---

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 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details 
/////////////////////////////////////////////////////////////////////////////
#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"

/**
 * This class defines an interface for specs which have multiple subspecs
 * containing sequence data.
 */
class GNDLLEXPORT gnMultiSpec : public gnBaseSpec
{
public:
        gnMultiSpec(){}
        /**
         * Destructor, frees memory.
         */
        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
        /**
         * Returns the number of subspecs this spec contains.
         * @return The number of subspecs this spec contains.
         */
        virtual uint32 GetSpecListLength() const = 0;
        /**
         * Get the spec at index i in the list of subspecs.
         * @param i The index of the spec
         * @return The spec.
         */
        virtual gnBaseSpec* GetSpec( const uint32 i ) const = 0;
        /**
         * Get the spec from the list of subspecs which contains the specified base pair.
         * @param baseI The base pair index.
         * @return The spec.
         */
        virtual gnBaseSpec* GetSpecByBase( const gnSeqI baseI ) const = 0;
        /**
         * Get the index of the subspec which contains the specified base pair.
         * @param baseI The base pair index.
         * @return The subspec index.
         */
        virtual uint32 GetSpecIndexByBase( const gnSeqI baseI ) const;
        /**
         * Get the index of the spec which has the given name.
         * @param name The name of the spec to find.
         * @return The spec index.
         */
        virtual uint32 GetSpecIndexByName( const string& name ) const;
        /**
         * Get the starting base pair, in this spec's sequence, of the given subspec.
         * @param specI The subspec index.
         * @return The subspec's starting base pair.
         */
        virtual gnSeqI GetSpecStartBase( const uint32 specI ) const;
        /**
         * Get the ending base pair, in this spec's sequence, of the given subspec.
         * @param specI The subspec index.
         * @return The subspec's ending base pair.
         */
        virtual gnSeqI GetSpecEndBase( const uint32 specI ) const;
        /**
         * Add a subspec to this spec.
         * Throws an exception if the insertion index i is out of range
         * @param spec The subspec to add.
         * @param i The subspec to insert before
         * @return True if successful
         */
        virtual void AddSpec( gnBaseSpec* spec, const uint32 i = UINT32_MAX ) = 0;
        /**
         * Remove a subspec from this spec.
         * @param i The index of the subspec to remove.
         */
        virtual void RemoveSpec( uint32 i ) = 0;

        /**
         * Returns the number of headers this spec contains.
         * @return The number of headers this spec contains.
         */
        virtual uint32 GetHeaderListLength() const;
        /**
         * Add a header to this spec, adds to the end of the header list by default.
         * @param head The header to add.
         * @param i The header to insert before.  If i is larger than the size of the header list
         * the header will be added to the end of the list.
         */
        virtual void AddHeader( gnBaseHeader *head, const uint32 i = UINT32_MAX);
        /**
         * Get the headers at index i in the list of headers.
         * Throws a HeaderIndexOutOfBounds exception if a nonexistant header is referenced
         * @param i The index of the header
         * @return The header.
         */
        virtual gnBaseHeader* GetHeader( const uint32 i ) const;
        /**
         * Find the first header with the specified name, starting at index i.
         * @param name The name of the header to find.
         * @param i The index to start looking at.
         * @return The header or NULL if none was found.
         */
        virtual gnBaseHeader* GetHeader( const string& name, uint32& i) const;
        /**
         * Remove a header from this spec.
         * Throws a HeaderIndexOutOfBounds exception if a nonexistant header is referenced
         * @param i The index of the header to remove.
         */
        virtual void RemoveHeader( uint32 i );

        /**
         * Add a feature to this spec.
         * @param feat The feature to add.
         * @return True if successful
         */
        uint32 AddFeature( gnBaseFeature* feat );
        /**
         * Returns the number of features this spec contains.
         * @return The number of features this spec contains.
         */
        virtual uint32 GetFeatureListLength() const = 0;
        /**
         * Get the feature at index i in the list of features.
         * @param i The index of the feature
         * @return The feature.
         */
        virtual gnBaseFeature* GetFeature( const uint32 i ) const = 0;
        /**
         * Creates a list of all features which are contained by coordinates specified.
         * @param lt The coordinates containing the features to return.
         * @param feature_vector The vector to store features in.
         * @param index_vector A vector of indices which correspond to the features.
         */
        virtual void GetContainedFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const = 0;
        /**
         * Creates a list of all features which intersect the coordinates specified.
         * @param lt The coordinates intersecting the features to return.
         * @param feature_vector The vector to store features in.
         * @param index_vector A vector of indices which correspond to the features.
         */
        virtual void GetIntersectingFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector, vector<uint32>& index_vector) const = 0;
        /**
         * Creates a list of features which may have been broken by an edit.
         * @param lt The coordinates containing the features to return.
         * @param feature_vector The vector to store features in.
         */
        virtual void GetBrokenFeatures(const gnLocation& lt, vector<gnBaseFeature*>& feature_vector) const = 0;
        /**
         * Remove a feature from this spec.
         * @param i The index of the feature to remove.
         * @return True if successful
         */
        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_

---