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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 _TRACEALIGN_HPP_
#define _TRACEALIGN_HPP_
#include <mutlib.h>
#include <array.hpp> // For Array<T> objects
#include <trace.hpp> // For Trace objects
#include <align.hpp> // For Alignment object
#include <muttag.hpp> // For MutTag objects
void TraceAlignDestroyCache( tracealign_t* ta );
void TraceAlignDestroyResults( tracealign_t* ta );
mutlib_result_t TraceAlignValidateInput( tracealign_t* ta );
void TraceAlignInterpolate( char cPad, SimpleArray<char>& Envelope, Trace& Tin, int nClipL, Trace& Tout );
void TraceAlignInsertBases( char cPad, SimpleArray<char>& Envelope, Trace& Tin, Trace& Tout, int nOverlap[2] );
void TraceAlignQuantiseEnvelope( NumericArray<int>& e, SimpleArray<char>& qe, int nLevels, int nLower, int nUpper );
#endif
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