ost::seq Namespace Reference

Namespaces
namespace	alg
namespace	impl
Data Structures
class	AlignedColumn
	Provides access to a column in a aligned region or a sequence alignment. More...
class	AlignedColumnIterator
class	AlignedRegion
	represents a region in a sequence alignment More...
class	AlignmentHandle
	representation of a multiple sequence alignemnt consisting of two or more sequences More...
class	InvalidSequence
class	InvalidAlignment
class	ConstSequenceHandle
	immutable sequence More...
class	SequenceHandle
	mutable sequence handle. More...
class	ConstSequenceList
	list of immutable sequences. More...
class	SequenceList
	list of sequences. More...
Typedefs
typedef std::vector < AlignedRegion >	AlignedRegionList
typedef std::vector < AlignmentHandle >	AlignmentList
Functions
DLLEXPORT_OST_SEQ std::ostream &	operator<< (std::ostream &os, const AlignedColumn &col)
AlignmentHandle DLLEXPORT_OST_SEQ	CreateAlignment ()
AlignmentHandle DLLEXPORT_OST_SEQ	AlignmentFromSequenceList (const SequenceList &seq_list)
SequenceHandle DLLEXPORT_OST_SEQ	CreateSequence (const String &name, const String &seq)
void DLLEXPORT_OST_SEQ	SequenceToInfo (const ConstSequenceHandle &sequence, info::InfoGroup &group)
SequenceHandle DLLEXPORT_OST_SEQ	SequenceFromInfo (info::InfoGroup &group)
DLLEXPORT_OST_SEQ std::ostream &	operator<< (std::ostream &os, const ConstSequenceHandle &sequence)
SequenceList DLLEXPORT_OST_SEQ	CreateSequenceList ()
ConstSequenceList DLLEXPORT_OST_SEQ	CreateConstSequenceList ()
void DLLEXPORT_OST_SEQ	SequenceListToInfo (const ConstSequenceList &seq_list, info::InfoGroup &group)
SequenceList DLLEXPORT_OST_SEQ	SequenceListFromInfo (info::InfoGroup &group)
SequenceHandle DLLEXPORT_OST_SEQ	SequenceFromChain (const String &name, const mol::ChainHandle &chain)
SequenceHandle DLLEXPORT_OST_SEQ	SequenceFromChain (const String &name, const mol::ChainView &chain)
std::pair< mol::EntityView, mol::EntityView > DLLEXPORT_OST_SEQ	ViewsFromSequences (const ConstSequenceHandle &seq1, const ConstSequenceHandle &seq2)
std::pair< mol::EntityView, mol::EntityView > DLLEXPORT_OST_SEQ	ViewsFromAlignment (const AlignmentHandle &aln, int index1=0, int index2=1)

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Typedef Documentation

typedef std::vector<AlignedRegion> AlignedRegionList

Definition at line 92 of file aligned_region.hh.

typedef std::vector<AlignmentHandle> AlignmentList

Definition at line 174 of file alignment_handle.hh.

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Function Documentation

AlignmentHandle DLLEXPORT_OST_SEQ ost::seq::AlignmentFromSequenceList

(

const SequenceList &

seq_list

)

convert alignment from sequence list

If the sequences in the SequenceList have different lengths, an InvalidAlignment exception is thrown.

Returns:

alignment consisting of the sequences in seq_list.

AlignmentHandle DLLEXPORT_OST_SEQ ost::seq::CreateAlignment

(

)

ConstSequenceList DLLEXPORT_OST_SEQ ost::seq::CreateConstSequenceList

(

)

SequenceHandle DLLEXPORT_OST_SEQ ost::seq::CreateSequence	(	const String &	name,
		const String &	seq
	)

SequenceList DLLEXPORT_OST_SEQ ost::seq::CreateSequenceList

(

)

DLLEXPORT_OST_SEQ std::ostream& ost::seq::operator<<	(	std::ostream &	os,
		const ConstSequenceHandle &	sequence
	)

DLLEXPORT_OST_SEQ std::ostream& ost::seq::operator<<	(	std::ostream &	os,
		const AlignedColumn &	col
	)

SequenceHandle DLLEXPORT_OST_SEQ ost::seq::SequenceFromChain	(	const String &	name,
		const mol::ChainView &	chain
	)

get sequence from chain

SequenceHandle DLLEXPORT_OST_SEQ ost::seq::SequenceFromChain	(	const String &	name,
		const mol::ChainHandle &	chain
	)

get sequence from chain

SequenceHandle DLLEXPORT_OST_SEQ ost::seq::SequenceFromInfo

(

info::InfoGroup &

group

)

create sequence from info

SequenceList DLLEXPORT_OST_SEQ ost::seq::SequenceListFromInfo

(

info::InfoGroup &

group

)

create sequence list object from info

void DLLEXPORT_OST_SEQ ost::seq::SequenceListToInfo	(	const ConstSequenceList &	seq_list,
		info::InfoGroup &	group
	)

export sequence list to info

void DLLEXPORT_OST_SEQ ost::seq::SequenceToInfo	(	const ConstSequenceHandle &	sequence,
		info::InfoGroup &	group
	)

export sequence to info

std::pair<mol::EntityView, mol::EntityView> DLLEXPORT_OST_SEQ ost::seq::ViewsFromAlignment	(	const AlignmentHandle &	aln,
		int	index1 = 0,
		int	index2 = 1
	)

std::pair<mol::EntityView, mol::EntityView> DLLEXPORT_OST_SEQ ost::seq::ViewsFromSequences	(	const ConstSequenceHandle &	seq1,
		const ConstSequenceHandle &	seq2
	)