rename things

cmd/internal/graph/dot/graph.go

@@ -0,0 +1,53 @@
+/*
+Copyright © 2025 filifa
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+*/
+package dot
+
+import (
+	"math"
+
+	igraph "scm.dairydemon.net/filifa/gv2adj/cmd/internal/graph"
+
+	"gonum.org/v1/gonum/graph"
+	"gonum.org/v1/gonum/graph/multi"
+)
+
+// DOTDirectedGraph is a graph representing an absorbing Markov chain.
+type DOTDirectedGraph struct {
+	*igraph.DirectedGraph
+}
+
+// NewDOTDirectedGraph returns an absorbing Markov chain with no nodes or
+// edges.
+func NewDOTDirectedGraph() *DOTDirectedGraph {
+	return &DOTDirectedGraph{DirectedGraph: igraph.NewDirectedGraph()}
+}
+
+// NewLine returns a DOT-aware weighted line.
+func (g *DOTDirectedGraph) NewLine(from, to graph.Node) graph.Line {
+	e := g.DirectedGraph.NewWeightedLine(from, to, math.NaN()).(multi.WeightedLine)
+	return &weightedLine{WeightedLine: e}
+}
+
+// NewNode returns a DOT-aware Node.
+func (g *DOTDirectedGraph) NewNode() graph.Node {
+	return &Node{Node: g.DirectedGraph.NewNode()}
+}
+
+// SetLine adds a DOT-aware weighted line to the Markov chain.
+func (g *DOTDirectedGraph) SetLine(e graph.Line) {
+	g.DirectedGraph.SetWeightedLine(e.(*weightedLine))
+}

cmd/internal/graph/dot/nodes_edges.go

@@ -0,0 +1,65 @@
+/*
+Copyright © 2025 filifa
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+*/
+package dot
+
+import (
+	"errors"
+	"strconv"
+
+	"gonum.org/v1/gonum/graph"
+	"gonum.org/v1/gonum/graph/encoding"
+	"gonum.org/v1/gonum/graph/multi"
+)
+
+// Node is a DOT-aware graph.Node.
+type Node struct {
+	graph.Node
+	dotID string
+}
+
+// SetDOTID sets the node's DOT ID. It enables storing the node name read from
+// a DOT file.
+func (n *Node) SetDOTID(id string) {
+	n.dotID = id
+}
+
+// DOTID returns the node's DOT ID.
+func (n *Node) DOTID() string {
+	return n.dotID
+}
+
+// weightedLine is a DOT-aware multi.WeightedLine. By being a
+// multi.WeightedLine, it allows for self-loops, which are important for
+// absorbing Markov chains.
+type weightedLine struct {
+	multi.WeightedLine
+}
+
+// SetAttribute enables storing the weight read from a DOT file. It errors if
+// an attribute is read that can't be stored in a weightedLine.
+func (e *weightedLine) SetAttribute(attr encoding.Attribute) error {
+	var err error
+
+	switch attr.Key {
+	case "weight":
+		e.W, err = strconv.ParseFloat(attr.Value, 64)
+	default:
+		err = errors.New("unknown key:" + attr.Key)
+	}
+
+	return err
+}

cmd/internal/graph/graph.go

@@ -0,0 +1,84 @@
+/*
+Copyright © 2025 filifa
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.
+*/
+package graph
+
+import (
+	"gonum.org/v1/gonum/graph"
+	"gonum.org/v1/gonum/graph/multi"
+	"gonum.org/v1/gonum/graph/simple"
+	"gonum.org/v1/gonum/mat"
+)
+
+// DirectedGraph embeds a multi.WeightedDirectedGraph (as opposed to
+// simple.WeightedDirectedGraph) to handle self loops.
+type DirectedGraph struct {
+	*multi.WeightedDirectedGraph
+}
+
+// NewDirectedGraph returns a graph with no nodes or edges.
+func NewDirectedGraph() *DirectedGraph {
+	return &DirectedGraph{WeightedDirectedGraph: multi.NewWeightedDirectedGraph()}
+}
+
+// AbsorbingNodes returns all the nodes in the Markov chain identified as
+// absorbing nodes.
+func (g *DirectedGraph) AbsorbingNodes() []graph.Node {
+	absorbingNodes := make([]graph.Node, 0)
+	for nodes := g.Nodes(); nodes.Next(); {
+		u := nodes.Node()
+		successors := g.From(u.ID())
+		if successors.Len() != 1 {
+			continue
+		}
+
+		successors.Next()
+		v := successors.Node()
+		if u == v {
+			absorbingNodes = append(absorbingNodes, u)
+		}
+	}
+
+	return absorbingNodes
+}
+
+// AdjacencyMatrix returns the graph's adjacency matrix.
+func (g *DirectedGraph) AdjacencyMatrix() *mat.Dense {
+	adj := simple.NewDirectedMatrix(g.Nodes().Len(), 0, 0, 0)
+	for edges := g.WeightedEdges(); edges.Next(); {
+		e := edges.WeightedEdge()
+		if e.From() == e.To() {
+			continue
+		}
+
+		adj.SetWeightedEdge(e)
+	}
+
+	a := mat.DenseCopyOf(adj.Matrix())
+
+	nodes := adj.Nodes()
+	for i := 0; nodes.Next(); i++ {
+		id := nodes.Node().ID()
+		u := g.Node(id)
+
+		e := g.WeightedEdge(u.ID(), u.ID())
+		if e != nil {
+			a.Set(i, i, e.Weight())
+		}
+	}
+
+	return a
+}