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gnFileContig.h

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/////////////////////////////////////////////////////////////////////////////
// File:            gnFileContig.h
// Purpose:         File Position holder.
// Description:     
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnFileContig_h_
#define _gnFileContig_h_

#include "gn/gnDefs.h"

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

/**
 * gnFileContig is used by source classes to track the location of
 * sequence data on disk.  gnFileContig stores the start and end byte
 * offset, and the size of a repeated gap in the sequence data.
 * Also stores whether the sequence data is in the expected format or
 * if it is corrupted.
 */
class GNDLLEXPORT gnFileContig : public gnClone
{
public:
        gnFileContig();
        gnFileContig( string nameStr, const uint64 pos, const uint64 len );
        gnFileContig( const gnFileContig& fc );
        ~gnFileContig();

        gnFileContig* Clone() const;
        void Clear();

        string GetName() const;
        gnSeqI GetSeqLength() const;
        pair<uint64,uint64> GetFileStartEnd() const;
        uint64 GetFileLength() const;
        pair<uint64,uint64> GetSectStartEnd( const gnContigSection i ) const;
        uint64 GetSectLength( gnContigSection i ) const;
        boolean HasRepeatSeqGap() const;
        pair<uint32,uint32> GetRepeatSeqGapSize() const;

        boolean SetName( string nameStr );
        boolean SetSeqLength( const gnSeqI len );
        boolean AddToSeqLength( const gnSeqI len );
        boolean SetFileStart( const uint64 s );
        boolean SetFileEnd( const uint64 e );
        boolean SetFileStartEnd( const pair<uint64,uint64> se );
        boolean SetSectStart( const gnContigSection i, const uint64 s );
        boolean SetSectEnd( const gnContigSection i, const uint64 e );
        boolean SetSectStartEnd( const gnContigSection i, const pair<uint64,uint64> se);
        boolean SetRepeatSeqGap( const boolean rsg );
        boolean SetRepeatSeqGapSize( const pair<uint64,uint64> rsgSize );
        boolean SetRepeatSeqSize( const uint64 seqSize );
        boolean SetRepeatGapSize( const uint64 gapSize );
private:
        string m_name;
        gnSeqI m_seqLength;
        pair<uint64,uint64> m_fileStartEnd;
        
        pair<uint64,uint64> m_startEndArray[CONTIG_SECTION_SIZE];
        // sequence access
        boolean m_repeatSeqGap;  // if true, use m_repeatSeqGapSize
        pair< uint64, uint64 > m_repeatSeqGapSize;
};// class gnFileContig

  // Clone
inline
gnFileContig* gnFileContig::Clone() const
{
        return new gnFileContig( *this );
}
  // GET
inline
string gnFileContig::GetName() const
{
        return m_name;
}
inline
gnSeqI gnFileContig::GetSeqLength() const
{
        return m_seqLength;
}
inline
pair<uint64,uint64> gnFileContig::GetFileStartEnd() const
{
        return m_fileStartEnd;
}
inline
uint64 gnFileContig::GetFileLength() const
{
        return m_fileStartEnd.second - m_fileStartEnd.first + 1;
}
inline
pair<uint64,uint64> gnFileContig::GetSectStartEnd( const gnContigSection i ) const
{
        if( (uint32)i < CONTIG_SECTION_SIZE )
                return m_startEndArray[(uint32)i];
        return pair<uint64,uint64>(0,0);
}
inline
uint64 gnFileContig::GetSectLength( gnContigSection i ) const
{
        if( (uint32)i < CONTIG_SECTION_SIZE )
                return m_startEndArray[(uint32)i].second - m_startEndArray[(uint32)i].first + 1;
        return 0;
}
inline
boolean gnFileContig::HasRepeatSeqGap() const
{
        return m_repeatSeqGap;
}
inline
pair<uint32,uint32> gnFileContig::GetRepeatSeqGapSize() const
{
        return m_repeatSeqGapSize;
}
  // SET
inline
boolean gnFileContig::SetName( string nameStr )
{
        m_name = nameStr;
        return true;
}
inline
boolean gnFileContig::SetSeqLength( const gnSeqI len )
{
        m_seqLength = len;
        return true;
}
inline
boolean gnFileContig::AddToSeqLength( const gnSeqI len )
{
        m_seqLength += len;
        return true;
}
inline
boolean gnFileContig::SetFileStart( const uint64 s )
{
        m_fileStartEnd.first = s;
        return true;
}
inline
boolean gnFileContig::SetFileEnd( const uint64 e )
{
        m_fileStartEnd.second = e;
        return true;
}
inline
boolean gnFileContig::SetFileStartEnd( const pair<uint64,uint64> se )
{
        m_fileStartEnd = se;
        return true;    
}
inline
boolean gnFileContig::SetSectStart( const gnContigSection i, const uint64 s )
{
        if( (uint32)i < CONTIG_SECTION_SIZE )
        {
                m_startEndArray[(uint32)i].first = s;
                return true;
        }
        return false;
}
inline
boolean gnFileContig::SetSectEnd( const gnContigSection i, const uint64 e )
{
        if( (uint32)i < CONTIG_SECTION_SIZE )
        {
                m_startEndArray[(uint32)i].second = e;
                return true;
        }
        return false;
}
inline
boolean gnFileContig::SetSectStartEnd( const gnContigSection i, const pair<uint64,uint64> se )
{
        if( (uint32)i < CONTIG_SECTION_SIZE )
        {
                m_startEndArray[(uint32)i] = se;
                return true;
        }
        return false;
}
inline
boolean gnFileContig::SetRepeatSeqGap( const boolean rsg )
{
        m_repeatSeqGap = rsg;
        return true;
}
inline
boolean gnFileContig::SetRepeatSeqGapSize( const pair<uint64,uint64> rsgSize )
{
        return  SetRepeatSeqSize( rsgSize.first ) && 
                SetRepeatGapSize( rsgSize.second );
}


#endif
        // _gnFileContig_h_

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