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Public Types | Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes

CFaLookup Class Reference

Inheritance diagram for CFaLookup:
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Collaboration diagram for CFaLookup:
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List of all members.

Public Types

enum  EPrimerEnd { eLeft = 'l', eRight = 'r' }
typedef std::string string
typedef Uint8 TBigCount
typedef vector< TBigCount > TBranchStat
typedef std::vector< THashTable > TData
typedef Int4 THashElement
typedef std::vector< THashElement > THashList
typedef std::vector< THashList > THashTable
typedef std::vector< SFileDescTPathLst
typedef std::vector< SSeqDescTSeqLst
typedef vector< vector
< TBigCount > > 
TStatVector
typedef list< ISts * > TStsList

Public Member Functions

void AttachFile (const string &path)
TBigCount CalcStat (const char *primer, unsigned wd=0)
TBigCount CalcStat (THashElement hashval, unsigned wd=0)
void Find (IFaLookupCallback *cbk, ISts *sts, int window=0)
void Find (IFaLookupCallback *cbk, const TStsList &sts, bool syscall_optimize=true, int window=0)
void Find (IFaLookupCallback *cbk, const string &label, char report_strand, const string &primer)
const CHashSetGetHash () const
TBigCount GetStat (THashElement hashval, unsigned wd=0)
const TStatVector & GetStat () const
TBigCount GetStat (const char *primer, unsigned wd=0)
void SetAligner (IAlign *left, IAlign *right)
void Stat ()

Public Attributes

TPathLst m_Fapath
CHashSet m_Hash
TSeqLst m_Seqlst
std::vector< std::pair
< off64_t, off64_t > > 
m_Tabloc

Protected Member Functions

off64_t GetHashEntries (const char *table, off64_t tab_off, unsigned word, THashElement value, unsigned &size) const
void InitTableOffsets ()

Protected Attributes

IAlignm_AlignL
IAlignm_AlignR
TStatVector m_Counts
Uint4 m_ElSize
int m_Fd
vector< Uint4 > m_TableOffset
Uint4 m_Version

Detailed Description

Definition at line 184 of file fahash.hpp.


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

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