mems::RepeatMatchList Class Reference

#include <RepeatMatchList.h>

Inheritance diagram for mems::RepeatMatchList:

[legend]Collaboration diagram for mems::RepeatMatchList:

[legend]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.

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Constructor & Destructor Documentation

mems::RepeatMatchList::RepeatMatchList (   )

Definition at line 28 of file RepeatMatchList.cpp. References mems::MatchList.

mems::RepeatMatchList::RepeatMatchList (  const RepeatMatchList &  ml  )

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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.

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

• libMems/RepeatMatchList.h
• libMems/RepeatMatchList.cpp

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