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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

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.