gwdi

Documentation

Index

• type GWDI
  • func NewGWDI(r io.Reader) (*GWDI, error)
  • func (g *GWDI) AllGroups() ([]string, error)
  • func (g *GWDI) AnnotateMutant() error
  • func (g *GWDI) DedupID() error
  • func (g *GWDI) GroupMutant() error
  • func (g *GWDI) MutantReader(group string) GWDIMutantReader
• type GWDIMutantReader
  • func NewGWDIMutantIterator(itr iterator.Iterator) GWDIMutantReader
• type GWDIStrain
• type IDMapper
  • func NewIDMap() (IDMapper, error)
• type ListCacher
  • func NewListCache() (ListCacher, error)

Types

type GWDI

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

GWDI is for managing gwdi data

func NewGWDI

func NewGWDI(r io.Reader) (*GWDI, error)

func (*GWDI) AllGroups

func (g *GWDI) AllGroups() ([]string, error)

func (*GWDI) AnnotateMutant

func (g *GWDI) AnnotateMutant() error

func (*GWDI) DedupID

func (g *GWDI) DedupID() error

func (*GWDI) GroupMutant

func (g *GWDI) GroupMutant() error

func (*GWDI) MutantReader

func (g *GWDI) MutantReader(group string) GWDIMutantReader

type GWDIMutantReader

type GWDIMutantReader interface {
	Next() bool
	Value() (*GWDIStrain, error)
}

func NewGWDIMutantIterator

func NewGWDIMutantIterator(itr iterator.Iterator) GWDIMutantReader

type GWDIStrain

type GWDIStrain struct {
	Label       string                        `json:"label"`
	Name        string                        `json:"name"`
	Summary     string                        `json:"summary"`
	Genotype    string                        `json:"genotype"`
	Parent      string                        `json:"parent"`
	Plasmid     string                        `json:"plasmid,omitempty"`
	Species     string                        `json:"species"`
	Depositor   string                        `json:"depositor"`
	Publication string                        `json:"publication"`
	Characters  []string                      `json:"characters"`
	Genes       []string                      `json:"genes,omitempty"`
	Properties  map[string]*tsource.StockProp `json:"properties"`
}

GWDIStrain is the container for GWDI strain

type IDMapper

type IDMapper interface {
	Put(key []byte, value []byte) error
	Get(key []byte) (value []byte, err error)
	Remove(key []byte) error
	Exist(key []byte) (bool, error)
	Iterate() iterator.Iterator
}

func NewIDMap

func NewIDMap() (IDMapper, error)

type ListCacher

type ListCacher interface {
	StartBatch()
	AppendToBatch([]byte, []byte)
	CommitBatch() error
	Push([]byte, []byte) error
	PushAll([]byte, ...[]byte) error
	IterateByPrefix([]byte) iterator.Iterator
	CommonPrefixes() ([][]byte, error)
}

func NewListCache

func NewListCache() (ListCacher, error)