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/*
* Copyright (c) Medical Research Council 2000. 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 <cstring> // For strcpy(), strlen(), ...
#include <cstdio> // For sprintf()
#include <mutationtag.hpp>
//-------------
// Constructor
//-------------
MutationTag::MutationTag( const char* name )
{
assert(name != NULL);
assert(std::strlen(name)<5);
m_cBaseRef = '-';
m_cBaseInp[0] = '-';
m_cBaseInp[1] = '-';
m_cBaseInp[2] = '-';
m_nStrand = MUTLIB_STRAND_FORWARD;
m_nSNR = 0.0;
m_nPosition[0] = 0;
m_nPosition[1] = 0;
m_nPosition[2] = 0;
m_nPosition[3] = 0;
m_nAmplitude[0] = 0.0;
m_nAmplitude[1] = 0.0;
m_nAmplitude[2] = 0.0;
m_pComment[0] = 0;
m_bMarked = false;
m_nRow = 0;
m_nCol = 0;
Name( name );
}
//-------
// Clone
//-------
void MutationTag::Clone( const MutationTag& rhs )
{
// Ensures proper copy of list item pointers and contained strings
Copy( rhs );
m_cBaseRef = rhs.m_cBaseRef;
m_cBaseInp[0] = rhs.m_cBaseInp[0];
m_cBaseInp[1] = rhs.m_cBaseInp[1];
m_cBaseInp[2] = rhs.m_cBaseInp[2];
m_nStrand = rhs.m_nStrand;
m_nSNR = rhs.m_nSNR;
m_nPosition[0] = rhs.m_nPosition[0];
m_nPosition[1] = rhs.m_nPosition[1];
m_nPosition[2] = rhs.m_nPosition[2];
m_nPosition[3] = rhs.m_nPosition[3];
m_nAmplitude[0] = rhs.m_nAmplitude[0];
m_nAmplitude[1] = rhs.m_nAmplitude[1];
m_nAmplitude[2] = rhs.m_nAmplitude[2];
m_bMarked = rhs.m_bMarked;
m_nRow = rhs.m_nRow;
m_nCol = rhs.m_nCol;
std::strcpy( m_pName, rhs.m_pName );
std::strcpy( m_pComment, rhs.m_pComment );
}
//---------
// Comment
//---------
const char* MutationTag::Comment()
{
if( std::strcmp(m_pName,"HETE") == 0 )
{
std::sprintf( m_pComment, "%c->%c, SNR=%0.2fdB, PKD=%0.2f",
m_cBaseRef, m_cBaseInp[0], m_nSNR, m_nAmplitude[2] );
}
if( std::strcmp(m_pName,"MUTA") == 0 )
{
std::sprintf( m_pComment, "%c->%c, SNR=%0.2fdB",
m_cBaseRef, m_cBaseInp[0], m_nSNR );
}
// Check for overflow!
assert(std::strlen(m_pComment)<MAX_STRING);
return m_pComment;
}
//------
// Name
//------
void MutationTag::Name( const char* newname )
{
assert(newname != NULL);
assert(std::strlen(newname)==4);
std::strcpy( m_pName, newname );
}
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