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:

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Collaboration diagram for gnFileContig:

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List of all members.

Public Member Functions

boolean AddToSeqLength (const gnSeqI len)
void Clear ()
gnFileContigClone () const
uint64 GetFileLength () const
pair< uint64, uint64GetFileStartEnd () const
string GetName () const
pair< uint32, uint32GetRepeatSeqGapSize () const
uint64 GetSectLength (gnContigSection i) const
pair< uint64, uint64GetSectStartEnd (const gnContigSection i) const
gnSeqI GetSeqLength () const
 gnFileContig (const gnFileContig &fc)
 gnFileContig (string nameStr, const uint64 pos, const uint64 len)
 gnFileContig ()
boolean HasRepeatSeqGap () const
boolean SetFileEnd (const uint64 e)
boolean SetFileStart (const uint64 s)
boolean SetFileStartEnd (const pair< uint64, uint64 > se)
boolean SetName (string nameStr)
boolean SetRepeatGapSize (const uint64 gapSize)
boolean SetRepeatSeqGap (const boolean rsg)
boolean SetRepeatSeqGapSize (const pair< uint64, uint64 > rsgSize)
boolean SetRepeatSeqSize (const uint64 seqSize)
boolean SetSectEnd (const gnContigSection i, const uint64 e)
boolean SetSectStart (const gnContigSection i, const uint64 s)
boolean SetSectStartEnd (const gnContigSection i, const pair< uint64, uint64 > se)
boolean SetSeqLength (const gnSeqI len)
 ~gnFileContig ()

Private Attributes

pair< uint64, uint64m_fileStartEnd
string m_name
boolean m_repeatSeqGap
pair< uint64, uint64m_repeatSeqGapSize
gnSeqI m_seqLength
pair< uint64, uint64m_startEndArray [CONTIG_SECTION_SIZE]

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, m_name, and uint64.

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 gnSeqI, and 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.

Referenced by main().

string gnFileContig::GetName  )  const [inline]
 

Definition at line 80 of file gnFileContig.h.

References m_name.

Referenced by main().

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

Definition at line 119 of file gnFileContig.h.

References m_repeatSeqGapSize.

Referenced by main(), 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, uint32, and uint64.

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

Definition at line 100 of file gnFileContig.h.

References CONTIG_SECTION_SIZE, m_startEndArray, and uint32.

Referenced by main(), 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(), and main().

boolean gnFileContig::HasRepeatSeqGap  )  const [inline]
 

Definition at line 114 of file gnFileContig.h.

References m_repeatSeqGap.

Referenced by main(), 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, and uint64.

Referenced by gnFASSource::ParseStream().

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

Definition at line 143 of file gnFileContig.h.

References m_fileStartEnd, and uint64.

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, m_repeatSeqGapSize, and uint64.

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, m_repeatSeqGapSize, and uint64.

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, m_startEndArray, uint32, and uint64.

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, m_startEndArray, uint32, and uint64.

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, m_startEndArray, and uint32.

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

Definition at line 131 of file gnFileContig.h.

References gnSeqI, and 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 Mon Feb 14 19:29:51 2005 for libGenome by doxygen 1.3.8