src/Alignment.h File Reference

#include "libMems/gnAlignedSequences.h"
#include "libMems/Aligner.h"
#include "libGenome/gnSequence.h"
#include <vector>
#include "GisSplayTree.h"
#include "libMems/PhyloTree.h"

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Classes
class	Alignment
class	LCBLeftComparator
	Compares left_end coordinate of two LCBs. More...
class	SourceInterval
	This class describes an interval of a mutated sequence The interval of sequence is either a range of sequence from another source or is a string of gaps The GappedIntervalSequence will be a search tree of these that tracks sequence coordinates through insertions and deletions, allowing fast lookup of ungapped sequence coordinates in a gapped sequence. More...
Defines
#define	GappedIntervalSequence   GisSplayTree
Functions
	CREATE_EXCEPTION (EvolutionError)
int	debugCheckingLevel (int level_request=-1)
	Sets or checks the level of extra debug checking to perform.
bool	debugChecks (int set=-1)
	An auxiliary function to help debug checking.

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Define Documentation

#define GappedIntervalSequence   GisSplayTree

Definition at line 16 of file Alignment.h.

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Function Documentation

CREATE_EXCEPTION (  EvolutionError   )

int debugCheckingLevel (  int  level_request = -1  )

Sets or checks the level of extra debug checking to perform. 0 indicates no checking 1 indicates intermittent checks 2 specifies data structure consistency checks after every mutation operation This can be set using the --debug-checking=# command line switch Setting this to 2 will make the program _very_ slow Definition at line 15 of file Alignment.cpp. Referenced by AlignmentEvolver::evolve(), main(), and Alignment::writeAlignment().

bool debugChecks (  int  set = -1  )

An auxiliary function to help debug checking. Definition at line 24 of file Alignment.cpp. Referenced by Alignment::applyInversions(), AlignmentEvolver::evolve(), Deleter::mutate(), and Inserter::mutate().

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