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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_ANALYSIS_HPP_
#define _MUTSCAN_ANALYSIS_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
#include <list.hpp> // For List object
#include <mutationtag.hpp> // For MutationTag object
#include <mutscan_preprocess.hpp> // For MutScanPreprocessor object
/**
Analyses the preprocessed input data and traces for mutations.
*/
class MutScanAnalyser
{
public:
// Constructor/Destructor
MutScanAnalyser() { }
~MutScanAnalyser() { }
public:
// Data
SimpleMatrix<int> Map; // 8*max(PEAKS) peak alignment maps, r[0,1]=A, r[2,3]=C, r[4,5]=G, r[6,7]=T
int MapCount[4]; // 4*1 pair counts for each pair of Map rows
SimpleMatrix<double> ScaleFactor; // 4*max(PEAKS) peak pair scale factors, row 0=A, 1=C, 2=G, 3=T
double ScaleFactorMean[4]; // 4*1 vector containing mean value of scale factors
double ScaleFactorStdDev[4]; // 4*1 vector containing the std deviation of the scale factors
List<MutationTag> MutationTagList;
public:
// Services
mutlib_result_t Execute( mutscan_t* ms, MutScanPreprocessor Data[], Trace Tr[], Trace* DifferenceTrace );
private:
// Helpers
bool HasReferencePeak( int base, int pos );
void AnalysePotentialMutations( Trace Tr[] );
void AlignPeaks( MutScanPreprocessor Data[] );
void AllocatePeakMap( MutScanPreprocessor Data[] );
void ComputeScaleFactors( MutScanPreprocessor Data[] );
void ValidateMutationsAgainstDifference( Trace& DiffTrace );
void ComputeScaleFactorLimits( int r, double nosd, double data[2] );
void DoLevelCall( int pos, Trace& Tr, MutationTag& Tag, bool AllowAmbiguity );
void ScanForPotentialMutations( MutScanPreprocessor Data[], mutlib_strand_t Strand, Trace Tr[] );
private:
// Data
int m_nSearchWindow;
double m_nHetSNRThreshold;
double m_nUpperPeakDropThreshold;
double m_nLowerPeakDropThreshold;
};
#endif
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