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Improve docstring of TCRdistDistanceCalculator
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src/scirpy/ir_dist/metrics.py

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@@ -1188,11 +1188,12 @@ class TCRdistDistanceCalculator(_MetricDistanceCalculator):
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base_matrix:
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Amino acid distance matrix used by TCRdist. `"blosum62"` uses the original
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BLOSUM62-derived TCRdist distance matrix, while `"tcrblosum"` uses
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TCRBLOSUM-derived matrices.
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TCRBLOSUM-derived matrices. Depending on `chain_type`, either the
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TCRBLOSUM alpha- or beta-chain matrix is used.
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chain_type:
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Required when `base_matrix="tcrblosum"` and calling `sequence_dist`.
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`"VJ"` selects the alpha-chain matrix and `"VDJ"` selects the beta-chain matrix.
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In `ir_dist`, this value is set automatically and should not be provided.
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Required when `base_matrix="tcrblosum"`. `"VJ"` selects the alpha-chain matrix
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and `"VDJ"` selects the beta-chain matrix. When called via `ir_dist`, this value
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is set automatically and should not be provided.
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"""
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parasail_aa_alphabet = "ARNDCQEGHILKMFPSTWYVBZX"

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