cogent3.core.seqview.SeqDataView

class SeqDataView(*, parent: SeqsDataABC, alphabet: c3_alphabet.CharAlphabet[Any], parent_len: int, seqid: str | None = None, slice_record: SliceRecordABC | None = None, offset: int = 0)

A view class for SeqsData, providing methods for different representations of a single sequence.

Attributes:

alphabet

array_value

returns the sequence as a numpy array

bytes_value

returns the sequence as bytes

is_reversed

whether the sequence is reversed

offset

the annotation offset of this view

parent

parent_len

length of the parent sequence

parent_offset

returns the offset from the true parent

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
parent_coords(*[, apply_offset])	returns coordinates on parent
to_rich_dict()	returns a json serialisable dict.
with_offset(offset)	returns new instance with annotation offset set

Notes

str_value / array_value are not complemented, but can be reversed. The latter is done by the Sequence object which has a moltype.