AlignedDataView

class AlignedDataView(*, parent: AlignedSeqsDataABC, seqid: str, alphabet: AlphabetABC, slice_record: SliceRecord | None = None)

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

Attributes:

alphabet

array_value

bytes_value

gapped_array_value

gapped_bytes_value

gapped_str_value

is_reversed

map

offset

parent

parent_len

seqid

slice_record

str_value

Methods

parent_seq_coords()

returns seqid, start, stop, strand on the parent sequence

copy
get_seq_view
with_offset

Notes

str_value / array_value are not complemented, but can be reversed. The latter is done by the Aligned object which has a moltype. The slice_record attribute is shared with the containing Alignment.

alphabet

property array_value: ndarray

property bytes_value: bytes

copy(sliced: bool = False)

property gapped_array_value: ndarray

property gapped_bytes_value: bytes

property gapped_str_value: str

get_seq_view() → SeqViewABC

property is_reversed: bool

property map: IndelMap

property offset: int

parent

property parent_len: int

parent_seq_coords() → tuple[str, int, int, int]

returns seqid, start, stop, strand on the parent sequence

property seqid: str

property slice_record: SliceRecordABC

property str_value: str

with_offset(offset: int)