As discussed extensively on the "dev" ML, there are two competing designs (please review them on the dedicated git branch) for the refactoring of the basic functionality currently implemented in the org.apache.commons.math4.legacy.genetics "legacy" package.
- The discussion has pointed to major (from a maintenance POV) issues of the design proposed by the OP.
- The alternative (much simpler) design has been implemented as proof-of-concept (indicating that some corner might have been cut).
- The OP mentioned correctness issues in the "simple" design but did neither fix them nor provided answers on the LM to that effect.
- Questions concerning other possible "bloat" (e.g. on using a custom representation of the "binary chromosome" concept instead of the BitSet available from the JDK) were also left dangling.
- Refactoring of the "basic" GA functionality (the purpose of the "proof-of-concept") must be decoupled from the new feature which the OP wanted to implement ("adaptive probability generation").
- Unit tests (a.o. all those from the "legacy" code) must demonstrate that the refactored code does (or does not) behave correctly, and bugs should be fixed on the "simple" implementation, before implementing the new feature on top of it.