-sampled exp table. More... | |
static float | myPow (float a, float b) |
Internally used function; uses register shifts for fast computation of the power function. More... | |
static UInt | getMzPeakCutOffAtMonoPos (const double mass, const UInt z) |
static UInt | getNumPeakCutOff (const double mass, const UInt z) |
static UInt | getNumPeakCutOff (const double mz) |
Protected Member Functions | |
IsotopeWavelet () | |
Default Constructor. More... | |
IsotopeWavelet (const double max_m, const UInt max_charge) | |
Constructor. More... | |
virtual | ~IsotopeWavelet () |
Destructor. More... | |
Static Protected Member Functions | |
static void | preComputeExpensiveFunctions_ (const double max_m) |
Should be called once before values are drawn from the isotope wavelet function. The function is automatically called by the public constructor. More... | |
static void | computeIsotopeDistributionSize_ (const double max_m) |
Initializes the internally used averagine model; automatically called by the public constructor. More... | |
static float | myPow2_ (float i) |
Internally used function; uses register shifts for fast computation of the power function. The function follows http://www.dctsystems.co.uk/Software/power.html , code by Ian Stephenson, DCT Systems, NCCA Bournemouth University. More... | |
static float | myLog2_ (float i) |
Internally used function uses register shifts for fast computation of the power function. The function follows http://www.dctsystems.co.uk/Software/power.html , code by Ian Stephenson, DCT Systems, NCCA Bournemouth University. More... | |
Static Protected Attributes | |
static IsotopeWavelet * | me_ |
static UInt | max_charge_ |
static double | table_steps_ |
static double | inv_table_steps_ |
static std::vector< double > | gamma_table_ |
static std::vector< double > | gamma_table_new_ |
static std::vector< double > | exp_table_ |
static std::vector< double > | sine_table_ |
static CoarseIsotopePatternGenerator | solver_ |
static IsotopeDistribution | averagine_ |
static Size | gamma_table_max_index_ |
static Size | exp_table_max_index_ |
Implements the isotope wavelet function.
The IsotopeWavelet class implements the isotope wavelet as described by R. Hussong, A. Tholey, A. Hildebrandt: Efficient Analysis of Mass Spectrometry Data Using the Isotope Wavelet. Proceedings of the 3rd international Symposium in Computational Life Sciences (Complife07). American Institute of Physics (AIP) Proceedings (2007).
union OpenMS::IsotopeWavelet::fi_ |
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Default Constructor.
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Constructor.
max_m | The maximal de-convoluted mass that occurs in the current data set. |
max_charge | The maximal charge state we would like to analyze. |
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Destructor.
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staticprotected |
Initializes the internally used averagine model; automatically called by the public constructor.
max_m | The maximal de-convoluted mass that occurs in the current data set. |
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Deletes the singleton instance.
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Computes the averagine isotopic distribution we would expect at the de-convoluted mass.
m | The de-convoluted mass m. |
size | Returns the number of significant peaks within a pattern occurring at mass m . |
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inlinestatic |
Returns the largest possible index for the pre-sampled exp table.
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Returns the largest possible index for the pre-sampled gamma table.
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inlinestatic |
Returns an pointer to the current instance of the class.
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inlinestatic |
Returns the inv_table_steps_ parameter.
This is an internally used parameter controlling the precision of several pre-sampling steps. Normally, this parameter can be left unchanged.
Returns the mass-parameter lambda (linear fit).
Referenced by IsotopeWaveletTransform< PeakType >::getTransform(), IsotopeWaveletTransform< PeakType >::getTransformHighRes(), and IsotopeWaveletTransform< PeakType >::mapSeeds2Features().
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inlinestatic |
Returns the largest charge state we will consider.
Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::getTransform(), IsotopeWaveletTransform< PeakType >::getTransformHighRes(), IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform(), and IsotopeWaveletTransform< PeakType >::mapSeeds2Features().
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inlinestatic |
Returns the table_steps_ parameter.
This is an internally used parameter controlling the precision of several pre-sampling steps. Normally, this parameter can be left unchanged.
Returns the value of the isotope wavelet at position t
via a fast table lookup. Usually, you do not need to call this function. Please use.
Note that this functions returns the pure function value of psi and not the normalized (average=0) value given by Psi.
lambda | The mass-parameter lambda. |
tz1 | t (the position) times the charge (z) plus 1. |
Referenced by IsotopeWaveletTransform< PeakType >::getTransform(), and IsotopeWaveletTransform< PeakType >::getTransformHighRes().
Returns the value of the isotope wavelet at position t
. This function is usually significantly slower than the table lookup performed in.
Usually, you do not need to call this function. Please use
Note that this functions returns the pure function value of psi and not the normalized (average=0) value given by Psi.
lambda | The mass-parameter lambda. |
tz1 | t (the position) times the charge (z) plus 1. |
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inlinestatic |
Returns the value of the isotope wavelet at position t
. Usually, you do not need to call this function. Please use.
Note that this functions returns the pure function value of psi and not the normalized (average=0) value given by Psi.
t | The position at which the wavelet has to be drawn (within the coordinate system of the wavelet). |
m | The m/z position within the signal (i.e. the mass not de-charged) within the signal. |
z | The charge z we want to detect. |
mode | Indicates whether positive mode (+1) or negative mode (-1) has been used for ionization. |
References OpenMS::Constants::IW_PROTON_MASS.
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The init function; creates an instance of this singleton class.
Referenced by IsotopeWaveletTransform< PeakType >::IsotopeWaveletTransform().
Internally used function uses register shifts for fast computation of the power function. The function follows http://www.dctsystems.co.uk/Software/power.html , code by Ian Stephenson, DCT Systems, NCCA Bournemouth University.
Internally used function; uses register shifts for fast computation of the power function.
Internally used function; uses register shifts for fast computation of the power function. The function follows http://www.dctsystems.co.uk/Software/power.html , code by Ian Stephenson, DCT Systems, NCCA Bournemouth University.
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Should be called once before values are drawn from the isotope wavelet function. The function is automatically called by the public constructor.
The function pre-computes the expensive gamma function. Parameters related to this function are:
max_m | The maximal de-convoluted mass that occurs in the current data set. |
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inlinestatic |
Sets the max_charge
parameter.
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Sets the table_steps
parameter.
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Internal table for the precomputed values of the exponential function.
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Internal table for the precomputed values of the gamma function.
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This parameter determines the maximal charge state we will consider.
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The singleton pointer.
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Internal table for the precomputed values of the exponential function.
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Internally used averagine model.
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This parameter determines the sample rate for the pre-computation of the gamma function.