Alignment Class Reference

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Detailed Description

Definition at line 66 of file Alignment.hpp.

#include <Alignment.hpp>

List of all members.

Public Member Functions
	Alignment (AlignmentParams *params)
	Alignment (const Alignment &orig)
virtual	~Alignment ()
void	addGapInSeq0 (int i)
void	addGapInSeq1 (int j)
void	finalize ()
bool	isFinalized ()
vector< gap_sequence_t > *	getGapSequences ()
AlignmentParams *	getAlignmentParams () const
int	getRawScore () const
void	setRawScore (int rawScore)
vector< gap_t > *	getGaps (int seq)
void	setStart (int seq, int pos)
void	setEnd (int seq, int pos)
int	getStart (int seq)
int	getEnd (int seq)
string	getPruningFile () const
void	setPruningFile (string pruningFile)
int	getGapExtensions () const
void	setGapExtensions (int gapExtensions)
int	getGapOpen () const
void	setGapOpen (int gapOpen)
int	getMatches () const
void	setMatches (int matches)
int	getMismatches () const
void	setMismatches (int mismatches)
Private Member Functions
void	addGap (int seq, int i)
Private Attributes
int	start [2]
int	end [2]
int	rawScore
int	matches
int	mismatches
int	gapOpen
int	gapExtensions
bool	alignmentFinalized
AlignmentParams *	params
vector< gap_t >	gaps [2]
vector< gap_sequence_t >	gap_sequences
string	pruningFile

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Constructor & Destructor Documentation

Alignment::Alignment

(

AlignmentParams *

params

)

Definition at line 34 of file Alignment.cpp.

Alignment::Alignment

(

const Alignment &

orig

)

Definition at line 38 of file Alignment.cpp.

Alignment::~Alignment

(

)

[virtual]

Definition at line 42 of file Alignment.cpp.

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Member Function Documentation

void Alignment::addGap	(	int	seq,
		int	i
	)		[private]

Definition at line 208 of file Alignment.cpp.

void Alignment::addGapInSeq0

(

int

i

)

Definition at line 46 of file Alignment.cpp.

void Alignment::addGapInSeq1

(

int

j

)

Definition at line 50 of file Alignment.cpp.

void Alignment::finalize

(

)

Definition at line 115 of file Alignment.cpp.

AlignmentParams * Alignment::getAlignmentParams

(

)

const

Definition at line 140 of file Alignment.cpp.

int Alignment::getEnd

(

int

seq

)

Definition at line 164 of file Alignment.cpp.

int Alignment::getGapExtensions

(

)

const

Definition at line 176 of file Alignment.cpp.

int Alignment::getGapOpen

(

)

const

Definition at line 184 of file Alignment.cpp.

vector<gap_t>* Alignment::getGaps

(

int

seq

)

[inline]

Definition at line 85 of file Alignment.hpp.

vector< gap_sequence_t > * Alignment::getGapSequences

(

)

Definition at line 54 of file Alignment.cpp.

int Alignment::getMatches

(

)

const

Definition at line 192 of file Alignment.cpp.

int Alignment::getMismatches

(

)

const

Definition at line 200 of file Alignment.cpp.

string Alignment::getPruningFile

(

)

const

Definition at line 168 of file Alignment.cpp.

int Alignment::getRawScore

(

)

const

Definition at line 144 of file Alignment.cpp.

int Alignment::getStart

(

int

seq

)

Definition at line 160 of file Alignment.cpp.

bool Alignment::isFinalized

(

)

Definition at line 128 of file Alignment.cpp.

void Alignment::setEnd	(	int	seq,
		int	pos
	)

Definition at line 156 of file Alignment.cpp.

void Alignment::setGapExtensions

(

int

gapExtensions

)

Definition at line 180 of file Alignment.cpp.

void Alignment::setGapOpen

(

int

gapOpen

)

Definition at line 188 of file Alignment.cpp.

void Alignment::setMatches

(

int

matches

)

Definition at line 196 of file Alignment.cpp.

void Alignment::setMismatches

(

int

mismatches

)

Definition at line 204 of file Alignment.cpp.

void Alignment::setPruningFile

(

string

pruningFile

)

Definition at line 172 of file Alignment.cpp.

void Alignment::setRawScore

(

int

rawScore

)

Definition at line 148 of file Alignment.cpp.

void Alignment::setStart	(	int	seq,
		int	pos
	)

Definition at line 152 of file Alignment.cpp.

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Member Data Documentation

bool Alignment::alignmentFinalized [private]

Definition at line 114 of file Alignment.hpp.

int Alignment::end[2] [private]

Definition at line 106 of file Alignment.hpp.

vector<gap_sequence_t> Alignment::gap_sequences [private]

Definition at line 118 of file Alignment.hpp.

int Alignment::gapExtensions [private]

Definition at line 112 of file Alignment.hpp.

int Alignment::gapOpen [private]

Definition at line 111 of file Alignment.hpp.

vector<gap_t> Alignment::gaps[2] [private]

Definition at line 117 of file Alignment.hpp.

int Alignment::matches [private]

Definition at line 109 of file Alignment.hpp.

int Alignment::mismatches [private]

Definition at line 110 of file Alignment.hpp.

AlignmentParams* Alignment::params [private]

Definition at line 115 of file Alignment.hpp.

string Alignment::pruningFile [private]

Definition at line 119 of file Alignment.hpp.

int Alignment::rawScore [private]

Definition at line 108 of file Alignment.hpp.

int Alignment::start[2] [private]

Definition at line 105 of file Alignment.hpp.

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

• Alignment.hpp
• Alignment.cpp