Sequence Class Reference

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Detailed Description

Definition at line 34 of file Sequence.hpp.

#include <Sequence.hpp>

List of all members.

Public Member Functions
	Sequence (SequenceInfo *info, SequenceModifiers *modifiers)
	Sequence (const Sequence *orig)
virtual	~Sequence ()
void	copyData (const Sequence *orig)
void	trim (int delta0, int delta1)
void	reverse ()
int	getAbsolutePos (int relativePos) const
int	getLen () const
int	getTrimStart () const
int	getTrimEnd () const
SequenceInfo *	getInfo () const
void	setInfo (SequenceInfo *info)
SequenceModifiers *	getModifiers () const
const char *	getData (bool reverse=false) const
const char *	getForwardData () const
const char *	getReverseData () const
bool	isReversed () const
Private Member Functions
void	setBoundaries (int trimStart, int trimEnd)
Private Attributes
SequenceInfo *	info
SequenceModifiers *	modifiers
SequenceData *	data
int	reverseData
int	offset0
int	offset1
int	len
bool	dataOwner

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Constructor & Destructor Documentation

Sequence::Sequence	(	SequenceInfo *	info,
		SequenceModifiers *	modifiers
	)

Definition at line 28 of file Sequence.cpp.

Sequence::Sequence

(

const Sequence *

orig

)

Definition at line 56 of file Sequence.cpp.

Sequence::~Sequence

(

)

[virtual]

Definition at line 69 of file Sequence.cpp.

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Member Function Documentation

void Sequence::copyData

(

const Sequence *

orig

)

Definition at line 77 of file Sequence.cpp.

int Sequence::getAbsolutePos

(

int

relativePos

)

const

Definition at line 140 of file Sequence.cpp.

const char * Sequence::getData

(

bool

reverse = false

)

const

Definition at line 172 of file Sequence.cpp.

const char * Sequence::getForwardData

(

)

const

Definition at line 180 of file Sequence.cpp.

SequenceInfo * Sequence::getInfo

(

)

const

Definition at line 152 of file Sequence.cpp.

int Sequence::getLen

(

)

const

Definition at line 93 of file Sequence.cpp.

SequenceModifiers * Sequence::getModifiers

(

)

const

Definition at line 160 of file Sequence.cpp.

const char * Sequence::getReverseData

(

)

const

Definition at line 185 of file Sequence.cpp.

int Sequence::getTrimEnd

(

)

const

Definition at line 168 of file Sequence.cpp.

int Sequence::getTrimStart

(

)

const

Definition at line 164 of file Sequence.cpp.

bool Sequence::isReversed

(

)

const

Definition at line 148 of file Sequence.cpp.

void Sequence::reverse

(

)

Definition at line 98 of file Sequence.cpp.

void Sequence::setBoundaries	(	int	trimStart,
		int	trimEnd
	)		[private]

Definition at line 126 of file Sequence.cpp.

void Sequence::setInfo

(

SequenceInfo *

info

)

Definition at line 156 of file Sequence.cpp.

void Sequence::trim	(	int	delta0,
		int	delta1
	)

Definition at line 102 of file Sequence.cpp.

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Member Data Documentation

SequenceData* Sequence::data [private]

Definition at line 76 of file Sequence.hpp.

bool Sequence::dataOwner [private]

Definition at line 84 of file Sequence.hpp.

SequenceInfo* Sequence::info [private]

Definition at line 74 of file Sequence.hpp.

int Sequence::len [private]

Definition at line 82 of file Sequence.hpp.

SequenceModifiers* Sequence::modifiers [private]

Definition at line 75 of file Sequence.hpp.

int Sequence::offset0 [private]

Definition at line 80 of file Sequence.hpp.

int Sequence::offset1 [private]

Definition at line 81 of file Sequence.hpp.

int Sequence::reverseData [private]

Definition at line 79 of file Sequence.hpp.

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

• Sequence.hpp
• Sequence.cpp