/usr/include/libGenome-1.3/libGenome/gnSEQSource.h is in libgenome-1.3-dev 1.3.1-7.
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: gnSEQSource.h
// Purpose: Implements gnBaseSource for .SEQ files
// 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 _gnSEQSource_h_
#define _gnSEQSource_h_
#include "libGenome/gnDefs.h"
#include <string>
#include <fstream>
#include <vector>
#include "libGenome/gnFileSource.h"
#include "libGenome/gnFileContig.h"
#include "libGenome/gnSourceSpec.h"
#include "libGenome/gnSequence.h"
namespace genome {
/**
* gnSEQSource is a SEQ file reader.
* This class reads and writes the DNAStar SEQ file format.
* gnSEQSource is used by gnSourceFactory to read files and should only be used
* directly.when writing out files in SEQ file format by calling
* gnSEQSource::Write( mySpec, "C:\\mySeqFile.seq");
*/
class GNDLLEXPORT gnSEQSource : public gnFileSource
{
public:
/**
* Empty Constructor, does nothing.
*/
gnSEQSource();
/**
* Clone Constructor copies the specified gnSEQSource.
* @param s The gnSEQSource to copy.
*/
gnSEQSource( const gnSEQSource& s );
/**
* Destructor, frees memory.
*/
~gnSEQSource();
/**
* Returns an exact copy of this class.
*/
gnSEQSource* Clone() const;
// Contig Access methods
uint32 GetContigListLength() const;
boolean HasContig( const std::string& name ) const;
uint32 GetContigID( const std::string& name ) const;
std::string GetContigName( const uint32 i ) const;
gnSeqI GetContigSeqLength( const uint32 i ) const;
boolean SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS );
/**
* Writes the specified gnSequence to a .SEQ file named "filename".
* @param sequence The gnSequence to write out.
* @param filename The name of the file to write.
* @return True if successful, false otherwise.
*/
static boolean Write(gnSequence& sequence, const std::string& filename);
/**
* Writes the specified source to a .SEQ file named "filename".
* @param source The source to write out.
* @param filename The name of the file to write.
* @return True if successful, false otherwise.
*/
static boolean Write(gnBaseSource *source, const std::string& filename);
/**
* Writes the given spec to a .SEQ file named "filename".
* @param spec The spec to write out.
* @param filename The name of the file to write.
* @return True if successful, false otherwise.
*/
static boolean Write(gnGenomeSpec *spec, const std::string& filename);
gnGenomeSpec *GetSpec() const;
gnFileContig* GetFileContig( const uint32 contigI ) const;
private:
boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes );
boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
boolean ParseStream( std::istream& fin );
static std::string& Filler(uint32 length);
static void FormatString(std::string& data, uint32 offset, uint32 width);
static void BaseCount(const std::string& bases, gnSeqI& a_count, gnSeqI& c_count, gnSeqI& g_count, gnSeqI& t_count, gnSeqI& other_count);
// gnSeqI m_seqLength;
gnGenomeSpec *m_spec;
std::vector< gnFileContig* > m_contigList;
};// class gnSEQSource
// Clone
inline
gnSEQSource* gnSEQSource::Clone() const
{
return new gnSEQSource( *this );
}
// Contig Access methods
inline
uint32 gnSEQSource::GetContigListLength() const
{
return m_contigList.size();
}
inline
boolean gnSEQSource::Write(gnSequence& sequence, const std::string& filename){
return Write(sequence.GetSpec(), filename);
}
inline
boolean gnSEQSource::Write(gnBaseSource *source, const std::string& filename){
return Write(source->GetSpec(), filename);
}
inline
gnGenomeSpec *gnSEQSource::GetSpec() const{
return m_spec->Clone();
}
} // end namespace genome
#endif
// _gnSEQSource_h_
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