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gnBaseFeature.h

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// File:            gnBaseFeature.h
// Purpose:         abstract Feature class
// Description:     Provides an interface for Features in memory and on disk.
// 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 _gnBaseFeature_h_
#define _gnBaseFeature_h_

#include "gn/gnDefs.h"
#include <string>
#include <vector>
#include "gn/gnClone.h"
#include "gn/gnLocation.h"
#include "gn/gnBaseQualifier.h"

class gnFragmentSpec;

class GNDLLEXPORT gnBaseFeature : public gnClone
{
public:
        gnBaseFeature();
        gnBaseFeature( string& name, uint32 id = 0, gnFragmentSpec* spec = NULL, gnLocation::gnLocationType lt = gnLocation::LT_Nothing, boolean broken = false );
        ~gnBaseFeature();

        virtual gnBaseFeature* Clone() const = 0;
        virtual string GetName() const;
        virtual void SetName( const string& name );
        virtual uint32 GetID() const;
        virtual void SetID(uint32 id);
        virtual gnFragmentSpec* GetSpec() const;
        virtual void SetSpec(gnFragmentSpec* spec);
        virtual gnLocation::gnLocationType GetLocationType() const;
        virtual void SetLocationType( gnLocation::gnLocationType lType );
        virtual uint32 GetLocationListLength() const;
        virtual boolean AddLocation( const gnLocation& l, uint32 listI = 0);
        virtual gnLocation GetLocation( uint32 listI ) const;
        virtual boolean RemoveLocation( uint32 listI );
        virtual boolean SetLocation( const gnLocation& l, uint32 listI );
        virtual boolean MovePositive( const gnSeqI i );
        virtual boolean MoveNegative( const gnSeqI i );
        virtual boolean CropStart( const gnSeqI i );
        virtual boolean CropEnd( const gnSeqI i );
        virtual boolean Crop( const gnLocation& l );
        virtual boolean IsBroken() const;
        virtual void SetBroken(boolean broke);

        virtual boolean Contains( gnSeqI i ) const;
        virtual boolean Contains( const gnLocation& l ) const;
        virtual boolean Contains( gnBaseFeature* feature ) const;
        virtual boolean IsContainedBy( const gnLocation& l ) const;
        virtual boolean Intersects( const gnLocation& l ) const;
        virtual boolean Intersects( gnBaseFeature* feature ) const;

        virtual uint32 GetQualifierListLength() const;
        virtual boolean AddQualifier( gnBaseQualifier* qualifier );
        virtual boolean HasQualifier( const string& name ) const;
        virtual uint32 FirstIndexOfQualifier( const string& name, uint32 listI ) const;
        virtual uint32 LastIndexOfQualifier( const string& name, uint32 listI ) const;
        virtual string GetQualifierName( uint32 listI ) const;
        virtual string GetQualifierValue( uint32 listI ) const;
        virtual gnBaseQualifier* GetQualifier( uint32 listI );
        virtual boolean RemoveQualifier( uint32 listI );
        virtual boolean SetQualifier( string& name, string& value, uint32 listI );
        virtual boolean SetQualifierName( string& name, uint32 listI );
        virtual boolean SetQualifierValue( string& value, uint32 listI );
protected:
        uint32 m_id;
        string m_name;
        boolean m_broken;
        gnLocation::gnLocationType m_locationType;
        vector< gnLocation > m_locationList;
        vector< gnBaseQualifier* > m_qualifierList;
        gnFragmentSpec* m_spec;
};// class gnBaseFeature

inline
string gnBaseFeature::GetName() const{
        return m_name;
}
inline
void gnBaseFeature::SetName( const string& name ){
        m_name = name;
}
inline
uint32 gnBaseFeature::GetID() const{
        return m_id;
}
inline
void gnBaseFeature::SetID(uint32 id){
        m_id = id;
}
inline
gnFragmentSpec* gnBaseFeature::GetSpec() const{
        return m_spec;
}
inline
void gnBaseFeature::SetSpec(gnFragmentSpec* spec){
        m_spec = spec;
}
inline
boolean gnBaseFeature::IsBroken() const{
        return m_broken;
}
inline
void gnBaseFeature::SetBroken(boolean broke){
        m_broken = broke;
}

inline
gnLocation::gnLocationType gnBaseFeature::GetLocationType() const{
        return m_locationType;
}
inline
void gnBaseFeature::SetLocationType( gnLocation::gnLocationType lType ){
        m_locationType = lType;
}
inline
uint32 gnBaseFeature::GetLocationListLength() const{
        return m_locationList.size();
}
inline
boolean gnBaseFeature::Crop( const gnLocation& l ){
        return CropStart(l.GetStart()) && CropEnd(l.GetEnd());
}
inline
uint32 gnBaseFeature::GetQualifierListLength() const{
        return m_qualifierList.size();
}

#endif
        // _gnBaseFeature_h_

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