/usr/include/libGenome-1.3/libGenome/gnContigSpec.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: gnContigSpec.h
// Purpose: Abstract Contig Spec class
// Description: Defines an interface for contig 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 _gnContigSpec_h_
#define _gnContigSpec_h_
#include "libGenome/gnDefs.h"
#include <vector>
#include <string>
#include "libGenome/gnBaseSpec.h"
#include "libGenome/gnBaseFeature.h"
#include "libGenome/gnDebug.h"
namespace genome {
/**
* gnContigSpec is an interface for classes which store contigs, or reads,
* of DNA or protein sequence
*/
class GNDLLEXPORT gnContigSpec : public gnBaseSpec
{
public:
gnContigSpec(){}
/**
* Destructor, frees memory.
*/
virtual ~gnContigSpec(){}
virtual gnContigSpec* Clone() const = 0;
virtual gnContigSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const = 0;
/**
* Get the name of the source associated with this spec.
* @return The source name or an empty std::string if none exists.
*/
virtual std::string GetSourceName() const;
/**
* Get the base pair index where this contig starts inside of the sequence data.
* @return The starting base pair.
*/
virtual gnSeqI GetStart() const;
/**
* Get the length of this contig inside of the sequence data.
* @return This contigs length.
*/
virtual gnSeqI GetLength() const;
/**
* Get the length of the source for this spec.
* @return The source length.
*/
virtual gnSeqI GetSourceLength() const = 0;
/**
* Returns this contig's index in its source sequence.
* @return This contig's index in the source sequence.
*/
virtual uint32 GetSourceContigIndex() const;
/**
* Sets the name of the source associated with this contig.
* @param sourceName The new name.
* @return True if successful.
*/
virtual void SetSourceName( const std::string& sourceName );
/**
* Sets the starting base pair to read from in the contig's sequence.
* This does not affect the actual sequence data but only where to begin
* using it in this contig.
* @param start The new starting base pair.
* @return True if successful.
*/
virtual void SetStart( const gnSeqI start );
/**
* Sets the length of reads into this sequence.
* This does not affect the actual sequence data but only how much of it
* is used in this contig.
* @param len The new sequence length.
* @return True if successful.
*/
virtual void SetLength( const gnSeqI len );
/**
* Sets this contig's index in its source sequence.
* @param contigI This contig's index in the source sequence.
*/
virtual void SetSourceContigIndex( const uint32 contigI );
/**
* Sets the reverse complement bit for this contig.
* This routine will translate the start index to the reverse base pair.
* @param value True for reverse complement, false otherwise.
* @return True if successful.
*/
virtual void SetReverseComplement( const boolean value );
virtual void CropStart( gnSeqI cropLen );
virtual void CropEnd( gnSeqI cropLen );
virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen, const uint32 contigI ) const;
virtual void Clear();
protected:
gnSeqI m_start; //start within the genome.
gnSeqI m_length;
uint32 m_SourceContigIndex;
/**
* all derived classes must implement this!
* it simply reads the specified bases into buf, disregarding circularity and reverse complement.
*/
virtual boolean Read(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen ) const = 0;
private:
}; // class gnContigSpec
inline
std::string gnContigSpec::GetSourceName() const{
return m_sourceName;
}
inline
void gnContigSpec::SetSourceName(const std::string& sourceName){
m_sourceName = sourceName;
}
inline
gnSeqI gnContigSpec::GetStart() const
{
return m_start;
}
inline
gnSeqI gnContigSpec::GetLength() const
{
return m_length;
}
// SET
inline
void gnContigSpec::SetStart( const gnSeqI start )
{
m_start = start;
}
inline
void gnContigSpec::SetLength( const gnSeqI len )
{
m_length = len;
}
inline
uint32 gnContigSpec::GetSourceContigIndex() const{
return m_SourceContigIndex;
}
inline
void gnContigSpec::SetSourceContigIndex( const uint32 contigI ){
m_SourceContigIndex = contigI;
}
} // end namespace genome
#endif
// _gnContigSpec_h_
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