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gnFileContig Class Reference

gnFileContig is used by source classes to track the location of sequence data on disk. More...

#include <gnFileContig.h>

Inheritance diagram for gnFileContig:


Public Member Functions
	gnFileContig ()
	gnFileContig (string nameStr, const uint64 pos, const uint64 len)
	gnFileContig (const gnFileContig &fc)
	~gnFileContig ()
gnFileContig *	Clone () const
void	Clear ()
string	GetName () const
gnSeqI	GetSeqLength () const
pair< uint64, uint64 >	GetFileStartEnd () const
uint64	GetFileLength () const
pair< uint64, uint64 >	GetSectStartEnd (const gnContigSection i) const
uint64	GetSectLength (gnContigSection i) const
boolean	HasRepeatSeqGap () const
pair< uint32, uint32 >	GetRepeatSeqGapSize () const
boolean	SetName (string nameStr)
boolean	SetSeqLength (const gnSeqI len)
boolean	AddToSeqLength (const gnSeqI len)
boolean	SetFileStart (const uint64 s)
boolean	SetFileEnd (const uint64 e)
boolean	SetFileStartEnd (const pair< uint64, uint64 > se)
boolean	SetSectStart (const gnContigSection i, const uint64 s)
boolean	SetSectEnd (const gnContigSection i, const uint64 e)
boolean	SetSectStartEnd (const gnContigSection i, const pair< uint64, uint64 > se)
boolean	SetRepeatSeqGap (const boolean rsg)
boolean	SetRepeatSeqGapSize (const pair< uint64, uint64 > rsgSize)
boolean	SetRepeatSeqSize (const uint64 seqSize)
boolean	SetRepeatGapSize (const uint64 gapSize)
Private Attributes
string	m_name
gnSeqI	m_seqLength
pair< uint64, uint64 >	m_fileStartEnd
pair< uint64, uint64 >	m_startEndArray [CONTIG_SECTION_SIZE]
boolean	m_repeatSeqGap
pair< uint64, uint64 >	m_repeatSeqGapSize

Detailed Description

gnFileContig is used by source classes to track the location of sequence data on disk.

gnFileContig stores the start and end byte offset, and the size of a repeated gap in the sequence data. Also stores whether the sequence data is in the expected format or if it is corrupted.

Definition at line 28 of file gnFileContig.h.

Constructor & Destructor Documentation

gnFileContig::gnFileContig ( )

Definition at line 15 of file gnFileContig.cpp.
References Clear().
Referenced by Clone().

gnFileContig::gnFileContig ( string nameStr,

const uint64 pos,

const uint64 len

)

Definition at line 19 of file gnFileContig.cpp.
References Clear(), m_fileStartEnd, and m_name.

gnFileContig::gnFileContig ( const gnFileContig & fc )

Definition at line 26 of file gnFileContig.cpp.
References CONTIG_SECTION_SIZE, m_fileStartEnd, m_name, m_repeatSeqGap, m_repeatSeqGapSize, m_seqLength, m_startEndArray, and uint32.

gnFileContig::~gnFileContig ( )

Definition at line 36 of file gnFileContig.cpp.

Member Function Documentation

boolean gnFileContig::AddToSeqLength ( const gnSeqI len ) [inline]

Definition at line 137 of file gnFileContig.h.
References m_seqLength.
Referenced by gnFASSource::ParseStream().

void gnFileContig::Clear ( )

Definition at line 39 of file gnFileContig.cpp.
References CONTIG_SECTION_SIZE, m_fileStartEnd, m_name, m_repeatSeqGap, m_repeatSeqGapSize, m_seqLength, m_startEndArray, and uint32.
Referenced by gnFileContig().

gnFileContig * gnFileContig::Clone ( ) const [inline, virtual]

Implements gnClone.
Definition at line 74 of file gnFileContig.h.
References gnFileContig().
Referenced by gnRAWSource::gnRAWSource().

uint64 gnFileContig::GetFileLength ( ) const [inline]

Definition at line 95 of file gnFileContig.h.
References m_fileStartEnd, and uint64.

pair< uint64, uint64 > gnFileContig::GetFileStartEnd ( ) const [inline]

Definition at line 90 of file gnFileContig.h.
References m_fileStartEnd.

string gnFileContig::GetName ( ) const [inline]

Definition at line 80 of file gnFileContig.h.
References m_name.

pair< uint32, uint32 > gnFileContig::GetRepeatSeqGapSize ( ) const [inline]

Definition at line 119 of file gnFileContig.h.
References m_repeatSeqGapSize.
Referenced by gnSEQSource::ParseStream(), gnSEQSource::SeqStartPos(), and gnFASSource::SeqStartPos().

uint64 gnFileContig::GetSectLength ( gnContigSection i ) const [inline]

Definition at line 107 of file gnFileContig.h.
References CONTIG_SECTION_SIZE, m_startEndArray, and uint64.

pair< uint64, uint64 > gnFileContig::GetSectStartEnd ( const gnContigSection i ) const [inline]

Definition at line 100 of file gnFileContig.h.
References CONTIG_SECTION_SIZE, and m_startEndArray.
Referenced by gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), and gnFASSource::SeqStartPos().

gnSeqI gnFileContig::GetSeqLength ( ) const [inline]

Definition at line 85 of file gnFileContig.h.
References gnSeqI, and m_seqLength.
Referenced by gnRAWSource::GetContigSeqLength().

boolean gnFileContig::HasRepeatSeqGap ( ) const [inline]

Definition at line 114 of file gnFileContig.h.
References m_repeatSeqGap.
Referenced by gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), and gnFASSource::SeqStartPos().

boolean gnFileContig::SetFileEnd ( const uint64 e ) [inline]

Definition at line 149 of file gnFileContig.h.
References m_fileStartEnd.
Referenced by gnFASSource::ParseStream().

boolean gnFileContig::SetFileStart ( const uint64 s ) [inline]

Definition at line 143 of file gnFileContig.h.
References m_fileStartEnd.
Referenced by gnFASSource::ParseStream().

boolean gnFileContig::SetFileStartEnd ( const pair< uint64, uint64 > se ) [inline]

Definition at line 155 of file gnFileContig.h.
References m_fileStartEnd.

boolean gnFileContig::SetName ( string nameStr ) [inline]

Definition at line 125 of file gnFileContig.h.
References m_name.
Referenced by gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), and gnFASSource::ParseStream().

boolean gnFileContig::SetRepeatGapSize ( const uint64 gapSize )

Definition at line 64 of file gnFileContig.cpp.
References m_repeatSeqGap, and m_repeatSeqGapSize.
Referenced by gnSEQSource::ParseStream(), gnFASSource::ParseStream(), and SetRepeatSeqGapSize().

boolean gnFileContig::SetRepeatSeqGap ( const boolean rsg ) [inline]

Definition at line 191 of file gnFileContig.h.
References m_repeatSeqGap.
Referenced by gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), and gnFASSource::ParseStream().

boolean gnFileContig::SetRepeatSeqGapSize ( const pair< uint64, uint64 > rsgSize ) [inline]

Definition at line 197 of file gnFileContig.h.
References SetRepeatGapSize(), and SetRepeatSeqSize().

boolean gnFileContig::SetRepeatSeqSize ( const uint64 seqSize )

Definition at line 50 of file gnFileContig.cpp.
References m_repeatSeqGap, and m_repeatSeqGapSize.
Referenced by gnSEQSource::ParseStream(), gnFASSource::ParseStream(), and SetRepeatSeqGapSize().

boolean gnFileContig::SetSectEnd ( const gnContigSection i,

const uint64 e

) [inline]

Definition at line 171 of file gnFileContig.h.
References CONTIG_SECTION_SIZE, and m_startEndArray.
Referenced by gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), and gnFASSource::ParseStream().

boolean gnFileContig::SetSectStart ( const gnContigSection i,

const uint64 s

) [inline]

Definition at line 161 of file gnFileContig.h.
References CONTIG_SECTION_SIZE, and m_startEndArray.
Referenced by gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), and gnFASSource::ParseStream().

boolean gnFileContig::SetSectStartEnd ( const gnContigSection i,

const pair< uint64, uint64 > se

) [inline]

Definition at line 181 of file gnFileContig.h.
References CONTIG_SECTION_SIZE, and m_startEndArray.

boolean gnFileContig::SetSeqLength ( const gnSeqI len ) [inline]

Definition at line 131 of file gnFileContig.h.
References m_seqLength.
Referenced by gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), and gnGBKSource::ParseStream().

Member Data Documentation

pair<uint64,uint64> gnFileContig::m_fileStartEnd [private]

Definition at line 64 of file gnFileContig.h.
Referenced by Clear(), GetFileLength(), GetFileStartEnd(), gnFileContig(), SetFileEnd(), SetFileStart(), and SetFileStartEnd().

string gnFileContig::m_name [private]

Definition at line 62 of file gnFileContig.h.
Referenced by Clear(), GetName(), gnFileContig(), and SetName().

boolean gnFileContig::m_repeatSeqGap [private]

Definition at line 68 of file gnFileContig.h.
Referenced by Clear(), gnFileContig(), HasRepeatSeqGap(), SetRepeatGapSize(), SetRepeatSeqGap(), and SetRepeatSeqSize().

pair< uint64, uint64 > gnFileContig::m_repeatSeqGapSize [private]

Definition at line 69 of file gnFileContig.h.
Referenced by Clear(), GetRepeatSeqGapSize(), gnFileContig(), SetRepeatGapSize(), and SetRepeatSeqSize().

gnSeqI gnFileContig::m_seqLength [private]

Definition at line 63 of file gnFileContig.h.
Referenced by AddToSeqLength(), Clear(), GetSeqLength(), gnFileContig(), and SetSeqLength().

pair<uint64,uint64> gnFileContig::m_startEndArray[CONTIG_SECTION_SIZE] [private]

Definition at line 66 of file gnFileContig.h.
Referenced by Clear(), GetSectLength(), GetSectStartEnd(), gnFileContig(), SetSectEnd(), SetSectStart(), and SetSectStartEnd().

The documentation for this class was generated from the following files:

Generated on Fri May 9 12:57:57 2003 for libGenome by

1.3-rc3

gnFileContig Class Reference

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation