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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_TRACE_HPP_
#define _MUTLIB_TRACE_HPP_
#include <cassert>
#include <staden.h> // For Read* structure
class Trace
{
public:
// Constructors/destructor
Trace() { Init(); }
~Trace() { Close(); }
Trace( Read* r, bool AutoDestroy=true ) { Wrap(r,AutoDestroy); }
public:
// Services
void Sort();
void Close();
void Smooth();
void FillGaps();
double Mean( int n=-1 ) const;
Trace* CreateEnvelope() const;
Trace* Subtract( Trace& t );
void ScaleTo( Trace& t );
void FloorHalfwaves();
void Floor( int threshold );
void AvgFilt( double scale );
void FloorNarrowPeaks( int width_threshold );
void Range( int n1, int n2 );
bool Open( const char* pFileName );
void MaxAt( int n, int& c, int& m ) const;
void MinAt( int n, int& c, int& m ) const;
bool SaveAs( const char* pFileName, int fmt=TT_ZTR );
bool Create( int nSamples, int nBases, const char* pName=0 );
void Wrap( Read* r, bool AutoDestroy=true );
Trace* Clone( const char* pNewFileName=0 ) const;
int BaseNumberFromSamplePosition( int nPosition ) const;
int PosPeakFind( int n, int nBegin, int nEnd, int& nResume, int nSlopeCount=1 ) const;
int NegPeakFind( int n, int nBegin, int nEnd, int& nResume, int nSlopeCount=1 ) const;
int PosPeakFindLargest( int n, int nBegin, int nEnd, int& nCount, int nSlopeCount=1 ) const;
int NegPeakFindLargest( int n, int nBegin, int nEnd, int& nCount, int nSlopeCount=1 ) const;
int PosPeakWidth( int n, int nPos, int& nLeft, int& nRight ) const;
int PosPeakWidth( int n, int nPos, int& nLeft, int& nRight, int nMeasurementThreshold ) const;
int NegPeakWidth( int n, int nPos, int& nLeft, int& nRight, int nMeasurementThreshold ) const;
void WindowToLeftOf( int nPosition, int nSize, int& l, int& r ) const;
void WindowCentredAt( int nPosition, int nSize, int& l, int& r ) const;
int IntervalMin() { assert(m_pRead!=0); UpdateStatistics(); return m_nIntervalMin; }
int IntervalMax() { assert(m_pRead!=0); UpdateStatistics(); return m_nIntervalMax; }
int IntervalMode() { assert(m_pRead!=0); UpdateStatistics(); return m_nIntervalMode; }
double IntervalMean() { assert(m_pRead!=0); UpdateStatistics(); return m_nIntervalMean; }
double IntervalStdDev() { assert(m_pRead!=0); UpdateStatistics(); return m_nIntervalStdDev; }
void InvalidateStatistics() { m_bStatisticsCached=false; }
bool AutoDestroy() const { return m_bAutoDestroy; }
void AutoDestroy( bool s ) { m_bAutoDestroy=s; }
int Range() const { return m_nUpperLimit-m_nLowerLimit+1; }
Read* Raw() const { assert(m_pRead!=0); return m_pRead; }
int Max() const { assert(m_pRead!=0); return m_pRead->maxTraceVal; }
void Max( int n ) { assert(m_pRead!=0); m_pRead->maxTraceVal = n; }
const char* Name() const { assert(m_pRead!=0); return m_pRead->trace_name ? m_pRead->trace_name : ""; }
int Bases() const { assert(m_pRead!=0); return m_pRead->NBases; }
void Bases( int n ) { assert(m_pRead!=0); m_pRead->NBases=n; }
int Samples() const { assert(m_pRead!=0); return m_pRead->NPoints; }
void Samples( int n ) { assert(m_pRead!=0); m_pRead->NPoints=n; }
double SamplesPerBase() const { assert(m_pRead!=0); assert(m_pRead->NBases>0); return double(m_pRead->NPoints) / double(m_pRead->NBases); }
int Baseline() const { assert(m_pRead!=0); return m_pRead->baseline; }
char BaseChar( int n ) const { assert(m_pRead!=0); assert(n>=0); assert(n<m_pRead->NBases); return m_pRead->base[n]; }
int BasePosition( int n ) const { assert(m_pRead!=0); assert(n>=0); assert(n<m_pRead->NBases); return m_pRead->basePos[n]; }
int BaseConfidence( int n ) const;
void SetBase( int n, char b, int pos, int conf );
public:
// Operators
TRACE* operator[]( int n ) { assert(n<4); assert(n>=0); return m_pTrace[n]; }
private:
// Helpers
void Init();
void InitTraces();
void ZeroTraces();
void UpdateStatistics();
private:
// Data
Read* m_pRead;
TRACE* m_pTrace[4]; // Required due to poor Read structure design
int m_nLowerLimit;
int m_nUpperLimit;
bool m_bAutoDestroy;
bool m_bExternalTrace;
int m_nIntervalMin;
int m_nIntervalMax;
int m_nIntervalMode;
double m_nIntervalMean;
double m_nIntervalStdDev;
bool m_bStatisticsCached;
};
#endif
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