Add stats to codon tables (#350)

* add stats to codon tables * separate stats into its own codon analyzer struct * stats struct * turn codonTable into TranslationTable, which holds the required data for translation and optimisation * generate translation and optimisation maps in constructors * update the Compromise and Add funcs to copy the first table when merging (no risk of changing data through pointer) * add gene count to stats * DRY tests with new structures * DRY examples with new structures * update synthesis code to use the codontable's Optimize func * update amino acid weights through setter * bubble up table weight update errs * 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 * make translation table stats public rather than use a getter * move stats below other interfaces * add translate to table interface * update changelog * add weight update err test * newAminoAcidChoosers test * UpdateWeights test * Compromise/Add codon table tests * add an example for using manual codon weights --------- Co-authored-by: Willow Carretero Chavez <sandiegobutterflies@gmail.com>
bebop · Nov 15, 2023 · 96b5cff · 96b5cff
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Alternative start codons can now be used in the `synthesis/codon` DNA -> protein translation package (#305)
 - Added a parser and writer for the `pileup` sequence alignment format (#329)
+- Added statistics to the `synthesis/codon` package (keeping track of the observed start codon occurrences in a translation table) (#350)
 
 ### Fixed
 - `fastq` parser no longer becomes de-aligned when reading (#325)