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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.
*
*/
#include <cassert>
#include <new> // For bad_alloc()
#include <array.hpp>
#include <basecall.hpp>
#include <tracealign_preprocess.hpp>
//-------
// Flush
//-------
void TraceAlignPreprocessor::Flush()
{
m_oEnvelope.Empty();
}
//------------------
// Preprocess Trace
//------------------
void TraceAlignPreprocessor::PreprocessTrace( Trace& t, bool bCacheBaseIntervalStatistics )
{
// Sort the basecalls
t.Sort();
// Initialisation
m_nIntervalMin = 0;
m_nIntervalMax = 0;
m_nIntervalMode = 0;
m_nIntervalMean = 0.0;
m_nIntervalStdDev = 0.0;
// Compute base interval statistics
if( bCacheBaseIntervalStatistics )
{
m_nIntervalMin = t.IntervalMin();
m_nIntervalMax = t.IntervalMax();
m_nIntervalMode = t.IntervalMode();
m_nIntervalMean = t.IntervalMean();
m_nIntervalStdDev = t.IntervalStdDev();
}
// Create a trace envelope in the A channel
Trace& Envelope = *t.CreateEnvelope();
if( !(&Envelope) )
throw std::bad_alloc();
// Make copy of envelope
m_oEnvelope.Empty();
m_oEnvelope.Create( t.Samples() );
for( int n=0; n<t.Samples(); n++ )
m_oEnvelope[n] = Envelope[0][n];
// Cleanup
delete &Envelope;
}
void TraceAlignQuantiseEnvelope( NumericArray<int>& e, SimpleArray<char>& qe, int nLevels, int nLower, int nUpper )
{
/*
Quantises the envelope 'e' into 'nLevels' between 'nLower' and 'nUpper'.
*/
assert(nLevels>0);
assert(nLower<nUpper);
// Allocate storage for output
qe.Empty();
qe.Create( e.Range() );
// Determine quanta, round up
int nQuanta = nUpper / nLevels + 1;
// Do quantisation
int n, k;
for( k=0, n=e.RangeLowerLimit(); n<=e.RangeUpperLimit(); k++, n++ )
qe[k] = char( (e[n] / nQuanta) + nLower );
}
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