Implements the isotope wavelet function. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeWavelet.h>
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union | fi_ |
Internal union for fast computation of the power function. More... | |
Static Public Member Functions | |
static IsotopeWavelet * | init (const DoubleReal max_m, const UInt max_charge) |
static IsotopeWavelet * | getInstance () |
static void | destroy () |
static DoubleReal | getValueByMass (const DoubleReal t, const DoubleReal 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 DoubleReal | getValueByLambda (const DoubleReal lambda, const DoubleReal 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 DoubleReal | getValueByLambdaExtrapol (const DoubleReal lambda, const DoubleReal 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 DoubleReal | getValueByLambdaExact (const DoubleReal lambda, const DoubleReal 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 DoubleReal | getTableSteps () |
Returns the table_steps_ parameter. More... | |
static DoubleReal | getInvTableSteps () |
Returns the inv_table_steps_ parameter. More... | |
static void | setTableSteps (const DoubleReal table_steps) |
Sets the table_steps parameter. More... | |
static DoubleReal | getLambdaL (const DoubleReal m) |
Returns the mass-parameter lambda (linear fit). More... | |
static const IsotopeDistribution::ContainerType & | getAveragine (const DoubleReal m, UInt *size=NULL) |
Computes the averagine isotopic distribution we would expect at the deconvoluted 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 DoubleReal mass, const UInt z) |
static UInt | getNumPeakCutOff (const DoubleReal mass, const UInt z) |
static UInt | getNumPeakCutOff (const DoubleReal mz) |
Protected Member Functions | |
IsotopeWavelet () | |
Default Constructor. More... | |
IsotopeWavelet (const DoubleReal max_m, const UInt max_charge) | |
Constructor. More... | |
virtual | ~IsotopeWavelet () |
Destructor. More... | |
Static Protected Member Functions | |
static void | preComputeExpensiveFunctions_ (const DoubleReal 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 DoubleReal 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 DoubleReal | table_steps_ |
static DoubleReal | inv_table_steps_ |
static std::vector< DoubleReal > | gamma_table_ |
static std::vector< DoubleReal > | gamma_table_new_ |
static std::vector< DoubleReal > | exp_table_ |
static std::vector< DoubleReal > | sine_table_ |
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).
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Default Constructor.
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Constructor.
max_m | The maximal deconvoluted 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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Initializes the internally used averagine model; automatically called by the public constructor.
max_m | The maximal deconvoluted 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 deconvoluted mass.
m | The deconvoluted 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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inlinestatic |
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.
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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.
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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.
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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().
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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 decharged) 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().
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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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Internally used function; uses register shifts for fast computation of the power function.
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staticprotected |
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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staticprotected |
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 deconvoluted mass that occurs in the current data set. |
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inlinestatic |
Sets the max_charge
parameter.
Referenced by FeatureFinderAlgorithmIsotopeWavelet< OpenMS::Peak2D, FeatureType >::updateMembers_().
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inlinestatic |
Sets the table_steps
parameter.
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Internally used averagine model.
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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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This parameter determines the sample rate for the pre-computation of the gamma function.
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5 |