#include <alignment_handle.hh>

Public Types
typedef AlignedColumnIterator	iterator

Public Member Functions
	AlignmentHandle ()
int	GetPos (int seq_index, int residue_index) const
int	GetResidueIndex (int seq_index, int pos) const
mol::ResidueView	GetResidue (int seq_index, int pos) const
char	GetOneLetterCode (int seq_index, int pos) const
void	AddSequence (const ConstSequenceHandle &sequence)
ConstSequenceHandle	GetSequence (int seq_id) const
void	RemoveSequence (int seq_index)
String	ToString (int width=80) const
int	GetLength () const
AlignmentHandle	Copy () const
ConstSequenceHandle	FindSequence (const String &name) const
void	AttachView (int seq_index, const mol::EntityView &view)
void	AttachView (int seq_index, const mol::EntityView &view, const String &chain_name)
void	SetSequenceName (int seq_index, const String &name)
void	SetSequenceOffset (int seq_index, int offset)
int	GetSequenceOffset (int seq_index)
ConstSequenceList	GetSequences () const
AlignedRegion	MakeRegion (int start, int n, int master=-1) const
int	GetCount () const
bool	operator== (const AlignmentHandle &rhs) const
bool	operator!= (const AlignmentHandle &rhs) const
AlignedColumn	operator[] (int index) const
	AlignmentHandle (const impl::SequenceListImplPtr &impl)
void	Cut (int start, int end)
void	Replace (const AlignedRegion &rhs, int start, int end)
void	ShiftRegion (int start, int end, int amount, int master=-1)
iterator	begin () const
iterator	end () const
bool	IsValid () const
Real	GetCoverage (int seq_index) const

Detailed Description

representation of a multiple sequence alignemnt consisting of two or more sequences

A sequence alignment consists of two or more sequences. The number of sequences in the alignment can be obtained by GetCount(). All sequences are of length GetLength().

Typically sequence alignments are used column-based, i.e by looking at an aligned columns in the sequence alignment. To get a row-based (sequence) view on the sequence list, use AlignmentHandle::GetSequenceList(). For an overview of how to use the sequence module, see here

All operators that operate on an alignment will again produce a valid alignment. This mean that it is not possible to change the length of one sequence, without adjusting the other sequences, too.

Definition at line 53 of file alignment_handle.hh.

Member Typedef Documentation

typedef AlignedColumnIterator iterator

Definition at line 56 of file alignment_handle.hh.

Constructor & Destructor Documentation

AlignmentHandle ( )

AlignmentHandle ( const impl::SequenceListImplPtr & impl )

Member Function Documentation

void AddSequence ( const ConstSequenceHandle & sequence )

Add new sequence to multiple sequence alignment.

If the sequence length does not match with the length of the other sequences in the alignment, an InvalidSequence() exception is thrown.

void AttachView	(	int	seq_index,
		const mol::EntityView &	view
	)

attach view to given sequence

See also:: SequenceHandle::AttachView(const mol::EntityView&)

void AttachView	(	int	seq_index,
		const mol::EntityView &	view,
		const String &	chain_name
	)

attach view to given sequence

See also:: SequenceHandle::AttachView(const mol::EntityView&, const String&)

iterator begin ( ) const

Column iterator start-point.

AlignmentHandle Copy ( ) const

deep-copy multi sequence alignment

void Cut	(	int	start,
		int	end
	)

cut out half-closed interval start, end

iterator end ( ) const

Column iterator end-point.

ConstSequenceHandle FindSequence ( const String & name ) const

find sequence by name.

If several sequences have the same name, the first matching sequence will be returned.

int GetCount ( ) const

get number of sequences in alignment

Real GetCoverage ( int seq_index ) const

get coverage of a specifi sequence

returns a value representing how extensively the specified sequence covers the first sequence (sequence 0). The function return a value between 0 (no coverage) and 1 (full coverage)

int GetLength ( ) const

Get length of sequences in alignment.

char GetOneLetterCode	(	int	seq_index,
		int	pos
	)		const

int GetPos	(	int	seq_index,
		int	residue_index
	)		const

Get position in sequence with index seq_index that corresponds to the given residue index.

Identical to msa->GetSequence(seq_id)->GetPos(index)

mol::ResidueView GetResidue	(	int	seq_index,
		int	pos
	)		const

int GetResidueIndex	(	int	seq_index,
		int	pos
	)		const

Get residue index for seq_index and alignment position.

Identitical to msa->GetSequence(seq_id)->GetResidueIndex(pos)

ConstSequenceHandle GetSequence ( int seq_id ) const

Get sequence with given index.

Returns:: sequence or invalid handle if the index is out of bounds

int GetSequenceOffset ( int seq_index )

ConstSequenceList GetSequences ( ) const

Get list of sequences (read-only)

bool IsValid ( ) const

inline

Definition at line 160 of file alignment_handle.hh.

AlignedRegion MakeRegion	(	int	start,
		int	n,
		int	master = `-1`
	)		const

create an aligned region.

Parameters:

start	is the index of the first column
n	is the length of the sequence
master	is the reference system for operations such as shifting. If set to -1, no master sequence is defined and the operations will affect all sequences

If the aligned region is out of bounds, a std::out_of_bounds exeception will be thrown.

bool operator!= ( const AlignmentHandle & rhs ) const

bool operator== ( const AlignmentHandle & rhs ) const

AlignedColumn operator[] ( int index ) const

get aligned column at index

This method does not throw any exception. Upon accessing methods of the aligned column, exceptions might be thrown when the index is out of bounds.

void RemoveSequence ( int seq_index )

remove sequence at seq_index from alignment

void Replace	(	const AlignedRegion &	rhs,
		int	start,
		int	end
	)

Replace part of an alignment.

void SetSequenceName	(	int	seq_index,
		const String &	name
	)

set name of sequence

void SetSequenceOffset	(	int	seq_index,
		int	offset
	)

void ShiftRegion	(	int	start,
		int	end,
		int	amount,
		int	master = `-1`
	)

shift half-closed interval by amount

if master is -1, all sequences of the alignment will be shifted. Otherwise only the sequence with given index is affected.

String ToString ( int width = 80 ) const

Convert multiple sequence alignment to string.

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

stage/include/ost/seq/alignment_handle.hh

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation