#include <sequence_handle.hh>
Inherits ConstGenericPropContainer< ConstSequenceHandle >.
The ConstSequenceHandle provides all read-only methods of the sequence handle.
Definition at line 45 of file sequence_handle.hh.
| ConstSequenceHandle | ( | const impl::SequenceImplPtr & | impl | ) |
| SequenceHandle Copy | ( | ) | const |
create copy sequence The newly created sequence has the same attached view.
| mol::EntityView GetAttachedView | ( | ) | const |
get attached view. may be an invalid entity view
| int GetFirstNonGap | ( | ) | const |
Get position of first non-gap character in sequence.
| String GetGaplessString | ( | ) | const |
Get sequence as string ignoring gaps.
| int GetLastNonGap | ( | ) | const |
Get position of last non-gap character in sequence.
| int GetLength | ( | ) | const |
Get lenght of sequence, including gaps.
| const String& GetName | ( | ) | const |
| char GetOneLetterCode | ( | int | position | ) | const |
get one letter code of residue at position
| int GetPos | ( | int | residue_index | ) | const |
Get zero-based index for given residue number.
| out_of_range,if | number is not included in sequence. |
| mol::ResidueView GetResidue | ( | int | position | ) | const |
get residue at position
will return the residue view at the given sequence position or an invalid residue view when no view is attached, the index is out of bounds or the position contains a gap.
| int GetResidueIndex | ( | int | pos | ) | const |
Get residue index corresponding to given sequence position.
| pos | zero-based index |
| out_of_range | if pos is not in [0, length-1]. |
| int GetSequenceOffset | ( | ) | const |
| const String& GetString | ( | ) | const |
| const GenericPropContainerImpl* GpImpl | ( | ) | const [protected] |
| GenericPropContainerImpl* GpImpl | ( | ) | [protected] |
| bool HasAttachedView | ( | ) | const |
whether the sequence has an attached view
| impl::SequenceImplPtr& Impl | ( | ) | const |
| bool IsValid | ( | ) | const |
whether the sequence is valid
| bool operator!= | ( | const ConstSequenceHandle & | rhs | ) | const |
| bool operator== | ( | const ConstSequenceHandle & | rhs | ) | const |
| char operator[] | ( | int | index | ) | const |
friend class AlignmentHandle [friend] |
Definition at line 49 of file sequence_handle.hh.
friend class ConstGenericPropContainer< ConstSequenceHandle > [friend] |
Definition at line 48 of file sequence_handle.hh.
friend class ConstSequenceList [friend] |
Definition at line 50 of file sequence_handle.hh.
friend class SequenceList [friend] |
Definition at line 51 of file sequence_handle.hh.
1.5.8