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

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Co-authored-by: Willow Carretero Chavez <[email protected]>

Author: cachemoi

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)