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/*
* Copyright (c) Medical Research Council 2002. All rights reserved.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided that
* this copyright and notice appears in all copies.
*
* This file was written as part of the Staden Package at the MRC Laboratory
* of Molecular Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
*
* MRC disclaims all warranties with regard to this software.
*
*/
#ifndef _MUTSCAN_PREPROCESS_HPP_
#define _MUTSCAN_PREPROCESS_HPP_
#include <mutlib.h> // For mutlib types
#include <array.hpp> // For SimpleArray object
#include <matrix.hpp> // For SimpleMatrix object
#include <trace.hpp> // For Trace object
/**
Preprocesses the trace ready for further analysis by mutscan. One preprocessor
object is used for each trace.
*/
class MutScanPreprocessor
{
public:
// Constructor/Destructor
MutScanPreprocessor() { }
~MutScanPreprocessor() { }
public:
// Data
SimpleMatrix<int> Peak; // 5*SAMPLES peak matrix, value=amplitude, last row is logical OR of all peaks for every base
NumericArray<int> Noise; // 1*SAMPLES noise vector
NumericArray<int> PeakCount; // 4*1 peak count for each row of Peak
int PeakCountMax; // Maximum number of peaks for all 4-bases
double SearchWindow; // Search window in samples, derrived from trace stats
int PeakInterval; // Peak interval mode
public:
// Services
mutlib_result_t Execute( mutscan_t* ms, Trace& t, int n, int left, int right );
private:
// Helpers
void Init();
void CountPeaks();
void PeakClip();
void PeakSpacing();
void EstimateNoiseFloor( Trace& t, int n );
void PeakFind( Trace& t, int left, int right );
private:
// Data
double m_nNoiseThreshold[2];
};
#endif
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