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/*
* Copyright (c) Medical Research Council 2001. 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 _MUTLIB_BASECALL_HPP_
#define _MUTLIB_BASECALL_HPP_
#include <cstddef> // For size_t
// Useful structure
typedef struct
{
int a;
int b;
}mutlib_pair_t;
class BaseCall
{
/*
Used to record and manipulate all base call information.
*/
public:
// Original data
int Call; // 0=A, 1=C, 2=G, 3=T
int Position; // Base position in samples
int Amplitude; // Size of peak
int Confidence; // In phred units
// New Data
int PeakCall; // 0=A, 1=C, 2=G, 3=T
int PeakPosition[4]; // Centre points for each peak in samples
int PeakAmplitude[4]; // 0=A, 1=C, 2=G, 3=T
int PeakWidth[4]; // Useful measure of peak quality
public:
// Constructors
BaseCall();
BaseCall( int a, int c, int g, int t );
BaseCall( int call, int pos, int conf=-1 );
public:
// Services
char AsCharacter() const;
int PeakCount() const;
bool PeakPresent() const;
int PeakOfRank( int n );
int PeakOfRankAsIndex( int n );
private:
// Helpers
void Init();
int Rank( std::size_t n, bool bIndex ) const;
void Swap( mutlib_pair_t& a, mutlib_pair_t& b ) const;
};
#endif
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