mems::SimpleBreakpointScorer Class Reference

A breakpoint scorer that applies a fixed penalty for each breakpoint that exists in a set of two or more sequences. More...

#include <GreedyBreakpointElimination.h>

List of all members.

Public Member Functions
size_t	getMoveCount ()
bool	isValid (size_t lcbI, double move_score)
double	operator() (size_t lcbI)
	return the relative change in score if lcbI were to be removed
void	remove (uint lcbI, std::vector< std::pair< double, size_t > > &new_moves)
	call to indicate that the given LCB has been removed
double	score ()
	SimpleBreakpointScorer (std::vector< LCB > &adjacencies, double breakpoint_penalty, bool collinear)
Private Attributes
std::vector< mems::LCB >	adjs
size_t	bp_count
double	bp_penalty
bool	collinear
std::vector< double >	scores
double	total_weight

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Detailed Description

A breakpoint scorer that applies a fixed penalty for each breakpoint that exists in a set of two or more sequences.

Definition at line 596 of file GreedyBreakpointElimination.h.

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Constructor & Destructor Documentation

mems::SimpleBreakpointScorer::SimpleBreakpointScorer (  std::vector< LCB > &  adjacencies, double  breakpoint_penalty, bool  collinear )

Definition at line 877 of file GreedyBreakpointElimination.cpp. References adjs, bp_count, scores, and total_weight.

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Member Function Documentation

size_t mems::SimpleBreakpointScorer::getMoveCount (   )

Definition at line 889 of file GreedyBreakpointElimination.cpp. References adjs.

bool mems::SimpleBreakpointScorer::isValid (  size_t  lcbI, double  move_score )

Definition at line 900 of file GreedyBreakpointElimination.cpp. References adjs.

double mems::SimpleBreakpointScorer::operator() (  size_t  lcbI  )

return the relative change in score if lcbI were to be removed Definition at line 908 of file GreedyBreakpointElimination.cpp. References adjs, bp_count, collinear, mems::RemoveLCBandCoalesce(), score(), scores, total_weight, uint, and mems::undoLcbRemoval().

void mems::SimpleBreakpointScorer::remove (  uint  lcbI, std::vector< std::pair< double, size_t > > &  new_moves )

call to indicate that the given LCB has been removed Definition at line 924 of file GreedyBreakpointElimination.cpp. References adjs, bp_count, mems::RemoveLCBandCoalesce(), scores, total_weight, and uint.

double mems::SimpleBreakpointScorer::score (   )

Definition at line 894 of file GreedyBreakpointElimination.cpp. References bp_count, and total_weight. Referenced by operator()().

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Member Data Documentation

std::vector< mems::LCB > mems::SimpleBreakpointScorer::adjs [private]

Definition at line 614 of file GreedyBreakpointElimination.h. Referenced by getMoveCount(), isValid(), operator()(), remove(), and SimpleBreakpointScorer().

size_t mems::SimpleBreakpointScorer::bp_count [private]

Definition at line 618 of file GreedyBreakpointElimination.h. Referenced by operator()(), remove(), score(), and SimpleBreakpointScorer().

double mems::SimpleBreakpointScorer::bp_penalty [private]

Definition at line 615 of file GreedyBreakpointElimination.h.

bool mems::SimpleBreakpointScorer::collinear [private]

Definition at line 619 of file GreedyBreakpointElimination.h. Referenced by operator()().

std::vector< double > mems::SimpleBreakpointScorer::scores [private]

Definition at line 616 of file GreedyBreakpointElimination.h. Referenced by operator()(), remove(), and SimpleBreakpointScorer().

double mems::SimpleBreakpointScorer::total_weight [private]

Definition at line 617 of file GreedyBreakpointElimination.h. Referenced by operator()(), remove(), score(), and SimpleBreakpointScorer().

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

• libMems/GreedyBreakpointElimination.h
• libMems/GreedyBreakpointElimination.cpp

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