/usr/include/libGenome-1.3/libGenome/gnFragmentSpec.h is in libgenome-1.3-dev 1.3.1-8.
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: gnFragmentSpec.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 _gnFragmentSpec_h_
#define _gnFragmentSpec_h_
#include "libGenome/gnDefs.h"
#include <vector>
#include <string>
#include "libGenome/gnClone.h"
#include "libGenome/gnBaseFeature.h"
#include "libGenome/gnBaseHeader.h"
#include "libGenome/gnContigSpec.h"
#include "libGenome/gnMultiSpec.h"
#include "libGenome/gnException.h"
namespace genome {
/**
* gnFragmentSpec contains a list of specs which make up a sequence
* fragment. It also contains a list of features which relate to
* the sequence fragment. Finally it contains a list of sequence
* related header data. This class is usually created and filled by
* a file reader class like gnGBKSource.
*/
class GNDLLEXPORT gnFragmentSpec : public gnMultiSpec< gnContigSpec >
{
public:
gnFragmentSpec();
/**
* Destructor, frees memory.
*/
virtual ~gnFragmentSpec();
/**
* Copy constructor.
* @param s the gnGenomeSpec to copy.
*/
gnFragmentSpec( const gnFragmentSpec& s);
virtual gnFragmentSpec* Clone() const;
virtual void Clear();
// Base Spec stuff
virtual void SetReverseComplement( const boolean value );
//Multispec stuff
/* virtual uint32 GetSpecListLength() const;
virtual gnContigSpec* GetSpec( const uint32 i ) const;
virtual gnContigSpec* GetSpecByBase( const gnSeqI baseI ) const;
virtual void AddSpec( gnBaseSpec* spec, const uint32 i = UINT32_MAX );
virtual void RemoveSpec( uint32 i );
*/
virtual void CropStart( gnSeqI cropLen );
virtual void CropEnd( gnSeqI cropLen );
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 gnFragmentSpec. 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 gnFragmentSpec containing only the specified bases
*/
virtual gnFragmentSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const;
protected:
// std::vector <gnContigSpec*> m_SpecList;
//Feature stuff...
std::vector <gnBaseFeature*> m_featureList;
}; // class gnFragmentSpec
inline
gnFragmentSpec* gnFragmentSpec::Clone() const{
return new gnFragmentSpec(*this);
}
/*
inline
uint32 gnFragmentSpec::GetSpecListLength() const{
return m_SpecList.size();
}
inline
gnContigSpec *gnFragmentSpec::GetSpec( const uint32 i ) const{
if(i < m_SpecList.size())
return m_SpecList[i];
Throw_gnEx(ContigIndexOutOfBounds());
}
inline
gnContigSpec* gnFragmentSpec::GetSpecByBase( const gnSeqI baseI ) const{
return m_SpecList[GetSpecIndexByBase(baseI)];
}
inline
void gnFragmentSpec::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, (gnContigSpec*)spec);
}
}
inline
void gnFragmentSpec::RemoveSpec( uint32 i ){
if(i < GetSpecListLength()){
m_SpecList.erase(m_SpecList.begin() + i);
}else
Throw_gnEx(ContigIndexOutOfBounds());
}
*/
inline
uint32 gnFragmentSpec::AddFeature( gnBaseFeature* feat )
{
m_featureList.push_back(feat);
feat->SetSpec(this);
return m_featureList.size()-1;
}
inline
uint32 gnFragmentSpec::GetFeatureListLength() const
{
return m_featureList.size();
}
inline
gnBaseFeature* gnFragmentSpec::GetFeature(const uint32 i) const
{
return m_featureList[i]->Clone();
}
inline
void gnFragmentSpec::RemoveFeature( const uint32 i)
{
if(i >= m_featureList.size())
Throw_gnEx(FeatureIndexOutOfBounds());
delete m_featureList[i];
m_featureList.erase(m_featureList.begin() + i);
}
} // end namespace genome
#endif
// _gnFragmentSpec_h_
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