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.

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