---

gnBaseSpec.h

Go to the documentation of this file.

/////////////////////////////////////////////////////////////////////////////
// File:            gnBaseSpec.h
// Purpose:         abstract Spec class
// Description:     Defines a basic interface for all specs
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnBaseSpec_h_
#define _gnBaseSpec_h_

#include "gn/gnDefs.h"

#include <vector>
#include <string>

#include "gn/gnClone.h"
#include "gn/gnBaseFeature.h"
#include "gn/gnBaseHeader.h"

/**
 * gnBaseSpec is the class which stores genetic information and is best accessed using gnSequence.
 */
class GNDLLEXPORT gnBaseSpec : public gnClone
{
public:
        gnBaseSpec(){}
        /**
         * Destructor, frees memory.
         */
        virtual ~gnBaseSpec(){}
        virtual gnBaseSpec* Clone() const = 0;
        virtual gnBaseSpec* CloneRange( const uint32 startI, const uint32 len ) const = 0;
        /**
         * Get the name of the contig associated with this spec.
         * @return The contig name or an empty string if none exists.
         */
        virtual string GetName() const;
        /**
         * Sets the name for this contig
         * @param name The new name.
         * @return True if successful.  Honestly, I don't know how this could be unsuccessful...
         */
        virtual void SetName( const string& name );
        /**
         * Get the length of all the sequence data covered by this spec.
         * @return This spec's length in base pairs.
         */
        virtual gnSeqI GetLength() const = 0;
        /**
         * Returns true if this spec is read reverse complement.
         * @return True if this spec is read reverse complement.
         */
        virtual boolean IsReverseComplement() const;
        /**
         * Returns true if this spec's sequence is circular.
         * @return True if this spec's sequence is circular.
         */
        virtual boolean IsCircular() const;
        /**
         * Sets the reverse complement bit for this spec.
         * @param value True for reverse complement, false otherwise.
         */
        virtual void SetReverseComplement( const boolean value ) = 0;
        /**
         * Sets whether this spec should be read circular.
         * If circular is set, reads beyond the end of this spec will pick up
         * at the beginning and read up to the start index.
         * @param value True for circular, false otherwise.
         */
        virtual void SetCircular( const boolean value );
        /**
         * Crop the first cropLen bases from the sequence. CropStart will
         * delete features and headers associated with the cropped bases.
         * @param cropLen The number of base pairs to delete from the beginning.
         */
        virtual void CropStart( gnSeqI cropLen ) = 0;
        /**
         * Crop the last cropLen bases from the sequence. CropEnd will
         * delete features and headers associated with the cropped bases.
         * @param cropLen The number of base pairs to delete from the end.
         */
        virtual void CropEnd( gnSeqI cropLen ) = 0;

        /**
         * Reads sequence data from this spec.
         * SeqRead will attempt to read "bufLen" base pairs starting at "start", an offset into the sequence.
         * Reading inside a specific contig can be accomplished by supplying the "contigI" parameter with
         * a valid contig index.
         * SeqRead stores the sequence data in "buf" and returns the actual number of bases read in "bufLen".
         * SeqRead will return false if a serious error occurs.
         * @param start The base pair to start reading at.
         * @param buf The character array to store base pairs into.
         * @param bufLen The number of base pairs to read.  This will be modified to reflect the actual number of bases read.
         * @param contigI The index of the subspec to read or ALL_CONTIGS by default.
         * @return True if the operation was successful.
         */
        virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, uint32& bufLen, const uint32 contigI ) const = 0;
        /**
         * Clears all data from this spec.
         */
        virtual void Clear();
protected:
        boolean m_reverseComplement;
        boolean m_circular;
        
        string m_name;
        string m_sourceName;
        
}; // class gnBaseSpec

inline
string gnBaseSpec::GetName() const{
        return m_name;
}
inline
void gnBaseSpec::SetName( const string& name ){
        m_name = name;
}
inline
boolean gnBaseSpec::IsReverseComplement() const{
        return m_reverseComplement;
}
inline
boolean gnBaseSpec::IsCircular() const{
        return m_circular;
}
inline
void gnBaseSpec::SetCircular( const boolean value ){
        m_circular = value;
}
inline
void gnBaseSpec::Clear(){
        m_sourceName = "";
        m_name = "";
        m_reverseComplement = false;
        m_circular = false;
}

#endif
        // _gnBaseSpec_h_

---