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 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 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.
| 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.
| 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 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 | |||
| ) |
| _CreateAlignment = CreateAlignment |
Definition at line 22 of file __init__.py.
1.6.1
