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

returns the numpy array of indices for the ungapped sequence

bytes_value

returns the bytes value of the ungapped sequence

gapped_array_value

returns the numpy array of indices for the gapped sequence

gapped_bytes_value

returns the bytes value of the gapped sequence

gapped_str_value

returns the string value of the gapped sequence

is_reversed

whether the sliced view is reversed relative to the parent

map

indel map (gaps) for the sequence

offset

the annotation offset of this view

parent
parent_len

length of the parent sequence

seqid

the name of the sequence

slice_record

the slice record for this view

str_value

returns the string value of the ungapped sequence

Methods

copy([sliced])

just returns self

get_seq_view()

returns view of ungapped sequence data for seqid

parent_seq_coords()

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

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 Aligned object which has a moltype. The slice_record attribute is shared with the containing Alignment.

alphabet#
property array_value: ndarray#

returns the numpy array of indices for the ungapped sequence

property bytes_value: bytes#

returns the bytes value of the ungapped sequence

copy(sliced: bool = False) Self#

just returns self

property gapped_array_value: ndarray#

returns the numpy array of indices for the gapped sequence

property gapped_bytes_value: bytes#

returns the bytes value of the gapped sequence

property gapped_str_value: str#

returns the string value of the gapped sequence

get_seq_view() SeqViewABC#

returns view of ungapped sequence data for seqid

property is_reversed: bool#

whether the sliced view is reversed relative to the parent

property map: IndelMap#

indel map (gaps) for the sequence

property offset: int#

the annotation offset of this view

parent#
property parent_len: int#

length of the parent sequence

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

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

property seqid: str#

the name of the sequence

property slice_record: SliceRecordABC#

the slice record for this view

property str_value: str#

returns the string value of the ungapped sequence

with_offset(offset: int) Self#

returns new instance with annotation offset set