SeqDataView#
- class SeqDataView(*, parent: str | bytes | ndarray, alphabet: CharAlphabet, parent_len: int, seqid: str | None = None, slice_record: SliceRecordABC = 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
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
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 theSequence
object which has a moltype.- alphabet#
- property array_value: ndarray#
returns the sequence as a numpy array
- property bytes_value: bytes#
returns the sequence as bytes
- copy(sliced: bool = False) Self #
returns copy
- 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
- to_rich_dict() dict[str, str | dict[str, str]] #
returns a json serialisable dict.
Warning
This method is not intended to provide serialisation of this object, instead, it is intended for usage by an enclosing class.
Notes
This method will slice the underlying sequence to the start and stop values
- with_offset(offset: int) Self #
returns new instance with annotation offset set