mems::RepeatMatchList Class Reference

#include <RepeatMatchList.h>

Inheritance diagram for mems::RepeatMatchList:

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Collaboration diagram for mems::RepeatMatchList:

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List of all members.

Public Member Functions

void LoadSequences (std::ostream *log_stream)
void LoadSMLs (uint mer_size, std::ostream *log_stream)
void ReadList (std::istream &match_stream)
 Reads a MatchList from an input stream Sequence and SML file names are read into the seq_filename and sml_filename vectors, but the actual files are not opened.

 RepeatMatchList (const RepeatMatchList &ml)
 RepeatMatchList ()
void WriteList (std::ostream &match_stream) const
 Writes a MatchList to the designated output stream.


Constructor & Destructor Documentation

mems::RepeatMatchList::RepeatMatchList  ) 
 

Definition at line 28 of file RepeatMatchList.cpp.

References mems::MatchList.

mems::RepeatMatchList::RepeatMatchList const RepeatMatchList ml  ) 
 


Member Function Documentation

void mems::RepeatMatchList::LoadSequences std::ostream *  log_stream  ) 
 

Definition at line 33 of file RepeatMatchList.cpp.

References uint.

void mems::RepeatMatchList::LoadSMLs uint  mer_size,
std::ostream *  log_stream
 

Definition at line 73 of file RepeatMatchList.cpp.

References mems::GenericMatchList< MatchPtrType >::GetDefaultMerSize(), getSolidSeed(), mems::FileSML::LoadFile(), mems::SortedMerList::Seed(), uint, and mems::uint64.

void mems::RepeatMatchList::ReadList std::istream &  match_stream  ) 
 

Reads a MatchList from an input stream Sequence and SML file names are read into the seq_filename and sml_filename vectors, but the actual files are not opened.

The calling function should load them after using this method.

Parameters:
match_stream The input stream to read from

Definition at line 155 of file RepeatMatchList.cpp.

References mems::MatchHashEntry::CalculateOffset(), mems::MatchHashEntry::Copy(), mems::Match, mems::MatchID_t, mems::UngappedLocalAlignment< AbstractMatchImpl >::SetLength(), uint, and mems::uint32.

void mems::RepeatMatchList::WriteList std::ostream &  match_stream  )  const
 

Writes a MatchList to the designated output stream.

Parameters:
match_stream The output stream to write to

Definition at line 251 of file RepeatMatchList.cpp.

References mems::Match, and mems::MatchID_t.


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