/usr/include/libGenome-1.3/libGenome/gnSourceSpec.h is in libgenome-1.3-dev 1.3.1-9.
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: gnSourceSpec.h
// Purpose: implements gnBaseSpec for source specs
// Description:
// 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 _gnSourceSpec_h_
#define _gnSourceSpec_h_
#include "libGenome/gnDefs.h"
#include <string>
#include "libGenome/gnContigSpec.h"
#include "libGenome/gnBaseSource.h"
namespace genome {
/**
* gnSourceSpec stores sequence and annotation data from another source.
* @see gnContigSpec
* @see gnBaseSpec
*/
class GNDLLEXPORT gnSourceSpec : public gnContigSpec
{
public:
/**
* Empty constructor.
*/
gnSourceSpec();
/**
* Constructor, creates a gnSourceSpec using sequence data in the given source.
* A circular spec will be created if the end index is greater than the start.
* @param m_pSource The source to read base pairs from.
* @param m_ContigIndex The index of the contig in the source, ALL_CONTIGS by default.
* @param startI The index to start reading base pairs from the source.
* @param endI The index to stop reading base pairs from the source.
* @param revComp True if the sequence is read reverse complement.
*/
gnSourceSpec( gnBaseSource* m_pSource, const uint32 m_ContigIndex=ALL_CONTIGS, const gnSeqI startI=0, const gnSeqI endI=GNSEQI_END, const boolean revComp = false);
/**
* Copy constructor.
* @param s the gnSourceSpec to copy.
*/
gnSourceSpec( const gnSourceSpec& s );
~gnSourceSpec();
gnSourceSpec* Clone() const;
// Source Spec Specific functions
virtual void Clear();
virtual gnSeqI GetSourceLength() const;
virtual gnBaseSource *GetSource() const;
/**
* Copies a specified range of bases and returns a pointer to
* the resulting gnSourceSpec. 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 gnSourceSpec containing only the specified bases
*/
virtual gnSourceSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const;
protected:
virtual boolean Read(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen ) const;
gnBaseSource* m_pSource;
}; // class gnSourceSpec
inline
gnSourceSpec* gnSourceSpec::Clone() const
{
return new gnSourceSpec( *this );
}
inline
gnSeqI gnSourceSpec::GetSourceLength() const{
return m_pSource->GetContigSeqLength(m_SourceContigIndex);
}
inline
gnBaseSource* gnSourceSpec::GetSource() const
{
return m_pSource;
}
inline
boolean gnSourceSpec::Read(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen) const{
return m_pSource->SeqRead(start, buf, bufLen, m_SourceContigIndex);
}
} // end namespace genome
#endif
// _gnSourceSpec_h_
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