as if with a call to make-instance."))
-(defgeneric make-edge-for-graph (graph vertex-1 vertex-2
+(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
(: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
+ of :ignore, :force, :replace, :replace-value, :error, or a function. The
default is :ignore."))
(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
filled-out, depending on the following keywords passed to the optional
GRAPH-COMPLETION-METHOD argument:
-* NIL (default)
+* NIL (default)
New graph has only nodes that correspond to those in the original
graph that pass the test. NO LINKS are reproduced.
-* :COMPLETE-LINKS
+* :COMPLETE-LINKS
New graph has only nodes that pass, but reproduces corresponding
links between passing nodes in the original graph.
depth. This value is ignored in non closure options."))
-(defgeneric project-bipartite-graph
+(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
(defgeneric graph->dot (graph output
- &key
+ &key
graph-formatter
vertex-key
vertex-labeler
vertex-formatter
- edge-labeler
+ edge-labeler
edge-formatter)
- (:documentation
+ (:documentation
"Generates a description of `graph` in DOT file format. The
formatting can be altered using `graph->dot-properties,`
`vertex->dot,` and `edge->dot` as well as `edge-formatter,`
D->F []
}\"
-For more information about DOT file format, search the web for 'DOTTY' and
+For more information about DOT file format, search the web for 'DOTTY' and
'GRAPHVIZ'."))
of Large Random Networks \(see batagelj-generation-2005 in doab\)."))
-(defgeneric generate-undirected-graph-via-assortativity-matrix
+(defgeneric generate-undirected-graph-via-assortativity-matrix
(generator graph-class size edge-count kind-matrix assortativity-matrix
vertex-labeler &key)
(:documentation "This generates a random graph with 'size' vertexes.
ought to be."))
-(defgeneric generate-undirected-graph-via-vertex-probabilities
+(defgeneric generate-undirected-graph-via-vertex-probabilities
(generator graph-class size kind-matrix probability-matrix vertex-labeler)
(:documentation "Generate an Erd\"os-R/'enyi like random graph
having multiple vertex kinds. See the function Gnp for the simple one
batagelj-generation-2005 in moab\)."))
-(defgeneric generate-scale-free-graph
+(defgeneric generate-scale-free-graph
(generator graph size kind-matrix add-edge-count
other-vertex-kind-samplers vertex-labeler &key)
(:documentation "Generates a 'scale-free' graph using preferential
\(see batagelj-generation-2005 in moab\). Self-edges are possible."))
-(defgeneric generate-preferential-attachment-graph
- (generator graph size kind-matrix minimum-degree
- assortativity-matrix
+(defgeneric generate-preferential-attachment-graph
+ (generator graph size kind-matrix minimum-degree
+ assortativity-matrix
&key)
(:documentation "Generate a Barabasi-Albert type scale free graph
with multiple vertex kinds.
of `edge`. If the value-or-vertex is not part of edge, then an error
is signaled. [?? Should create a new condition for this]"))
-(defgeneric find-edge-between-vertexes-if
+(defgeneric find-edge-between-vertexes-if
(graph value-or-vertex-1 value-or-vertex-2 fn &key error-if-not-found?)
(:documentation "Finds and returns an edge between value-or-vertex-1
and value-or-vertex-2 if one exists. Unless error-if-not-found? is
((vertex-1 nil ir "One of the vertexes for which no connecting edge could be found.")
(vertex-2 nil ir "One of the vertexes for which no connecting edge could be found."))
(:report (lambda (c s)
- (format s "Edge between ~S and ~S not found in ~A"
+ (format s "Edge between ~S and ~S not found in ~A"
(vertex-1 c) (vertex-2 c) (graph c))))
(:export-p t)
(:export-slots-p t)
(:documentation "This condition is signaled when an edge cannot be found in a graph."))
-(defclass* basic-vertex (container-node-mixin)
+(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]")
(vertex-id 0 ir "`Vertex-id` is used internally to keep track of vertexes.")
(element :unbound ia :accessor value "The `element` is the value that this vertex represents.")
(when (and graph (not vertex-id))
(setf (slot-value object 'vertex-id)
(largest-vertex-id graph))
- (incf (slot-value graph 'largest-vertex-id))))
+ (incf (slot-value graph 'largest-vertex-id))))
(defmethod print-object ((vertex basic-vertex) stream)
(print-unreadable-object (vertex stream :identity nil)
- (format stream "~A"
+ (format stream "~A"
(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.")
(element nil ia :accessor value :initarg :value)
(defmethod print-object ((object basic-edge) stream)
- (print-unreadable-object (object stream :type t)
+ (print-unreadable-object (object stream :type t)
(format stream "<~A ~A>" (vertex-1 object) (vertex-2 object))))
"The class used to create directed edges in the graph. This must extend the base-class for edges of the graph type and directed-edge-mixin. E.g., the directed-edge-class of a graph-container must extend graph-container-edge and directed-edge-mixin.")
(undirected-edge-class 'basic-edge ir
"The class used to create undirected edges in the graph. This must extend the base-class for edges of the graph type. E.g., all edges of a graph-container must extend graph-container-edge")
- (contains-directed-edge-p nil ar
+ (contains-directed-edge-p nil ar
"Returns true if graph contains at least one directed edge. [?? Not sure if this is really keep up-to-date.]")
(contains-undirected-edge-p nil ar
"Returns true if graph contains at least one undirected edge. [?? Not sure if this is really keep up-to-date.]")
(defmethod initialize-instance :after ((object basic-graph) &key initial-size
&allow-other-keys)
- (setf (slot-value object 'graph-vertexes)
+ (setf (slot-value object 'graph-vertexes)
(make-vertex-container object initial-size))
- (setf (slot-value object 'graph-edges)
+ (setf (slot-value object 'graph-edges)
(make-edge-container object initial-size)))
(format stream "[~A,~A]" (size graph) (edge-count graph))))
-;;; internals
+;;; internals
(defmethod add-vertex
((graph basic-graph) (value basic-vertex) &key if-duplicate-do)
(values value))
-(defmethod make-vertex-for-graph ((graph basic-graph) &rest args &key
- (vertex-class (vertex-class graph))
+(defmethod make-vertex-for-graph ((graph basic-graph) &rest args &key
+ (vertex-class (vertex-class graph))
&allow-other-keys)
(remf args :vertex-class)
(assert (subtypep vertex-class (vertex-class graph)) nil
(apply #'make-instance vertex-class :graph graph args))
-(defmethod make-edge-for-graph ((graph basic-graph)
+(defmethod make-edge-for-graph ((graph basic-graph)
(vertex-1 basic-vertex) (vertex-2 basic-vertex)
&rest args &key
(edge-type (default-edge-type graph))
(eq edge-type :directed)
(eq edge-type :undirected)) nil
"Edge-type must be nil, :directed or :undirected.")
-
+
(assert (or (null edge-class)
(subtypep edge-class (directed-edge-class graph))
(subtypep edge-class (undirected-edge-class graph))) nil
"Edge-class must be nil or a subtype of ~A or ~A"
(undirected-edge-class graph)
(directed-edge-class graph))
-
+
(apply #'make-instance
(or edge-class
(ecase edge-type
(defmethod make-graph ((graph-type symbol) &rest args &key &allow-other-keys)
(apply #'make-instance graph-type args))
-;;; generic implementation
+;;; generic implementation
(defmethod undirected-edge-p ((edge basic-edge))
(not (directed-edge-p edge)))
;; :ignore, :force, :replace, <function>
-(defmethod add-vertex ((graph basic-graph) (value t) &rest args &key
+(defmethod add-vertex ((graph basic-graph) (value t) &rest args &key
(if-duplicate-do :ignore) &allow-other-keys)
(remf args :if-duplicate-do)
(let ((existing-vertex (find-vertex graph value nil)))
(if existing-vertex
(cond ((eq if-duplicate-do :ignore)
(values existing-vertex :ignore))
-
+
((eq if-duplicate-do :force)
(add-it :force))
-
+
((eq if-duplicate-do :replace)
(replace-vertex graph existing-vertex (make-it)))
-
+
((eq if-duplicate-do :replace-value)
(setf (element existing-vertex) value)
(values existing-vertex :replace-value))
-
+
+ ((eq if-duplicate-do :error)
+ (error "Attempting to insert a duplicate node in graph ~a" graph))
+
(t
(values (funcall if-duplicate-do existing-vertex)
:duplicate)))
-
+
;; not found, add
(add-it :new)))))
;; we need the graph and the new vertex to reference each other
;; we need every edge of the old vertex to use the new-vertex
;; we need to remove the old vertex
- ;;
+ ;;
;; since I'm tired today, let's ignore trying to make this elegant
-
+
;; first, we connect the edges to the new vertex so that they don't get deleted
;; when we delete the old vertex
- (iterate-edges
+ (iterate-edges
old
(lambda (e)
- (if (eq (vertex-1 e) old)
+ (if (eq (vertex-1 e) old)
(setf (slot-value e 'vertex-1) new) (setf (slot-value e 'vertex-2) new))
(add-edge-to-vertex e new)))
-
+
(delete-vertex graph old)
(add-vertex graph new))
;;; 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)
+(defmethod add-edge-between-vertexes ((graph basic-graph)
(v-1 basic-vertex) (v-2 basic-vertex)
- &rest args &key
+ &rest args &key
(value nil) (if-duplicate-do :ignore)
&allow-other-keys)
(declare (dynamic-extent args))
(remf args :if-duplicate-do)
-
+
(let ((edge (find-edge-between-vertexes graph v-1 v-2 :error-if-not-found? nil)))
(flet ((add-it (why)
- (values (add-edge
- graph
+ (values (add-edge
+ graph
(apply #'make-edge-for-graph graph v-1 v-2 args))
why)))
(if edge
- (cond
+ (cond
((eq if-duplicate-do :ignore)
(values edge :ignore))
-
+
((eq if-duplicate-do :force)
(add-it :force))
-
+
((eq if-duplicate-do :force-if-different-value)
(if (equal (value edge) value)
(values :ignore)
(add-it :force)))
-
-
+
+
((eq if-duplicate-do :replace)
(warn "replace edges isn't really implemented, maybe you can use :replace-value")
(delete-edge graph edge)
(add-it :replace))
-
+
((eq if-duplicate-do :replace-value)
(setf (element edge) value)
(values edge :replace-value))
-
+
(t
(setf edge (funcall if-duplicate-do edge))
(values edge :duplicate)))
-
+
;; not found, add
(add-it :new)))))
(unless (eq graph (graph vertex))
(error 'graph-vertex-not-found-error
:graph graph :vertex vertex))
-
- (iterate-edges
+
+ (iterate-edges
vertex
(lambda (edge)
(delete-edge graph edge)))
-
+
(empty! (vertex-edges vertex))
(values vertex graph))
-(defmethod delete-vertex :after ((graph basic-graph)
+(defmethod delete-vertex :after ((graph basic-graph)
(vertex basic-vertex))
(setf (slot-value vertex 'graph) nil)
(delete-item-at (graph-vertexes graph)
(defmethod adjacentp ((graph basic-graph) (vertex-1 basic-vertex) (vertex-2 basic-vertex))
- (iterate-neighbors
+ (iterate-neighbors
vertex-1
(lambda (vertex)
(when (eq vertex vertex-2)
(collect-elements (graph-vertexes graph))))
-(defmethod add-vertex :before ((graph basic-graph) (vertex basic-vertex)
+(defmethod add-vertex :before ((graph basic-graph) (vertex basic-vertex)
&key &allow-other-keys)
-
+
(assert (typep vertex (vertex-class graph)))
- (setf (item-at (graph-vertexes graph)
+ (setf (item-at (graph-vertexes graph)
(funcall (vertex-key graph) (element vertex))) vertex
(slot-value vertex 'graph) graph))
(iterate-vertexes
edge
(lambda (vertex)
- (when (funcall (vertex-test (graph edge))
+ (when (funcall (vertex-test (graph edge))
(funcall (vertex-key (graph edge)) (element vertex)) value)
(return-from find-vertex vertex))))
(when error-if-not-found?
(error "~A not found in ~A" vertex graph))))
(defmethod iterate-elements ((graph basic-graph) fn)
- (iterate-elements (graph-vertexes graph)
+ (iterate-elements (graph-vertexes graph)
(lambda (vertex) (funcall fn (element vertex)))))
(defmethod find-vertex-if ((graph basic-graph) fn &key key)
- (iterate-vertexes graph
+ (iterate-vertexes graph
(lambda (v)
- (when (funcall fn (if key (funcall key v) v))
+ (when (funcall fn (if key (funcall key v) v))
(return-from find-vertex-if v))))
(values nil))
root
(lambda (c)
(when (not (member c visited-list))
- (add-edge-between-vertexes
+ (add-edge-between-vertexes
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
+ (iterate-edges
graph
(lambda (edge)
(change-class edge (undirected-edge-class graph)))))
thing
(lambda (vertex)
(setf (tag vertex) marker)))
-
+
(iterate-elements
(graph-roots thing)
(lambda (vertex)
thing
(lambda (vertex)
(traverse-elements-helper vertex style marker fn)))
-
+
(funcall fn thing)))
(when (eq (tag thing) marker)
(setf (tag thing) nil)
(funcall fn thing))
-
+
(iterate-neighbors
thing
(lambda (vertex)
(when (eq (tag vertex) marker)
(funcall fn vertex))))
-
+
(iterate-neighbors
thing
(lambda (vertex)
&key (state= #'eql) old-states
(new-state-fn (error "argument required")))
"Find a state that satisfies goal-p. Start with states,
- and search according to successors and combiner.
+ and search according to successors and combiner.
Don't try the same state twice."
(cond ((null states) nil)
((funcall goal-p (first states)) (first states))
(defmethod in-cycle-p ((graph basic-graph) (start-vertex basic-vertex))
(let ((first-time? t))
(not (null
- (graph-search-for-cl-graph
+ (graph-search-for-cl-graph
(list start-vertex)
(lambda (v)
(if first-time?
(funcall successors (first states)))))))))
-(defmethod in-undirected-cycle-p
+(defmethod in-undirected-cycle-p
((graph basic-graph) (current basic-vertex)
&optional (marked (make-container 'simple-associative-container))
(previous nil))
(setf (item-at-1 marked current) t)
(iterate-children current
(lambda (child)
- (cond
+ (cond
((eq child previous) nil)
((item-at-1 marked child) (return-from do-it t))
(t
"Collects set of unique relatives of nodes in node-list."
(let ((unique-relatives nil))
(dolist (node node-list)
- (setf unique-relatives
+ (setf unique-relatives
(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
-in the transitive closure(s) of each of the vertices in the list
-(without duplicates). Optional DEPTH limits the depth (in _both_ the
-child and parent directions) to which the closure is gathered; default
+in the transitive closure(s) of each of the vertices in the list
+(without duplicates). Optional DEPTH limits the depth (in _both_ the
+child and parent directions) to which the closure is gathered; default
nil gathers the entire closure(s)."
(labels ((collect-transitive-closure (remaining visited depth)
- (if (and remaining
+ (if (and remaining
(typecase depth
(null t)
(fixnum (>= (decf depth) 0))))
-
+
(let* ((non-visited-relatives ;; list of relatives not yet visited
(remove-list visited
(get-nodelist-relatives remaining)))
;;; 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
-length"
+ "Apply fn to each path that starts at start-vertex and is of exactly length
+length"
;; a sort of depth first search
(labels ((follow-path (next-vertex current-path length)
(when (zerop length)
(funcall fn (reverse current-path)))
; (format t "~%~A ~A ~A" current-path next-vertex length)
(when (plusp length)
- (iterate-neighbors
+ (iterate-neighbors
next-vertex
(lambda (v)
(when (funcall filter v)
(unless (find-item current-path v)
(let ((new-path (copy-list current-path)))
(follow-path v (push v new-path) (1- length))))))))))
- (iterate-neighbors
+ (iterate-neighbors
start-vertex
(lambda (v)
(when (funcall filter v)
;;; project-bipartite-graph
-(defmethod 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
+(defmethod project-bipartite-graph
((new-graph basic-graph) graph vertex-class vertex-classifier)
(iterate-vertexes
graph
(lambda (v)
(when (eq (funcall vertex-classifier v) vertex-class)
(add-vertex new-graph (element v)))))
-
+
(iterate-vertexes
graph
(lambda (v)
(iterate-neighbors
v
(lambda (other-class-vertex)
- (iterate-neighbors
+ (iterate-neighbors
other-class-vertex
(lambda (this-class-vertex)
(when (< (vertex-id v) (vertex-id this-class-vertex))
- (add-edge-between-vertexes
+ (add-edge-between-vertexes
new-graph (element v) (element this-class-vertex)
:if-duplicate-do (lambda (e) (incf (weight e))))))))))))
-
+
new-graph)
-
+
#+Test
(pro:with-profiling
(setf (ds :g-5000-m-projection)
'undirected-graph-container
(ds :g-5000)
:m
- (lambda (v)
+ (lambda (v)
(let ((vertex-class (aref (symbol-name (element v)) 0)))
(cond ((member vertex-class '(#\a #\b) :test #'char-equal)
:m)
'undirected-graph-container
(ds :g-5000)
:h
- (lambda (v)
+ (lambda (v)
(let ((vertex-class (aref (symbol-name (element v)) 0)))
(cond ((member vertex-class '(#\a #\b) :test #'char-equal)
:m)
'undirected-graph-container
(ds :g-1000)
:m
- (lambda (v)
+ (lambda (v)
(let ((vertex-class (aref (symbol-name (element v)) 0)))
(cond ((member vertex-class '(#\x #\y) :test #'char-equal)
:m)
projects / cl-graph.git / commitdiff