ost::seq Namespace Reference


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...


typedef std::vector
< AlignedRegion
typedef std::vector
< AlignmentHandle
typedef boost::shared_ptr
< ProfileHandle
typedef boost::shared_ptr
< ProfileDB
typedef std::vector
< ProfileColumn


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


 _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 45 of file profile_handle.hh.

typedef boost::shared_ptr<ProfileDB> ProfileDBPtr

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.

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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