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Revert "Merge branch 'seq-collections-refactor' into develop" #1875

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merged 1 commit into from
May 22, 2024
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Revert "Merge branch 'seq-collections-refactor' into develop" #1875

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311 changes: 0 additions & 311 deletions src/cogent3/core/new_alignment.py
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10 changes: 3 additions & 7 deletions src/cogent3/core/sequence.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2312,21 +2312,17 @@ def __init__(
raise ValueError("step cannot be 0")
step = 1 if step is None else step

self._seq_len = self._checked_seq_len(seq, seq_len)
func = _input_vals_pos_step if step > 0 else _input_vals_neg_step
start, stop, step = func(self._seq_len, start, stop, step)
start, stop, step = func(len(seq), start, stop, step)
self.seq = seq
self.start = start
self.stop = stop
self.step = step
self._offset = offset
self._seqid = seqid

def _checked_seq_len(self, seq, seq_len) -> int:
if seq_len is not None and seq_len != len(seq):
raise AssertionError(f"{seq_len} != {len(seq)})")
seq_len = seq_len or len(seq)
return seq_len
raise AssertionError(f"{seq_len} != {len(self.seq)})")
self._seq_len = seq_len or len(self.seq)

@property
def _zero_slice(self):
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