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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::

List of all members.

Public Methods
	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

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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 31 of file gnFileContig.h.

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Constructor & Destructor Documentation

gnFileContig::gnFileContig ( )

Definition at line 16 of file gnFileContig.cpp. Referenced by Clone().

gnFileContig::gnFileContig ( string nameStr, const uint64 pos, const uint64 len )

Definition at line 20 of file gnFileContig.cpp.

gnFileContig::gnFileContig ( const gnFileContig & fc )

Definition at line 27 of file gnFileContig.cpp.

gnFileContig::~gnFileContig ( )

Definition at line 37 of file gnFileContig.cpp.

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Member Function Documentation

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

Definition at line 140 of file gnFileContig.h. Referenced by gnFASSource::ParseStream().

void gnFileContig::Clear ( )

Definition at line 40 of file gnFileContig.cpp. Referenced by gnFileContig().

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

Reimplemented from gnClone. Definition at line 77 of file gnFileContig.h.

uint64 gnFileContig::GetFileLength ( ) const [inline]

Definition at line 98 of file gnFileContig.h.

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

Definition at line 93 of file gnFileContig.h. Referenced by main().

string gnFileContig::GetName ( ) const [inline]

Definition at line 83 of file gnFileContig.h. Referenced by gnSEQSource::GetContigID(), gnGBKSource::GetContigID(), gnFASSource::GetContigID(), gnSEQSource::GetContigName(), gnGBKSource::GetContigName(), gnFASSource::GetContigName(), gnABISource::GetContigName(), gnSEQSource::HasContig(), gnGBKSource::HasContig(), gnFASSource::HasContig(), and main().

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

Definition at line 122 of file gnFileContig.h. Referenced by gnSEQSource::ParseStream(), gnSEQSource::SeqStartPos(), gnFASSource::SeqStartPos(), and main().

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

Definition at line 110 of file gnFileContig.h.

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

Definition at line 103 of file gnFileContig.h. Referenced by gnFASSource::GetSpec(), gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), gnFASSource::SeqStartPos(), and main().

gnSeqI gnFileContig::GetSeqLength ( ) const [inline]

Definition at line 88 of file gnFileContig.h. Referenced by gnSEQSource::GetContigSeqLength(), gnRAWSource::GetContigSeqLength(), gnGBKSource::GetContigSeqLength(), gnFASSource::GetContigSeqLength(), gnABISource::GetContigSeqLength(), gnSEQSource::SeqRead(), gnGBKSource::SeqRead(), gnFASSource::SeqRead(), and main().

boolean gnFileContig::HasRepeatSeqGap ( ) const [inline]

Definition at line 117 of file gnFileContig.h. Referenced by gnSEQSource::SeqStartPos(), gnGBKSource::SeqStartPos(), gnFASSource::SeqStartPos(), and main().

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

Definition at line 152 of file gnFileContig.h. Referenced by gnFASSource::ParseStream().

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

Definition at line 146 of file gnFileContig.h. Referenced by gnFASSource::ParseStream().

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

Definition at line 158 of file gnFileContig.h.

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

Definition at line 128 of file gnFileContig.h. Referenced by gnSEQSource::ParseStream(), gnGBKSource::ParseStream(), and gnFASSource::ParseStream().

boolean gnFileContig::SetRepeatGapSize ( const uint64 gapSize )

Definition at line 65 of file gnFileContig.cpp. Referenced by gnSEQSource::ParseStream(), gnFASSource::ParseStream(), and SetRepeatSeqGapSize().

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

Definition at line 194 of file gnFileContig.h. Referenced by gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), and gnFASSource::ParseStream().

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

Definition at line 200 of file gnFileContig.h.

boolean gnFileContig::SetRepeatSeqSize ( const uint64 seqSize )

Definition at line 51 of file gnFileContig.cpp. Referenced by gnSEQSource::ParseStream(), gnFASSource::ParseStream(), and SetRepeatSeqGapSize().

boolean gnFileContig::SetSectEnd ( const gnContigSection i, const uint64 e ) [inline]

Definition at line 174 of file gnFileContig.h. Referenced by gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), gnGBKSource::ParseStream(), and gnFASSource::ParseStream().

boolean gnFileContig::SetSectStart ( const gnContigSection i, const uint64 s ) [inline]

Definition at line 164 of file gnFileContig.h. 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 184 of file gnFileContig.h.

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

Definition at line 134 of file gnFileContig.h. Referenced by gnSEQSource::ParseStream(), gnRAWSource::ParseStream(), and gnGBKSource::ParseStream().

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Member Data Documentation

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

Definition at line 67 of file gnFileContig.h.

string gnFileContig::m_name [private]

Definition at line 65 of file gnFileContig.h.

boolean gnFileContig::m_repeatSeqGap [private]

Definition at line 71 of file gnFileContig.h.

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

Definition at line 72 of file gnFileContig.h.

gnSeqI gnFileContig::m_seqLength [private]

Definition at line 66 of file gnFileContig.h.

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

Definition at line 69 of file gnFileContig.h.

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

• gnFileContig.h
• gnFileContig.cpp

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