---

gnMultiSpec.h

Go to the documentation of this file.

// File:            gnMultiSpec.h
// Purpose:         abstract multiple spec class
// Description:     For specs which can contain multiple data sources
// 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 _gnMultiSpec_h_
#define _gnMultiSpec_h_

#include "gn/gnDefs.h"

#include <vector>
#include <string>

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

class GNDLLEXPORT gnMultiSpec : public gnBaseSpec
{
public:
        gnMultiSpec(){}
        virtual ~gnMultiSpec(){}
        virtual gnMultiSpec* Clone() const = 0;

// Base Spec stuff
        virtual gnSeqI GetLength() const;
        virtual void CropStart( gnSeqI cropLen );
        virtual void CropEnd( gnSeqI cropLen );

        virtual string GetSourceName() const;
        virtual void SetSourceName(const string& sourceName);
        virtual void Clear();

        virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, uint32& bufLen, const uint32 contigI ) const;

//Multispec stuff
        virtual uint32 GetSpecListLength() const = 0;
        virtual gnBaseSpec* GetSpec( const uint32 i ) const = 0;
        virtual gnBaseSpec* GetSpecByBase( const gnSeqI baseI ) const = 0;
        virtual uint32 GetSpecIndexByBase( const gnSeqI baseI ) const;
        virtual uint32 GetSpecIndexByName( const string& name ) const;
        virtual gnSeqI GetSpecStartBase( const uint32 specI ) const;
        virtual gnSeqI GetSpecEndBase( const uint32 specI ) const;
        virtual void AddSpec( gnBaseSpec* spec, const uint32 i = UINT32_MAX ) = 0;
        virtual void RemoveSpec( uint32 i ) = 0;

        virtual uint32 GetHeaderListLength() const;
        virtual void AddHeader( gnBaseHeader *head, const uint32 i = UINT32_MAX);
        virtual gnBaseHeader* GetHeader( const uint32 i ) const;
        virtual gnBaseHeader* GetHeader( const string& name, uint32& i) const;
        virtual void RemoveHeader( uint32 i );

        uint32 AddFeature( gnBaseFeature* feat );
        virtual uint32 GetFeatureListLength() const = 0;
        virtual gnBaseFeature* GetFeature( const uint32 i ) const = 0;
        virtual void GetContainedFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const = 0;
        virtual void GetIntersectingFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const = 0;
        virtual void GetBrokenFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector) const = 0;
        virtual void RemoveFeature( const uint32 i ) = 0;
        
protected:
        string m_sourceName;
        
        vector <gnBaseHeader*> m_headerList;
private:

}; // class gnMultiSpec

inline
uint32 gnMultiSpec::GetHeaderListLength() const
{
        return m_headerList.size();
}
inline
gnBaseHeader* gnMultiSpec::GetHeader(const uint32 i) const
{
        if(i < m_headerList.size()){
                return m_headerList[i];
        }
        return 0;
}

inline
string gnMultiSpec::GetSourceName() const{
        return m_sourceName;
}

inline
void gnMultiSpec::SetSourceName(const string& sourceName){
        m_sourceName = sourceName;
}

#endif
        // _gnMultiSpec_h_

---