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70 lines
1.9 KiB
Python
70 lines
1.9 KiB
Python
from typing import Type
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from sequence_align.pairwise import hirschberg, needleman_wunsch
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from .registry import BaseRegistry
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class AlignerRegistry(BaseRegistry[Type["BaseAligner"]]):
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"""A registry for aligners."""
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class BaseAligner:
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def __init__(self, *args, **kwargs):
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super().__init__()
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def align(self, gold: list[str], pred: list[str]) -> tuple[list[str], list[str]]:
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raise NotImplementedError()
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@AlignerRegistry.add("hirschberg")
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class HirschbergAligner(BaseAligner):
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def __init__(
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self,
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match_score: float = 1.0,
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mismatch_score: float = -1.0,
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indel_score: float = -1.0,
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gap_token: str = "▓",
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):
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self.match_score = match_score
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self.mismatch_score = mismatch_score
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self.indel_score = indel_score
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self.gap_token = gap_token
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super().__init__()
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def align(self, gold: list[str], pred: list[str]) -> tuple[list[str], list[str]]:
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return hirschberg(
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gold,
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pred,
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match_score=self.match_score,
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mismatch_score=self.mismatch_score,
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indel_score=self.indel_score,
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gap=self.gap_token,
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)
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@AlignerRegistry.add("needleman-wunsch")
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class NeedlemanWunschAligner(BaseAligner):
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def __init__(
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self,
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match_score: float = 1.0,
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mismatch_score: float = -1.0,
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indel_score: float = -1.0,
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gap_token: str = "▓",
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):
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self.match_score = match_score
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self.mismatch_score = mismatch_score
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self.indel_score = indel_score
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self.gap_token = gap_token
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super().__init__()
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def align(self, gold: list[str], pred: list[str]) -> tuple[list[str], list[str]]:
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return needleman_wunsch(
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gold,
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pred,
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match_score=self.match_score,
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mismatch_score=self.mismatch_score,
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indel_score=self.indel_score,
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gap=self.gap_token,
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)
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