StochHMM::ambigCharacter Class Reference

Define the ambiguous characters symbol and index number for digitizing ambiguous characters in the sequence For example in DNA N = [ACGT] = [0,1,2,3]. More...

#include <track.h>

List of all members.

Public Member Functions
	ambigCharacter (track *, std::string &, std::vector< std::string > &)
std::string	getSymbol ()
std::vector< size_t > &	getDef ()

Private Attributes
std::string	symbol
std::vector< size_t >	setDefinition

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Detailed Description

Define the ambiguous characters symbol and index number for digitizing ambiguous characters in the sequence For example in DNA N = [ACGT] = [0,1,2,3].

Definition at line 60 of file track.h.

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Constructor & Destructor Documentation

StochHMM::ambigCharacter::ambigCharacter	(	track *	tr,
		std::string &	ambChar,
		std::vector< std::string > &	defs
	)

Create an ambiguous character For example in DNA N = [ACGT] = [0,1,2,3]

Parameters:

tr	Track to use for ambiguity code
ambChar	String representation of the character/symbol/word for ambiguous character
defs	vector of strings where each string is a non-ambiguous character defined in the track

Definition at line 36 of file track.cpp.

References setDefinition, symbol, and StochHMM::track::symbolIndex().

                                                                                           {
        symbol=ambChar;
        for(size_t i=0;i<defs.size();i++){
            setDefinition.push_back(tr->symbolIndex(defs[i]));
        }
        sort(setDefinition.begin(),setDefinition.end());
        return;
    }

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Member Function Documentation

std::vector<size_t>& StochHMM::ambigCharacter::getDef ( )

inline

Get the characters that the characters defines. For example in DNA N = [ACGT] = [0,1,2,3]

Returns:

std::vector<int> Digitized value of characters that are represented by the given symbol

Definition at line 74 of file track.h.

{return setDefinition;};

std::string StochHMM::ambigCharacter::getSymbol ( )

inline

Get Ambiguous String/Alphabet character symbol

Returns:

std::string Symbol of character/word

Definition at line 67 of file track.h.

References symbol.

{return symbol;};

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Member Data Documentation

std::vector<size_t> StochHMM::ambigCharacter::setDefinition

private

Definition at line 78 of file track.h.

Referenced by ambigCharacter().

std::string StochHMM::ambigCharacter::symbol

private

Definition at line 74 of file track.h.

Referenced by ambigCharacter(), and getSymbol().

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

• track.h
• track.cpp