cogent3.core.seqview.AlignedDataView

class AlignedDataView(*, parent: AlignedSeqsDataABC, seqid: str, alphabet: c3_alphabet.CharAlphabet[Any], slice_record: SliceRecordABC | 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 slice offset of this view

parent

parent_len

length of the parent sequence

parent_offset

returns the offset from the true parent

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_coords(*[, seq_coords, apply_offset])	returns seqid, start, stop, strand on the parent
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.