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Documentation

Index

• Constants
• func AddSpeciesTips(t *tree.Tree)
• func Format(format string) int
• func ParseNcbiNames(reader io.Reader) (map[string]string, error)
• func ParseNcbiTree(reader io.Reader) (*tree.Tree, error)
• func RenameTreeNodes(t *tree.Tree, namemap map[string]string)
• func StrFormat(format int) string
• type ImageDownloader
• type ItolImageDownloader
  • func NewItolImageDownloader(config map[string]string) *ItolImageDownloader
  • func (d *ItolImageDownloader) Download(id string, format int) ([]byte, error)
• type NcbiTreeDownloader
  • func NewNcbiTreeDownloader() *NcbiTreeDownloader
  • func (d *NcbiTreeDownloader) Download(id string) (*tree.Tree, error)
• type TreeDownloader

Constants

const (
	IMGFORMAT_SVG     = 0
	IMGFORMAT_PNG     = 1
	IMGFORMAT_EPS     = 2
	IMGFORMAT_PDF     = 3
	IMGFORMAT_UNKNOWN = 4
)

Functions

func AddSpeciesTips

func AddSpeciesTips(t *tree.Tree)

if an internal node is a species, then we add a new tip

func Format

func Format(format string) int

func ParseNcbiNames

func ParseNcbiNames(reader io.Reader) (map[string]string, error)

Parse name file and convert names with the following rules: Special characters are replaces with "_" -> '(', ')', '[', ']', ':', ',', ' ', ';'

func ParseNcbiTree

func ParseNcbiTree(reader io.Reader) (*tree.Tree, error)

Build a gotree.tree.Tree

func RenameTreeNodes

func RenameTreeNodes(t *tree.Tree, namemap map[string]string)

func StrFormat

func StrFormat(format int) string

Types

type ImageDownloader

type ImageDownloader interface {
	Download(id string, format int) ([]byte, error) // Downdload a tree image from a server
}

type ItolImageDownloader

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

func NewItolImageDownloader

func NewItolImageDownloader(config map[string]string) *ItolImageDownloader

func (*ItolImageDownloader) Download

func (d *ItolImageDownloader) Download(id string, format int) ([]byte, error)

Down a tree image from ITOL

type NcbiTreeDownloader

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

func NewNcbiTreeDownloader

func NewNcbiTreeDownloader() *NcbiTreeDownloader

NCBI taxonomy downloader

func (*NcbiTreeDownloader) Download

func (d *NcbiTreeDownloader) Download(id string) (*tree.Tree, error)

Download the NCBI taxonomy as a tree.Tree

type TreeDownloader

type TreeDownloader interface {
	Download(id string) (*tree.Tree, error) // Download a tree from a server
}