Namespaces | Data Structures | Typedefs | Functions | Variables
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  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


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)
void DLLEXPORT_OST_SEQ SequenceToInfo (const ConstSequenceHandle &sequence, info::InfoGroup &group)
SequenceHandle DLLEXPORT_OST_SEQ SequenceFromInfo (info::InfoGroup &group)
DLLEXPORT_OST_SEQ std::ostream & operator<< (std::ostream &os, const ConstSequenceHandle &sequence)
SequenceList DLLEXPORT_OST_SEQ CreateSequenceList ()
ConstSequenceList DLLEXPORT_OST_SEQ CreateConstSequenceList ()
void DLLEXPORT_OST_SEQ SequenceListToInfo (const ConstSequenceList &seq_list, info::InfoGroup &group)
SequenceList DLLEXPORT_OST_SEQ SequenceListFromInfo (info::InfoGroup &group)
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 >
ViewsFromSequences (const ConstSequenceHandle &seq1, const ConstSequenceHandle &seq2)
std::pair< mol::EntityView,
mol::EntityView >
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 185 of file alignment_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

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 
def ost.seq.CreateSequenceList (   seqs)

Definition at line 30 of file

SequenceList DLLEXPORT_OST_SEQ ost::seq::CreateSequenceList ( )
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

SequenceHandle DLLEXPORT_OST_SEQ ost::seq::SequenceFromInfo ( info::InfoGroup &  group)

create sequence from info

SequenceList DLLEXPORT_OST_SEQ ost::seq::SequenceListFromInfo ( info::InfoGroup &  group)

create sequence list object from info

void DLLEXPORT_OST_SEQ ost::seq::SequenceListToInfo ( const ConstSequenceList &  seq_list,
info::InfoGroup &  group 

export sequence list to info

void DLLEXPORT_OST_SEQ ost::seq::SequenceToInfo ( const ConstSequenceHandle &  sequence,
info::InfoGroup &  group 

export sequence to info

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