---

gnRAWSource.h

Go to the documentation of this file.

/////////////////////////////////////////////////////////////////////////////
// File:            gnRAWSource.h
// Purpose:         Implements gnBaseSource for raw data files
// Description:     
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details 
/////////////////////////////////////////////////////////////////////////////

#ifndef _gnRAWSource_h_
#define _gnRAWSource_h_

#include "gn/gnDefs.h"

#include <string>
#include <fstream>
#include <vector>
#include "gn/gnFileSource.h"
#include "gn/gnFileContig.h"
#include "gn/gnSourceSpec.h"
#include "gn/gnSequence.h"

/**
 * gnRAWSource reads raw sequence data from a text file.
 * This class reads and writes raw sequence to and from files.
 * A raw sequence does not contain any newlines, fragment delimiters, or other
 * type of annotation.
 * gnRAWSource is used by gnSourceFactory to read files and should only be used 
 * directly.when writing out raw files by calling gnRAWSource::Write( mySpec, "C:\\myFile.txt");
 */

class GNDLLEXPORT gnRAWSource : public gnFileSource
{
public:
        /**
         * Empty Constructor, does nothing.
         */
        gnRAWSource();  
        /**
         * Clone Constructor copies the specified gnRAWSource.
         * @param s The gnRAWSource to copy.
         */
        gnRAWSource( const gnRAWSource& s );
        /**
         * Destructor, frees memory.
         */
        ~gnRAWSource();
        /**
         * Returns an exact copy of this class.
         */
        gnRAWSource* Clone() const;
// Contig Access methods        
        uint32 GetContigListLength() const;
        boolean HasContig( const string& name ) const;
        uint32 GetContigID( const string& name ) const;
        string GetContigName( const uint32 i ) const;
        gnSeqI GetContigSeqLength( const uint32 i ) const;

        boolean SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS );

        /**
         * Writes the specified gnSequence to a raw file named "filename".
         * @param sequence The gnSequence to write out.
         * @param filename The name of the file to write.
         * @return True if successful, false otherwise.
         */
        static boolean Write(gnSequence& sequence, const string& filename);
        /**
         * Writes the specified source to a raw file named "filename".
         * @param source The source to write out.
         * @param filename The name of the file to write.
         * @return True if successful, false otherwise.
         */
        static boolean Write(gnBaseSource *source, const string& filename);
        gnGenomeSpec *GetSpec() const;
        gnFileContig* GetFileContig( const uint32 contigI ) const;

        static boolean CheckRawData( boolean set = false, boolean check = false );
private:
        boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes );
        boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
        boolean ParseStream( istream& fin );
        
        gnFileContig* m_contig; 
        gnGenomeSpec* m_spec;
};// class gnRAWSource
// Clone        
inline
gnRAWSource* gnRAWSource::Clone() const
{
        return new gnRAWSource( *this );
}
// Contig Access methods        
inline
uint32 gnRAWSource::GetContigListLength() const
{
        return m_contig == NULL? 0 : 1;
}
inline
boolean gnRAWSource::Write(gnBaseSource *source, const string& filename){
        gnSequence gns(*source->GetSpec());
        return Write(gns, filename);
}

inline
boolean gnRAWSource::CheckRawData( boolean set, boolean check ){
        static boolean check_raw_data = false;
        if( set ){
                check_raw_data = check;
        }
        return check_raw_data;
}
#endif
        // _gnRAWSource_h_

---