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Documentation

Index

• Variables
• func AddRank(cs []Clade)
• type Clade
• type CladesDist
• type Context
  • func New(h []Hierarch, threshold float32) Context
• type Hierarch
• type Rank
  • func NewRank(s string) Rank
  • func (r Rank) Index() int
  • func (r Rank) String() string

Variables

var RankStr = map[Rank]string{
	Empty:      "empty",
	Unknown:    "unknown",
	SubSpecies: "subspecies",
	Species:    "species",
	Genus:      "genus",
	Family:     "family",
	Order:      "order",
	Class:      "class",
	Phylum:     "phylum",
	Kingdom:    "kingdom",
}

var StrRank = func() map[string]Rank {
	res := make(map[string]Rank)
	for k, v := range RankStr {
		res[v] = k
	}
	return res
}()

Functions

func AddRank

func AddRank(cs []Clade)

Types

type Clade

type Clade struct {
	ID, Name, RankStr string
	Rank
}

type CladesDist

type CladesDist struct {
	NamesNum   int
	Name       string
	Percentage float32
}

type Context

type Context struct {
	NamesNum                             int
	Kingdom, Context                     Clade
	KingdomPercentage, ContextPercentage float32
	Kingdoms                             []CladesDist
}

func New

func New(
	h []Hierarch,
	threshold float32,
) Context

New takes several items that include bio-clasification and returns back the kingdom where most of items belong to (if rank 'kingdom' is provided), percentage of how many items belong to that kingdom, and the highest ranking clade that includes a certain percentage of species. The percentage is provided via threshold parameter.

The algorithm assumes that all items belong to the same classification tree and that classification does not skip clades from item to item.

type Hierarch

type Hierarch interface {
	// Clades method produces a slice of clades that represent a path in a
	// hierarchy.
	Clades() []Clade
}

An interface that allows to produce a normalized verion of a hierarchy as a slice of clades, ordered accorting from more general to more specific clades.

type Rank

type Rank int

const (
	Empty Rank = iota
	Unknown
	SubSpecies
	Species
	Genus
	Family
	Order
	Class
	Phylum
	Kingdom
)

func NewRank

func NewRank(s string) Rank

func (Rank) Index

func (r Rank) Index() int

func (Rank) String

func (r Rank) String() string