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c90dd6f265
* Alignment: use a simplified ragged type for performance This introduces the AlignmentArray type, which is a simplified version of Ragged that performs better on the simple(r) indexing performed for alignment. * AlignmentArray: raise an error when using unsupported index * AlignmentArray: move error messages to Errors * AlignmentArray: remove simlified ... with simplifications * AlignmentArray: fix typo that broke a[n:n] indexing
23 lines
614 B
Python
23 lines
614 B
Python
from typing import List
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from dataclasses import dataclass
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from .align import get_alignments
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from .alignment_array import AlignmentArray
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@dataclass
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class Alignment:
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x2y: AlignmentArray
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y2x: AlignmentArray
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@classmethod
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def from_indices(cls, x2y: List[List[int]], y2x: List[List[int]]) -> "Alignment":
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x2y = AlignmentArray(x2y)
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y2x = AlignmentArray(y2x)
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return Alignment(x2y=x2y, y2x=y2x)
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@classmethod
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def from_strings(cls, A: List[str], B: List[str]) -> "Alignment":
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x2y, y2x = get_alignments(A, B)
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return Alignment.from_indices(x2y=x2y, y2x=y2x)
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