SequenceListImpl Class Reference

#include <sequence_list_impl.hh>

Public Types
typedef SequenceImplListConstIterator	ConstIterator
typedef SequenceImplListIterator	Iterator

Public Member Functions
	SequenceListImpl ()
void	AddSequence (const SequenceImplPtr &sequence)
int	GetCount () const
SequenceImplPtr &	GetSequence (int i)
const SequenceImplPtr &	GetSequence (unsigned int i) const
void	RemoveSequence (int index)
int	GetPos (int seq_index, int residue_index) const
int	GetResidueIndex (int seq_index, int pos) const
SequenceImplPtr	FindSequence (const String &name) const
int	FindSequenceIndex (const String &name) const
String	ToString (int width=80) const
SequenceListImplPtr	Slice (int first, int n) const
int	GetMinLength () const
int	GetMaxLength () const
bool	SequencesHaveEqualLength () const
Real	GetCoverage (int seq_index) const
SequenceListImplPtr	Copy () const
Iterator	Begin ()
Iterator	End ()
ConstIterator	Begin () const
ConstIterator	End () const

Detailed Description

Definition at line 33 of file sequence_list_impl.hh.

Member Typedef Documentation

typedef SequenceImplListConstIterator ConstIterator

Definition at line 35 of file sequence_list_impl.hh.

typedef SequenceImplListIterator Iterator

Definition at line 36 of file sequence_list_impl.hh.

Constructor & Destructor Documentation

SequenceListImpl ( )

inline

Definition at line 37 of file sequence_list_impl.hh.

Member Function Documentation

void AddSequence

(

const SequenceImplPtr &

sequence

)

add sequence

Iterator Begin ( )

inline

Definition at line 87 of file sequence_list_impl.hh.

ConstIterator Begin ( ) const

inline

Definition at line 89 of file sequence_list_impl.hh.

SequenceListImplPtr Copy

(

)

const

Iterator End ( )

inline

Definition at line 88 of file sequence_list_impl.hh.

ConstIterator End ( ) const

inline

Definition at line 90 of file sequence_list_impl.hh.

SequenceImplPtr FindSequence

(

const String &

name

)

const

int FindSequenceIndex

(

const String &

name

)

const

int GetCount ( ) const

inline

get number of sequences in list

Definition at line 42 of file sequence_list_impl.hh.

Real GetCoverage

(

int

seq_index

)

const

int GetMaxLength

(

)

const

int GetMinLength

(

)

const

int GetPos	(	int	seq_index,
		int	residue_index
	)		const

int GetResidueIndex	(	int	seq_index,
		int	pos
	)		const

SequenceImplPtr& GetSequence ( int  i )

inline

Definition at line 44 of file sequence_list_impl.hh.

const SequenceImplPtr& GetSequence ( unsigned int  i ) const

inline

Definition at line 52 of file sequence_list_impl.hh.

void RemoveSequence

(

int

index

)

bool SequencesHaveEqualLength ( ) const

inline

Definition at line 78 of file sequence_list_impl.hh.

SequenceListImplPtr Slice	(	int	first,
		int	n
	)		const

String ToString

(

int

width = 80

)

const

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

• stage/include/ost/seq/impl/sequence_list_impl.hh