Namespaces
namespace	alg

namespace	impl

Data Structures
class	AlignedColumn

class	AlignedColumnIterator

class	AlignedRegion

class	AlignmentHandle

class	ConstSequenceHandle

class	ConstSequenceList

class	HMMData

class	InvalidAlignment

class	InvalidSequence

class	ProfileColumn

class	ProfileDB

class	ProfileHandle

class	SequenceHandle

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)

	CreateAlignment (*seqs)

	CreateSequenceList (*seqs)

Variables
	_CreateAlignment = CreateAlignment

	_CreateSequenceList = CreateSequenceList

Typedef Documentation

◆ AlignedRegionList

typedef std::vector<AlignedRegion> AlignedRegionList

Definition at line 92 of file aligned_region.hh.

◆ AlignmentList

typedef std::vector<AlignmentHandle> AlignmentList

Definition at line 193 of file alignment_handle.hh.

◆ HMMDataPtr

typedef boost::shared_ptr<HMMData> HMMDataPtr

Definition at line 45 of file profile_handle.hh.

◆ ProfileColumnList

typedef std::vector<ProfileColumn> ProfileColumnList

Definition at line 48 of file profile_handle.hh.

◆ ProfileDBPtr

typedef boost::shared_ptr<ProfileDB> ProfileDBPtr

Definition at line 47 of file profile_handle.hh.

◆ ProfileHandleList

typedef std::vector<ProfileHandlePtr> ProfileHandleList

Definition at line 46 of file profile_handle.hh.

◆ ProfileHandlePtr

typedef boost::shared_ptr<ProfileHandle> ProfileHandlePtr

Definition at line 44 of file profile_handle.hh.

Enumeration Type Documentation

◆ HMMTransition

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

◆ AlignmentFromSequenceList()

AlignmentHandle DLLEXPORT_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.

◆ CreateAlignment() [1/2]

AlignmentHandle DLLEXPORT_OST_SEQ CreateAlignment ( )

◆ CreateAlignment() [2/2]

CreateAlignment ( * seqs )

Definition at line 23 of file __init__.py.

◆ CreateConstSequenceList()

ConstSequenceList DLLEXPORT_OST_SEQ CreateConstSequenceList ( )

◆ CreateSequence()

SequenceHandle DLLEXPORT_OST_SEQ CreateSequence	(	const String &	name,
		const String &	seq,
		const String &	role = `"UNKNOWN"`
	)

◆ CreateSequenceList() [1/2]

SequenceList DLLEXPORT_OST_SEQ CreateSequenceList ( )

◆ CreateSequenceList() [2/2]

CreateSequenceList ( * seqs )

Definition at line 30 of file __init__.py.

◆ Match() [1/2]

bool DLLEXPORT_OST_SEQ Match	(	const ConstSequenceHandle &	s1,
		const ConstSequenceHandle &	s2
	)

◆ Match() [2/2]

bool DLLEXPORT_OST_SEQ Match	(	const String &	s1,
		const String &	s2
	)

◆ operator<<() [1/2]

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

◆ operator<<() [2/2]

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

◆ SequenceFromChain() [1/2]

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

get sequence from chain

◆ SequenceFromChain() [2/2]

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

get sequence from chain

◆ ViewsFromAlignment()

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

◆ ViewsFromSequences()

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

Variable Documentation

◆ _CreateAlignment

_CreateAlignment = CreateAlignment

protected

Definition at line 22 of file __init__.py.

◆ _CreateSequenceList

_CreateSequenceList = CreateSequenceList