/usr/include/libGenome-1.3/libGenome/gnGenomeSpec.h is in libgenome-1.3-dev 1.3.1-6.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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
/////////////////////////////////////////////////////////////////////////////
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#ifndef _gnGenomeSpec_h_
#define _gnGenomeSpec_h_
#include "libGenome/gnDefs.h"
#include <vector>
#include <string>
#include "libGenome/gnClone.h"
#include "libGenome/gnBaseFeature.h"
#include "libGenome/gnBaseHeader.h"
#include "libGenome/gnMultiSpec.h"
#include "libGenome/gnFragmentSpec.h"
#include "libGenome/gnException.h"
namespace genome {
/**
* 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< gnFragmentSpec >
{
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, std::vector<gnBaseFeature*>& feature_vector, std::vector<uint32>& index_vector) const;
virtual void GetIntersectingFeatures(const gnLocation& lt, std::vector<gnBaseFeature*>& feature_vector, std::vector<uint32>& index_vector) const;
virtual void GetBrokenFeatures(const gnLocation& lt, std::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:
// std::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);
}
}
*/
} // end namespace genome
#endif
// _gnGenomeSpec_h_
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