/usr/include/libGenome-1.3/libGenome/gnContigSpec.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 | /////////////////////////////////////////////////////////////////////////////
// File: gnContigSpec.h
// Purpose: Abstract Contig Spec class
// Description: Defines an interface for contig specs
// 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 _gnContigSpec_h_
#define _gnContigSpec_h_
#include "libGenome/gnDefs.h"
#include <vector>
#include <string>
#include "libGenome/gnBaseSpec.h"
#include "libGenome/gnBaseFeature.h"
#include "libGenome/gnDebug.h"
namespace genome {
/**
* gnContigSpec is an interface for classes which store contigs, or reads,
* of DNA or protein sequence
*/
class GNDLLEXPORT gnContigSpec : public gnBaseSpec
{
public:
gnContigSpec(){}
/**
* Destructor, frees memory.
*/
virtual ~gnContigSpec(){}
virtual gnContigSpec* Clone() const = 0;
virtual gnContigSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const = 0;
/**
* Get the name of the source associated with this spec.
* @return The source name or an empty std::string if none exists.
*/
virtual std::string GetSourceName() const;
/**
* Get the base pair index where this contig starts inside of the sequence data.
* @return The starting base pair.
*/
virtual gnSeqI GetStart() const;
/**
* Get the length of this contig inside of the sequence data.
* @return This contigs length.
*/
virtual gnSeqI GetLength() const;
/**
* Get the length of the source for this spec.
* @return The source length.
*/
virtual gnSeqI GetSourceLength() const = 0;
/**
* Returns this contig's index in its source sequence.
* @return This contig's index in the source sequence.
*/
virtual uint32 GetSourceContigIndex() const;
/**
* Sets the name of the source associated with this contig.
* @param sourceName The new name.
* @return True if successful.
*/
virtual void SetSourceName( const std::string& sourceName );
/**
* Sets the starting base pair to read from in the contig's sequence.
* This does not affect the actual sequence data but only where to begin
* using it in this contig.
* @param start The new starting base pair.
* @return True if successful.
*/
virtual void SetStart( const gnSeqI start );
/**
* Sets the length of reads into this sequence.
* This does not affect the actual sequence data but only how much of it
* is used in this contig.
* @param len The new sequence length.
* @return True if successful.
*/
virtual void SetLength( const gnSeqI len );
/**
* Sets this contig's index in its source sequence.
* @param contigI This contig's index in the source sequence.
*/
virtual void SetSourceContigIndex( const uint32 contigI );
/**
* Sets the reverse complement bit for this contig.
* This routine will translate the start index to the reverse base pair.
* @param value True for reverse complement, false otherwise.
* @return True if successful.
*/
virtual void SetReverseComplement( const boolean value );
virtual void CropStart( gnSeqI cropLen );
virtual void CropEnd( gnSeqI cropLen );
virtual boolean SeqRead(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen, const uint32 contigI ) const;
virtual void Clear();
protected:
gnSeqI m_start; //start within the genome.
gnSeqI m_length;
uint32 m_SourceContigIndex;
/**
* all derived classes must implement this!
* it simply reads the specified bases into buf, disregarding circularity and reverse complement.
*/
virtual boolean Read(const gnSeqI start, gnSeqC* buf, gnSeqI& bufLen ) const = 0;
private:
}; // class gnContigSpec
inline
std::string gnContigSpec::GetSourceName() const{
return m_sourceName;
}
inline
void gnContigSpec::SetSourceName(const std::string& sourceName){
m_sourceName = sourceName;
}
inline
gnSeqI gnContigSpec::GetStart() const
{
return m_start;
}
inline
gnSeqI gnContigSpec::GetLength() const
{
return m_length;
}
// SET
inline
void gnContigSpec::SetStart( const gnSeqI start )
{
m_start = start;
}
inline
void gnContigSpec::SetLength( const gnSeqI len )
{
m_length = len;
}
inline
uint32 gnContigSpec::GetSourceContigIndex() const{
return m_SourceContigIndex;
}
inline
void gnContigSpec::SetSourceContigIndex( const uint32 contigI ){
m_SourceContigIndex = contigI;
}
} // end namespace genome
#endif
// _gnContigSpec_h_
|