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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.
*
*/
#include <caller.hpp>
int Caller::LoadPeaks( SimpleMatrix<int>& Peak, int nPos, int nAmbiguityWindow, call_t data[4] )
{
assert(data != NULL);
assert(nPos>=0);
assert(nAmbiguityWindow>0);
int peaks = 0;
// Load in default data
for( int n=0; n<4; n++ )
{
data[n].Index = n;
data[n].Position = -1;
data[n].Amplitude = Peak[n][nPos];
}
// For each base that has no peak at nPos, search within ambiguity window
// for another very close peak. Work outwards from middle position.
const int rows = 4;
const int cols = Peak.Cols();
for( int r=0; r<rows; r++ )
{
// If base has a peak at nPos, record the position
if( data[r].Amplitude )
{
data[r].Position = nPos;
peaks++;
continue;
}
// No peak, search for one nearby, within window
int j = nPos;
int off = 1;
int win = nAmbiguityWindow;
while( (win>0) && ((j-off)>=0) && ((j+off)<cols) )
{
if( Peak[r][j-off] > 0 )
{
data[r].Position = j-off;
data[r].Amplitude = Peak[r][j-off];
peaks++;
break;
}
if( Peak[r][j+off] > 0 )
{
data[r].Position = j+off;
data[r].Amplitude = Peak[r][j+off];
peaks++;
break;
}
off++;
win--;
}
}
return peaks;
}
void Caller::SortAscending( call_t data[4] )
{
// Sort into amplitude order, lowest to highest
if( data[0].Amplitude > data[1].Amplitude ) // 1st pair
Swap( data[0], data[1] );
if( data[2].Amplitude > data[3].Amplitude ) // 2nd pair
Swap( data[2], data[3] );
if( data[0].Amplitude > data[2].Amplitude ) // Tops
Swap( data[0], data[2] );
if( data[1].Amplitude > data[3].Amplitude ) // Bottoms
Swap( data[1], data[3] );
if( data[1].Amplitude > data[2].Amplitude ) // Middle
Swap( data[1], data[2] );
}
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