cogent3.core.seqview.SeqView

class SeqView(*, parent: str | bytes | NumpyIntArrayType | SeqsDataABC, alphabet: c3_alphabet.CharAlphabet[Any], parent_len: int, seqid: str | None = None, slice_record: SliceRecordABC | None = 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

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
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.