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gnGenomeSpec.h

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/////////////////////////////////////////////////////////////////////////////
// File:            gnGenomeSpec.h
// Purpose:         abstract Spec class
// Description:     Genome level spec class
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnGenomeSpec_h_
#define _gnGenomeSpec_h_

#include "gn/gnDefs.h"

#include <vector>
#include <string>

#include "gn/gnClone.h"
#include "gn/gnBaseFeature.h"
#include "gn/gnBaseHeader.h"
#include "gn/gnMultiSpec.h"
#include "gn/gnFragmentSpec.h"
#include "gn/gnException.h"

/**
 * This class contains references to the sequence data, annotation,
 * and other related header data for an organism's genome.  The genome
 * is organized into a list of sequence fragments (specs), a list of
 * features, and a list of headers.
 */
class GNDLLEXPORT gnGenomeSpec : public gnMultiSpec
{
public:
        gnGenomeSpec();
        /**
         * Copy constructor.
         * @param s the gnGenomeSpec to copy.
         */
        gnGenomeSpec( const gnGenomeSpec& s);
        /**
         * Destructor, frees memory.
         */
        virtual ~gnGenomeSpec();
// Clone
        virtual gnGenomeSpec* Clone() const;
        virtual void Clear();
// Base Spec stuff
        virtual void SetReverseComplement( const boolean value );

//Multispec stuff
        virtual uint32 GetSpecListLength() const;
        virtual gnFragmentSpec* GetSpec( const uint32 i ) const;
        virtual gnFragmentSpec* GetSpecByBase( const gnSeqI baseI ) const;
        virtual void AddSpec( gnBaseSpec* spec, const uint32 i = UINT32_MAX );
        virtual void RemoveSpec( uint32 i );
        virtual void MergeFragments( const uint32 startC, const uint32 endC);

        virtual uint32 AddFeature( gnBaseFeature* feat );
        virtual uint32 GetFeatureListLength() const;
        virtual gnBaseFeature* GetFeature( const uint32 i ) const;
        virtual void GetContainedFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const;
        virtual void GetIntersectingFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const;
        virtual void GetBrokenFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector) const;
        virtual void RemoveFeature( const uint32 i );
        /**
         * Copies a specified range of bases and returns a pointer to
         * the resulting gnGenomeSpec.  You must delete the copy when you
         * are finished with it.
         * @param startI The first base pair to copy
         * @param len The length of the piece to copy
         * @return A copy of the gnGenomeSpec containing only the specified bases
         */
        virtual gnGenomeSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const;

protected:
        vector <gnFragmentSpec*> m_SpecList;
        
}; // class gnGenomeSpec

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

inline
uint32 gnGenomeSpec::GetSpecListLength() const{
        return m_SpecList.size();
}

inline
gnFragmentSpec* gnGenomeSpec::GetSpec( const uint32 i ) const{
        if(i < m_SpecList.size())
                return m_SpecList[i];
        Throw_gnEx(FragmentIndexOutOfBounds());
}

inline
gnFragmentSpec* gnGenomeSpec::GetSpecByBase( const gnSeqI baseI ) const{
        return m_SpecList[GetSpecIndexByBase(baseI)];
}

inline
void gnGenomeSpec::AddSpec( gnBaseSpec* spec, const uint32 i ){
        uint32 index = i == UINT32_MAX ? m_SpecList.size() : i;
        if(index <= m_SpecList.size()){
                m_SpecList.insert(m_SpecList.begin() + index, (gnFragmentSpec*)spec);
        }
}

inline
void gnGenomeSpec::RemoveSpec( uint32 i ){
        if(i < GetSpecListLength()){
                m_SpecList.erase(m_SpecList.begin() + i);
        }
}

#endif
        // _gnGenomeSpec_h_

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