mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
Add obiminion first version
Former-commit-id: aa5ace7bd4d2266333715fca7094d1c3cbbb5e6d
This commit is contained in:
Eric Coissac
327
pkg/obigraph/graph.go
Normal file
327
pkg/obigraph/graph.go
Normal file
@ -0,0 +1,327 @@
|
||||
package obigraph
|
||||
|
||||
import (
|
||||
"bytes"
|
||||
"fmt"
|
||||
"io"
|
||||
"math"
|
||||
"os"
|
||||
"text/template"
|
||||
|
||||
log "github.com/sirupsen/logrus"
|
||||
)
|
||||
|
||||
type Edge[T any] struct {
|
||||
From int
|
||||
To int
|
||||
Data *T
|
||||
}
|
||||
|
||||
type Edges[T any] map[int]map[int]*T
|
||||
type Graph[V any, T any] struct {
|
||||
Name string
|
||||
Vertices *[]V
|
||||
Edges *Edges[T]
|
||||
ReverseEdges *Edges[T]
|
||||
VertexWeight func(int) float64
|
||||
VertexId func(int) string
|
||||
EdgeWeight func(int, int) float64
|
||||
}
|
||||
|
||||
func NewEdges[T any]() *Edges[T] {
|
||||
e := make(map[int]map[int]*T)
|
||||
|
||||
return (*Edges[T])(&e)
|
||||
}
|
||||
|
||||
// AddEdge adds an edge to the graph between two vertices.
|
||||
//
|
||||
// Parameters:
|
||||
// - from: the index of the starting vertex.
|
||||
// - to: the index of the ending vertex.
|
||||
// - data: a pointer to the data associated with the edge.
|
||||
func (e *Edges[T]) AddEdge(from, to int, data *T) {
|
||||
|
||||
fnode, ok := (*e)[from]
|
||||
if !ok {
|
||||
fnode = make(map[int]*T)
|
||||
(*e)[from] = fnode
|
||||
}
|
||||
fnode[to] = data
|
||||
}
|
||||
|
||||
// NewGraph creates a new graph with the specified name and vertices.
|
||||
//
|
||||
// Parameters:
|
||||
// - name: a string representing the name of the graph.
|
||||
// - vertices: a slice of vertices of type V.
|
||||
//
|
||||
// Returns:
|
||||
// - Graph[V, T]: the newly created graph.
|
||||
func NewGraph[V, T any](name string, vertices *[]V) *Graph[V, T] {
|
||||
return &Graph[V, T]{
|
||||
Name: name,
|
||||
Vertices: vertices,
|
||||
Edges: NewEdges[T](),
|
||||
ReverseEdges: NewEdges[T](),
|
||||
VertexWeight: func(i int) float64 {
|
||||
return 1.0
|
||||
},
|
||||
EdgeWeight: func(i, j int) float64 {
|
||||
return 1.0
|
||||
},
|
||||
VertexId: func(i int) string {
|
||||
return fmt.Sprintf("V%d", i)
|
||||
},
|
||||
}
|
||||
}
|
||||
|
||||
// AddEdge adds an edge between two vertices in the graph.
|
||||
//
|
||||
// Parameters:
|
||||
// - from: the index of the starting vertex.
|
||||
// - to: the index of the ending vertex.
|
||||
// - data: a pointer to the data associated with the edge.
|
||||
func (g *Graph[V, T]) AddEdge(from, to int, data *T) {
|
||||
lv := len(*g.Vertices)
|
||||
if from >= lv || to >= lv {
|
||||
log.Errorf("out of bounds vertex index: %d or %d (max: %d)", from, to, lv-1)
|
||||
}
|
||||
|
||||
g.Edges.AddEdge(from, to, data)
|
||||
g.Edges.AddEdge(to, from, data)
|
||||
g.ReverseEdges.AddEdge(to, from, data)
|
||||
g.ReverseEdges.AddEdge(from, to, data)
|
||||
}
|
||||
|
||||
// AddDirectedEdge adds a directed edge from one vertex to another in the graph.
|
||||
//
|
||||
// Parameters:
|
||||
// - from: an integer representing the index of the starting vertex.
|
||||
// - to: an integer representing the index of the ending vertex.
|
||||
// - data: a pointer to the data associated with the edge.
|
||||
func (g *Graph[V, T]) AddDirectedEdge(from, to int, data *T) {
|
||||
lv := len(*g.Vertices)
|
||||
|
||||
if from >= lv || to >= lv {
|
||||
log.Errorf("out of bounds vertex index: %d or %d (max: %d)", from, to, lv-1)
|
||||
}
|
||||
|
||||
g.Edges.AddEdge(from, to, data)
|
||||
g.ReverseEdges.AddEdge(to, from, data)
|
||||
}
|
||||
|
||||
// SetAsDirectedEdge sets the edge from one vertex to another as directed in the graph.
|
||||
//
|
||||
// Parameters:
|
||||
// - from: an integer representing the index of the starting vertex.
|
||||
// - to: an integer representing the index of the ending vertex.
|
||||
func (g *Graph[V, T]) SetAsDirectedEdge(from, to int) {
|
||||
lv := len(*g.Vertices)
|
||||
|
||||
if from >= lv || to >= lv {
|
||||
log.Errorf("out of bounds vertex index: %d or %d (max: %d)", from, to, lv-1)
|
||||
}
|
||||
|
||||
if _, ok := (*g.Edges)[from][to]; ok {
|
||||
if _, ok := (*g.Edges)[to][from]; ok {
|
||||
delete((*g.Edges)[to], from)
|
||||
delete((*g.Edges)[from], to)
|
||||
}
|
||||
|
||||
return
|
||||
}
|
||||
|
||||
log.Error("no edge from ", from, " to ", to)
|
||||
|
||||
}
|
||||
|
||||
// Neighbors generates a list of neighbor vertices for a given vertex index in the graph.
|
||||
//
|
||||
// Parameters:
|
||||
// - v: an integer representing the index of the vertex.
|
||||
// Returns:
|
||||
// - []int: a list of neighbor vertices.
|
||||
func (g *Graph[V, T]) Neighbors(v int) []int {
|
||||
if neighbors, ok := (*g.Edges)[v]; ok {
|
||||
rep := make([]int, 0, len(neighbors))
|
||||
|
||||
for k := range neighbors {
|
||||
rep = append(rep, k)
|
||||
}
|
||||
|
||||
return rep
|
||||
}
|
||||
|
||||
return nil
|
||||
|
||||
}
|
||||
|
||||
// Degree calculates the degree of a vertex in a graph.
|
||||
//
|
||||
// Parameters:
|
||||
// - v: an integer representing the index of the vertex.
|
||||
//
|
||||
// Returns:
|
||||
// - an integer representing the degree of the vertex.
|
||||
func (g *Graph[V, T]) Degree(v int) int {
|
||||
if neighbors, ok := (*g.Edges)[v]; ok {
|
||||
return len(neighbors)
|
||||
}
|
||||
return 0
|
||||
}
|
||||
|
||||
// Parents returns a list of parent vertices for a given vertex index in the graph.
|
||||
//
|
||||
// Parameters:
|
||||
// - v: an integer representing the index of the vertex.
|
||||
//
|
||||
// Returns:
|
||||
// - []int: a list of parent vertices.
|
||||
func (g *Graph[V, T]) Parents(v int) []int {
|
||||
if parents, ok := (*g.ReverseEdges)[v]; ok {
|
||||
rep := make([]int, 0, len(parents))
|
||||
|
||||
for k := range parents {
|
||||
rep = append(rep, k)
|
||||
}
|
||||
|
||||
return rep
|
||||
}
|
||||
|
||||
return nil
|
||||
}
|
||||
|
||||
// ParentDegree calculates the degree of a vertex in a graph by counting the number of its parent vertices.
|
||||
//
|
||||
// Parameters:
|
||||
// - v: an integer representing the index of the vertex.
|
||||
//
|
||||
// Returns:
|
||||
// - an integer representing the degree of the vertex.
|
||||
func (g *Graph[V, T]) ParentDegree(v int) int {
|
||||
if parents, ok := (*g.ReverseEdges)[v]; ok {
|
||||
return len(parents)
|
||||
}
|
||||
return 0
|
||||
|
||||
}
|
||||
|
||||
type gml_graph[V any, T any] struct {
|
||||
Graph *Graph[V, T]
|
||||
As_directed bool
|
||||
Min_degree int
|
||||
Threshold float64
|
||||
Scale int
|
||||
}
|
||||
|
||||
// Gml generates a GML representation of the graph.
|
||||
//
|
||||
// as_directed: whether the graph should be treated as directed or undirected.
|
||||
// threshold: the threshold value.
|
||||
// scale: the scaling factor.
|
||||
// string: the GML representation of the graph.
|
||||
func (g *Graph[V, T]) Gml(as_directed bool, min_degree int, threshold float64, scale int) string {
|
||||
// (*seqs)[1].Count
|
||||
var gml bytes.Buffer
|
||||
|
||||
data := gml_graph[V, T]{
|
||||
Graph: g,
|
||||
As_directed: as_directed,
|
||||
Min_degree: min_degree,
|
||||
Threshold: threshold,
|
||||
Scale: scale,
|
||||
}
|
||||
|
||||
digraphTpl := template.New("gml_digraph")
|
||||
|
||||
digraph := ` {{$context := .}}
|
||||
graph [
|
||||
comment "{{ if $context.As_directed }}Directed graph{{ else }}Undirected graph{{ end }} {{ Name }}"
|
||||
directed {{ if $context.As_directed }}1{{ else }}0{{ end }}
|
||||
|
||||
{{range $index, $data:= $context.Graph.Vertices}}
|
||||
{{ if (ge (Degree $index) $context.Min_degree)}}
|
||||
node [
|
||||
id {{$index}}
|
||||
graphics [
|
||||
type "{{ Shape $index }}"
|
||||
h {{ Sqrt (VertexWeight $index) }}
|
||||
w {{ Sqrt (VertexWeight $index) }}
|
||||
]
|
||||
]
|
||||
{{ end }}
|
||||
{{ end }}
|
||||
|
||||
{{range $source, $data:= $context.Graph.Edges}}
|
||||
{{range $target, $edge:= $data}}
|
||||
{{ if and (ge $source $context.Min_degree) (ge $target $context.Min_degree) (or $context.As_directed (lt $source $target))}}
|
||||
edge [ source {{$source}}
|
||||
target {{$target}}
|
||||
color "#00FF00"
|
||||
]
|
||||
{{ end }}
|
||||
{{ end }}
|
||||
{{ end }}
|
||||
|
||||
]
|
||||
`
|
||||
|
||||
tmpl, err := digraphTpl.Funcs(template.FuncMap{
|
||||
"Sqrt": func(i float64) int { return scale * int(math.Floor(math.Sqrt(i))) },
|
||||
"Name": func() string { return g.Name },
|
||||
"VertexId": func(i int) string { return g.VertexId(i) },
|
||||
"Degree": func(i int) int { return g.Degree(i) },
|
||||
"VertexWeight": func(i int) float64 { return g.VertexWeight(i) },
|
||||
"Shape": func(i int) string {
|
||||
if g.VertexWeight(i) >= threshold {
|
||||
return "circle"
|
||||
} else {
|
||||
return "rectangle"
|
||||
}
|
||||
},
|
||||
}).Parse(digraph)
|
||||
|
||||
if err != nil {
|
||||
panic(err)
|
||||
}
|
||||
|
||||
err = tmpl.Execute(&gml, data)
|
||||
|
||||
if err != nil {
|
||||
panic(err)
|
||||
}
|
||||
|
||||
return gml.String()
|
||||
|
||||
}
|
||||
|
||||
// WriteGml writes the GML representation of the graph to an io.Writer.
|
||||
//
|
||||
// w: the io.Writer to write the GML representation to.
|
||||
// as_directed: whether the graph should be treated as directed or undirected.
|
||||
// threshold: the threshold value.
|
||||
// scale: the scaling factor.
|
||||
func (g *Graph[V, T]) WriteGml(w io.Writer, as_directed bool, min_degree int, threshold float64, scale int) {
|
||||
|
||||
_, err := w.Write([]byte(g.Gml(as_directed, min_degree, threshold, scale)))
|
||||
if err != nil {
|
||||
panic(err)
|
||||
}
|
||||
}
|
||||
|
||||
// WriteGmlFile writes the graph in GML format to the specified file.
|
||||
//
|
||||
// filename: the name of the file to write the GML representation to.
|
||||
// as_directed: whether the graph should be treated as directed or undirected.
|
||||
// threshold: the threshold value.
|
||||
// scale: the scaling factor.
|
||||
func (g *Graph[V, T]) WriteGmlFile(filename string, as_directed bool, min_degree int, threshold float64, scale int) {
|
||||
|
||||
f, err := os.Create(filename)
|
||||
if err != nil {
|
||||
panic(err)
|
||||
}
|
||||
defer f.Close()
|
||||
g.WriteGml(f, as_directed, min_degree, threshold, scale)
|
||||
}
|
||||
104
pkg/obigraph/graphbuffer.go
Normal file
104
pkg/obigraph/graphbuffer.go
Normal file
@ -0,0 +1,104 @@
|
||||
package obigraph
|
||||
|
||||
import (
|
||||
"io"
|
||||
"os"
|
||||
)
|
||||
|
||||
type GraphBuffer[V, T any] struct {
|
||||
Graph *Graph[V, T]
|
||||
Channel chan Edge[T]
|
||||
}
|
||||
|
||||
// NewGraphBuffer creates a new GraphBuffer with the given name and vertices.
|
||||
//
|
||||
// Parameters:
|
||||
// - name: the name of the GraphBuffer.
|
||||
// - vertices: a slice of vertices to initialize the GraphBuffer.
|
||||
//
|
||||
// Returns:
|
||||
// - GraphBuffer[V, T]: the newly created GraphBuffer.
|
||||
func NewGraphBuffer[V, T any](name string, vertices *[]V) *GraphBuffer[V, T] {
|
||||
buffer := GraphBuffer[V, T]{
|
||||
Graph: NewGraph[V, T](name, vertices),
|
||||
Channel: make(chan Edge[T]),
|
||||
}
|
||||
|
||||
go func() {
|
||||
for edge := range buffer.Channel {
|
||||
buffer.Graph.AddEdge(edge.From, edge.To, edge.Data)
|
||||
}
|
||||
}()
|
||||
|
||||
return &buffer
|
||||
}
|
||||
|
||||
// AddEdge adds an edge to the GraphBuffer.
|
||||
//
|
||||
// Parameters:
|
||||
// - from: the index of the starting vertex.
|
||||
// - to: the index of the ending vertex.
|
||||
// - data: a pointer to the data associated with the edge.
|
||||
func (g *GraphBuffer[V, T]) AddEdge(from, to int, data *T) {
|
||||
g.Channel <- Edge[T]{
|
||||
From: from,
|
||||
To: to,
|
||||
Data: data,
|
||||
}
|
||||
}
|
||||
|
||||
// AddDirectedEdge adds a directed edge from one vertex to another in the GraphBuffer.
|
||||
//
|
||||
// Parameters:
|
||||
// - from: the index of the starting vertex.
|
||||
// - to: the index of the ending vertex.
|
||||
// - data: a pointer to the data associated with the edge.
|
||||
func (g *GraphBuffer[V, T]) AddDirectedEdge(from, to int, data *T) {
|
||||
g.Channel <- Edge[T]{
|
||||
From: from,
|
||||
To: to,
|
||||
Data: data,
|
||||
}
|
||||
}
|
||||
|
||||
// Gml generates a GML representation of the graph.
|
||||
//
|
||||
// as_directed: whether the graph should be treated as directed or undirected.
|
||||
// min_degree: the minimum degree of vertices to include in the GML representation.
|
||||
// threshold: the threshold value.
|
||||
// scale: the scaling factor.
|
||||
// string: the GML representation of the graph.
|
||||
func (g *GraphBuffer[V, T]) Gml(as_directed bool, min_degree int, threshold float64, scale int) string {
|
||||
return g.Graph.Gml(as_directed, min_degree, threshold, scale)
|
||||
}
|
||||
|
||||
func (g *GraphBuffer[V, T]) WriteGmlFile(filename string, as_directed bool, min_degree int, threshold float64, scale int) {
|
||||
|
||||
f, err := os.Create(filename)
|
||||
if err != nil {
|
||||
panic(err)
|
||||
}
|
||||
defer f.Close()
|
||||
g.WriteGml(f, as_directed, min_degree, threshold, scale)
|
||||
}
|
||||
|
||||
// WriteGml writes the GML representation of the graph to an io.Writer.
|
||||
//
|
||||
// w: the io.Writer to write the GML representation to.
|
||||
// as_directed: whether the graph should be treated as directed or undirected.
|
||||
// min_degree: the minimum degree of vertices to include in the GML representation.
|
||||
// threshold: the threshold value.
|
||||
// scale: the scaling factor.
|
||||
func (g *GraphBuffer[V, T]) WriteGml(w io.Writer, as_directed bool, min_degree int, threshold float64, scale int) {
|
||||
_, err := w.Write([]byte(g.Gml(as_directed, min_degree, threshold, scale)))
|
||||
if err != nil {
|
||||
panic(err)
|
||||
}
|
||||
}
|
||||
|
||||
// Close closes the GraphBuffer by closing its channel.
|
||||
//
|
||||
// No parameters.
|
||||
func (g *GraphBuffer[V, T]) Close() {
|
||||
close(g.Channel)
|
||||
}
|
||||
Reference in New Issue
Block a user