/usr/include/libGenome-1.3/libGenome/gnDNASequence.h is in libgenome-1.3-dev 1.3.1-10.
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: gnDNASequence.h
// Purpose: Sequence class
// Description: Provides a high level sequence interface to all types of
// sequence data.
// 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 _gnDNASequence_h_
#define _gnDNASequence_h_
#include "libGenome/gnDefs.h"
#include <string>
#include <list>
#include "libGenome/gnSequence.h"
#include "libGenome/gnFilter.h"
namespace genome {
/**
* gnDNASequence is a special kind of gnSequence which can be used for DNA sequences
* It sets the default filters and comparators to the DNA filters and comparators.
*/
class GNDLLEXPORT gnDNASequence : public gnSequence
{
public:
/**
* Empty Constructor, creates an empty gnDNASequence.
*/
gnDNASequence();
/**
* Creates a gnDNASequence with a single contig containing the bases in "seq".
* @param seq The null terminated array of base pairs to use.
*/
gnDNASequence( const gnSeqC* seq );
/**
* Creates a gnDNASequence with a single contig containing the bases in "str".
* @param str The base pairs to use.
*/
gnDNASequence( const std::string& str );
/**
* Creates a gnDNASequence with the contigs stored in "gngs".
* @param gngs the gnGenomeSpec to get contigs from.
*/
gnDNASequence( const gnGenomeSpec& gngs );
/**
* Creates a gnDNASequence with the contigs stored in "gnfs".
* @param gnfs the gnFragmentSpec to get contigs from.
*/
gnDNASequence( const gnFragmentSpec& gnfs );
/**
* Creates a gnDNASequence with the contigs stored in "gncs".
* @param gncs the gnContigSpec to get contigs from.
*/
gnDNASequence( const gnContigSpec& gncs );
/**
* Creates a gnDNASequence with a single contig containing the bases in "bases".
* @param bases The base pairs to use
* @param length The length of the base pair array.
*/
gnDNASequence( gnSeqC *bases, const gnSeqI length);
/**
* Copies the gnDNASequence "seq".
* @param seq The gnDNASequence to copy.
*/
gnDNASequence( const gnDNASequence& seq);
private:
gnGenomeSpec *spec;
list<const gnBaseFilter*> filter_list;
const gnCompare* comparator;
}; // class gnDNASequence
inline
gnDNASequence::gnDNASequence() : gnSequence(){
filter_list.push_back(gnFilter::fullDNASeqFilter());
comparator = gnCompare::DNASeqCompare();
}
inline
gnDNASequence::gnDNASequence( const gnSeqC* seq ) : gnSequence(seq){
filter_list.push_back(gnFilter::fullDNASeqFilter());
comparator = gnCompare::DNASeqCompare();
}
inline
gnDNASequence::gnDNASequence( const std::string& str ) : gnSequence(str){
filter_list.push_back(gnFilter::fullDNASeqFilter());
comparator = gnCompare::DNASeqCompare();
}
inline
gnDNASequence::gnDNASequence( const gnGenomeSpec& gngs ) : gnSequence(gngs){
filter_list.push_back(gnFilter::fullDNASeqFilter());
comparator = gnCompare::DNASeqCompare();
}
inline
gnDNASequence::gnDNASequence( const gnFragmentSpec& gnfs ) : gnSequence(gnfs){
filter_list.push_back(gnFilter::fullDNASeqFilter());
comparator = gnCompare::DNASeqCompare();
}
inline
gnDNASequence::gnDNASequence( const gnContigSpec& gncs ) : gnSequence(gncs){
filter_list.push_back(gnFilter::fullDNASeqFilter());
comparator = gnCompare::DNASeqCompare();
}
inline
gnDNASequence::gnDNASequence( gnSeqC *bases, const gnSeqI length) : gnSequence(bases, length){
filter_list.push_back(gnFilter::fullDNASeqFilter());
comparator = gnCompare::DNASeqCompare();
}
inline
gnDNASequence::gnDNASequence( const gnDNASequence& seq) : gnSequence(seq){
filter_list.push_back(gnFilter::fullDNASeqFilter());
comparator = gnCompare::DNASeqCompare();
}
} // end namespace genome
#endif
// _gnDNASequence_h_
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