(in-package #:cl-graph)
-;;; ---------------------------------------------------------------------------
(defgeneric make-vertex-container (graph initial-size)
(:documentation "Make-vertex-container is called during graph creation and can be used to create specialized containers to hold graph vertexes."))
-;;; ---------------------------------------------------------------------------
(defgeneric make-edge-container (graph initial-size)
(:documentation "Make-edge-container is called during graph creation and can be used to create specialized containers to hold graph edges."))
-;;; ---------------------------------------------------------------------------
;;; API
-;;; ---------------------------------------------------------------------------
(defgeneric make-graph (graph-type &key &allow-other-keys)
(:documentation "Create a new graph of type `graph-type'. Graph type can be
classes as superclasses will be found (or created). In either case, the new graph will
be created as if with a call to make-instance."))
-;;; ---------------------------------------------------------------------------
(defgeneric make-edge-for-graph (graph vertex-1 vertex-2
&key edge-type edge-class &allow-other-keys)
(:documentation "It should not usually necessary to call this in user code. Creates a new edge between vertex-1 and vertex-2 for the graph. If the edge-type and edge-class are not specified, they will be determined from the defaults of the graph."))
-;;; ---------------------------------------------------------------------------
(defgeneric add-edge (graph edge &rest args &key force-new?)
(:documentation "Add-edge adds an existing edge to a graph. As add-edge-between-vertexes is generally more natural to use, this method is rarely called."))
-;;; ---------------------------------------------------------------------------
(defgeneric add-edge-between-vertexes (graph value-or-vertex-1 value-or-vertex-2
&rest args &key if-duplicate-do
added between the two vertexes; if it is a function, then this function will
be called with the previous edge."))
-;;; ---------------------------------------------------------------------------
(defgeneric delete-edge (graph edge)
(:documentation "Delete the `edge' from the `graph' and returns it."))
-;;; ---------------------------------------------------------------------------
(defgeneric delete-edge-between-vertexes (graph value-or-vertex-1
value-or-vertex-2 &rest args)
(:documentation "Finds an edge in the graph between the two specified vertexes. If values (i.e., non-vertexes) are passed in, then the graph will be searched for matching vertexes."))
-;;; ---------------------------------------------------------------------------
(defgeneric add-vertex (graph value-or-vertex &key if-duplicate-do &allow-other-keys)
(:documentation "Adds a vertex to a graph. If called with a vertex, then this vertex is added. If called with a value, then a new vertex is created to hold the value. If-duplicate-do can be one of :ignore, :force, :replace, :replace-value or a function. The default is :ignore."))
-;;; ---------------------------------------------------------------------------
(defgeneric delete-vertex (graph value-or-vertex)
(:documentation "Remove a vertex from a graph. The 'vertex-or-value' argument can be
graph-vertex-not-found-error will be raised if the vertex is not found or is not part of
the graph."))
-;;; ---------------------------------------------------------------------------
(defgeneric find-vertex (graph value &optional error-if-not-found?)
(:documentation "Search 'graph' for a vertex with element 'value'. The search is fast but inflexible because it uses an associative-container. If you need more flexibity, see search-for-vertex."))
-;;; ---------------------------------------------------------------------------
(defgeneric search-for-vertex (graph value &key key test error-if-not-found?)
(:documentation "Search 'graph' for a vertex with element 'value'. The 'key' function is applied to each element before that element is compared with the value. The comparison is done using the function 'test'. If you don't need to use key or test, then consider using find-vertex instead."))
-;;; ---------------------------------------------------------------------------
(defgeneric find-edge (graph edge &optional error-if-not-found?)
(:documentation "Search `graph` for an edge whose vertexes match `edge`. This means that `vertex-1` of the edge in the graph must match `vertex-1` of `edge` and so forth. Wil signal an error of type `graph-edge-not-found-error` unless `error-if-not-found?` is nil. [?? Unused. Remove?]"))
-;;; ---------------------------------------------------------------------------
(defgeneric find-edge-between-vertexes (graph value-or-vertex-1 value-or-vertex-2
&key error-if-not-found?)
(:documentation "Searches `graph` for an edge that connects vertex-1 and vertex-2. [?? Ignores error-if-not-found? Does directedness matter? need test]"))
-;;; ---------------------------------------------------------------------------
(defgeneric source-vertex (edge)
(:documentation "Returns the source-vertex of a directed edge. Compare with `vertex-1`."))
-;;; ---------------------------------------------------------------------------
(defgeneric target-vertex (edge)
(:documentation "Returns the target-vertex of a directed edge. Compare with `vertex-2`."))
-;;; ---------------------------------------------------------------------------
(defgeneric iterate-edges (graph-or-vertex fn)
(:documentation "Calls `fn` on each edge of graph or vertex."))
-;;; ---------------------------------------------------------------------------
(defgeneric iterate-source-edges (vertex fn)
(:documentation "In a directed graph, calls `fn` on each edge of a vertex that begins at vertex. In an undirected graph, this is equivalent to `iterate-edges`."))
-;;; ---------------------------------------------------------------------------
(defgeneric iterate-target-edges (vertex fn)
(:documentation "In a directed graph, calls `fn` on each edge of a vertex that ends at vertex. In an undirected graph, this is equivalent to `iterate-edges`."))
-;;; ---------------------------------------------------------------------------
(defgeneric iterate-children (vertex fn)
(:documentation "Calls fn on every vertex that is either connected to vertex by an undirected edge or is at the target end of a directed edge."))
-;;; ---------------------------------------------------------------------------
(defgeneric has-children-p (vertex)
(:documentation "In a directed graph, returns true if vertex has any edges that point from vertex to some other vertex (cf. iterate-target-edges). In an undirected graph, `has-children-p` is testing only whether or not the vertex has any edges."))
-;;; ---------------------------------------------------------------------------
(defgeneric has-parent-p (vertex)
(:documentation "In a directed graph, returns true if vertex has any edges that point from some other vertex to this vertex (cf. iterate-source-edges). In an undirected graph, `has-parent-p` is testing only whether or not the vertex has any edges."))
-;;; ---------------------------------------------------------------------------
(defgeneric iterate-parents (vertex fn)
(:documentation "Calls fn on every vertex that is either connected to vertex by an undirected edge or is at the source end of a directed edge."))
-;;; ---------------------------------------------------------------------------
(defgeneric iterate-neighbors (vertex fn)
(:documentation "Calls fn on every vertex adjecent to vertex See also iterate-children and iterate-parents."))
-;;; ---------------------------------------------------------------------------
(defgeneric renumber-vertexes (graph)
(:documentation "Assign a number to each vertex in a graph in some unspecified order. [?? internal]"))
-;;; ---------------------------------------------------------------------------
(defgeneric renumber-edges (graph)
(:documentation "Assign a number to each edge in a graph in some unspecified order. [?? internal]"))
-;;; ---------------------------------------------------------------------------
(defgeneric generate-directed-free-tree (graph root)
(:documentation "Returns a version of graph which is a directed free tree
rooted at root."))
-;;; ---------------------------------------------------------------------------
(defgeneric in-undirected-cycle-p (graph start-vertex &optional marked previous)
(:documentation "Return true if-and-only-if an undirected cycle in graph is reachable from start-vertex."))
-;;; ---------------------------------------------------------------------------
(defgeneric undirected-edge-p (edge)
(:documentation "Returns true if-and-only-if edge is undirected"))
-;;; ---------------------------------------------------------------------------
(defgeneric directed-edge-p (edge)
(:documentation "Returns true if-and-only-if edge is directed"))
-;;; ---------------------------------------------------------------------------
(defgeneric tagged-edge-p (edge)
(:documentation "Returns true if-and-only-if edge's tag slot is t"))
-;;; ---------------------------------------------------------------------------
(defgeneric untagged-edge-p (edge)
(:documentation "Returns true if-and-only-if edge's tage slot is nil"))
-;;; ---------------------------------------------------------------------------
(defgeneric adjacentp (graph vertex-1 vertex-2)
(:documentation "Return true if vertex-1 and vertex-2 are connected by an edge. [?? compare with vertices-share-edge-p and remove one or maybe call one directed-adjacentp]"))
-;;; ---------------------------------------------------------------------------
(defgeneric make-filtered-graph (old-graph test-fn &key
graph-completion-method depth
that all vertexes are to be included, no matter their depth. This
value is ignored in non closure options."))
-;;; ---------------------------------------------------------------------------
(defgeneric project-bipartite-graph
(new-graph existing-graph vertex-class vertex-classifier)
(:documentation "Creates the unimodal bipartite projects of existing-graph with
vertexes for each vertex of existing graph whose `vertex-classifier` is eq to `vertex-class` and where an edge existing between two vertexes of the graph if and only if they are connected to a shared vertex in the existing-graph."))
-;;; ---------------------------------------------------------------------------
(defgeneric assortativity-coefficient (mixing-matrix)
(:documentation "An assortative graph is one where vertexes of the same type are more likely to
Mixing Patterns in Networks by Mark Newman. See the citation 'newman200-mixing' in moab
or the URL 'http://arxiv.org/abs/cond-mat/0209450'."))
-;;; ---------------------------------------------------------------------------
(defgeneric graph->dot (graph output
&key
For more information about DOT file format, search the web for 'DOTTY' and
'GRAPHVIZ'."))
-;;; ---------------------------------------------------------------------------
(defgeneric graph->dot-properties (g stream)
(:documentation "Unless a different graph-formatter is specified, this method is called by graph->dot to output graph-properties onto a stream. The function can assume that the openning and closing brackets will be taken care of by the graph->dot."))
-;;; ---------------------------------------------------------------------------
(defgeneric vertex->dot (vertex stream)
(:documentation "Unless a different vertex-formatter is specified with a keyword argument, this is used by graph->dot to output vertex formatting for `vertex` onto the `stream`. The function can assume that openning and closing square brackets and label have already been taken care of."))
-;;; ---------------------------------------------------------------------------
(defgeneric edge->dot (edge stream)
(:documentation "Used by graph->dot to output edge formatting for `edge` onto the `stream`. The function can assume that openning and closing square brackets and label have already been taken care of."))
-;;; ---------------------------------------------------------------------------
(defgeneric generate-gnm (generator graph n m &key)
(:documentation "Generate a 'classic' random graph G(n, m) with n vertexes and m edges."))
-;;; ---------------------------------------------------------------------------
(defgeneric generate-gnp (generator graph n p &key)
(:documentation "Generate the Erd\"os-R\'enyi random graph G\(n, p\). I.e., a graph with n vertexes where
each possible edge appears with probability p. This implementation is from Efficient Generation
of Large Random Networks \(see batagelj-generation-2005 in doab\)."))
-;;; ---------------------------------------------------------------------------
(defgeneric generate-undirected-graph-via-assortativity-matrix
(generator graph-class size edge-count kind-matrix assortativity-matrix
The vertex-labeler is a function of two parameters: the vertex kind and the index. It should return whatever the 'value' of the vertex ought to be."))
-;;; ---------------------------------------------------------------------------
(defgeneric generate-undirected-graph-via-vertex-probabilities
(generator graph-class size kind-matrix probability-matrix vertex-labeler)
The clever sequential sampling technique in this implementation is from Efficient Generation
of Large Random Networks \(see batagelj-generation-2005 in moab\)."))
-;;; ---------------------------------------------------------------------------
(defgeneric generate-scale-free-graph
(generator graph size kind-matrix add-edge-count
other-vertex-kind-samplers are confusing...; and
vertex-labeler is used to create vertex elements \(as in other generators\)."))
-;;; ---------------------------------------------------------------------------
(defgeneric generate-assortative-graph-with-degree-distributions
(generator graph
&key)
(:documentation ""))
-;;; ---------------------------------------------------------------------------
(defgeneric generate-simple-preferential-attachment-graph (generator graph size minimum-degree)
(:documentation "Generate a simple scale-free graph using the preferential attachment
mechanism of Barabasi and Albert. The implementation is from Efficient Generation
of Large Random Networks \(see batagelj-generation-2005 in moab\). Self-edges are possible."))
-;;; ---------------------------------------------------------------------------
(defgeneric generate-preferential-attachment-graph
(generator graph size kind-matrix minimum-degree
of Large Random Networks \(see batagelj-generation-2005 in moab\)."))
-;;; ---------------------------------------------------------------------------
;;; more
-;;; ---------------------------------------------------------------------------
(defgeneric make-vertex-for-graph (graph &key &allow-other-keys)
(:documentation "Creates a new vertex for graph `graph`. The keyword arguments include:
and any other initialization arguments that make sense for the vertex class."))
-;;; ---------------------------------------------------------------------------
(defgeneric tag-all-edges (thing)
(:documentation "Sets the `tag` of all the edges of `thing` to true. [?? why does this exist?\]"))
-;;; ---------------------------------------------------------------------------
(defgeneric untag-all-edges (thing)
(:documentation "Sets the `tag` of all the edges of `thing` to nil. [?? why does this exist?\]"))
-;;; ---------------------------------------------------------------------------
(defgeneric untag-edges (edges)
(:documentation "Sets the `tag` of all the edges of `thing` to true. [?? why does this exist?\]"))
-;;; ---------------------------------------------------------------------------
(defgeneric tag-edges (edges)
(:documentation "Sets the `tag` of all the edges of `thing` to true. [?? why does this exist?\]"))
-;;; ---------------------------------------------------------------------------
(defgeneric replace-vertex (graph old new)
(:documentation "Replace vertex `old` in graph `graph` with vertex `new`. The edge structure of the graph is maintained."))
-;;; ---------------------------------------------------------------------------
(defgeneric add-edge-to-vertex (edge vertex)
(:documentation "Attaches the edge `edge` to the vertex `vertex`."))
-;;; ---------------------------------------------------------------------------
(defgeneric source-edges (vertex &optional filter)
(:documentation "Returns a list of the source edges of `vertex`. I.e.,
the edges that begin at `vertex`."))
-;;; ---------------------------------------------------------------------------
(defgeneric target-edges (vertex &optional filter)
(:documentation "Returns a list of the target edges of `vertex`.
I.e., the edges that end at `vertex`."))
-;;; ---------------------------------------------------------------------------
(defgeneric child-vertexes (vertex &optional filter)
(:documentation "Returns a list of the vertexes to which `vertex`
If the connecting edge is undirected, then the vertex is always
counted as a source. [?? Could be a defun]."))
-;;; ---------------------------------------------------------------------------
(defgeneric parent-vertexes (vertex &optional filter)
(:documentation "Returns a list of the vertexes to which `vertex` is connected by an edge and for which `vertex` is the target vertex. If the connecting edge is undirected, then the vertex is always counted as a target. [?? Could be a defun]."))
-;;; ---------------------------------------------------------------------------
(defgeneric neighbor-vertexes (vertex &optional filter)
(:documentation "Returns a list of the vertexes to which `vertex` is connected by an edge disregarding edge direction. In a directed graph, neighbor-vertexes is the union of parent-vertexes and child-vertexes. [?? Could be a defun]."))
-;;; ---------------------------------------------------------------------------
(defgeneric number-of-neighbors (vertex)
(:documentation "Returns the number of neighbors of `vertex` (cf. `neighbor-vertexes`). [?? could be a defun]"))
-;;; ---------------------------------------------------------------------------
(defgeneric in-cycle-p (graph start-vertex)
(:documentation "Returns true if `start-vertex` is in some cycle in `graph`. This uses child-vertexes to generate the vertexes adjacent to a vertex."))
-;;; ---------------------------------------------------------------------------
(defgeneric iterate-vertexes (thing fn)
(:documentation "Calls `fn` on each of the vertexes of `thing`."))
-;;; ---------------------------------------------------------------------------
(defgeneric edges (thing)
(:documentation "Returns a list of the edges of `thing`."))
-;;; ---------------------------------------------------------------------------
(defgeneric vertex-count (graph)
(:documentation "Returns the number of vertexes in `graph`. [?? could be a defun]"))
-;;; ---------------------------------------------------------------------------
(defgeneric vertexes (thing)
(:documentation "Returns a list of the vertexes of `thing`."))
-;;; ---------------------------------------------------------------------------
(defgeneric source-edge-count (vertex)
(:documentation "Returns the number of source edges of vertex (cf. source-edges). [?? could be a defun]"))
-;;; ---------------------------------------------------------------------------
(defgeneric target-edge-count (vertex)
(:documentation "Returns the number of target edges of vertex (cf. target-edges). [?? could be a defun]"))
-;;; ---------------------------------------------------------------------------
(defgeneric graph-roots (graph)
(:documentation "Returns a list of the roots of graph. A root is defined as a vertex with no source edges \(i.e., all of the edges are out-going\). (cf. rootp) [?? could be a defun]"))
-;;; ---------------------------------------------------------------------------
(defgeneric rootp (vertex)
(:documentation "Returns true if `vertex` is a root vertex \(i.e., it has no incoming \(source\) edges\)."))
-;;; ---------------------------------------------------------------------------
(defgeneric find-vertex-if (thing predicate &key key)
(:documentation "Returns the first vertex in `thing` for which the `predicate` function returns non-nil. If the `key` is supplied, then it is applied to the vertex before the predicate is."))
-;;; ---------------------------------------------------------------------------
(defgeneric find-edge-if (graph fn &key key)
(:documentation "Returns the first edge in `thing` for which the `predicate` function returns non-nil. If the `key` is supplied, then it is applied to the edge before the predicate is."))
-;;; ---------------------------------------------------------------------------
(defgeneric find-edges-if (thing predicate)
(:documentation "Returns a list of edges in `thing` for which the `predicate` returns non-nil. [?? why no key function?]"))
-;;; ---------------------------------------------------------------------------
(defgeneric find-vertexes-if (thing predicate)
(:documentation "Returns a list of vertexes in `thing` for which the `predicate` returns non-nil. [?? why no key function?]"))
-;;; ---------------------------------------------------------------------------
(defgeneric force-undirected (graph)
(:documentation "Ensures that the graph is undirected (possibly by calling change-class on the edges)."))
-;;; ---------------------------------------------------------------------------
(defgeneric traverse-elements (thing style fn)
(:documentation "WIP"))
(defgeneric subgraph-containing (graph vertex &key)
(:documentation "Returns a new graph that is a subset of `graph` that contains `vertex` and all of the other vertexes that can be reached from vertex by paths of less than or equal of length `depth`. If depth is not specified, then the entire sub-graph reachable from vertex will be returned. [?? Edge weights are always assumed to be one.]"))
-;;; ---------------------------------------------------------------------------
(defgeneric weight (edge)
(:documentation "Returns the weight of an edge. This defaults to 1.0 and can only be altered if the edge is a sub-class of `weighted-edge-mixin`."))
(in-package #:metabang.graph)
-;;; ---------------------------------------------------------------------------
;;;
-;;; ---------------------------------------------------------------------------
(defstruct (vertex-datum (:conc-name node-) (:type list))
(color nil)
(depth most-positive-fixnum)
(parent nil))
-;;; ---------------------------------------------------------------------------
(defmethod initialize-vertex-data ((graph basic-graph))
(let ((vertex-data (make-container 'simple-associative-container)))
(make-vertex-datum :color :white))))
(values vertex-data)))
-;;; ---------------------------------------------------------------------------
;;; breadth-first-search by GWK
-;;; ---------------------------------------------------------------------------
(defmethod breadth-first-visitor ((graph basic-graph) (source t) fn)
(breadth-first-visitor graph (find-vertex graph source) fn))
-;;; ---------------------------------------------------------------------------
(defmethod breadth-first-visitor ((graph basic-graph) (source basic-vertex) fn)
;; initialize
vertex-data)))
-;;; ---------------------------------------------------------------------------
(defmethod breadth-first-search-graph ((graph basic-graph) (source t))
(breadth-first-search-graph graph (find-vertex graph source)))
-;;; ---------------------------------------------------------------------------
(defmethod breadth-first-search-graph ((graph basic-graph) (source basic-vertex))
;; initialize
vertex-data)))
-;;; ---------------------------------------------------------------------------
;;; single-source-shortest-paths - gwk
-;;; ---------------------------------------------------------------------------
#+NotYet
(defmethod single-source-shortest-paths ((graph basic-graph))
(setf (node-depth source-datum) 0))
))
-;;; ---------------------------------------------------------------------------
;;; connected-components - gwk
-;;; ---------------------------------------------------------------------------
(defmethod connected-components ((graph basic-graph))
(let ((union (make-container 'union-find-container)))
(iterate-elements union 'find-set)
union))
-;;; ---------------------------------------------------------------------------
(defmethod connected-component-count ((graph basic-graph))
;;?? Gary King 2005-11-28: Super ugh
-;;; ---------------------------------------------------------------------------
;;; minimum-spanning-tree based on kruskal's algorithm detailed in clrs2 -jjm
-;;; ---------------------------------------------------------------------------
(defmethod mst-find-set ((vertex basic-vertex))
#+ignore
(setf (previous-node vertex) (mst-find-set (previous-node vertex))))
(previous-node vertex))
-;;; ---------------------------------------------------------------------------
(defmethod mst-make-set ((vertex basic-vertex))
(setf (previous-node vertex) vertex
(rank vertex) 0))
-;;; ---------------------------------------------------------------------------
(defmethod mst-tree-union ((v1 basic-vertex) (v2 basic-vertex))
(mst-link (mst-find-set v1) (mst-find-set v2)))
-;;; ---------------------------------------------------------------------------
(defmethod mst-link ((v1 basic-vertex) (v2 basic-vertex))
(cond ((> (rank v1) (rank v2))
(when (= (rank v1) (rank v2))
(incf (rank v2))))))
-;;; ---------------------------------------------------------------------------
;;; jjm's implementation of mst depends on this
;;; todo - figure out some what to add and edge we create to a graph rather
;;; than always using add-edge-between-vertexes interface
-;;; ---------------------------------------------------------------------------
(defmethod add-edges-to-graph ((graph basic-graph) (edges list)
&key (if-duplicate-do :ignore))
:if-duplicate-do if-duplicate-do))))
graph)
-;;; ---------------------------------------------------------------------------
(defmethod edge-lessp-by-weight ((e1 basic-edge) (e2 basic-edge))
(< (weight e1) (weight e2)))
-;;; ---------------------------------------------------------------------------
;;; minumum spanning tree
-;;; ---------------------------------------------------------------------------
(defmethod minimum-spanning-tree ((graph basic-graph)
(values t result))
(t (values nil result)))))))
-;;; ---------------------------------------------------------------------------
#+ignore ;;; shoot
(defmethod minimum-spanning-tree ((vertex-list list)
(values t result))
(t (values nil result)))))))
-;;; ---------------------------------------------------------------------------
;;; uses mst to determine if the graph is connected
-;;; ---------------------------------------------------------------------------
(defmethod connected-graph-p ((graph basic-graph) &key
(edge-sorter 'edge-lessp-by-weight))
(minimum-spanning-tree graph :edge-sorter edge-sorter))
-;;; ---------------------------------------------------------------------------
#+test
(let ((g (make-container 'graph-container)))
:if-duplicate-do :force)
(minimum-spanning-tree g))
-;;; ---------------------------------------------------------------------------
;;; GWK's implementation of kruskal's - slightly faster, but it doesn't return
;;; a tree (still faster even if it does). Will decide later if which to use
;;; ignoring for now -jjm
-;;; ---------------------------------------------------------------------------
#+not-yet
(defmethod minimum-spanning-tree ((graph basic-graph) &key (weight 'weight))
(values a)))
-;;; ---------------------------------------------------------------------------
#+test
(loop for f in '(mst-kruskal minimum-spanning-tree-kruskal) do
(declare (ignore a b))
0)))))))
-;;; ---------------------------------------------------------------------------
;;; end minimum spanning tree
-;;; ---------------------------------------------------------------------------
-;;; ---------------------------------------------------------------------------
;;; depth-first-search - clrs2
;;; todo - figure out how to name this depth-first-search, which is already
;;; defined in search.lisp
-;;; ---------------------------------------------------------------------------
-;;; ---------------------------------------------------------------------------
;;; should probably make this special
-;;; ---------------------------------------------------------------------------
(defparameter *depth-first-search-timer* -1)
-;;; ---------------------------------------------------------------------------
;;; undirected edges are less than edges that are directed
-;;; ---------------------------------------------------------------------------
#+ignore ;;; incorrect, methinks - jjm
(defmethod edge-lessp-by-direction ((e1 basic-edge) (e2 basic-edge))
(defmethod edge-lessp-by-direction ((e1 basic-edge) (e2 basic-edge))
(and (undirected-edge-p e1) (directed-edge-p e2)))
-;;; ---------------------------------------------------------------------------
(defmethod out-edge-for-vertex-p ((edge basic-edge) (vertex basic-vertex))
(cond ((and (directed-edge-p edge)
t)
(t nil)))
-;;; ---------------------------------------------------------------------------
;;; depth-first-search
-;;; ---------------------------------------------------------------------------
(defmethod dfs ((graph basic-graph) (root t) fn &key
(out-edge-sorter #'edge-lessp-by-direction))
(dfs graph (find-vertex graph root) fn :out-edge-sorter out-edge-sorter))
-;;; ---------------------------------------------------------------------------
(defmethod dfs ((graph basic-graph) (root basic-vertex) fn &key
(out-edge-sorter #'edge-lessp-by-direction))
(sort (copy-list (vertexes graph)) #'< :key #'finish-time)
graph))
-;;; ---------------------------------------------------------------------------
(defmethod dfs-visit ((graph graph-container) (u basic-vertex)
fn sorter)
(setf (color u) :black
(finish-time u) *depth-first-search-timer*))
-;;; ---------------------------------------------------------------------------
;;; from clrs2
-;;; ---------------------------------------------------------------------------
#+test
(let ((g (make-container 'graph-container)))
(assert (equal '(:X :Y :V :U :Z :W)
(mapcar #'element (dfs g :u #'identity)))))
-;;; ---------------------------------------------------------------------------
(defmethod dfs-tree-edge-p ((edge graph-container-edge))
(eql (color edge) :white))
-;;; ---------------------------------------------------------------------------
(defmethod dfs-back-edge-p ((edge graph-container-edge))
(eql (color edge) :gray))
-;;; ---------------------------------------------------------------------------
;;; not correct - has to look at combination of discovery-time and finish-time
-;;; ---------------------------------------------------------------------------
(defmethod dfs-forward-edge-p ((edge graph-container-edge))
(warn "implementation is not correct.")
(< (discovery-time (source-vertex edge))
(discovery-time (target-vertex edge)))))
-;;; ---------------------------------------------------------------------------
;;; not correct - has to look at combination of discovery-time and finish-time
-;;; ---------------------------------------------------------------------------
(defmethod dfs-cross-edge-p ((edge graph-container-edge))
(warn "implementation is not correct.")
(> (discovery-time (source-vertex edge))
(discovery-time (target-vertex edge)))))
-;;; ---------------------------------------------------------------------------
(defmethod dfs-edge-type ((edge graph-container-edge))
(cond ((dfs-tree-edge-p edge)
:cross)
(t nil)))
-;;; ---------------------------------------------------------------------------
;;; end dfs
-;;; ---------------------------------------------------------------------------
-;;; ---------------------------------------------------------------------------
;;; mapping functions
-;;; ---------------------------------------------------------------------------
-;;; ---------------------------------------------------------------------------
;;; over vertexes
-;;; ---------------------------------------------------------------------------
(defmethod map-over-all-combinations-of-k-vertexes ((graph basic-graph) k fn)
(let* ((vertex-count (size graph))
(nth-element vertexes vertex-index))
vertex-indexes)))))))
-;;; ---------------------------------------------------------------------------
#+test
(let ((result nil)
(push graph-from-vertexes result)))))
result)
-;;; ---------------------------------------------------------------------------
;;; over edges
;;; todo: merge these two defs
-;;; ---------------------------------------------------------------------------
(defmethod map-over-all-combinations-of-k-edges ((graph basic-graph) k fn)
(let* ((edge-count (edge-count graph))
(nth-element edges edge-index))
edge-indexes)))))))
-;;; ---------------------------------------------------------------------------
(defmethod map-over-all-combinations-of-k-edges ((vertex basic-vertex) k fn)
(let* ((edge-count (edge-count vertex))
(funcall fn (mapcar (lambda (edge-index)
(nth-element edges edge-index))
edge-indexes)))))))
-;;; ---------------------------------------------------------------------------
#+test
(map-over-all-combinations-of-k-edges
(in-package #:metabang.graph)
-;;; ---------------------------------------------------------------------------
;;; class defs
-;;; ---------------------------------------------------------------------------
(defclass* graph-container (iteratable-container-mixin
non-associative-container-mixin
(:export-p t)
(:documentation "A graph container is essentially an adjacency list graph representation [?? The Bad name comes from it being implemented with containers... ugh]"))
-;;; ---------------------------------------------------------------------------
(defclass* graph-container-edge (basic-edge)
((vertex-1 nil ir "`Vertex-1` is one of the two vertexes that an edge connects. In a directed-edge, `vertex-1` is also the `source-edge`.")
(:export-p t)
(:documentation "This is the root class for edges in graph-containers. It adds vertex-1 and vertex-2 slots."))
-;;; ---------------------------------------------------------------------------
(defmethod print-object ((object graph-container-edge) stream)
(print-unreadable-object (object stream :type t)
(format stream "<~A ~A ~A>" (vertex-1 object) (vertex-2 object)
(value object))))
-;;; ---------------------------------------------------------------------------
(defclass* weighted-edge (weighted-edge-mixin graph-container-edge)
()
(:export-p t)
(:documentation "A weighted edge is both a weighted-edge-mixin and a graph-container-edge."))
-;;; ---------------------------------------------------------------------------
(defclass* graph-container-vertex (basic-vertex)
((vertex-edges nil r))
:vertex-edges-container-class 'vector-container)
(:documentation "A graph container vertex keeps track of its edges in the the vertex-edges slot. The storage for this defaults to a vector-container but can be changed using the vertex-edges-container-class initarg."))
-;;; ---------------------------------------------------------------------------
(defmethod make-vertex-edges-container ((vertex graph-container-vertex)
container-class &rest args)
(apply #'make-container container-class args))
-;;; ---------------------------------------------------------------------------
(defmethod initialize-instance :after ((object graph-container-vertex) &key
vertex-edges-container-class)
(setf (slot-value object 'vertex-edges)
(make-vertex-edges-container object vertex-edges-container-class)))
-;;; ---------------------------------------------------------------------------
(defmethod make-vertex-container ((graph graph-container) initial-size)
(make-container 'simple-associative-container
:initial-size initial-size
:test (vertex-test graph)))
-;;; ---------------------------------------------------------------------------
(defmethod make-edge-container ((graph graph-container) initial-size)
(make-container 'vector-container :initial-size initial-size
:fill-pointer 0))
-;;; ---------------------------------------------------------------------------
;;; graph-container-directed-edge
-;;; ---------------------------------------------------------------------------
(defclass* graph-container-directed-edge (directed-edge-mixin
graph-container-edge)
(:export-p t)
(:documentation "A graph-container-directed-edge is both a directed-edge-mixin and a graph-container-edge."))
-;;; ---------------------------------------------------------------------------
(defmethod initialize-instance :after ((object graph-container-directed-edge)
&key source-vertex target-vertex)
(when target-vertex
(setf (slot-value object 'vertex-2) target-vertex)))
-;;; ---------------------------------------------------------------------------
;;; vertex-1 is defined to be the source vertex of an undirected edge
-;;; ---------------------------------------------------------------------------
(defmethod source-vertex ((edge graph-container-edge))
(vertex-1 edge))
-;;; ---------------------------------------------------------------------------
;;; vertex-2 is defined to be the target vertex of an undirected edge
-;;; ---------------------------------------------------------------------------
(defmethod target-vertex ((edge graph-container-edge))
(vertex-2 edge))
-;;; ---------------------------------------------------------------------------
(defmethod other-vertex ((edge graph-container-edge)
(v graph-container-vertex))
(t (error "Vertex ~A not part of Edge ~A" v edge))))
-;;; ---------------------------------------------------------------------------
(defmethod other-vertex ((edge graph-container-edge)
(value t))
(other-vertex edge (find-vertex edge value)))
-;;; ---------------------------------------------------------------------------
(defmethod add-edge ((graph graph-container) (edge graph-container-edge)
&key force-new?)
(push edge (item-at-1 (vertex-pair->edge graph) (cons vertex-1 vertex-2))))
edge)
-;;; ---------------------------------------------------------------------------
(defmethod add-edge-to-vertex :around ((edge graph-container-edge)
(vertex graph-container-vertex))
(insert-item (vertex-edges vertex) edge))
-;;; ---------------------------------------------------------------------------
(defmethod make-node-for-container ((graph graph-container) (node t) &key)
(make-vertex-for-graph graph :element node))
-;;; ---------------------------------------------------------------------------
(defmethod find-edge-between-vertexes ((graph graph-container)
(vertex-1 graph-container-vertex)
:vertex-1 vertex-1 :vertex-2 vertex-1))
(first value)))
-;;; ---------------------------------------------------------------------------
(defmethod find-edge-between-vertexes-if ((graph graph-container)
(vertex-1 graph-container-vertex)
:vertex-1 vertex-1 :vertex-2 vertex-1))
it))
-;;; ---------------------------------------------------------------------------
(defmethod find-edge-between-vertexes-if ((graph graph-container)
(value-1 t)
(when error-if-not-found?
(error 'graph-edge-not-found-error :vertex-1 v1 :vertex-2 v2)))))
-;;; ---------------------------------------------------------------------------
(defmethod find-edge ((graph graph-container) (edge graph-container-edge)
&optional error-if-not-found?)
graph (vertex-1 edge) (vertex-2 edge)
:error-if-not-found? error-if-not-found?))
-;;; ---------------------------------------------------------------------------
(defmethod delete-edge ((graph graph-container) (edge graph-container-edge))
(let ((vertex-1 (vertex-1 edge))
(empty! (vertex-pair->edge graph))
graph)
-;;; ---------------------------------------------------------------------------
(defmethod empty! :after ((graph graph-container))
(empty! (vertex-pair->edge graph)))
-;;; ---------------------------------------------------------------------------
;;; iteration
-;;; ---------------------------------------------------------------------------
(defmethod iterate-edges ((graph graph-container) fn)
(iterate-elements (graph-edges graph) fn))
-;;; ---------------------------------------------------------------------------
(defmethod iterate-edges ((vertex graph-container-vertex) fn)
(iterate-elements (vertex-edges vertex) fn))
-;;; ---------------------------------------------------------------------------
(defmethod iterate-source-edges ((vertex graph-container-vertex) fn)
(iterate-elements (vertex-edges vertex)
(eq vertex (source-vertex edge)))
(funcall fn edge)))))
-;;; ---------------------------------------------------------------------------
(defmethod iterate-target-edges ((vertex graph-container-vertex) fn)
(iterate-elements (vertex-edges vertex)
(eq vertex (target-vertex edge)))
(funcall fn edge)))))
-;;; ---------------------------------------------------------------------------
(defmethod iterate-children ((vertex graph-container-vertex) fn)
(iterate-source-edges vertex
(lambda (edge)
(funcall fn (other-vertex edge vertex)))))
-;;; ---------------------------------------------------------------------------
(defmethod iterate-parents ((vertex graph-container-vertex) fn)
(iterate-target-edges vertex
(lambda (edge)
(funcall fn (other-vertex edge vertex)))))
-;;; ---------------------------------------------------------------------------
(defmethod iterate-neighbors ((vertex graph-container-vertex) fn)
(iterate-edges vertex
(lambda (edge)
(funcall fn (other-vertex edge vertex)))))
-;;; ---------------------------------------------------------------------------
(defmethod vertexes ((edge graph-container-edge))
(collect-using #'iterate-vertexes nil edge))
-;;; ---------------------------------------------------------------------------
(defmethod has-children-p ((vertex graph-container-vertex))
(iterate-target-edges vertex
(return-from has-children-p t)))
(values nil))
-;;; ---------------------------------------------------------------------------
(defmethod has-parent-p ((vertex graph-container-vertex))
(iterate-source-edges vertex
(return-from has-parent-p t)))
(values nil))
-;;; ---------------------------------------------------------------------------
(defmethod vertices-share-edge-p ((vertex-1 graph-container-vertex)
(vertex-2 graph-container-vertex))
(values nil))
-;;; ---------------------------------------------------------------------------
(defmethod edge-count ((graph graph-container))
(size (graph-edges graph)))
poisson-vertex-degree-distribution
power-law-vertex-degree-distribution)))
-;;; ---------------------------------------------------------------------------
;;; classes
-;;; ---------------------------------------------------------------------------
(defclass* generated-graph-mixin ()
((generation-method nil ir)
(random-seed nil ir)))
-;;; ---------------------------------------------------------------------------
(defun save-generation-information (graph generator method)
;; No
(setf (slot-value graph 'generation-method) method
(slot-value graph 'random-seed) (random-seed generator)))
-;;; ---------------------------------------------------------------------------
(defun simple-group-id-generator (kind count)
(form-keyword "H" (format nil "~2,'0D~4,'0D" kind count)))
-;;; ---------------------------------------------------------------------------
(defun simple-group-id-parser (vertex)
(parse-integer (subseq (symbol-name (element vertex)) 1 3)))
-;;; ---------------------------------------------------------------------------
;;; generate-gnp
-;;; ---------------------------------------------------------------------------
(defmethod generate-gnp (generator (graph-class symbol) n p &key (label 'identity))
(generate-gnp
generator (make-instance graph-class) n p :label label))
-;;; ---------------------------------------------------------------------------
(defmethod generate-gnp (generator (graph basic-graph) n p &key (label 'identity))
(let ((v 1)
graph))
-;;; ---------------------------------------------------------------------------
;;; generate-gnm
-;;; ---------------------------------------------------------------------------
(defmethod generate-gnm (generator (graph-class symbol) n p &key (label 'identity))
(generate-gnm
generator (make-instance graph-class) n p :label label))
-;;; ---------------------------------------------------------------------------
(defmethod generate-gnm (generator (graph basic-graph) n m &key (label 'identity))
(let ((max-edge-index (1- (combination-count n 2))))
'graph-container 10000 (floor (* 0.0001 (combination-count 10000 2)))))
)
-;;; ---------------------------------------------------------------------------
(defun vertex-group (v)
(aref (symbol-name (element v)) 1))
-;;; ---------------------------------------------------------------------------
(defun in-group-degree (v &key (key 'vertex-group))
(vertex-degree
(declare (ignore e))
(in-same-group-p v ov key))))
-;;; ---------------------------------------------------------------------------
(defun in-same-group-p (v1 v2 key)
(eq (funcall key v1) (funcall key v2)))
-;;; ---------------------------------------------------------------------------
(defun out-group-degree (v &key (key 'vertex-group))
(vertex-degree
(declare (ignore e))
(not (in-same-group-p v ov key)))))
-;;; ---------------------------------------------------------------------------
;;; generate-undirected-graph-via-assortativity-matrix
-;;; ---------------------------------------------------------------------------
(defmethod generate-undirected-graph-via-assortativity-matrix
(generator (graph-class symbol) size edge-count
kind-matrix assortativity-matrix vertex-creator
:duplicate-edge-function duplicate-edge-function))
-;;; ---------------------------------------------------------------------------
(defmethod generate-undirected-graph-via-assortativity-matrix
(generator graph size edge-count
(values graph)))
-;;; ---------------------------------------------------------------------------
;;; generate-undirected-graph-via-verex-probabilities
-;;; ---------------------------------------------------------------------------
(defmethod generate-undirected-graph-via-vertex-probabilities
(generator (graph-class symbol) size
generator (make-instance graph-class) size
kind-matrix probability-matrix vertex-creator))
-;;; ---------------------------------------------------------------------------
(defmethod generate-undirected-graph-via-vertex-probabilities
(generator graph size
(lambda (kind count)
(form-keyword "H" (format nil "~2,'0D~4,'0D" kind count))))
-;;; ---------------------------------------------------------------------------
(defun sample-edges-of-same-kind (generator n p fn)
(when (plusp p)
#+Test
(sample-edges-of-same-kind *random-generator* 10 0.2 (lambda (a b) (print (list a b))))
-;;; ---------------------------------------------------------------------------
(defun sample-edges-of-different-kinds (generator rows cols p fn)
(when (plusp p)
(when (< v rows)
(funcall fn v w)))))))
-;;; ---------------------------------------------------------------------------
(defun poisson-vertex-degree-distribution (z k)
(/ (* (expt z k) (expt cl-mathstats:+e+ (- z)))
from this distribution
|#
-;;; ---------------------------------------------------------------------------
(defun power-law-vertex-degree-distribution (kappa k)
(* (- 1 (expt cl-mathstats:+e+ (- (/ kappa))))
(expt cl-mathstats:+e+ (- (/ k kappa)))))
-;;; ---------------------------------------------------------------------------
(defun create-specified-vertex-degree-distribution (degrees)
(lambda (z k)
(declare (ignore z k))
degrees))
-;;; ---------------------------------------------------------------------------
(defun make-degree-sampler (p_k &key (generator *random-generator*)
(max-degree 1000)
(lambda ()
(first (next-element wsc)))))
-;;; ---------------------------------------------------------------------------
#+Old
(defun sample-edges-for-assortative-graph (generator edge-count assortativity-matrix)
(loop repeat edge-count collect
(next-element c))))
-;;; ---------------------------------------------------------------------------
(defun sample-edges-for-assortative-graph (generator edge-count assortativity-matrix)
(let ((s (make-edge-sampler-for-assortative-graph generator assortativity-matrix)))
(loop repeat edge-count collect
(funcall s))))
-;;; ---------------------------------------------------------------------------
(defun make-edge-sampler-for-assortative-graph (generator assortativity-matrix)
(let ((c (make-container 'weighted-sampling-container
(insert-item c (list i j))))
(lambda () (next-element c))))
-;;; ---------------------------------------------------------------------------
(defun sample-vertexes-for-mixed-graph (generator size kind-matrix)
(cond ((every-element-p kind-matrix (lambda (x) (fixnump x)))
mixing-matrix)))
-;;; ---------------------------------------------------------------------------
;;; girvan-newman-test-graphs
-;;; ---------------------------------------------------------------------------
(defun generate-girvan-newman-graph (generator graph-class z-in)
(warn "This is broken!")
(values g)))
-;;; ---------------------------------------------------------------------------
(defun gn-id->group (id)
(parse-integer (subseq (symbol-name id) 1 2)))
-;;; ---------------------------------------------------------------------------
(defun collect-edge-counts (g)
(let ((vertexes (make-container 'simple-associative-container
#'string-lessp
:key #'first)))
-;;; ---------------------------------------------------------------------------
(defclass* weighted-sampler-with-lookup-container ()
((sampler nil r)
(lookup nil r)))
-;;; ---------------------------------------------------------------------------
(defmethod initialize-instance :after ((object weighted-sampler-with-lookup-container)
&key random-number-generator key)
(slot-value object 'lookup)
(make-container 'simple-associative-container)))
-;;; ---------------------------------------------------------------------------
(defmethod insert-item ((container weighted-sampler-with-lookup-container)
(item t))
(assert (not (null node)))
(setf (item-at-1 (lookup container) item) node)))
-;;; ---------------------------------------------------------------------------
(defmethod find-node ((container weighted-sampler-with-lookup-container)
(item t))
(item-at-1 (lookup container) item))
-;;; ---------------------------------------------------------------------------
(defmethod delete-node ((container weighted-sampler-with-lookup-container)
(node t))
;; not going to worry about the hash table
(delete-node (sampler container) node))
-;;; ---------------------------------------------------------------------------
(defmethod next-element ((container weighted-sampler-with-lookup-container))
(next-element (sampler container)))
-;;; ---------------------------------------------------------------------------
(defmethod generate-scale-free-graph
(generator graph size kind-matrix add-edge-count
graph)))
-;;; ---------------------------------------------------------------------------
#+Test
(defun poisson-connector (count generator)
|#
-;;; ---------------------------------------------------------------------------
;;; generate-assortative-graph-with-degree-distributions
-;;; ---------------------------------------------------------------------------
#+Ignore
(define-debugging-class generate-assortative-graph-with-degree-distributions ())
-;;; ---------------------------------------------------------------------------
(defmethod generate-assortative-graph-with-degree-distributions
(generator (graph-class symbol)
(0.2222222222222222 0.4444444444444444))))
:test #'eq)
-;;; ---------------------------------------------------------------------------
;;; generate-graph-by-resampling-edges
-;;; ---------------------------------------------------------------------------
#|
doesn't take edge weights into account when sampling
((generator nil ir)
(graph nil ir)))
-;;; ---------------------------------------------------------------------------
(defmethod next-element ((sampler basic-edge-sampler))
(sample-element (graph-edges (graph sampler)) (generator sampler)))
-;;; ---------------------------------------------------------------------------
(defclass* weighted-edge-sampler (basic-edge-sampler)
((weight-so-far 0 a)
(edge-iterator nil r)
(size nil ir)))
-;;; ---------------------------------------------------------------------------
(defmethod initialize-instance :after ((object weighted-edge-sampler) &key)
(let ((generator (generator object))
(slot-value object 'edge-iterator)
(make-iterator (graph-edges (graph object))))))
-;;; ---------------------------------------------------------------------------
(defmethod next-element ((object weighted-edge-sampler))
(let ((edge-iterator (edge-iterator object))
(generate-graph-by-resampling-edges
*random-generator* g 'weighted-edge-sampler (edge-count g)))))))))
-;;; ---------------------------------------------------------------------------
;;; some preferential attachment algorithms
-;;; ---------------------------------------------------------------------------
#+Ignore
(define-debugging-class generate-preferential-attachment-graph
(graph-generation))
-;;; ---------------------------------------------------------------------------
(defmethod generate-simple-preferential-attachment-graph
(generator (graph-class symbol) size minimum-degree)
(generate-simple-preferential-attachment-graph
generator (make-instance graph-class) size minimum-degree))
-;;; ---------------------------------------------------------------------------
(defmethod generate-simple-preferential-attachment-graph
(generator graph size minimum-degree)
:sort #'>
:sort-on :values)
-;;; ---------------------------------------------------------------------------
(defmethod generate-preferential-attachment-graph
(generator (graph-class symbol) size kind-matrix minimum-degree
:vertex-labeler vertex-labeler
:duplicate-edge-function duplicate-edge-function))
-;;; ---------------------------------------------------------------------------
(defmethod generate-preferential-attachment-graph
(generator (graph basic-graph) size kind-matrix minimum-degree
graph))
-;;; ---------------------------------------------------------------------------
(defun make-edge-sampler-for-preferential-attachment-graph (generator assortativities)
(let ((c (make-container 'weighted-sampling-container
(0.02 0.25 0.25)
(0.02 0.25 0.25))))
-;;; ---------------------------------------------------------------------------
(defmethod generate-acquaintance-network
generator graph death-probability duplicate-edge-function))
(values graph))
-;;; ---------------------------------------------------------------------------
(defmethod generate-acquaintance-network-until-stable
(generator graph size death-probability step-count
(values graph))
-;;; ---------------------------------------------------------------------------
(defun add-acquaintance-and-maybe-kill-something
(generator graph death-probability duplicate-edge-function)
-;;; ---------------------------------------------------------------------------
;;; vertex-iterator
-;;; ---------------------------------------------------------------------------
(u:defclass* vertex-iterator (containers::forward-iterator)
())
-;;; ---------------------------------------------------------------------------
(defmethod initialize-instance :after ((object vertex-iterator) &key)
(reset object))
-;;; ---------------------------------------------------------------------------
(defmethod reset ((iterator vertex-iterator))
(let ((vertex (containers::initial-container iterator)))
:transform (lambda (e) (other-vertex e vertex)))))
iterator)
-;;; ---------------------------------------------------------------------------
(defmethod containers::base-class-for-iteratee ((container basic-vertex))
'vertex-iterator)
-;;; ---------------------------------------------------------------------------
(defmethod containers::base-class-for-iteratee ((container basic-vertex))
(containers::base-class-for-iteratee (vertex-edges container)))
|#
(in-package #:metabang.graph)
-;;; ---------------------------------------------------------------------------
(defclass* graph-matrix (basic-graph)
((adjencency-matrix nil r))
(:export-p t)
(:documentation "Stub for matrix based graph. Not implemented."))
-;;; ---------------------------------------------------------------------------
(defmethod initialize-instance :after ((object graph-matrix) &key)
(setf (slot-value object 'adjencency-matrix)
nil))
-;;; ---------------------------------------------------------------------------
(defmethod make-vertex-container ((graph graph-matrix) initial-size)
(make-container 'vector-container :initial-size initial-size
:fill-pointer 0))
-;;; ---------------------------------------------------------------------------
(defmethod make-edge-container ((graph graph-matrix) initial-size)
(make-container 'vector-container :initial-size initial-size
:fill-pointer 0))
-;;; ---------------------------------------------------------------------------
(defclass* graph-matrix-edge (basic-edge)
()
(:export-p t)
(:documentation "Stub for matrix based graph. Not implemented."))
-;;; ---------------------------------------------------------------------------
(defclass* graph-matrix-vertex (basic-vertex)
()
(:export-p t)
(:documentation "Stub for matrix based graph. Not implemented."))
-;;; ---------------------------------------------------------------------------
(incf (item-at c (edge-count v)))))
c))
-;;; ---------------------------------------------------------------------------
(defun average-vertex-degree (graph &key
(vertex-filter (constantly t))
(values (float (/ total size)))
nil)))
-;;; ---------------------------------------------------------------------------
(defun vertex-degree (vertex &key
(edge-filter (constantly t))
(declare (inline %vertex-degree))
(%vertex-degree vertex edge-filter edge-size))
-;;; ---------------------------------------------------------------------------
(defun %vertex-degree (vertex edge-filter edge-size)
"Called internally by `vertex-degree` and `average-vertex-degree`."
(incf degree (funcall edge-size e)))))
degree))
-;;; ---------------------------------------------------------------------------
(defun vertex-degree-summary (graph vertex-classifier
&key (edge-size (constantly 1)))
"Average vertex degree between ~A and ~A:"
k-1 k-2))))))
-;;; ---------------------------------------------------------------------------
#|
Transitivity or Clustering.
(float (/ (vertex-triangle-count vertex)
(combination-count (edge-count vertex) 2)))))
-;;; ---------------------------------------------------------------------------
(defun vertex-triangle-count (vertex)
(let ((neighbors (neighbor-vertexes vertex)))
(member v neighbors))
(neighbor-vertexes neighbor)) 2))))
-;;; ---------------------------------------------------------------------------
(defun row-sums (matrix)
(let* ((row-count (array-dimension matrix 1))
(incf (aref result row) (aref matrix column row))))
result))
-;;; ---------------------------------------------------------------------------
(defun column-sums (matrix)
(let* ((column-count (array-dimension matrix 0))
(incf (aref result column) (aref matrix column row))))
result))
-;;; ---------------------------------------------------------------------------
(defmethod assortativity-coefficient ((matrix array))
(values 1)
(values (/ (- trace sum-squared) (- 1 sum-squared))))))
-;;; ---------------------------------------------------------------------------
(defmethod graph-edge-mixture-matrix ((graph basic-graph) vertex-classifier &key
(edge-weight (constantly 1)))
(0.013 0.023 0.306 0.035)
(0.005 0.007 0.024 0.016)))
-;;; ---------------------------------------------------------------------------
;;OPT we call the classifier a lot, probably better to make a new ht for that
(in-package #:metabang.graph)
-;;; ---------------------------------------------------------------------------
;;; classes
-;;; ---------------------------------------------------------------------------
(defcondition graph-error (error)
((graph nil ir))
(:export-slots-p t)
(:documentation "This is the root condition for errors that occur while running code in CL-Graph."))
-;;; ---------------------------------------------------------------------------
(defcondition edge-error (graph-error)
((edge nil ir "The `edge` that is implicated in the condition."))
(:export-slots-p t)
(:documentation "This is the root condition for graph errors that have to do with edges."))
-;;; ---------------------------------------------------------------------------
(defcondition graph-vertex-not-found-error (graph-error)
((vertex nil ir "The vertex or value that could not be found in the graph."))
(:export-slots-p t)
(:documentation "This condition is signaled when a vertex can not be found in a graph."))
-;;; ---------------------------------------------------------------------------
(defcondition graph-vertex-not-found-in-edge-error (edge-error)
((vertex nil ir))
(:export-p t)
(:documentation "This condition is signaled when a vertex can not be found in an edge."))
-;;; ---------------------------------------------------------------------------
(defcondition graph-edge-not-found-error (graph-error)
((vertex-1 nil ir "One of the vertexes for which no connecting edge could be found.")
(:export-slots-p t)
(:documentation "This condition is signaled when an edge cannot be found in a graph."))
-;;; ---------------------------------------------------------------------------
(defclass* basic-vertex (container-node-mixin)
((depth-level 0 ia :type number "`Depth-level` is used by some algorithms for bookkeeping. [?? Should be in a mixin]")
(:make-load-form-p t)
(:documentation "This is the root class for all vertexes in CL-Graph."))
-;;; ---------------------------------------------------------------------------
(defmethod initialize-instance :after ((object basic-vertex) &key graph vertex-id)
(when (and graph (not vertex-id))
(largest-vertex-id graph))
(incf (slot-value graph 'largest-vertex-id))))
-;;; ---------------------------------------------------------------------------
(defmethod print-object ((vertex basic-vertex) stream)
(print-unreadable-object (vertex stream :identity nil)
(if (and (slot-exists-p vertex 'element) (slot-boundp vertex 'element))
(element vertex) "#unbound#"))))
-;;; ---------------------------------------------------------------------------
(defclass* basic-edge ()
((edge-id 0 ia "The `edge-id` is used internally by CL-Graph for bookkeeping.")
(:make-load-form-p t)
(:documentation "This is the root class for all edges in CL-Graph."))
-;;; ---------------------------------------------------------------------------
(defmethod initialize-instance :after ((object basic-edge) &key graph edge-id)
(when (and graph (not edge-id))
(largest-edge-id graph))
(incf (slot-value graph 'largest-edge-id))))
-;;; ---------------------------------------------------------------------------
(defmethod print-object ((object basic-edge) stream)
(print-unreadable-object (object stream :type t)
(format stream "<~A ~A>" (vertex-1 object) (vertex-2 object))))
-;;; ---------------------------------------------------------------------------
(defclass* directed-edge-mixin () ()
(:export-p t)
(:documentation "This mixin class is used to indicate that an edge is directed."))
-;;; ---------------------------------------------------------------------------
(defclass* weighted-edge-mixin ()
((weight 1d0 ia "The value of the weight of this edge. Defaults to 1.0d0"))
(:export-p t)
(:documentation "This mixin class adds a `weight` slot to an edge."))
-;;; ---------------------------------------------------------------------------
(defmethod weight ((edge basic-edge)) (values 1.0))
-;;; ---------------------------------------------------------------------------
(defclass* basic-graph ()
((graph-vertexes :unbound ir)
:initial-size 25)
(:documentation "This is the root class for all graphs in CL-Graph."))
-;;; ---------------------------------------------------------------------------
(defmethod initialize-instance :after ((object basic-graph) &key initial-size
&allow-other-keys)
(setf (slot-value object 'graph-edges)
(make-edge-container object initial-size)))
-;;; ---------------------------------------------------------------------------
(defmethod print-object ((graph basic-graph) stream)
(print-unreadable-object (graph stream :type t :identity t)
(format stream "[~A,~A]" (size graph) (edge-count graph))))
-;;; ---------------------------------------------------------------------------
;;; internals
-;;; ---------------------------------------------------------------------------
(defmethod add-vertex
((graph basic-graph) (value basic-vertex) &key if-duplicate-do)
(declare (ignore if-duplicate-do))
(values value))
-;;; ---------------------------------------------------------------------------
(defmethod make-vertex-for-graph ((graph basic-graph) &rest args &key
(vertex-class (vertex-class graph))
"Vertex class '~A' must be a subtype of ~A" vertex-class (vertex-class graph))
(apply #'make-instance vertex-class :graph graph args))
-;;; ---------------------------------------------------------------------------
(defmethod make-edge-for-graph ((graph basic-graph)
(vertex-1 basic-vertex) (vertex-2 basic-vertex)
:graph graph
:vertex-1 vertex-1 :vertex-2 vertex-2 args))
-;;; ---------------------------------------------------------------------------
(defmethod make-graph ((graph-type symbol) &rest args &key &allow-other-keys)
(apply #'make-instance graph-type args))
-;;; ---------------------------------------------------------------------------
;;; generic implementation
-;;; ---------------------------------------------------------------------------
(defmethod undirected-edge-p ((edge basic-edge))
(not (directed-edge-p edge)))
-;;; ---------------------------------------------------------------------------
(defmethod directed-edge-p ((edge basic-edge))
(typep edge 'directed-edge-mixin))
-;;; ---------------------------------------------------------------------------
(defmethod tagged-edge-p ((edge basic-edge))
(tag edge))
-;;; ---------------------------------------------------------------------------
(defmethod untagged-edge-p ((edge basic-edge))
(null (tag edge)))
-;;; ---------------------------------------------------------------------------
(defmethod tag-all-edges ((graph basic-graph))
(iterate-edges
(lambda (e)
(setf (tag e) t))))
-;;; ---------------------------------------------------------------------------
(defmethod tag-all-edges ((vertex basic-vertex))
(iterate-edges
(lambda (e)
(setf (tag e) t))))
-;;; ---------------------------------------------------------------------------
(defmethod untag-all-edges ((graph basic-graph))
(iterate-edges
(lambda (e)
(setf (tag e) nil))))
-;;; ---------------------------------------------------------------------------
(defmethod untag-all-edges ((vertex basic-vertex))
(iterate-edges
(lambda (e)
(setf (tag e) nil))))
-;;; ---------------------------------------------------------------------------
(defmethod untag-edges ((edges list))
(iterate-nodes
(lambda (e)
(setf (tag e) nil))))
-;;; ---------------------------------------------------------------------------
(defmethod tag-edges ((edges list))
(iterate-nodes
(setf (tag e) t))))
-;;; ---------------------------------------------------------------------------
(defmethod (setf element) :around ((value t) (vertex basic-vertex))
(with-changing-vertex (vertex)
(call-next-method)))
-;;; ---------------------------------------------------------------------------
;; :ignore, :force, :replace, <function>
;; not found, add
(add-it :new)))))
-;;; ---------------------------------------------------------------------------
(defmethod replace-vertex ((graph basic-graph) (old basic-vertex) (new basic-vertex))
;; we need the graph and the new vertex to reference each other
(delete-vertex graph old)
(add-vertex graph new))
-;;; ---------------------------------------------------------------------------
(defmethod add-edge-between-vertexes ((graph basic-graph) (value-1 t) (value-2 t)
&rest args &key (if-duplicate-do :ignore)
(add-vertex graph value-2 :if-duplicate-do :replace))))
(apply #'add-edge-between-vertexes graph v1 v2 args)))
-;;; ---------------------------------------------------------------------------
;;; to-do - add-edge-between-vertexes needs to be able to grab the weight and
;;; color from edges that inherit from weight and color mixins
-;;; ---------------------------------------------------------------------------
(defmethod add-edge-between-vertexes ((graph basic-graph)
(v-1 basic-vertex) (v-2 basic-vertex)
(add-it :new)))))
-;;; ---------------------------------------------------------------------------
(defmethod add-edge-to-vertex ((edge basic-edge) (vertex basic-vertex))
(values))
-;;; ---------------------------------------------------------------------------
(defmethod find-edge-between-vertexes
((graph basic-graph) (value-1 t) (value-2 t)
(error 'graph-edge-not-found-error
:graph graph :vertex-1 v1 :vertex-2 v2)))))
-;;; ---------------------------------------------------------------------------
(defmethod delete-edge-between-vertexes ((graph basic-graph)
(value-or-vertex-1 t)
(when edge
(delete-edge graph edge))))
-;;; ---------------------------------------------------------------------------
(defmethod delete-edge :after ((graph basic-graph) (edge basic-edge))
(delete-item (graph-edges graph) edge)
(empty! (graph-edges graph))
graph)
-;;; ---------------------------------------------------------------------------
(defmethod delete-vertex ((graph basic-graph) value-or-vertex)
(delete-vertex graph (find-vertex graph value-or-vertex)))
-;;; ---------------------------------------------------------------------------
(defmethod delete-vertex ((graph basic-graph) (vertex basic-vertex))
(unless (eq graph (graph vertex))
(empty! (vertex-edges vertex))
(values vertex graph))
-;;; ---------------------------------------------------------------------------
(defmethod delete-vertex :after ((graph basic-graph)
(vertex basic-vertex))
(delete-item-at (graph-vertexes graph)
(funcall (vertex-key graph) (element vertex))))
-;;; ---------------------------------------------------------------------------
(defmethod insert-item ((graph basic-graph) value)
(add-vertex graph value))
-;;; ---------------------------------------------------------------------------
(defmethod source-edges ((vertex basic-vertex) &optional filter)
(collect-using #'iterate-source-edges filter vertex))
-;;; ---------------------------------------------------------------------------
(defmethod target-edges ((vertex basic-vertex) &optional filter)
(collect-using #'iterate-target-edges filter vertex))
-;;; ---------------------------------------------------------------------------
(defmethod child-vertexes (vertex &optional filter)
(collect-using #'iterate-children filter vertex))
-;;; ---------------------------------------------------------------------------
(defmethod parent-vertexes (vertex &optional filter)
(collect-using #'iterate-parents filter vertex))
-;;; ---------------------------------------------------------------------------
(defmethod neighbor-vertexes (vertex &optional filter)
(collect-using #'iterate-neighbors filter vertex))
-;;; ---------------------------------------------------------------------------
(defmethod adjacentp ((graph basic-graph) vertex-1 vertex-2)
(adjacentp graph (find-vertex graph vertex-1) (find-vertex graph vertex-2)))
-;;; ---------------------------------------------------------------------------
(defmethod adjacentp ((graph basic-graph) (vertex-1 basic-vertex) (vertex-2 basic-vertex))
(iterate-neighbors
(return-from adjacentp t))))
(values nil))
-;;; ---------------------------------------------------------------------------
(defmethod number-of-neighbors (vertex)
(count-using #'iterate-neighbors nil vertex))
-;;; ---------------------------------------------------------------------------
(defmethod in-cycle-p ((graph basic-graph) (vertex t))
(in-cycle-p graph (find-vertex graph vertex)))
-;;; ---------------------------------------------------------------------------
(defmethod renumber-vertexes ((graph basic-graph))
(let ((count 0))
(incf count)))
(setf (slot-value graph 'largest-vertex-id) count)))
-;;; ---------------------------------------------------------------------------
(defmethod renumber-edges ((graph basic-graph))
(let ((count 0))
(incf count)))
(setf (slot-value graph 'largest-edge-id) count)))
-;;; ---------------------------------------------------------------------------
(deprecated
(defmethod container->list ((graph basic-graph))
(collect-elements (graph-vertexes graph))))
-;;; ---------------------------------------------------------------------------
(defmethod add-vertex :before ((graph basic-graph) (vertex basic-vertex)
&key &allow-other-keys)
(funcall (vertex-key graph) (element vertex))) vertex
(slot-value vertex 'graph) graph))
-;;; ---------------------------------------------------------------------------
(defmethod add-edge :before ((graph basic-graph) (edge basic-edge) &key force-new?)
(declare (ignore force-new?))
(progn (setf (contains-directed-edge-p graph) t))
(progn (setf (contains-undirected-edge-p graph) t))))
-;;; ---------------------------------------------------------------------------
(defmethod find-vertex ((graph basic-graph) (value t)
&optional (error-if-not-found? t))
(iterate-elements (graph-vertexes graph)
(lambda (vertex) (funcall fn (element vertex)))))
-;;; ---------------------------------------------------------------------------
(defmethod iterate-nodes ((graph basic-graph) fn)
(iterate-nodes (graph-vertexes graph) fn))
-;;; ---------------------------------------------------------------------------
(defmethod iterate-vertexes ((graph basic-graph) fn)
(iterate-nodes (graph-vertexes graph) fn))
-;;; ---------------------------------------------------------------------------
(defmethod iterate-vertexes ((edge basic-edge) fn)
(funcall fn (vertex-1 edge))
(funcall fn (vertex-2 edge)))
-;;; ---------------------------------------------------------------------------
(defmethod size ((graph basic-graph))
(size (graph-vertexes graph)))
-;;; ---------------------------------------------------------------------------
(defmethod edges ((graph basic-graph))
(collect-using #'iterate-edges nil graph))
-;;; ---------------------------------------------------------------------------
(defmethod edges ((vertex basic-vertex))
(collect-using #'iterate-edges nil vertex))
-;;; ---------------------------------------------------------------------------
(deprecated
"Use size instead"
(defmethod vertex-count ((graph basic-graph))
(size graph)))
-;;; ---------------------------------------------------------------------------
(defmethod vertexes ((graph basic-graph))
(collect-elements (graph-vertexes graph)))
-;;; ---------------------------------------------------------------------------
(defmethod source-edge-count ((vertex basic-vertex))
(count-using 'iterate-source-edges nil vertex))
-;;; ---------------------------------------------------------------------------
(defmethod target-edge-count ((vertex basic-vertex))
(count-using 'iterate-target-edges nil vertex))
-;;; ---------------------------------------------------------------------------
(defmethod graph-roots ((graph basic-graph))
(collect-elements (graph-vertexes graph) :filter #'rootp))
-;;; ---------------------------------------------------------------------------
(defmethod rootp ((vertex basic-vertex))
;;?? this is inefficient in the same way that (zerop (length <list>)) is...
(zerop (source-edge-count vertex)))
-;;; ---------------------------------------------------------------------------
(defmethod find-vertex-if ((graph basic-graph) fn &key key)
(iterate-vertexes graph
(return-from find-vertex-if v))))
(values nil))
-;;; ---------------------------------------------------------------------------
(defmethod find-vertex-if ((edge basic-edge) fn &key key)
(iterate-vertexes edge
(return-from find-vertex-if v))))
(values nil))
-;;; ---------------------------------------------------------------------------
(defmethod find-edge-if ((graph basic-graph) fn &key key)
(iterate-edges graph
(return-from find-edge-if e))))
(values nil))
-;;; ---------------------------------------------------------------------------
(defmethod find-edges-if ((graph basic-graph) fn)
(collect-using 'iterate-edges fn graph))
-;;; ---------------------------------------------------------------------------
(defmethod find-vertexes-if ((graph basic-graph) fn)
(collect-using 'iterate-vertexes fn graph))
-;;; ---------------------------------------------------------------------------
(defmethod empty! ((graph basic-graph))
(empty! (graph-edges graph))
(renumber-vertexes graph)
(values))
-;;; ---------------------------------------------------------------------------
(defun neighbors-to-children (new-graph root &optional visited-list)
(pushnew root visited-list)
new-graph (value root) (value c) :edge-type :directed)
(neighbors-to-children new-graph c visited-list)))))
-;;; ---------------------------------------------------------------------------
(defmethod generate-directed-free-tree ((graph basic-graph) root)
(generate-directed-free-tree graph (find-vertex graph root)))
-;;; ---------------------------------------------------------------------------
(defmethod force-undirected ((graph basic-graph))
(iterate-edges
-;;; ---------------------------------------------------------------------------
;;; traversal
-;;; ---------------------------------------------------------------------------
(defmethod traverse-elements ((thing basic-graph) (style symbol) fn)
(let ((marker (gensym)))
(lambda (vertex)
(traverse-elements-helper vertex style marker fn)))))
-;;; ---------------------------------------------------------------------------
(defmethod traverse-elements-helper ((thing basic-vertex) (style (eql :depth)) marker fn)
(when (eq (tag thing) marker)
(funcall fn thing)))
-;;; ---------------------------------------------------------------------------
(defmethod traverse-elements-helper ((thing basic-vertex) (style (eql :breadth)) marker fn)
(when (eq (tag thing) marker)
(setf (tag vertex) nil)
(traverse-elements-helper vertex style marker fn)))))
-;;; ---------------------------------------------------------------------------
;; also in metatilites
(defun graph-search-for-cl-graph (states goal-p successors combiner
(member state old-states :test state=))))
(funcall successors (first states)))))))))
-;;; ---------------------------------------------------------------------------
(defmethod in-undirected-cycle-p
((graph basic-graph) (current basic-vertex)
(t
(in-undirected-cycle-p graph child marked current)))))))
-;;; ---------------------------------------------------------------------------
(defmethod any-undirected-cycle-p ((graph basic-graph))
(let ((marked (make-container 'simple-associative-container)))
(return-from any-undirected-cycle-p v)))))
(values nil)))
-;;; ---------------------------------------------------------------------------
(defun remove-list (original target)
"Removes all elements in original from target."
(member target-element original))
target))
-;;; ---------------------------------------------------------------------------
(defun get-nodelist-relatives (node-list)
"Collects set of unique relatives of nodes in node-list."
(append-unique (neighbor-vertexes node) unique-relatives)))
unique-relatives))
-;;; ---------------------------------------------------------------------------
(defun get-transitive-closure (vertex-list &optional (depth nil))
"Given a list of vertices, returns a combined list of all of the nodes
(values visited))))
(collect-transitive-closure vertex-list vertex-list depth)))
-;;; ---------------------------------------------------------------------------
(defmethod edge-count ((graph basic-graph))
(count-using #'iterate-edges nil graph))
-;;; ---------------------------------------------------------------------------
(defmethod edge-count ((vertex basic-vertex))
(size (vertex-edges vertex)))
-;;; ---------------------------------------------------------------------------
(defmethod topological-sort ((graph basic-graph))
(assign-level graph 0)
(sort (collect-elements (graph-vertexes graph)) #'<
:key (lambda (x) (depth-level x))))
-;;; ---------------------------------------------------------------------------
(defmethod assign-level ((graph basic-graph) (level number))
(loop for node in (graph-roots graph)
do (assign-level node 0)))
-;;; ---------------------------------------------------------------------------
(defmethod assign-level ((node basic-vertex) (level number))
(if (or (not (depth-level node))
(setf (depth-level node) level))
(iterate-children node (lambda (x) (assign-level x (1+ level)))))
-;;; ---------------------------------------------------------------------------
(defmethod depth ((graph basic-graph))
(assign-level graph 0)
(setf depth (depth-level vertex)))))
depth))
-;;; ---------------------------------------------------------------------------
;;; mapping
-;;; ---------------------------------------------------------------------------
(defun map-paths (graph start-vertex length fn &key (filter (constantly t)))
"Apply fn to each path that starts at start-vertex and is of exactly length
(follow-path v (list v start-vertex) (1- length))))))
(values graph))
-;;; ---------------------------------------------------------------------------
(defun map-shortest-paths
(graph start-vertex depth fn &key (filter (constantly t)))
:filter filter))))
-;;; ---------------------------------------------------------------------------
;;; utilities
-;;; ---------------------------------------------------------------------------
(defun append-unique (list1 list2)
(remove-duplicates (append list1 list2)))
-;;; ---------------------------------------------------------------------------
;;; project-bipartite-graph
-;;; ---------------------------------------------------------------------------
(defmethod project-bipartite-graph
((new-graph symbol) graph vertex-class vertex-classifier)
(project-bipartite-graph
(make-instance new-graph) graph vertex-class vertex-classifier))
-;;; ---------------------------------------------------------------------------
(defmethod project-bipartite-graph
((new-graph basic-graph) graph vertex-class vertex-classifier)
(in-package #:cl-graph)
-;;; ---------------------------------------------------------------------------
;;; make-filtered-graph
-;;; ---------------------------------------------------------------------------
(defmethod complete-links ((new-graph basic-graph)
(old-graph basic-graph))
:value (value edge)
:edge-type edge-type))))))))))
-;;; ---------------------------------------------------------------------------
(defmethod make-filtered-graph ((old-graph basic-graph)
test-fn
(complete-links new-graph old-graph)))
new-graph)
-;;; ---------------------------------------------------------------------------
(defmethod subgraph-containing ((graph basic-graph) (vertex basic-vertex)
&rest args &key (depth nil) (new-graph nil))
:graph-completion-method :complete-closure-with-links
args))
-;;; ---------------------------------------------------------------------------
;;; for completeness
-;;; ---------------------------------------------------------------------------
(defmethod make-graph-from-vertexes ((vertex-list list))
(bind ((edges-to-keep nil)
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