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/////////////////////////////////////////////////////////////////////////////
// File: gnBaseFilter.h
// Purpose: Generic filter interface
// Description: Filters sequences, translates, reverse complement, converts
// additions, etc.
// Changes:
// Version: libGenome 0.5.1
// Author: Aaron Darling
// Modified by:
// Copyright: (c) Aaron Darling
// Licenses: See COPYING file for details
/////////////////////////////////////////////////////////////////////////////
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#ifndef _gnBaseFilter_h_
#define _gnBaseFilter_h_
#include "libGenome/gnDefs.h"
#include <string>
#include "libGenome/gnClone.h"
#include "libGenome/gnDefs.h"
namespace genome {
class GNDLLEXPORT gnBaseFilter : public gnClone
{
public:
virtual gnBaseFilter* Clone() const = 0;
/**
* Gets the name of this filter
* @return the filter name
*/
virtual std::string GetName() const;
/**
* Sets the name of this filter
* @param name the new filter name
*/
virtual void SetName( std::string name );
/**
* Filter the given character
* @param ch The character to filter
* @return The filtered character
*/
virtual gnSeqC Filter( const gnSeqC ch ) const = 0;
/**
* Filter the given character array
* @param seq A pointer to the character array
* @param len the length of the character array to filter
* @return The filtered character
*/
virtual void Filter( gnSeqC** seq, gnSeqI& len ) const = 0;
/**
* Filters the given std::string
* @param seq The std::string to filter
*/
virtual void Filter( std::string &seq ) const = 0;
protected:
std::string m_name;
};//class gnBaseFilter
inline
std::string gnBaseFilter::GetName() const
{
return m_name;
}
inline
void gnBaseFilter::SetName( std::string name )
{
m_name = name;
}
} // end namespace genome
#endif
// _gnBaseFilter_h_
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