spqr-tree 4.0.0

A representation of the SPQR tree in Rust with support for I/O
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152

use bidirected_adjacency_array::{
    graph::BidirectedAdjacencyArray,
    index::{EdgeIndex, GraphIndexInteger, NodeIndex},
    io::gfa1::GfaNodeData,
};

use crate::graph::{NamedNodeData, StaticGraph};

impl<IndexType: GraphIndexInteger, NodeData: NamedNodeData, EdgeData> StaticGraph
    for BidirectedAdjacencyArray<IndexType, NodeData, EdgeData>
{
    type IndexType = IndexType;

    type NodeIndex = NodeIndex<IndexType>;

    type EdgeIndex = EdgeIndex<IndexType>;

    fn node_indices(&self) -> impl Iterator<Item = Self::NodeIndex> {
        self.iter_nodes()
    }

    fn edge_indices(&self) -> impl Iterator<Item = Self::EdgeIndex> {
        self.iter_edges()
    }

    fn node_count(&self) -> usize {
        BidirectedAdjacencyArray::node_count(self)
    }

    fn edge_count(&self) -> usize {
        BidirectedAdjacencyArray::edge_count(self)
    }

    fn node_name(&self, node_index: Self::NodeIndex) -> std::borrow::Cow<'_, str> {
        self.node_data(node_index).name()
    }

    fn incident_edges(&self, node: Self::NodeIndex) -> impl Iterator<Item = Self::EdgeIndex> {
        self.iter_incident_edges(node)
    }

    fn edge_endpoints(&self, edge: Self::EdgeIndex) -> (Self::NodeIndex, Self::NodeIndex) {
        let edge_data = self.edge(edge);
        (
            edge_data.from().into_bidirected(),
            edge_data.to().into_bidirected(),
        )
    }

    fn edges_between(
        &self,
        u: Self::NodeIndex,
        v: Self::NodeIndex,
    ) -> impl Iterator<Item = Self::EdgeIndex> {
        self.iter_incident_edges(u).filter(move |edge| {
            let endpoints = self.edge_endpoints(*edge);
            if u == v {
                endpoints.0 == v && endpoints.1 == v
            } else {
                endpoints.0 == v || endpoints.1 == v
            }
        })
    }
}

impl<T: GfaNodeData> NamedNodeData for T {
    fn name(&'_ self) -> std::borrow::Cow<'_, str> {
        GfaNodeData::name(self)
    }
}

#[cfg(test)]
mod tests {
    use bidirected_adjacency_array::graph::{BidirectedAdjacencyArray, BidirectedEdge};
    use itertools::Itertools;
    use tagged_vec::TaggedVec;

    use crate::graph::{NamedNodeData, StaticGraph};

    #[test]
    fn test_edges_between() {
        struct NodeData(u8);
        impl NamedNodeData for NodeData {
            fn name(&'_ self) -> std::borrow::Cow<'_, str> {
                std::borrow::Cow::Owned(format!("n{}", self.0))
            }
        }

        let nodes = [1, 2, 3].into_iter().map(NodeData).collect();
        let edges = TaggedVec::from(vec![
            BidirectedEdge::new(3.into(), 0.into(), 1),
            BidirectedEdge::new(0.into(), 1.into(), 2),
            BidirectedEdge::new(4.into(), 4.into(), 3),
            BidirectedEdge::new(0.into(), 4.into(), 4),
            BidirectedEdge::new(0.into(), 3.into(), 5),
        ]);

        let graph = BidirectedAdjacencyArray::<u8, NodeData, u8>::new(nodes, edges);

        for n1 in graph.node_indices() {
            for n2 in graph.node_indices() {
                let edges_between = graph.edges_between(n1, n2).sorted().collect::<Vec<_>>();
                let edges_between_reversed =
                    graph.edges_between(n2, n1).sorted().collect::<Vec<_>>();
                assert_eq!(edges_between, edges_between_reversed);
            }
        }

        assert_eq!(
            graph
                .edges_between(0.into(), 0.into())
                .sorted()
                .collect::<Vec<_>>(),
            vec![1.into()]
        );
        assert_eq!(
            graph
                .edges_between(0.into(), 1.into())
                .sorted()
                .collect::<Vec<_>>(),
            vec![0.into(), 4.into()]
        );
        assert_eq!(
            graph
                .edges_between(0.into(), 2.into())
                .sorted()
                .collect::<Vec<_>>(),
            vec![3.into()]
        );
        assert_eq!(
            graph
                .edges_between(1.into(), 1.into())
                .sorted()
                .collect::<Vec<_>>(),
            vec![]
        );
        assert_eq!(
            graph
                .edges_between(1.into(), 2.into())
                .sorted()
                .collect::<Vec<_>>(),
            vec![]
        );
        assert_eq!(
            graph
                .edges_between(2.into(), 2.into())
                .sorted()
                .collect::<Vec<_>>(),
            vec![2.into()]
        );
    }
}