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package module
v0.0.19 Latest Latest
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 Go to latest Published: Apr 27, 2021 License: GPL-2.0 Imports: 34 Imported by: 3

README

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Index

Constants

This section is empty.

Variables

This section is empty.

Functions

func Asset 

func Asset(name string) ([]byte, error)

Asset loads and returns the asset for the given name. It returns an error if the asset could not be found or could not be loaded.

func AssetDir 

func AssetDir(name string) ([]string, error)

AssetDir returns the file names below a certain directory embedded in the file by go-bindata. For example if you run go-bindata on data/... and data contains the following hierarchy: 

data/
  foo.txt
  img/
    a.png
    b.png

then AssetDir("data") would return []string{"foo.txt", "img"} AssetDir("data/img") would return []string{"a.png", "b.png"} AssetDir("foo.txt") and AssetDir("notexist") would return an error AssetDir("") will return []string{"data"}.

func AssetInfo 

func AssetInfo(name string) (os.FileInfo, error)

AssetInfo loads and returns the asset info for the given name. It returns an error if the asset could not be found or could not be loaded.

func AssetNames 

func AssetNames() []string

AssetNames returns the names of the assets.

func IterEntry 

func IterEntry(d DataManager) chan Entry

func MustAsset 

func MustAsset(name string) []byte

MustAsset is like Asset but panics when Asset would return an error. It simplifies safe initialization of global variables.

func ParseSimpleWb 

func ParseSimpleWb(xlFile *SimpleWorkbook) ([]dataIndex, error)

JSON -> Simple Workbook parsed already

func RestoreAsset 

func RestoreAsset(dir, name string) error

RestoreAsset restores an asset under the given directory

func RestoreAssets 

func RestoreAssets(dir, name string) error

RestoreAssets restores an asset under the given directory recursively

func SaveIndex 

func SaveIndex(uri string, root string) error

Types

type Band 

type Band struct {
	Chr   string `json:"chr"`
	Start int    `json:"start"`
	End   int    `json:"end"`
	Id    string `json:"id"`
	Value string `json:"value"`
}

type Bed3 

type Bed3 interface {
	Chr() string
	Start() int
	End() int
}

type Bed4 

type Bed4 struct {
	// contains filtered or unexported fields
}

func (Bed4) Chr 

func (b Bed4) Chr() string

func (Bed4) End 

func (b Bed4) End() int

func (Bed4) Id 

func (b Bed4) Id() string

func (Bed4) Start 

func (b Bed4) Start() int

type BigBedManager 

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

func InitBigBedManager 

func InitBigBedManager(dbname string, root string) *BigBedManager

func NewBigBedManager 

func NewBigBedManager(uri string, dbname string, root string) *BigBedManager

func (*BigBedManager) Add 

func (m *BigBedManager) Add(key string, reader io.ReadSeeker, uri string) error

func (*BigBedManager) AddURI 

func (bb *BigBedManager) AddURI(uri string, key string) error

func (*BigBedManager) Del 

func (m *BigBedManager) Del(key string) error

func (*BigBedManager) Get 

func (m *BigBedManager) Get(key string) (string, bool)

func (*BigBedManager) GetAttr 

func (m *BigBedManager) GetAttr(key string) (map[string]interface{}, bool)

func (*BigBedManager) List 

func (m *BigBedManager) List() []string

func (*BigBedManager) Move 

func (m *BigBedManager) Move(key1 string, key2 string) bool

func (*BigBedManager) ServeTo 

func (m *BigBedManager) ServeTo(router *mux.Router)

func (*BigBedManager) SetAttr 

func (m *BigBedManager) SetAttr(key string, value map[string]interface{}) error

type BigWigManager 

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

func InitBigWigManager 

func InitBigWigManager(dbname string, indexRoot string) *BigWigManager

func NewBigWigManager 

func NewBigWigManager(uri string, dbname string, indexRoot string) *BigWigManager

func (*BigWigManager) Add 

func (m *BigWigManager) Add(key string, reader io.ReadSeeker, uri string) error

func (*BigWigManager) AddURI 

func (m *BigWigManager) AddURI(uri string, key string) error

func (*BigWigManager) Del 

func (m *BigWigManager) Del(key string) error

func (*BigWigManager) Get 

func (m *BigWigManager) Get(key string) (string, bool)

func (*BigWigManager) GetAttr 

func (m *BigWigManager) GetAttr(key string) (map[string]interface{}, bool)

func (*BigWigManager) List 

func (m *BigWigManager) List() []string

func (*BigWigManager) Move 

func (m *BigWigManager) Move(key1 string, key2 string) bool

func (*BigWigManager) ServeTo 

func (m *BigWigManager) ServeTo(router *mux.Router)

TODO ls Add Attr

func (*BigWigManager) SetAttr 

func (m *BigWigManager) SetAttr(key string, value map[string]interface{}) error

type CytoBand 

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

type CytoBandManager 

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

func InitCytoBandManager 

func InitCytoBandManager(id string) *CytoBandManager

func NewCytoBandManager 

func NewCytoBandManager(id string) *CytoBandManager

func (*CytoBandManager) Add 

func (m *CytoBandManager) Add(genome string) error

func (*CytoBandManager) AddURI 

func (m *CytoBandManager) AddURI(uri string, key string) error

func (*CytoBandManager) Del 

func (m *CytoBandManager) Del(genome string) error

func (*CytoBandManager) Get 

func (m *CytoBandManager) Get(genome string) (string, bool)

func (*CytoBandManager) List 

func (m *CytoBandManager) List() []string

func (*CytoBandManager) Move 

func (m *CytoBandManager) Move(key1 string, key2 string) bool

func (*CytoBandManager) ServeTo 

func (m *CytoBandManager) ServeTo(router *mux.Router)

type DataLoader 

type DataLoader interface {
	Load(interface{}) error
}

type DataManager 

type DataManager interface {
	DataRouter
	AddURI(uri string, key string) error
	Del(string) error
	List() []string
	Get(string) (string, bool)
	Move(key1 string, key2 string) bool
}

type DataRouter 

type DataRouter interface {
	ServeTo(*mux.Router)
}

type DataServer 

type DataServer interface {
	DataRouter
	DataLoader
}

type Entry 

type Entry struct {
	Name string
	URI  string
}

type FileManager 

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

func InitFileManager 

func InitFileManager(dbname string) *FileManager

func NewFileManager 

func NewFileManager(uri string, dbname string) *FileManager

func (*FileManager) AddURI 

func (m *FileManager) AddURI(uri string, key string) error

func (*FileManager) Del 

func (m *FileManager) Del(key string) error

func (*FileManager) Get 

func (m *FileManager) Get(key string) (string, bool)

func (*FileManager) List 

func (m *FileManager) List() []string

func (*FileManager) Move 

func (m *FileManager) Move(key1 string, key2 string) bool

func (*FileManager) ServeTo 

func (m *FileManager) ServeTo(router *mux.Router)

type HicManager 

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

func InitHicManager 

func InitHicManager(dbname string) *HicManager

func NewHicManager 

func NewHicManager(uri string, dbname string) *HicManager

func (*HicManager) Add 

func (m *HicManager) Add(key string, reader io.ReadSeeker, uri string) error

func (*HicManager) AddURI 

func (m *HicManager) AddURI(uri string, key string) error

func (*HicManager) Del 

func (m *HicManager) Del(key string) error

func (*HicManager) Get 

func (m *HicManager) Get(key string) (string, bool)

func (*HicManager) GetAttr 

func (m *HicManager) GetAttr(key string) (map[string]interface{}, bool)

func (*HicManager) List 

func (m *HicManager) List() []string

func (*HicManager) Move 

func (m *HicManager) Move(key1 string, key2 string) bool

func (*HicManager) ServeTo 

func (m *HicManager) ServeTo(router *mux.Router)

func (*HicManager) SetAttr 

func (m *HicManager) SetAttr(key string, value map[string]interface{}) error

type IndexEntry 

type IndexEntry struct {
	Genome string
	Id     string
	Type   string
	Nc     int
	Vc     []int
}

TODO THIS add more interface

type Loader 

type Loader struct {
	IndexRoot string
	Plugins   map[string]func(string, interface{}) (DataRouter, error)
	Data      map[string]DataRouter
	// contains filtered or unexported fields
}

func NewLoader 

func NewLoader(root string) *Loader

func (*Loader) AddDataMiddleware 

func (m *Loader) AddDataMiddleware(uri string, h http.Handler) http.Handler

func (*Loader) AddLoader 

func (e *Loader) AddLoader(format string, f func(string, interface{}) (DataRouter, error)) error

func (*Loader) Factory 

func (e *Loader) Factory(dbname string, data interface{}, format string) func(string, interface{}) (DataRouter, error)

func (*Loader) Load 

func (m *Loader) Load(uri string, router *mux.Router) error

func (*Loader) LoadWorkbook 

func (m *Loader) LoadWorkbook(wb *SimpleWorkbook, router *mux.Router) error

func (*Loader) Refresh 

func (e *Loader) Refresh(dbname string, data interface{}, format string) error

func (*Loader) Reload 

func (m *Loader) Reload(uri string) error

type Manager 

type Manager interface {
	DataManager
	Add(key string, reader io.ReadSeeker, uri string) error
	SetAttr(key string, values map[string]interface{}) error
	GetAttr(key string) (map[string]interface{}, bool)
}

type MapManager 

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

func InitMapManager 

func InitMapManager(name string) *MapManager

func NewMapManager 

func NewMapManager(uri string, name string) *MapManager

func (*MapManager) AddURI 

func (m *MapManager) AddURI(uri string, key string) error

func (*MapManager) Del 

func (m *MapManager) Del(key string) error

func (*MapManager) Get 

func (m *MapManager) Get(key string) (string, bool)

func (*MapManager) List 

func (m *MapManager) List() []string

func (*MapManager) Move 

func (m *MapManager) Move(key1 string, key2 string) bool

func (*MapManager) ServeTo 

func (m *MapManager) ServeTo(router *mux.Router)

type NamedIndexEntry 

type NamedIndexEntry struct {
	Genome string
	Id     string
	Type   string
	Nid    string
	Vids   []string
}

type ShortBed 

type ShortBed interface {
	Chr() string
	Start() int
	End() int
}

type SimpleWorkbook 

type SimpleWorkbook struct {
	SheetNames []string
	Sheets     map[string][][]string
}

type TabixManager 

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

func InitTabixManager 

func InitTabixManager(dbname string) *TabixManager

func NewTabixManager 

func NewTabixManager(uri string, dbname string) *TabixManager

func (*TabixManager) AddURI 

func (T *TabixManager) AddURI(uri string, key string) error

func (*TabixManager) Del 

func (m *TabixManager) Del(key string) error

func (*TabixManager) Get 

func (m *TabixManager) Get(key string) (string, bool)

func (*TabixManager) GetAttr 

func (m *TabixManager) GetAttr(key string) (map[string]interface{}, bool)

func (*TabixManager) List 

func (m *TabixManager) List() []string

func (*TabixManager) Move 

func (m *TabixManager) Move(key1 string, key2 string) bool

func (*TabixManager) ServeTo 

func (T *TabixManager) ServeTo(router *mux.Router)

func (*TabixManager) SetAttr 

func (m *TabixManager) SetAttr(key string, value map[string]interface{}) error

type TrackManager 

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

func InitTrackManager 

func InitTrackManager(dbname string, root string) *TrackManager

func NewTrackManager 

func NewTrackManager(uri string, dbname string, root string) *TrackManager

func (*TrackManager) Add 

func (m *TrackManager) Add(key string, reader io.ReadSeeker, uri string) error

func (*TrackManager) AddURI 

func (m *TrackManager) AddURI(uri string, key string) error

func (*TrackManager) Del 

func (m *TrackManager) Del(k string) error

func (*TrackManager) Get 

func (m *TrackManager) Get(key string) (string, bool)

func (*TrackManager) GetAttr 

func (m *TrackManager) GetAttr(key string) (map[string]interface{}, bool)

func (*TrackManager) List 

func (m *TrackManager) List() []string

func (*TrackManager) Move 

func (m *TrackManager) Move(key1 string, key2 string) bool

func (*TrackManager) ServeTo 

func (m *TrackManager) ServeTo(router *mux.Router)

func (*TrackManager) SetAttr 

func (m *TrackManager) SetAttr(key string, values map[string]interface{}) error

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