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gnDNXSource.h

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/////////////////////////////////////////////////////////////////////////////
// File:            gnDNXSource.h
// Purpose:         Implements gnBaseSource for .DNX files
// Description:     
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnDNXSource_h_
#define _gnDNXSource_h_

#include "gn/gnDefs.h"


#include <string>
#include <vector>
#include <fstream>
#include <time.h>

#include "gn/gnSetup.h"
#include "gn/gnFileSource.h"
#include "gn/gnSourceSpec.h"
#include "gn/gnSequence.h"

/**
 * gnDNXSource implements the DNX file source.
 * This class reads and writes the Blattner Lab DNX file format.
 * DNX files may be written by calling:
 * gnDNXSource::Write( mySpec, "C:\\myFile.dnx");
 */

class GNDLLEXPORT gnDNXSource : public gnFileSource
{
public:
        /**
         * Empty Constructor, does nothing.
         */
        gnDNXSource();  
        /**
         * The copy constructor copies the given gnDNXSource.
         * @param s A gnDNXSource to copy.
         */
        gnDNXSource( const gnDNXSource& s );
        /**
         * Destructor, frees memory.
         */
        ~gnDNXSource();

        gnDNXSource* Clone() const;

        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, uint32& bufLen, const uint32 contigI=ALL_CONTIGS ) ;

        /**
         * Writes the given gnSequence to a DNX file named "filename".
         * Actual sequence and annotation data will be written to GenBank
         * files.  The DNX file will then reference any created GenBank files.
         * @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);
        /**
         * This method is deprecated.
         * Writes the given gnBaseSource to a DNX file named "filename".
         * Actual sequence and annotation data will be written to GenBank
         * files.  The DNX file will then reference any created GenBank files.
         * @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);
        /**
         * Writes the given gnGenomeSpec to a DNX file named "filename".
         * Actual sequence and annotation data will be written to GenBank
         * files.  The DNX file will then reference any created GenBank files.
         * @param spec The spec to write out.
         * @param filename The name of the file to write.
         * @return True if successful, false otherwise.
         */
        static boolean Write(gnGenomeSpec *spec, const string& filename);

        gnGenomeSpec* GetSpec() const;
        gnFileContig* GetFileContig( const uint32 contigI ) const;
private:
        boolean ParseStream( istream& fin );
        static void ValidateName(string& name);

        gnGenomeSpec *m_DNXSpec;
};// class gnDNXSource

inline
gnDNXSource* gnDNXSource::Clone() const
{
        return new gnDNXSource( *this );
}

inline
uint32 gnDNXSource::GetContigListLength() const
{
        return m_DNXSpec->GetSpecListLength();
}
//read sequence data from the file
inline
boolean gnDNXSource::SeqRead( const gnSeqI start, char* buf, uint32& bufLen, const uint32 contigI ) 
{
        return m_DNXSpec->SeqRead(start, buf, bufLen, contigI);
}

inline
boolean gnDNXSource::Write(gnSequence& sequence, const string& filename){
        return Write(sequence.GetSpec(), filename);
}
inline
boolean gnDNXSource::Write(gnBaseSource *source, const string& filename){
        return Write(source->GetSpec(), filename);
}
inline
gnGenomeSpec *gnDNXSource::GetSpec() const{
        return m_DNXSpec->Clone();
}

#endif
        // _gnDNXSource_h_

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