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gnSourceHeader.h

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/////////////////////////////////////////////////////////////////////////////
// File:            gnSourceHeader.h
// Purpose:         Source Header class
// Description:     Provides an interface for Headers on disk.
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnSourceHeader_h_
#define _gnSourceHeader_h_

#include "gn/gnDefs.h"

#include <string>
#include "gn/gnBaseHeader.h"
#include "gn/gnBaseSource.h"

#include <utility>

/**
 * gnSourceHeader is used to store a sequence header which resides in another source.
 * gnSourceHeaders are created by gnSEQSource and other sources and placed into a spec.
 */
class GNDLLEXPORT gnSourceHeader : public gnBaseHeader
{
public:
        /**
         * Empty constructor.
         */
        gnSourceHeader();
        /**
         * Constructor, records the header's name and byte offset in the source.
         * @param source The source which contains the header.
         * @param name The name of the header.
         * @param begin The offset into the source where the header starts.
         * @param length The length of the header.
         */
        gnSourceHeader( gnBaseSource* source, const string& name, const uint32 begin, const uint32 length );
        /**
         * Copy constructor.
         * @param s The gnSourceHeader to copy.
         */
        gnSourceHeader( const gnSourceHeader& s );
        /**
         * Destructor, frees memory.
         */
        ~gnSourceHeader();

        gnSourceHeader* Clone() const;

        string GetHeader() const;
        string GetHeaderName() const;
        /// Not implemented, use gnStringHeader. 
//      void SetHeader(const string& header){};
        /// Not implemented, use gnStringHeader. 
//      void SetHeaderName(const string& name){};
        
        uint32 GetLength() const;
        /**
         * Get the header's start position within the source.
         * @return The byte offset of the header's start position.
         */
        uint32 GetHeaderStart() const;
        /**
         * Get the header's start position and length within the source.
         * @return The header start position and length as a pair.
         */
        pair<uint32, uint32> GetHeaderLoc() const;

        /**
         * Set the header's start position within the source.
         * @param start The header start position.
         */
        void SetHeaderStart(const uint32 start);
        /**
         * Get the header's length within the source.
         * @param length The header length.
         */
        void SetHeaderLength(const uint32 length);
        /**
         * Set the header's start position and length within the source.
         * @param startLen The header start position and length as a pair.
         */
        void SetHeaderLoc(const pair<uint32, uint32> startLen);

private:
        string m_name;
        uint32 m_start, m_length;
        gnBaseSource *m_source;
}; //class gnSourceHeader

inline 
gnSourceHeader* gnSourceHeader::Clone() const{
        return new gnSourceHeader(*this);
}
inline
string gnSourceHeader::GetHeaderName() const{
        return m_name;
}
inline
uint32 gnSourceHeader::GetHeaderStart() const{
        return m_start;
}
inline
uint32 gnSourceHeader::GetLength() const{
        return m_length;
}
inline
pair<uint32, uint32> gnSourceHeader::GetHeaderLoc() const{
        pair<uint32, uint32> p;
        p.first = m_start;
        p.second = m_length;
        return p;
}
inline
void gnSourceHeader::SetHeaderStart(const uint32 start){
        m_start = start;
}
inline
void gnSourceHeader::SetHeaderLength(const uint32 length){
        m_length = length;
}
inline
void gnSourceHeader::SetHeaderLoc(const pair<uint32, uint32> startLen){
        m_start = startLen.first;
        m_length = startLen.second;
}


#endif
        // _gnSourceHeader_h_

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