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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 <tracealign_cache.hpp>
//-------
// Flush
//-------
void TraceAlignCache::Flush()
{
RefData[0].Flush();
RefData[1].Flush();
AlignmentMatrix.Empty();
}
//-------------------------
// Create Alignment Matrix
//-------------------------
void TraceAlignCache::CreateAlignmentMatrix( int nMatrixSize, int nLevels, int nOffset )
{
int r, c;
assert(nLevels>0);
assert(nOffset>=0);
// Create matrix
if( AlignmentMatrix.Raw() )
AlignmentMatrix.Empty();
AlignmentMatrix.Create( nMatrixSize, nMatrixSize );
// Fill the score matrix in toeplitz form according to number of
// characters and offset. For example, a 4-level matrix would look
// like this (the zero character is not used because it looks like
// a null terminator to the alignment routines):
//
// 0 0 0 0 0
// 0 4 3 2 1
// 0 3 4 3 2
// 0 2 3 4 3
// 0 1 2 3 4
//
// Anything along the diagonal, indicating a perfect match, gets the
// highest score. The score falls off linearly as the amplitude
// difference increases.
for( r=nOffset; r<nMatrixSize-1; r++ )
{
for( c=nOffset; c<nMatrixSize-1; c++ )
{
if( (r-c) <= 0 )
{
AlignmentMatrix[r][c] = (r-c) + nLevels;
}
else
{
AlignmentMatrix[r][c] = (c-r) + nLevels;
}
}
}
}
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