#
# VaxPress
#
# Copyright 2023 Hyeshik Chang
#
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# a copy of this software and associated documentation files (the
# “Software”), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish,
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# permit persons to whom the Software is furnished to do so, subject to
# the following conditions:
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# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
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# THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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#

from . import ScoringFunction

class MFEFitness(ScoringFunction):

    name = 'mfe'
    description = 'RNA Folding (MFE)'
    priority = 40
    uses_folding = True

    arguments = [
        ('weight', dict(
            type=float, default=3.0, metavar='WEIGHT',
            help='scoring weight for MFE (default: 3.0)')),
    ]

    def __init__(self, weight, _length_cds):
        self.weight = -weight / _length_cds

    def score(self, seqs, foldings):
        mfe = [folding['mfe'] for folding in foldings]
        score = [m * self.weight for m in mfe]

        return {'mfe': score}, {'mfe': mfe}

    def annotate_sequence(self, seq, folding):
        return {'mfe': folding['mfe']}
