Optimization

type Assembly struct {
	Method    AssemblyMethod
	Raw       []string
	Assembled []string
}

type AssemblyMethod interface {
	Name() string                                             // what is this method called
	Type() string                                             // method classification
	CanAssemble([]string) bool                                // can these parts work?
	Validate([]string, string) (bool, error)                  // do these parts make this output?
	Assemble([]string) ([]string, error)                      // what do these parts make?
	Disassemble(string, AssemblyParameters) ([]string, error) // split this sequence into parts
	RawToParts([]string) ([]string, error)                    // convert each part
	PartsToRaw([]string) ([]string, error)                    // return each part to its raw state
}

type AssemblyOptimizer interface {
	OptimizeAssembly(sequences []string, environment AssemblyOptimizerEnvironment, parameters AssemblyOptimizerParameters) AssemblyStrategy
}

type AssemblyOptimizerEnvironment struct {
	AssemblyMethods   []AssemblyMethod
	SequenceProviders []SequenceProvider
}

type AssemblyOptimizerParameters interface {
	MethodName() string
	MaxIterations() int
	Set(string, interface{})
	GetInt(string) (int, bool)
	GetFloat(string) (float64, bool)
	GetString(string) (string, bool)
	GetBool(string) (bool, bool)
}

type AssemblyParameters interface {
	SplitPoints() []int
}

type AssemblyProblem struct {
	Mutations PointSet2D // set of mutations
	Seq       string     // actual sequence
}

type AssemblyStep struct {
	Assemblies []Assembly
}

type AssemblyStrategy struct {
	Cost   int            // in pence
	Steps  []AssemblyStep // ordered
	Orders map[string]SequenceProvider
}

type Constraints struct {
	MaxSplits     int
	MinLen        int
	MaxLen        int
	MinDistToMut  int
	Query         string
	EndsToAvoid   []string
	EndLen        int
	NoTransitions bool
}

type FitnessValues struct {
	Fit        []int
	BestScore  int
	BestMember PointSet1D
}

type GAParameters struct {
	// contains filtered or unexported fields
}

type Point2D struct {
	X int
	Y int
}

type Point3D struct {
	X int
	Y int
	Z int
}

type PointSet1D []int

type PointSet2D []Point2D

type PointSet3D []Point3D

type Population struct {
	Members     []PointSet1D
	Problem     AssemblyProblem
	FitnessTest func(f int, fs []int) bool
}

type SeqSet []string

type SequenceProvider interface {
	Name() string
	MethodsImplemented() []string
	GetMethod(string) AssemblyMethod
}