/usr/include/libGenome-1.3/libGenome/gnGBKSource.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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 | /////////////////////////////////////////////////////////////////////////////
// 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_
|