mandos.analysis.enrichment.EnrichmentCalculation.create() - Code Metrics - Inspection of "feature: skeleton for plot commands" - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

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Push — main ( a80564...ec3fe3 )

by Douglas

created 2021-07-07 20:15 UTC

EnrichmentCalculation.create() A

↳ Parent: mandos.analysis.enrichment

Complexity

Conditions

Size

Total Lines	4
Code Lines	4

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	4
nop	2
dl	0
loc	4
rs	10
c	0
b	0
f	0

"""
Scoring (regression and enrichment) calculations.
"""
import abc
import enum
import math
from typing import Generic, Mapping, Sequence, Type, TypeVar, Union

import pandas as pd

from typeddfs import TypedDfs


from mandos.analysis import AnalysisUtils as Au
from mandos.model import CleverEnum
from mandos.model.hits import AbstractHit, HitFrame, HitUtils, Pair

S = TypeVar("S", bound=Union[int, float, bool])



EnrichmentDf = (
    TypedDfs.typed("EnrichmentDf")
    .require("predicate", "object", dtype=str)
    .require("samples", dtype=int)
).build()
# extra cols are, e.g., alpha(score_1), alpha(is_hit)


ScoreDf = (TypedDfs.typed("ScoreDf").require("inchikey", dtype=str).reserve("score")).build()
# extra cols are, e.g., score_1, score_hello


IsHitDf = TypedDfs.typed("IsHitDf").require("inchikey", dtype=str)
# extra calls are is_hit, etc.


def _vars(self: ScoreDf) -> Sequence[str]:
    return [
        col
        for col in self.columns
        if (isinstance(self, ScoreDf) and (col == "score" or col.startswith("score_")))
        or (isinstance(self, IsHitDf) and col.startswith("is_"))
    ]


def _var_map(self: ScoreDf) -> Mapping[str, Mapping[str, S]]:
    results = {}
    for c in self.score_cols:

        results[c] = self[c].to_dict()
    return results


ScoreDf.vars = _vars
ScoreDf.var_map = _var_map
IsHitDf.vars = _vars
IsHitDf.var_map = _var_map


class EnrichmentCalculator(Generic[S], metaclass=abc.ABCMeta):

    def __init__(self, alg_name: str):
        self.alg_name = alg_name

    def calc_many(self, data: HitFrame, score_df: ScoreDf):

        hits = HitUtils.df_to_hits(data)
        samples_per_pair = {k: len(v) for k, v in Au.hit_multidict(hits, "pair").items()}
        results = {}
        for col, scores in score_df.var_map():
            calculated = self.calc(hits, scores)
            results[col] = calculated
        return EnrichmentDf(
            [
                pd.Series(self._results_row(pair, n_samples, results))
                for pair, n_samples in samples_per_pair.items()
            ]
        )

    def _results_row(
        self, pair: Pair, n_samples: int, results

    ) -> Mapping[str, Union[str, int, float]]:
        return {
            **dict(
                predicate=pair.pred,
                object=pair.obj,
                samples=n_samples,
            ),
            **{self._col_name(col): vs[pair] for col, vs in results.items()},
        }

    def _col_name(self, col: str) -> str:
        return self.alg_name + "(" + col + ")"

    def calc(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> Mapping[Pair, float]:

        pair_to_hits = Au.hit_multidict(hits, "to_pair")
        results = {}
        for pair, the_hits in pair_to_hits.items():

            results[pair] = self.for_pair(hits, scores)
        return results

    def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:

        raise NotImplementedError()


class AlphaCalculator(EnrichmentCalculator[S]):

    def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:

        source_to_hits = Au.hit_multidict(hits, "data_source")
        terms = []
        for source, source_hits in source_to_hits.items():

            terms.append(self._calc_term(source_hits, scores))
        return math.fsum(terms) / len(terms)

    def _calc_term(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
class Foo:
    def some_method(self, x, y):
        return x + y;
        values = [
            Au.elle(hit.weight) * (2 * float(scores[hit.origin_inchikey] - 1)) ** 2 for hit in hits
        ]
        return math.fsum(values) / len(values)


class FoldUnweightedCalc(EnrichmentCalculator[bool]):

    def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
class Foo:
    def some_method(self, x, y):
        return x + y;
        numerator = len([hit for hit in hits if scores[hit.origin_inchikey]])
        denominator = len([hit for hit in hits if not scores[hit.origin_inchikey]])
        if denominator == 0:
            return float("inf")
        return numerator / denominator


class FoldWeightedCalc(EnrichmentCalculator[bool]):

    def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
class Foo:
    def some_method(self, x, y):
        return x + y;
        yes = [hit for hit in hits if scores[hit.origin_inchikey]]
        no = [hit for hit in hits if not scores[hit.origin_inchikey]]

        numerator = math.fsum((hit.weight for hit in yes))

        denominator = math.fsum((hit.weight for hit in no))
        if denominator == 0:
            return float("inf")
        return numerator / denominator


class SumWeightedCalc(EnrichmentCalculator[S]):

    def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
class Foo:
    def some_method(self, x, y):
        return x + y;
        return math.fsum([scores[hit.origin_inchikey] * hit.weight for hit in hits]) / len(hits)


class SumUnweightedCalc(EnrichmentCalculator[S]):

    def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
class Foo:
    def some_method(self, x, y):
        return x + y;
        return math.fsum([scores[hit.origin_inchikey] for hit in hits]) / len(hits)


class EnrichmentAlg(CleverEnum):

    """ """

    alpha = enum.auto()
    fold = enum.auto()
    fold_w = enum.auto()
    sum = enum.auto()
    sum_w = enum.auto()

    @property
    def description(self) -> str:

        s = self.symbol

        return {
            EnrichmentAlg.alpha: rf"[float] {s}(p) = Mean product of rescaled weights and scores; see the docs",

            EnrichmentAlg.fold: rf"[bool] {s}(p) = #(c has p and hit) / #(c has p and not hit)",
            EnrichmentAlg.fold_w: rf"[bool] {s}(p) = ∑(w(c, pair) s.t. c is hit) / ∑(w(c, pair) s.t. c not hit)",

            EnrichmentAlg.sum: rf"{s}(p) = ∑(score(c) s.t. c has p)",
            EnrichmentAlg.sum_w: rf"{s}(p) = ∑(score(c) × w(c, p) for all c)",
        }[self]

    @property
    def symbol(self) -> str:

        return {
            EnrichmentAlg.alpha: "α",
            EnrichmentAlg.fold: r"β",
            EnrichmentAlg.fold_w: "β*",
            EnrichmentAlg.sum: r"γ",
            EnrichmentAlg.sum_w: r"γ*",
        }[self]

    @property
    def clazz(self) -> Type[EnrichmentCalculator]:

        return {
            EnrichmentAlg.alpha: AlphaCalculator,
            EnrichmentAlg.fold: FoldUnweightedCalc,
            EnrichmentAlg.fold_w: FoldWeightedCalc,
            EnrichmentAlg.sum: SumUnweightedCalc,
            EnrichmentAlg.sum_w: SumWeightedCalc,
        }[self.name]


class EnrichmentCalculation:

    @classmethod
    def create(cls, algorithm: Union[str, EnrichmentAlg]) -> EnrichmentDf:

        alg_clazz = EnrichmentDf.of(algorithm).clazz
        return alg_clazz()


__all__ = [
    "AlphaCalculator",
    "EnrichmentCalculator",
    "FoldUnweightedCalc",
    "FoldWeightedCalc",
    "SumUnweightedCalc",
    "SumWeightedCalc",
    "EnrichmentCalculation",
    "EnrichmentAlg",
    "EnrichmentDf",
    "ScoreDf",
]


1			"""
2			Scoring (regression and enrichment) calculations.
3			"""
4			import abc
5			import enum
6			import math
7			from typing import Generic, Mapping, Sequence, Type, TypeVar, Union
8
9			import pandas as pd
			0 ignored issues – show introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Unable to import 'pandas' Loading history...
10			from typeddfs import TypedDfs
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Unable to import 'typeddfs' Loading history...
11
12			from mandos.analysis import AnalysisUtils as Au
13			from mandos.model import CleverEnum
14			from mandos.model.hits import AbstractHit, HitFrame, HitUtils, Pair
15
16			S = TypeVar("S", bound=Union[int, float, bool])
			0 ignored issues – show Coding Style Naming introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Class name "S" doesn't conform to PascalCase naming style ('[^\\W\\da-z][^\\W_]+$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
17
18
19			EnrichmentDf = (
20			TypedDfs.typed("EnrichmentDf")
21			.require("predicate", "object", dtype=str)
22			.require("samples", dtype=int)
23			).build()
24			# extra cols are, e.g., alpha(score_1), alpha(is_hit)
25
26
27			ScoreDf = (TypedDfs.typed("ScoreDf").require("inchikey", dtype=str).reserve("score")).build()
28			# extra cols are, e.g., score_1, score_hello
29
30
31			IsHitDf = TypedDfs.typed("IsHitDf").require("inchikey", dtype=str)
32			# extra calls are is_hit, etc.
33
34
35			def _vars(self: ScoreDf) -> Sequence[str]:
36			return [
37			col
38			for col in self.columns
39			if (isinstance(self, ScoreDf) and (col == "score" or col.startswith("score_")))
40			or (isinstance(self, IsHitDf) and col.startswith("is_"))
41			]
42
43
44			def _var_map(self: ScoreDf) -> Mapping[str, Mapping[str, S]]:
45			results = {}
46			for c in self.score_cols:
			0 ignored issues – show Coding Style Naming introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Variable name "c" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
47			results[c] = self[c].to_dict()
48			return results
49
50
51			ScoreDf.vars = _vars
52			ScoreDf.var_map = _var_map
53			IsHitDf.vars = _vars
54			IsHitDf.var_map = _var_map
55
56
57			class EnrichmentCalculator(Generic[S], metaclass=abc.ABCMeta):
			0 ignored issues – show introduced 2021-06-30 04:51 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
58			def __init__(self, alg_name: str):
59			self.alg_name = alg_name
60
61			def calc_many(self, data: HitFrame, score_df: ScoreDf):
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62			hits = HitUtils.df_to_hits(data)
63			samples_per_pair = {k: len(v) for k, v in Au.hit_multidict(hits, "pair").items()}
64			results = {}
65			for col, scores in score_df.var_map():
66			calculated = self.calc(hits, scores)
67			results[col] = calculated
68			return EnrichmentDf(
69			[
70			pd.Series(self._results_row(pair, n_samples, results))
71			for pair, n_samples in samples_per_pair.items()
72			]
73			)
74
75			def _results_row(
76			self, pair: Pair, n_samples: int, results
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77			) -> Mapping[str, Union[str, int, float]]:
78			return {
79			**dict(
80			predicate=pair.pred,
81			object=pair.obj,
82			samples=n_samples,
83			),
84			**{self._col_name(col): vs[pair] for col, vs in results.items()},
85			}
86
87			def _col_name(self, col: str) -> str:
88			return self.alg_name + "(" + col + ")"
89
90			def calc(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> Mapping[Pair, float]:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
91			pair_to_hits = Au.hit_multidict(hits, "to_pair")
92			results = {}
93			for pair, the_hits in pair_to_hits.items():
			0 ignored issues – show Unused Code introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report The variable `the_hits` seems to be unused. Loading history...
94			results[pair] = self.for_pair(hits, scores)
95			return results
96
97			def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
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98			raise NotImplementedError()
99
100
101			class AlphaCalculator(EnrichmentCalculator[S]):
			0 ignored issues – show introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Missing class docstring Loading history... introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Value 'EnrichmentCalculator' is unsubscriptable Loading history...
102			def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
103			source_to_hits = Au.hit_multidict(hits, "data_source")
104			terms = []
105			for source, source_hits in source_to_hits.items():
			0 ignored issues – show Unused Code introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report The variable `source` seems to be unused. Loading history...
106			terms.append(self._calc_term(source_hits, scores))
107			return math.fsum(terms) / len(terms)
108
109			def _calc_term(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
			0 ignored issues – show Coding Style introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
110			values = [
111			Au.elle(hit.weight) * (2 * float(scores[hit.origin_inchikey] - 1)) ** 2 for hit in hits
112			]
113			return math.fsum(values) / len(values)
114
115
116			class FoldUnweightedCalc(EnrichmentCalculator[bool]):
			0 ignored issues – show introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Missing class docstring Loading history... introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Value 'EnrichmentCalculator' is unsubscriptable Loading history...
117			def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
			0 ignored issues – show Coding Style introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history... introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
118			numerator = len([hit for hit in hits if scores[hit.origin_inchikey]])
119			denominator = len([hit for hit in hits if not scores[hit.origin_inchikey]])
120			if denominator == 0:
121			return float("inf")
122			return numerator / denominator
123
124
125			class FoldWeightedCalc(EnrichmentCalculator[bool]):
			0 ignored issues – show introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Missing class docstring Loading history... introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Value 'EnrichmentCalculator' is unsubscriptable Loading history...
126			def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
127			yes = [hit for hit in hits if scores[hit.origin_inchikey]]
128			no = [hit for hit in hits if not scores[hit.origin_inchikey]]
			0 ignored issues – show Coding Style Naming introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Variable name "no" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
129			numerator = math.fsum((hit.weight for hit in yes))
			0 ignored issues – show Comprehensibility Best Practice introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report The variable `hit` does not seem to be defined. Loading history...
130			denominator = math.fsum((hit.weight for hit in no))
131			if denominator == 0:
132			return float("inf")
133			return numerator / denominator
134
135
136			class SumWeightedCalc(EnrichmentCalculator[S]):
			0 ignored issues – show introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Missing class docstring Loading history... introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Value 'EnrichmentCalculator' is unsubscriptable Loading history...
137			def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
138			return math.fsum([scores[hit.origin_inchikey] * hit.weight for hit in hits]) / len(hits)
139
140
141			class SumUnweightedCalc(EnrichmentCalculator[S]):
			0 ignored issues – show introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Missing class docstring Loading history... introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Value 'EnrichmentCalculator' is unsubscriptable Loading history...
142			def for_pair(self, hits: Sequence[AbstractHit], scores: Mapping[str, S]) -> float:
			0 ignored issues – show Coding Style introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history... introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
143			return math.fsum([scores[hit.origin_inchikey] for hit in hits]) / len(hits)
144
145
146			class EnrichmentAlg(CleverEnum):
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147			""" """
148
149			alpha = enum.auto()
150			fold = enum.auto()
151			fold_w = enum.auto()
152			sum = enum.auto()
153			sum_w = enum.auto()
154
155			@property
156			def description(self) -> str:
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157			s = self.symbol
			0 ignored issues – show Coding Style Naming introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Variable name "s" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
158			return {
159			EnrichmentAlg.alpha: rf"[float] {s}(p) = Mean product of rescaled weights and scores; see the docs",
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160			EnrichmentAlg.fold: rf"[bool] {s}(p) = #(c has p and hit) / #(c has p and not hit)",
161			EnrichmentAlg.fold_w: rf"[bool] {s}(p) = ∑(w(c, pair) s.t. c is hit) / ∑(w(c, pair) s.t. c not hit)",
			0 ignored issues – show Coding Style introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (113/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
162			EnrichmentAlg.sum: rf"{s}(p) = ∑(score(c) s.t. c has p)",
163			EnrichmentAlg.sum_w: rf"{s}(p) = ∑(score(c) × w(c, p) for all c)",
164			}[self]
165
166			@property
167			def symbol(self) -> str:
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168			return {
169			EnrichmentAlg.alpha: "α",
170			EnrichmentAlg.fold: r"β",
171			EnrichmentAlg.fold_w: "β*",
172			EnrichmentAlg.sum: r"γ",
173			EnrichmentAlg.sum_w: r"γ*",
174			}[self]
175
176			@property
177			def clazz(self) -> Type[EnrichmentCalculator]:
			0 ignored issues – show introduced 2021-07-05 03:20 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
178			return {
179			EnrichmentAlg.alpha: AlphaCalculator,
180			EnrichmentAlg.fold: FoldUnweightedCalc,
181			EnrichmentAlg.fold_w: FoldWeightedCalc,
182			EnrichmentAlg.sum: SumUnweightedCalc,
183			EnrichmentAlg.sum_w: SumWeightedCalc,
184			}[self.name]
185
186
187			class EnrichmentCalculation:
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188			@classmethod
189			def create(cls, algorithm: Union[str, EnrichmentAlg]) -> EnrichmentDf:
			0 ignored issues – show introduced 2021-07-05 18:49 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history...
190			alg_clazz = EnrichmentDf.of(algorithm).clazz
191			return alg_clazz()
192
193
194			__all__ = [
195			"AlphaCalculator",
196			"EnrichmentCalculator",
197			"FoldUnweightedCalc",
198			"FoldWeightedCalc",
199			"SumUnweightedCalc",
200			"SumWeightedCalc",
201			"EnrichmentCalculation",
202			"EnrichmentAlg",
203			"EnrichmentDf",
204			"ScoreDf",
205			]
206

dmyersturnbull / mandos

Push — main ( a80564...ec3fe3 )

EnrichmentCalculation.create() A

Complexity

Size

Duplication

Importance

Duplication Side-by-Side

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