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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 <cassert>
#include <dnatable.hpp>
const char DNATable::m_IndexTable[4][4] = {
{ 'A', 'M', 'R', 'W'},
{ 'M', 'C', 'S', 'Y'},
{ 'R', 'S', 'G', 'K'},
{ 'W', 'Y', 'K', 'T'}};
int DNATable::LookupIndex( char c ) const
{
// Convert characters to indices
int index;
switch( c )
{
case 'A':
case 'a': index = 0; break;
case 'C':
case 'c': index = 1; break;
case 'G':
case 'g': index = 2; break;
case 'T':
case 't': index = 3; break;
case 'K':
case 'k': index = 4; break;
case 'M':
case 'm': index = 5; break;
case 'R':
case 'r': index = 6; break;
case 'S':
case 's': index = 7; break;
case 'W':
case 'w': index = 8; break;
case 'Y':
case 'y': index = 9; break;
default: index =-1; break;
}
return index;
}
char DNATable::LookupBase( int index ) const
{
if( (index<0) || (index>3) )
return '-';
return m_IndexTable[index][index];
}
char DNATable::LookupBase( int index1, int index2 ) const
{
if( (index1<0) || (index1>3) )
return '-';
if( (index2<0) || (index2>3) )
return '-';
return m_IndexTable[index1][index2];
}
char DNATable::LookupBase( char char1, char char2 ) const
{
// Convert characters to indices
int index[2] = { char1, char2 };
for( int n=0; n<2; n++ )
{
switch( index[n] )
{
case 'A':
case 'a': index[n] = 0; break;
case 'C':
case 'c': index[n] = 1; break;
case 'G':
case 'g': index[n] = 2; break;
case 'T':
case 't': index[n] = 3; break;
default: index[n] =-1;
}
}
return LookupBase( index[0], index[1] );
}
bool DNATable::IsBaseAmbiguous( char c ) const
{
switch( c )
{
case 'K':
case 'k':
case 'M':
case 'm':
case 'R':
case 'r':
case 'S':
case 's':
case 'W':
case 'w':
case 'Y':
case 'y':
return true;
}
return false;
}
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