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gnBaseFilter.h

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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 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnBaseFilter_h_
#define _gnBaseFilter_h_

#include "gn/gnDefs.h"

#include <string>
#include "gn/gnClone.h"
#include "gn/gnDefs.h"

class GNDLLEXPORT gnBaseFilter : public gnClone
{
public:         
        virtual gnBaseFilter* Clone() const = 0;
        
        /**
         * Gets the name of this filter
         * @return the filter name 
         */
        virtual string GetName() const;
        /**
         * Sets the name of this filter
         * @param name the new filter name
         */
        virtual void SetName( 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, uint32& len ) const = 0;

        /**
         * Filters the given string
         * @param seq The string to filter
         */
        virtual void Filter( string &seq ) const = 0;

protected:
        string m_name;

};//class gnBaseFilter

inline
string gnBaseFilter::GetName() const
{
        return m_name;
}
inline
void gnBaseFilter::SetName( string name )
{
        m_name = name;
}

#endif
        // _gnBaseFilter_h_

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