SeqView#
- class SeqView(*, parent: str | bytes | ndarray, alphabet: CharAlphabet, parent_len: int, seqid: str | None = None, slice_record: SliceRecordABC = None, offset: int = 0)#
Provides a view of a sequence with support for slicing operations.
This class represents a view of a sequence. It uses
SliceRecord
to enable efficient slicing without altering the original sequence data.- Parameters:
- parent
the original sequence data
- alphabet
the alphabet object defining valid characters for the sequence
- seqid
the name or identifier of the sequence
- parent_len
the length of the sequence. Defaults to the length of the input sequence
- Attributes:
- alphabet
array_value
returns the sequence as a array of indices
bytes_value
returns the sequence as a bytes string
is_reversed
whether the sequence is reversed
offset
the annotation offset of this view
- parent
parent_len
length of the parent sequence
seqid
name of the sequence
slice_record
the slice state of this view
str_value
returns the sequence as a string
Methods
copy
([sliced])returns copy
with_offset
(offset)returns new instance with annotation offset set
Notes
It utilises the alphabet object to allow providing different types such as strings or numpy arrays, corresponding to its underlying data.
- alphabet#
- property array_value: ndarray[int]#
returns the sequence as a array of indices
- property bytes_value: bytes#
returns the sequence as a bytes string
- copy(sliced: bool = False) Self #
returns copy
- Parameters:
- sliced
if True, the underlying sequence is truncated and the start/stop adjusted
- property is_reversed: bool#
whether the sequence is reversed
- property offset: int#
the annotation offset of this view
- parent#
- property parent_len: int#
length of the parent sequence
- property seqid: str | None#
name of the sequence
- property slice_record: SliceRecordABC#
the slice state of this view
- property str_value: str#
returns the sequence as a string
- with_offset(offset: int) Self #
returns new instance with annotation offset set