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.


Define Documentation

#define GappedIntervalSequence   GisSplayTree
 

Definition at line 16 of file Alignment.h.


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().


Generated on Mon Aug 19 06:00:51 2013 for sgEvolver by doxygen 1.3.6