Sequence::stateCounter Class Reference
[Function objects defined in the library]

keep track of state counts at a site in an alignment or along a sequence More...

#include <Sequence/stateCounter.hpp>

List of all members.

Public Member Functions
	stateCounter (const char &gapchar= '-')
void	operator() (const char &ch) const
unsigned	nStates (void) const
Public Attributes
unsigned	a
unsigned	g
unsigned	c
unsigned	t
unsigned	zero
unsigned	one
unsigned	gap
unsigned	n
bool	ndna

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Detailed Description

keep track of state counts at a site in an alignment or along a sequence

Warning:

class data are public. Use responsibly.

Examples:

baseComp.cc.

Definition at line 39 of file stateCounter.hpp.

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Constructor & Destructor Documentation

Sequence::stateCounter::stateCounter

(

const char &

gapchar = '-'

)

Parameters:

gapchar

charcter representing a gap in an alignment

Definition at line 57 of file stateCounter.cc.

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Member Function Documentation

unsigned Sequence::stateCounter::nStates

(

void

)

const

Returns:

the number of states counted, excluding gaps and missing data

Definition at line 106 of file stateCounter.cc.

void Sequence::stateCounter::operator()

(

const char &

ch

)

const

Parameters:

ch

the character in position i,j in an alignment

Definition at line 64 of file stateCounter.cc.

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Member Data Documentation

unsigned Sequence::stateCounter::a [mutable]

the number of times the character 'a' or 'A' has been counted

Examples:

baseComp.cc.

Definition at line 44 of file stateCounter.hpp.

unsigned Sequence::stateCounter::c [mutable]

the number of times the character 'c' or 'C' has been counted

Examples:

baseComp.cc.

Definition at line 44 of file stateCounter.hpp.

unsigned Sequence::stateCounter::g [mutable]

the number of times the character 'g' or 'G' has been counted

Examples:

baseComp.cc.

Definition at line 44 of file stateCounter.hpp.

unsigned Sequence::stateCounter::gap [mutable]

the number of times the gap character has been counted

Examples:

baseComp.cc.

Definition at line 44 of file stateCounter.hpp.

unsigned Sequence::stateCounter::n [mutable]

the number of times the missing data character 'N' has been counted

Examples:

baseComp.cc.

Definition at line 44 of file stateCounter.hpp.

bool Sequence::stateCounter::ndna [mutable]

true if a non-DNA character has been encountered, false otherwise

Examples:

baseComp.cc.

Definition at line 45 of file stateCounter.hpp.

unsigned Sequence::stateCounter::one [mutable]

the number of times the character '1' has been counted

Definition at line 44 of file stateCounter.hpp.

unsigned Sequence::stateCounter::t [mutable]

the number of times the character 't' or 'T' has been counted

Examples:

baseComp.cc.

Definition at line 44 of file stateCounter.hpp.

unsigned Sequence::stateCounter::zero [mutable]

the number of times the character '0' has been counted

Definition at line 44 of file stateCounter.hpp.

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

• stateCounter.hpp
• stateCounter.cc