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mems::RepeatHash Class Reference

Finds repeats within a single sequence. More...

#include <RepeatHash.h>

Inheritance diagram for mems::RepeatHash:

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Collaboration diagram for mems::RepeatHash:

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List of all members.

Public Member Functions

virtual RepeatHash * Clone () const
virtual boolean CreateMatches ()
 Generates exact matches for the sequences loaded into this MemHash.


Protected Member Functions

virtual boolean EnumerateMatches (IdmerList &match_list)
virtual SortedMerList * GetSar (uint32 sarI) const
virtual boolean HashMatch (IdmerList &match_list)
 Called whenever a mer match is found.

Detailed Description

Finds repeats within a single sequence.

This class extends the functionality of MemHash to search for repetitive matches within a single sequence.

Definition at line 25 of file RepeatHash.h.

Member Function Documentation

RepeatHash * mems::RepeatHash::Clone (   )  const [virtual]
 

Reimplemented from mems::MemHash.

Definition at line 21 of file RepeatHash.cpp.

boolean mems::RepeatHash::CreateMatches (   )  [virtual]
 

Generates exact matches for the sequences loaded into this MemHash.

Reimplemented from mems::MemHash.

Definition at line 25 of file RepeatHash.cpp.

boolean mems::RepeatHash::EnumerateMatches (  IdmerList &  match_list  )  [protected, virtual]
 

Reimplemented from mems::MemHash.

Definition at line 34 of file RepeatHash.cpp.

References HashMatch(), and mems::IdmerList.

SortedMerList * mems::RepeatHash::GetSar (  uint32  sarI  )  const [inline, protected, virtual]
 

Reimplemented from mems::MatchFinder.

Definition at line 38 of file RepeatHash.h.

References mems::uint32.

Referenced by HashMatch().

boolean mems::RepeatHash::HashMatch (  IdmerList &  match_list  )  [protected, virtual]
 

Called whenever a mer match is found.

Reimplemented from mems::MemHash.

Definition at line 40 of file RepeatHash.cpp.

References mems::MemHash::AddHashEntry(), mems::MatchHashEntry::CalculateOffset(), GetSar(), mems::idmer_position_lessthan(), mems::IdmerList, mems::SortedMerList::SeedLength(), mems::MemHash::SetDirection(), mems::UngappedLocalAlignment< AbstractMatchImpl >::SetLength(), and mems::uint32.

Referenced by EnumerateMatches().

The documentation for this class was generated from the following files:
Generated on Fri Mar 14 06:01:43 2008 for libMems by doxygen 1.3.6