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refactoring scoring (tracker issue) #205

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CunliangGeng opened this issue Feb 2, 2024 · 0 comments

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refactor codebase

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CunliangGeng commented Feb 2, 2024 •

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This is a collection of issues on refactoring scorings.
The number of 🔻 roughly indicates the complexity level of the legacy code.

refactor shared classes 🔻

class ScoringMethod
- add abstract base class for scoring methods #247
class ObjectLink and class LinkCollection
- Add LinkGraph to replace ObjectLink and LinkCollection #252

refactor metcalf scoring 🔻🔻

module linking, including
- class DataLinks
  - merge DataLinks to MetcalfScoring class #249
  - merge DataLinks get_common_strains to ObjectLink #250
- class LinkFinder
  - merge LinkFinder to MetcalfScoring class #248
class MetcalfScoring
- refactor MetcalfScoring methods #254

👉 To do the following if time allows

refactor rosetta scoring 🔻🔻🔻

class RosettaScoring
module rosetta, including classes RosettaHit, Rosetta, SpecLib
module parsers, including classes KCBJSONParser and KCBTextParser

NPClass scoring 🔻🔻🔻🔻

a huge class NPClassScoring

The text was updated successfully, but these errors were encountered:

CunliangGeng added the Tracker-issue label

CunliangGeng changed the title ~~refactoring scoring~~ refactoring scoring (tracker issue)

CunliangGeng self-assigned this

CunliangGeng added this to the refactor codebase milestone

CunliangGeng added this to dev

CunliangGeng moved this to In progress in dev

CunliangGeng moved this from In progress to Done in dev

CunliangGeng closed this as completed

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