/usr/include/libGenome-1.3/libGenome/gnBaseSpec.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: gnBaseSpec.h
// Purpose: abstract Spec class
// Description: Defines a basic interface for all specs
// 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 _gnBaseSpec_h_
#define _gnBaseSpec_h_
#include "libGenome/gnDefs.h"
#include <vector>
#include <string>
#include "libGenome/gnClone.h"
#include "libGenome/gnBaseFeature.h"
#include "libGenome/gnBaseHeader.h"
namespace genome {
/**
* gnBaseSpec is the class which stores genetic information and is best accessed using gnSequence.
*/
class GNDLLEXPORT gnBaseSpec : public gnClone
{
public:
gnBaseSpec(){}
/**
* Destructor, frees memory.
*/
virtual ~gnBaseSpec(){}
virtual gnBaseSpec* Clone() const = 0;
virtual gnBaseSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const = 0;
/**
* Get the name of the contig associated with this spec.
* @return The contig name or an empty std::string if none exists.
*/
virtual std::string GetName() const;
/**
* Sets the name for this contig
* @param name The new name.
* @return True if successful. Honestly, I don't know how this could be unsuccessful...
*/
virtual void SetName( const std::string& name );
/**
* Get the length of all the sequence data covered by this spec.
* @return This spec's length in base pairs.
*/
virtual gnSeqI GetLength() const = 0;
/**
* Returns true if this spec is read reverse complement.
* @return True if this spec is read reverse complement.
*/
virtual boolean IsReverseComplement() const;
/**
* Returns true if this spec's sequence is circular.
* @return True if this spec's sequence is circular.
*/
virtual boolean IsCircular() const;
/**
* Sets the reverse complement bit for this spec.
* @param value True for reverse complement, false otherwise.
*/
virtual void SetReverseComplement( const boolean value ) = 0;
/**
* Sets whether this spec should be read circular.
* If circular is set, reads beyond the end of this spec will pick up
* at the beginning and read up to the start index.
* @param value True for circular, false otherwise.
*/
virtual void SetCircular( const boolean value );
/**
* Crop the first cropLen bases from the sequence. CropStart will
* delete features and headers associated with the cropped bases.
* @param cropLen The number of base pairs to delete from the beginning.
*/
virtual void CropStart( gnSeqI cropLen ) = 0;
/**
* Crop the last cropLen bases from the sequence. CropEnd will
* delete features and headers associated with the cropped bases.
* @param cropLen The number of base pairs to delete from the end.
*/
virtual void CropEnd( gnSeqI cropLen ) = 0;
/**
* Reads sequence data from this spec.
* SeqRead will attempt to read "bufLen" base pairs starting at "start", an offset into the sequence.
* Reading inside a specific contig can be accomplished by supplying the "contigI" parameter with
* a valid contig index.
* SeqRead stores the sequence data in "buf" and returns the actual number of bases read in "bufLen".
* SeqRead will return false if a serious error occurs.
* @param start The base pair to start reading at.
* @param buf The character array to store base pairs into.
* @param bufLen The number of base pairs to read. This will be modified to reflect the actual number of bases read.
* @param contigI The index of the subspec to read or ALL_CONTIGS by default.
* @return True if the operation was successful.
*/
virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen, const uint32 contigI ) const = 0;
/**
* Clears all data from this spec.
*/
virtual void Clear();
protected:
boolean m_reverseComplement;
boolean m_circular;
std::string m_name;
std::string m_sourceName;
}; // class gnBaseSpec
inline
std::string gnBaseSpec::GetName() const{
return m_name;
}
inline
void gnBaseSpec::SetName( const std::string& name ){
m_name = name;
}
inline
boolean gnBaseSpec::IsReverseComplement() const{
return m_reverseComplement;
}
inline
boolean gnBaseSpec::IsCircular() const{
return m_circular;
}
inline
void gnBaseSpec::SetCircular( const boolean value ){
m_circular = value;
}
inline
void gnBaseSpec::Clear(){
m_sourceName = "";
m_name = "";
m_reverseComplement = false;
m_circular = false;
}
} // end namespace genome
#endif
// _gnBaseSpec_h_
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