/usr/include/libGenome-1.3/libGenome/gnGBKSource.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: gnGBKSource.h
// Purpose: Implements gnBaseSource for GenBank 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 _gnGBKSource_h_
#define _gnGBKSource_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 {
const uint32 SEQ_COLUMN_WIDTH = 80;
const uint32 SEQ_HEADER_NAME_LENGTH = 11;
const uint32 SEQ_SUBTAG_COLUMN = 5;
const uint32 SEQ_LOCUS_CIRCULAR_COLUMN = 43;
const uint32 SEQ_LOCUS_NAME_COLUMN = 13;
const uint32 SEQ_LOCUS_NAME_LENGTH = 10;
const uint32 SEQ_LOCUS_SIZE_LENGTH = 10;
const uint32 SEQ_LOCUS_DNATYPE_OFFSET = 33;
const uint32 SEQ_LOCUS_DNATYPE_LENGTH = 7;
const uint32 SEQ_LOCUS_DIVCODE_OFFSET = 52;
const uint32 SEQ_LOCUS_DIVCODE_LENGTH = 3;
const uint32 SEQ_LOCUS_DATE_OFFSET = 62;
const uint32 SEQ_LOCUS_DATE_LENGTH = 11;
const uint32 SEQ_FEATURE_LOC_OFFSET = 21;
const uint32 SEQ_BASES_INDEX_END = 9;
/**
* gnGBKSource is a GenBank sequence file reader.
* This class reads and writes the GenBank file format.
* gnGBKSource is used by gnSourceFactory to read files and should only be used
* directly when writing out files in GBK file format by calling
* gnGBKSource::Write( mySpec, "C:\\mySeqFile.gbk");
*/
class GNDLLEXPORT gnGBKSource : public gnFileSource
{
public:
/**
* Empty Constructor, does nothing.
*/
gnGBKSource();
/**
* Clone Constructor copies the specified gnGBKSource.
* @param s The gnGBKSource to copy.
*/
gnGBKSource( const gnGBKSource& s );
/**
* Destructor, frees memory.
*/
~gnGBKSource();
/**
* Returns an exact copy of this class.
*/
gnGBKSource* 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 .GBK file named "filename".
* @param seq The gnSequence to write out.
* @param filename The name of the file to write.
* @return True if successful, false otherwise.
*/
static boolean Write(gnSequence& seq, const std::string& filename);
/**
* Writes the specified source to a .GBK 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);
gnGenomeSpec *GetSpec() const;
gnFileContig* GetFileContig( const uint32 contigI ) const;
private:
boolean SeqReadImpl( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS );
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);
// gnSeqI m_seqLength;
gnGenomeSpec *m_spec;
std::vector< gnFileContig* > m_contigList;
};// class gnGBKSource
template< class SubSpec >
void WriteHeader(gnMultiSpec< SubSpec >* spec, const std::string& hdr, std::ofstream& m_ofstream);
// Clone
inline
gnGBKSource* gnGBKSource::Clone() const
{
return new gnGBKSource( *this );
}
// Contig Access methods
inline
uint32 gnGBKSource::GetContigListLength() const
{
return m_contigList.size();
}
inline
boolean gnGBKSource::Write(gnBaseSource *source, const std::string& filename){
gnSequence gns(*source->GetSpec());
return Write(gns, filename);
}
inline
gnGenomeSpec *gnGBKSource::GetSpec() const{
return m_spec->Clone();
}
} // end namespace genome
#endif
// _gnGBKSource_h_
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