core.seqview.SeqView

core.seqview.SeqView(
    parent,
    alphabet,
    parent_len,
    seqid=None,
    slice_record=None,
    offset=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

Name	Type	Description	Default
parent	str \| bytes \| NumpyIntArrayType \| SeqsDataABC	the original sequence data	required
alphabet	c3_alphabet.CharAlphabet[Any]	the alphabet object defining valid characters for the sequence	required
seqid	str \| None	the name or identifier of the sequence	`None`
parent_len	int	the length of the sequence. Defaults to the length of the input sequence	required

It utilises the alphabet object to allow providing different types such as strings or numpy arrays, corresponding to its underlying data.

Name	Description
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_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

Name	Description
copy	returns copy
parent_coords	returns coordinates on parent
with_offset	returns new instance with annotation offset set

core.seqview.SeqView.copy(sliced=False)

returns copy

Name	Type	Description	Default
sliced	bool	if True, the underlying sequence is truncated and the start/stop adjusted	`False`

core.seqview.SeqView.parent_coords(apply_offset=False, **kwargs)

returns coordinates on parent

Name	Type	Description	Default
apply_offset	bool	if True adds annotation offset from parent	`False`

Name	Type	Description
	parent seqid, start, stop, strand

core.seqview.SeqView.with_offset(offset)

returns new instance with annotation offset set