AlignEntry Class Reference

#include <align.hpp>

List of all members.

Public Member Functions
	AlignEntry (long i, long j)
	AlignEntry ()
	operator const AlignState () const
Public Attributes
Pair	pair
double	posterior

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Detailed Description

An entry for each atom of an alignment. Extend this class to obtain a richer set of information for each alignment.

Definition at line 148 of file align.hpp.

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Constructor & Destructor Documentation

AlignEntry::AlignEntry	(	long	i,
		long	j
	)			[inline]

construct a pair of positons for alignments. sets posterior to 0

Parameters:

	i	position in the first sequence (-1 for deletions)
	j	position in the second sequence (-1 for insertions)

Definition at line 167 of file align.hpp.

AlignEntry::AlignEntry

(

)

[inline]

default constructor sets pair.i=-1, pair.j=-1 and posterior = 0

Definition at line 172 of file align.hpp.

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Member Function Documentation

AlignEntry::operator const AlignState

(

)

const [inline]

cast operator to type AlignState

Returns:

StateInsert if pair.i == -1, StateDelete if pair.j == -1 and StateMatch otherwise

Definition at line 178 of file align.hpp.

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Member Data Documentation

Pair AlignEntry::pair

Pair of positions in the sequnce. pair.i == -1 deletions pair.j == -1 insertions pair.i != -1 and pair.j != -1 match

Definition at line 156 of file align.hpp.

double AlignEntry::posterior

posterior probability

Definition at line 160 of file align.hpp.

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

• src/align.hpp