Namespaces | Data Structures | Typedefs | Enumerations | Functions
ost::seq Namespace Reference



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


typedef std::vector< AlignedRegionAlignedRegionList
typedef std::vector< AlignmentHandleAlignmentList
typedef boost::shared_ptr< ProfileHandleProfileHandlePtr
typedef boost::shared_ptr< HMMDataHMMDataPtr
typedef std::vector< ProfileHandlePtrProfileHandleList
typedef boost::shared_ptr< ProfileDBProfileDBPtr
typedef std::vector< ProfileColumnProfileColumnList


enum  HMMTransition {
  HMM_M2M = 0 , HMM_M2I = 1 , HMM_M2D = 2 , HMM_I2M = 3 ,
  HMM_I2I = 4 , HMM_D2M = 5 , HMM_D2D = 6


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 (*seqs)
def CreateSequenceList (*seqs)

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


Definition at line 50 of file profile_handle.hh.

Function Documentation

◆ AlignmentFromSequenceList()

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.

◆ CreateAlignment() [1/2]

AlignmentHandle DLLEXPORT_OST_SEQ ost::seq::CreateAlignment ( )

◆ CreateAlignment() [2/2]

def ost.seq.CreateAlignment ( seqs)

Definition at line 23 of file

◆ CreateConstSequenceList()

ConstSequenceList DLLEXPORT_OST_SEQ ost::seq::CreateConstSequenceList ( )

◆ CreateSequence()

SequenceHandle DLLEXPORT_OST_SEQ ost::seq::CreateSequence ( const String name,
const String seq,
const String role = "UNKNOWN" 

◆ CreateSequenceList() [1/2]

SequenceList DLLEXPORT_OST_SEQ ost::seq::CreateSequenceList ( )

◆ CreateSequenceList() [2/2]

def ost.seq.CreateSequenceList ( seqs)

Definition at line 30 of file

◆ Match() [1/2]

bool DLLEXPORT_OST_SEQ ost::seq::Match ( const ConstSequenceHandle s1,
const ConstSequenceHandle s2 

◆ Match() [2/2]

bool DLLEXPORT_OST_SEQ ost::seq::Match ( const String s1,
const String s2 

◆ operator<<() [1/2]

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

◆ operator<<() [2/2]

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

◆ SequenceFromChain() [1/2]

SequenceHandle DLLEXPORT_OST_SEQ ost::seq::SequenceFromChain ( const String name,
const mol::ChainHandle chain 

get sequence from chain

◆ SequenceFromChain() [2/2]

SequenceHandle DLLEXPORT_OST_SEQ ost::seq::SequenceFromChain ( const String name,
const mol::ChainView chain 

get sequence from chain

◆ ViewsFromAlignment()

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

◆ ViewsFromSequences()

std::pair<mol::EntityView, mol::EntityView> DLLEXPORT_OST_SEQ ost::seq::ViewsFromSequences ( const ConstSequenceHandle seq1,
const ConstSequenceHandle seq2