From cfebf3d77b7584b542f7cdfba5b0cc9c64a3a9be Mon Sep 17 00:00:00 2001
From: Iago Bonnici <iago.bonnici@umontpellier.fr>
Date: Thu, 1 Aug 2024 14:51:18 +0200
Subject: [PATCH] =?UTF-8?q?=F0=9F=9A=A7=20Expose=20`adjacency=5Fmatrix()`?=
 =?UTF-8?q?=20and=20variants.?=
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---
 src/basic_topology_queries.jl | 46 +++++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/src/basic_topology_queries.jl b/src/basic_topology_queries.jl
index e32da046a..cdb104814 100644
--- a/src/basic_topology_queries.jl
+++ b/src/basic_topology_queries.jl
@@ -312,6 +312,52 @@ function live_tops(g::Topology, tops_indices)
 end
 export live_tops
 
+# ==========================================================================================
+# Adjacency matrices.
+
+"""
+    adjacency_matrix(g::Topology, source, edge, target; transpose = false; prune = true)
+
+Produce a boolean sparse matrix representing the connections of the given edge type,
+from the given source node compartment (lines) \
+to the given target node compartment (colums).
+Flip dimensions if `transpose` is set.
+Lower `prune` to keep lines and columns for the nodes marked as removed.
+See [`topology`](@ref).
+"""
+function adjacency_matrix(
+    g::Topology,
+    source::Symbol,
+    edge::Symbol,
+    target::Symbol;
+    transpose = false,
+    prune = true,
+)
+    # Same, but with stricter input signature.
+    Topologies.adjacency_matrix(g, source, edge, target; transpose, prune)
+end
+export adjacency_matrix
+
+"""
+    species_adjacency_matrix(g::Topology, edge::Symbol; kwargs...)
+
+Restriction of [`adjacency_matrix`](@ref) to only `:species` compartments.
+"""
+function species_adjacency_matrix(g::Topology, edge::Symbol; kwargs...)
+    adjacency_matrix(g, :species, edge, :species; kwargs...)
+end
+export species_adjacency_matrix
+
+"""
+    foodweb_matrix(g::Topology; kwargs...)
+
+Restriction of [`species_adjacency_matrix`](@ref)
+to only `:species` compartment and `:trophic` links.
+"""
+foodweb_matrix(g::Topology; kwargs...) = species_adjacency_matrix(g, :trophic; kwargs...)
+export foodweb_matrix
+
+
 # ==========================================================================================
 # Common checks to raise useful error messages.