ost::seq Namespace Reference

Namespaces
	alg
	impl

Data Structures
class	AlignedColumn
class	AlignedColumnIterator
class	AlignedRegion
class	AlignmentHandle
class	InvalidSequence
class	InvalidAlignment
class	HMMData
class	ProfileColumn
class	ProfileHandle
class	ProfileDB
class	ConstSequenceHandle
class	SequenceHandle
class	ConstSequenceList
class	SequenceList

Typedefs
typedef std::vector < AlignedRegion >	AlignedRegionList
typedef std::vector < AlignmentHandle >	AlignmentList
typedef boost::shared_ptr < ProfileHandle >	ProfileHandlePtr
typedef boost::shared_ptr < HMMData >	HMMDataPtr
typedef std::vector < ProfileHandlePtr >	ProfileHandleList
typedef boost::shared_ptr < ProfileDB >	ProfileDBPtr
typedef std::vector < ProfileColumn >	ProfileColumnList

Enumerations
enum	HMMTransition {   HMM_M2M = 0, HMM_M2I = 1, HMM_M2D = 2, HMM_I2M = 3,   HMM_I2I = 4, HMM_D2M = 5, HMM_D2D = 6 }

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, const String &role="UNKNOWN")
DLLEXPORT_OST_SEQ std::ostream &	operator<< (std::ostream &os, const ConstSequenceHandle &sequence)
bool DLLEXPORT_OST_SEQ	Match (const ConstSequenceHandle &s1, const ConstSequenceHandle &s2)
bool DLLEXPORT_OST_SEQ	Match (const String &s1, const String &s2)
SequenceList DLLEXPORT_OST_SEQ	CreateSequenceList ()
ConstSequenceList DLLEXPORT_OST_SEQ	CreateConstSequenceList ()
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)
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 boost::shared_ptr<HMMData> HMMDataPtr

Definition at line 45 of file profile_handle.hh.

typedef std::vector<ProfileColumn> ProfileColumnList

Definition at line 48 of file profile_handle.hh.

typedef boost::shared_ptr<ProfileDB> ProfileDBPtr

Definition at line 47 of file profile_handle.hh.

typedef std::vector<ProfileHandlePtr> ProfileHandleList

Definition at line 46 of file profile_handle.hh.

typedef boost::shared_ptr<ProfileHandle> ProfileHandlePtr

Definition at line 43 of file profile_handle.hh.

Enumeration Type Documentation

enum HMMTransition

Enumerator
HMM_M2M
HMM_M2I
HMM_M2D
HMM_I2M
HMM_I2I
HMM_D2M
HMM_D2D

Definition at line 50 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 DLLEXPORT_OST_SEQ ost::seq::CreateConstSequenceList

(

)

SequenceHandle DLLEXPORT_OST_SEQ 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 DLLEXPORT_OST_SEQ ost::seq::CreateSequenceList

(

)

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

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

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

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

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

get sequence from chain

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

get sequence from chain

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
	)

Variable Documentation

_CreateAlignment = CreateAlignment

Definition at line 22 of file __init__.py.