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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 0.1.0 
// Author:          Aaron Darling 
// Last Edited:     April 15, 2001, 10:34:50pm 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        Proprietary 
#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"

class GNDLLEXPORT gnGenomeSpec : public gnMultiSpec
{
public:
        gnGenomeSpec();
        gnGenomeSpec( const gnGenomeSpec& s);
        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 );
        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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