#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/IsotopeWavelet.h>
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).
Public Member Functions | |
virtual | ~IsotopeWavelet () throw () |
Destructor. | |
Static Public Member Functions | |
static IsotopeWavelet * | init (const DoubleReal max_m, const UInt max_charge) throw () |
static IsotopeWavelet * | getInstance () throw () |
static DoubleReal | getValueByMass (const DoubleReal t, const DoubleReal m, const UInt z, const Int mode=+1) throw () |
Returns the value of the isotope wavelet at position t . Usually, you do not need to call this function. Please use. | |
static DoubleReal | getValueByLambda (const DoubleReal lambda, const DoubleReal tz1) throw () |
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. | |
static DoubleReal | getValueByLambdaExtrapol (const DoubleReal lambda, const DoubleReal tz1) throw () |
Returns the value of the isotope wavelet at position t . This function is usually significantly slower than the table lookup performed in. | |
static UInt | getMaxCharge () throw () |
Returns the largest charge state we will consider. | |
static void | setMaxCharge (const UInt max_charge) throw () |
Sets the max_charge parameter. | |
static DoubleReal | getTableSteps () throw () |
Returns the table_steps_ parameter. | |
static void | setTableSteps (const DoubleReal table_steps) throw () |
Sets the table_steps parameter. | |
static DoubleReal | getLambdaL (const DoubleReal m) throw () |
Returns the mass-parameter lambda (linear fit). | |
static DoubleReal | getLambdaQ (const DoubleReal m) throw () |
Returns the mass-parameter lambda (quadratic fit). | |
static const IsotopeDistribution::ContainerType & | getAveragine (const DoubleReal m, UInt *size=NULL) throw () |
Computes the averagine isotopic distribution we would expect at the deconvoluted mass. | |
Protected Member Functions | |
IsotopeWavelet () throw () | |
Default Constructor. | |
IsotopeWavelet (const DoubleReal max_m, const UInt max_charge) throw () | |
Constructor. | |
Static Protected Member Functions | |
static void | preComputeExpensiveFunctions_ (const DoubleReal max_m) throw () |
Should be called once before values are drawn from the isotope wavelet function. The function is automatically called by the public constructor. | |
static void | computeIsotopeDistributionSize_ (const DoubleReal max_m) throw () |
Initializes the internally used averagine model; automatically called by the public constructor. | |
static float | myPow_ (float a, float b) throw () |
Internally used function; uses register shifts for fast computation of the power function. | |
static float | myPow2_ (float i) throw () |
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. | |
static float | myLog2_ (float i) throw () |
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. | |
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 > | exp_table_ |
static IsotopeDistribution | averagine_ |
Classes | |
union | fi_ |
Internal union for fast computation of the power function. More... |
virtual ~IsotopeWavelet | ( | ) | throw () [virtual] |
Destructor.
IsotopeWavelet | ( | ) | throw () [protected] |
Default Constructor.
IsotopeWavelet | ( | const DoubleReal | max_m, | |
const UInt | max_charge | |||
) | throw () [protected] |
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. |
static IsotopeWavelet* init | ( | const DoubleReal | max_m, | |
const UInt | max_charge | |||
) | throw () [static] |
The init function; creates an instance of this singleton class.
static IsotopeWavelet* getInstance | ( | ) | throw () [inline, static] |
Returns an pointer to the current instance of the class.
static DoubleReal getValueByMass | ( | const DoubleReal | t, | |
const DoubleReal | m, | |||
const UInt | z, | |||
const Int | mode = +1 | |||
) | throw () [inline, static] |
Returns the value of the isotope wavelet at position t
. Usually, you do not need to call this function. Please use.
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. |
static DoubleReal getValueByLambda | ( | const DoubleReal | lambda, | |
const DoubleReal | tz1 | |||
) | throw () [static] |
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.
lambda | The mass-parameter lambda. | |
tz1 | t (the position) times the charge (z) plus 1. |
static DoubleReal getValueByLambdaExtrapol | ( | const DoubleReal | lambda, | |
const DoubleReal | tz1 | |||
) | throw () [static] |
Returns the value of the isotope wavelet at position t
. This function is usually significantly slower than the table lookup performed in.
lambda | The mass-parameter lambda. | |
tz1 | t (the position) times the charge (z) plus 1. |
static UInt getMaxCharge | ( | ) | throw () [inline, static] |
Returns the largest charge state we will consider.
static void setMaxCharge | ( | const UInt | max_charge | ) | throw () [inline, static] |
Sets the max_charge
parameter.
static DoubleReal getTableSteps | ( | ) | throw () [inline, static] |
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.
static void setTableSteps | ( | const DoubleReal | table_steps | ) | throw () [inline, static] |
Sets the table_steps
parameter.
static DoubleReal getLambdaL | ( | const DoubleReal | m | ) | throw () [static] |
Returns the mass-parameter lambda (linear fit).
getLambdaQ is pure hardcoding.
static DoubleReal getLambdaQ | ( | const DoubleReal | m | ) | throw () [static] |
Returns the mass-parameter lambda (quadratic fit).
static const IsotopeDistribution::ContainerType& getAveragine | ( | const DoubleReal | m, | |
UInt * | size = NULL | |||
) | throw () [static] |
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 . |
static void preComputeExpensiveFunctions_ | ( | const DoubleReal | max_m | ) | throw () [static, protected] |
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:
peak_cutoff_. If both of these are set correctly
getValue will never compute the gamma function online.
max_m | The maximal deconvoluted mass that occurs in the current data set. |
static void computeIsotopeDistributionSize_ | ( | const DoubleReal | max_m | ) | throw () [static, protected] |
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. |
static float myPow_ | ( | float | a, | |
float | b | |||
) | throw () [static, protected] |
Internally used function; uses register shifts for fast computation of the power function.
static float myPow2_ | ( | float | i | ) | throw () [static, protected] |
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.
static float myLog2_ | ( | float | i | ) | throw () [static, protected] |
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.
IsotopeWavelet* me_ [static, protected] |
The singleton pointer.
UInt max_charge_ [static, protected] |
This parameter determines the maximal charge state we will consider.
DoubleReal table_steps_ [static, protected] |
This parameter determines the sample rate for the pre-computation of the gamma function.
DoubleReal inv_table_steps_ [static, protected] |
std::vector<DoubleReal> gamma_table_ [static, protected] |
Internal table for the precomputed values of the gamma function.
std::vector<DoubleReal> exp_table_ [static, protected] |
Internal table for the precomputed values of the exponential function.
IsotopeDistribution averagine_ [static, protected] |
Internally used averagine model.
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