analyze

Documentation

Index

• Variables
• func Execute(cmd *cobra.Command, args []string) error
• func ExportCytoscapeJS(pg graph.Graph[*engine.Object, engine.EdgeBitmap], filename string) error
• func ExportGraphViz(pg graph.Graph[*engine.Object, engine.EdgeBitmap], filename string) error
• func NewWebservice() *webservice
• type AnalysisResults
  • func AnalyzeObjects(opts AnalyzeObjectsOptions) AnalysisResults
• type AnalyzeObjectsOptions
  • func NewAnalyzeObjectsOptions() AnalyzeObjectsOptions
• type CytoElements
• type CytoFlatElement
• type CytoGraph
  • func GenerateCytoscapeJS(pg graph.Graph[*engine.Object, engine.EdgeBitmap], alldetails bool) (CytoGraph, error)
• type CytoGraphData
• type GraphNode
• type MapStringInterface
• type MethodMap
• type PostProcessorFunc
• type Prefs
  • func (p *Prefs) Get(key string) any
  • func (p *Prefs) Load() error
  • func (p *Prefs) Save() error
  • func (p *Prefs) Set(key string, val any)
• type UnionFS
  • func (ufs *UnionFS) AddFS(newfs http.FileSystem)
  • func (ufs UnionFS) Exists(prefix, filename string) bool
  • func (ufs UnionFS) Open(filename string) (http.File, error)
• type XGMMLAttribute
• type XGMMLEdge
• type XGMMLGraph
  • func NewXGMMLGraph() XGMMLGraph
• type XGMMLNode

Variables

var (
	Command = &cobra.Command{
		Use:   "analyze [-options]",
		Short: "Lanunches the interactive discovery tool in your browser",
	}

	WebService = NewWebservice()
)

var EdgeMemberOfGroup = engine.NewEdge("MemberOfGroup") // Get rid of this

var PostProcessors []PostProcessorFunc

var SortBy engine.Attribute = engine.NonExistingAttribute

Functions

func Execute

func Execute(cmd *cobra.Command, args []string) error

func ExportCytoscapeJS

func ExportCytoscapeJS(pg graph.Graph[*engine.Object, engine.EdgeBitmap], filename string) error

func ExportGraphViz

func ExportGraphViz(pg graph.Graph[*engine.Object, engine.EdgeBitmap], filename string) error

func NewWebservice

func NewWebservice() *webservice

Types

type AnalysisResults

type AnalysisResults struct {
	Graph   graph.Graph[*engine.Object, engine.EdgeBitmap]
	Removed int
}

func AnalyzeObjects

func AnalyzeObjects(opts AnalyzeObjectsOptions) AnalysisResults

type AnalyzeObjectsOptions

type AnalyzeObjectsOptions struct {
	Objects                   *engine.Objects
	StartFilter               query.NodeFilter
	MiddleFilter              query.NodeFilter
	EndFilter                 query.NodeFilter
	ObjectTypesF              []engine.ObjectType
	ObjectTypesM              []engine.ObjectType
	ObjectTypesL              []engine.ObjectType
	MethodsL                  engine.EdgeBitmap
	MethodsM                  engine.EdgeBitmap
	MethodsF                  engine.EdgeBitmap
	MaxDepth                  int
	MaxOutgoingConnections    int
	Direction                 engine.EdgeDirection
	Backlinks                 int // Backlink depth
	MinEdgeProbability        engine.Probability
	MinAccumulatedProbability engine.Probability
	PruneIslands              bool
	NodeLimit                 int
	DontExpandAUEO            bool
}

func NewAnalyzeObjectsOptions

func NewAnalyzeObjectsOptions() AnalyzeObjectsOptions

type CytoElements

type CytoElements []CytoFlatElement

type CytoFlatElement

type CytoFlatElement struct {
	Data  MapStringInterface `json:"data"`
	Group string             `json:"group"` // nodes or edges
}

type CytoGraph

type CytoGraph struct {
	FormatVersion            string        `json:"format_version"`
	GeneratedBy              string        `json:"generated_by"`
	TargetCytoscapeJSVersion string        `json:"target_cytoscapejs_version"`
	Data                     CytoGraphData `json:"data"`
	Elements                 CytoElements  `json:"elements"`
}

func GenerateCytoscapeJS

func GenerateCytoscapeJS(pg graph.Graph[*engine.Object, engine.EdgeBitmap], alldetails bool) (CytoGraph, error)

type CytoGraphData

type CytoGraphData struct {
	SharedName string `json:"shared_name"`
	Name       string `json:"name"`
	SUID       int    `json:"SUID"`
}

type GraphNode

type GraphNode struct {
	CanExpand int
	// contains filtered or unexported fields
}

type MapStringInterface

type MapStringInterface map[string]any

type MethodMap

type MethodMap map[string]bool

type PostProcessorFunc

type PostProcessorFunc func(pg graph.Graph[*engine.Object, engine.EdgeBitmap]) graph.Graph[*engine.Object, engine.EdgeBitmap]

type Prefs

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

func (*Prefs) Get

func (p *Prefs) Get(key string) any

func (*Prefs) Load

func (p *Prefs) Load() error

func (*Prefs) Save

func (p *Prefs) Save() error

func (*Prefs) Set

func (p *Prefs) Set(key string, val any)

type UnionFS

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

func (*UnionFS) AddFS

func (ufs *UnionFS) AddFS(newfs http.FileSystem)

func (UnionFS) Exists

func (ufs UnionFS) Exists(prefix, filename string) bool

func (UnionFS) Open

func (ufs UnionFS) Open(filename string) (http.File, error)

type XGMMLAttribute

type XGMMLAttribute struct {
	XMLName xml.Name `xml:"att"`
	Name    string   `xml:"name,attr"`
	Value   string   `xml:"value,attr"`
}

type XGMMLEdge

type XGMMLEdge struct {
	XMLName    xml.Name        `xml:"edge"`
	Source     engine.ObjectID `xml:"source,attr"`
	Target     engine.ObjectID `xml:"target,attr"`
	Label      string          `xml:"label,attr"`
	Attributes []XGMMLAttribute
}

type XGMMLGraph

type XGMMLGraph struct {
	XMLName    xml.Name `xml:"graph"`
	XMLNS      string   `xml:"xmlns,attr"`
	XMLNSDC    string   `xml:"xmlns:dc,attr"`
	XMLNSXLINK string   `xml:"xmlns:xlink,attr"`
	XMLNSRDF   string   `xml:"xmlns:rdf,attr"`
	XMLNSCY    string   `xml:"xmlns:cy,attr"`

	Directed int    `xml:"directed,attr"`
	Label    string `xml:"label,attr,omitempty"`
	RootNode int    `xml:"Rootnode,attr,omitempty"`

	Nodes []XGMMLNode
	Edges []XGMMLEdge
}

func NewXGMMLGraph

func NewXGMMLGraph() XGMMLGraph

type XGMMLNode

type XGMMLNode struct {
	XMLName    xml.Name        `xml:"node"`
	Id         engine.ObjectID `xml:"id,attr"`
	Label      string          `xml:"label,attr"`
	Weight     int             `xml:"weight,attr,omitempty"`
	Attributes []XGMMLAttribute
}