Code

Add stats to codon tables#350

Code

Merged

TimothyStiles merged 38 commits intobebop:mainbebop/poly:mainfrom cachemoi:FEAT-262/start-codon-statscachemoi/poly:FEAT-262/start-codon-statsCopy head branch name to clipboardNov 15, 2023

+664-431

Commits

Commits on Nov 5, 2023

• add stats to codon tables

  cachemoi

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  14d574a

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• revert unintended error message removal

  cachemoi

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  9e5dc10

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• separate stats into its own codon analyzer struct

  cachemoi

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  1b3009f

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• Update synthesis/codon/analyzer_test.go

  Show description for e21ea46
  

  cachemoi

  and

  carreter

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  e21ea46

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• remove analyzer

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• stats struct

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  57c2b06

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• turn codonTable into TranslationTable, which holds the required data for translation and optimisation

  cachemoi

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  35f8854

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• generate translation and optimisation maps in constructors

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• return pointer

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• return pointer, table interface no longer necessary

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  ad22177

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• update the Compromise and Add funcs to copy the first table when merging (no risk of changing data through pointer)

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  6f6fa7b

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• imports and error

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  a371a42

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• add gene count to stats

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  7d0e6a9

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• DRY tests with new structures

  cachemoi

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  8f21d0b

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• DRY examples with new structures

  cachemoi

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  7938cd8

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• update synthesis code to use the codontable's Optimize func

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  888d800

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• update amino acid weights through setter

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  fdaa508

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• bubble up table weight update errs

  cachemoi

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  0e2a1a3

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• make stats part of the table struct so we can track them across a table's lifetime, which is probably closer to what we want

  cachemoi

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  03e99bc

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• add comments

  cachemoi

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  a2f8fc7

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• make translation table stats public rather than use a getter

  cachemoi

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  299e45a

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• add table test for optimisation

  cachemoi

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  6429150

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• fix fatal err case

  cachemoi

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  4d8020b

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• add test case

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• missed an item in updateWeights

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  4fcd51e

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• proper gene count

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  436ed93

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• move stats below other interfaces

  cachemoi

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• add translate to table interface

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  04b7c82

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• update comments

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  d3a9454

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• update comment

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  08becb9

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• update changelog

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  58a511c

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Commits on Nov 8, 2023

• comment NewStats

  cachemoi

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• add weight update err test

  cachemoi

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• newAminoAcidChoosers test

  cachemoi

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• UpdateWeights test

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• Compromise/Add codon table tests

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• add an example for using manual codon weights

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Commits on Nov 13, 2023

• fix lint

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