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	ProfileColumn
	Defines profile of 20 frequencies for one residue. More...
class	ProfileHandle
	Provides a profile for a sequence. More...
class	ProfileDB
	Contains a DB of profiles (identified by a unique name (String)). More...
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
typedef boost::shared_ptr < ProfileHandle >	ProfileHandlePtr
typedef std::vector < ProfileHandlePtr >	ProfileHandleList
typedef boost::shared_ptr < ProfileDB >	ProfileDBPtr
typedef std::vector < ProfileColumn >	ProfileColumnList
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 DLLIMPORT	CreateSequence (const String &name, const String &seq, const String &role="UNKNOWN")
void DLLIMPORT	SequenceToInfo (const ConstSequenceHandle &sequence, info::InfoGroup &group)
SequenceHandle DLLIMPORT	SequenceFromInfo (info::InfoGroup &group)
DLLIMPORT std::ostream &	operator<< (std::ostream &os, const ConstSequenceHandle &sequence)
bool DLLIMPORT	Match (const ConstSequenceHandle &s1, const ConstSequenceHandle &s2)
bool DLLIMPORT	Match (const String &s1, const String &s2)
SequenceList DLLIMPORT	CreateSequenceList ()
ConstSequenceList DLLIMPORT	CreateConstSequenceList ()
void DLLIMPORT	SequenceListToInfo (const ConstSequenceList &seq_list, info::InfoGroup &group)
SequenceList DLLIMPORT	SequenceListFromInfo (info::InfoGroup &group)
SequenceHandle DLLIMPORT	SequenceFromChain (const String &name, const mol::ChainHandle &chain)
SequenceHandle DLLIMPORT	SequenceFromChain (const String &name, const mol::ChainView &chain)
std::pair< mol::EntityView, mol::EntityView > DLLIMPORT	ViewsFromSequences (const ConstSequenceHandle &seq1, const ConstSequenceHandle &seq2)
std::pair< mol::EntityView, mol::EntityView > DLLIMPORT	ViewsFromAlignment (const AlignmentHandle &aln, int index1=0, int index2=1)
def	CreateAlignment
def	CreateSequenceList
Variables
	_CreateAlignment = CreateAlignment

---

Typedef Documentation

typedef std::vector<AlignedRegion> AlignedRegionList

Definition at line 92 of file aligned_region.hh.

typedef std::vector<AlignmentHandle> AlignmentList

Definition at line 193 of file alignment_handle.hh.

typedef std::vector<ProfileColumn> ProfileColumnList

Definition at line 46 of file profile_handle.hh.

typedef boost::shared_ptr<ProfileDB> ProfileDBPtr

Definition at line 45 of file profile_handle.hh.

typedef std::vector<ProfileHandlePtr> ProfileHandleList

Definition at line 44 of file profile_handle.hh.

typedef boost::shared_ptr<ProfileHandle> ProfileHandlePtr

Definition at line 42 of file profile_handle.hh.

---

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.

def ost::seq::CreateAlignment

(

seqs

)

Definition at line 23 of file __init__.py.

AlignmentHandle DLLEXPORT_OST_SEQ ost::seq::CreateAlignment

(

)

ConstSequenceList DLLIMPORT ost::seq::CreateConstSequenceList

(

)

SequenceHandle DLLIMPORT ost::seq::CreateSequence	(	const String &	name,
		const String &	seq,
		const String &	role = "UNKNOWN"
	)

def ost::seq::CreateSequenceList

(

seqs

)

Definition at line 30 of file __init__.py.

SequenceList DLLIMPORT ost::seq::CreateSequenceList

(

)

bool DLLIMPORT ost::seq::Match	(	const String &	s1,
		const String &	s2
	)

bool DLLIMPORT ost::seq::Match	(	const ConstSequenceHandle &	s1,
		const ConstSequenceHandle &	s2
	)

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

get sequence from chain

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

get sequence from chain

SequenceHandle DLLIMPORT ost::seq::SequenceFromInfo

(

info::InfoGroup &

group

)

create sequence from info

SequenceList DLLIMPORT ost::seq::SequenceListFromInfo

(

info::InfoGroup &

group

)

create sequence list object from info

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

export sequence list to info

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

export sequence to info

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

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

---

Variable Documentation

_CreateAlignment = CreateAlignment

Definition at line 22 of file __init__.py.