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;;; suffiex-tree.el --- Ukkonen algorithm for building a suffix tree -*- lexical-binding: t; -*-
;; Our node is represented as a list with the following elements:
;; start,
;; which is the starting index of the edge going from its parent
;; node
;; end, the index of the end index
;; suffix-link, the index of the node its suffix-link points to
;; children,
;; a hash-table of pairs of integers and indices of its
;; children
;; To compute the length of the edge going into NODE we use:
;; (- (min end (1+ st-position)) start)
;; which is actually how far the position is on that edge,
;; if it is on that edge.
;;;###autoload
(defun st-min (&rest args)
"Return the minimum among ARGS.
If an argument is 'infty, then it is considered greater than
every number."
(apply #'min (delq nil
(mapcar
(lambda (arg)
(cond
((number-or-marker-p arg) arg)
((eq arg 'infty) nil)))
args))))
;;;###autoload
(defun st-edge-length (node position)
"Return the length of the edge into NODE.
See the comment above this function for the reason
POSITION is here."
(- (st-min (car (cdr node)) (1+ position))
(car node)))
;;;###autoload
(defun st-new-node (tree last-added start &optional end)
"Make a new node with START and END as the coming edge.
Then add the new node to TREE.
LAST-ADDED is the number of elements already in the TREE."
(let* ((end (or end 'infty) ;; 'infty represents the index of a leaf
)
(suffix-link 0) ;; The suffix link is initially 0
(new-node
(list start end
suffix-link
(make-hash-table))))
(puthash (1+ last-added) new-node tree)
(1+ last-added)))
;;;###autoload
(defun st-add-suffix-link (tree need-sl node)
"If NEED-SL is positive, then add the suffix link.
In particular, the node corresponding to NEED-SL in TREE
gets a suffix link pointing to NODE.
This always returns NODE."
(cond
((> need-sl 0)
(setcar (cdr (cdr (gethash need-sl tree))) node)))
node)
;;;###autoload
(defun st-canonize (tree node position active-edge-index active-length active-node)
"Walk down TREE to find the correct active point."
(let ((node-edge-length (st-edge-length (gethash node tree) position)))
(cond
((>= active-length node-edge-length)
(list t
(+ active-edge-index
node-edge-length)
(- active-length
node-edge-length)
node))
(t
(list nil
active-edge-index
active-length
active-node)))))
;;; For review later
;;;###autoload
;; (defun st-init)
;; {
;; needSL = 0, last_added = 0, pos = -1,
;; remainder = 0, active_node = 0, active_e = 0, active_len = 0;
;; root = active_node = new_node(-1, -1);
;; }
;;;###autoload
(defun st-extend-tree (tree last-added position remain
active-node active-edge-index
active-length character str)
"Extend a tree by CHARACTER.
The return value is
(tree last-added remain active-node
active-edge-index active-length)"
(let* ((need-sl 0)
(remain (1+ remain))
continue-p breakp)
(while (and (not breakp) (> remain 0))
(cond
((= active-length 0)
(setq active-edge-index position)))
(let* ((actual-node (gethash active-node tree))
(nxt (cond
(actual-node
(gethash (aref str active-edge-index)
(cadr (cdr (cdr actual-node))))))))
;; (cond ((null actual-node) (user-error "active-node: %S" active-node)))
;; (message "aei: %S" active-edge-index)
;; (message "act: %S" (gethash active-node tree))
(cond
((null nxt)
(let ((leaf (st-new-node tree last-added position)))
(setq last-added leaf)
(puthash (aref str active-edge-index)
leaf
(cadr (cdr (cdr (gethash active-node tree)))))
(setq need-sl (st-add-suffix-link tree need-sl active-node))
;; rule 2
))
(t
(let* ((result (st-canonize
tree nxt position active-edge-index
active-length active-node)))
(cond
((car result)
;; observation 2
(setq active-edge-index (cadr result))
(setq active-length (caddr result))
(setq active-node (cadr (cddr result)))
(setq continue-p t))
(t
(cond
((eq (aref str (+ active-length
(car (gethash nxt tree))))
character)
;; observation 1
(setq active-length (1+ active-length))
(setq need-sl (st-add-suffix-link tree need-sl active-node))
(setq breakp t)))
(cond
(breakp)
(t ;; splitting
(let ((split (st-new-node
tree last-added (car (gethash nxt tree))
(+ (car (gethash nxt tree)) active-length))))
(setq last-added split)
(puthash
(aref str active-edge-index)
split (cadr (cdr (cdr (gethash active-node tree)))))
(let ((leaf (st-new-node tree last-added position)))
(setq last-added leaf)
(puthash character leaf
(cadddr (gethash split tree)))
(setcar (gethash nxt tree)
(+ (car (gethash nxt tree))
active-length))
(puthash (aref str (car (gethash nxt tree))) nxt
(cadddr (gethash split tree)))
;; rule 2
(setq need-sl
(st-add-suffix-link tree need-sl split)))))))))))
(cond
((or continue-p breakp))
(t
(setq remain (1- remain))
(cond
((and (eq active-node 1) ; root
(> active-length 0))
(setq active-length (1- active-length))
(setq active-edge-index
(1+ (- position remain))))
(t
(setq active-node
(let ((slink (caddr (gethash active-node tree))))
(cond
((> slink 0) slink)
; or root
(t 1))))))))))
;; (message "remain is %d" remain)
(list tree last-added remain active-node
active-edge-index active-length)))
;;;###autoload
(defun st-build-for-str (str)
"Build the suffix tree for STR."
(let* ((position 0)
(character (ignore-error 'error (aref str position)))
(tree (make-hash-table))
(last-added 0)
(remain 0)
(active-node (st-new-node tree last-added -1 -1))
(active-edge-index 0)
(active-length 0)
result)
(setq last-added active-node)
(while character
(setq result (st-extend-tree tree last-added position remain
active-node active-edge-index
active-length character str))
(setq tree (pop result))
(setq last-added (pop result))
(setq remain (pop result))
(setq active-node (pop result))
(setq active-edge-index (pop result))
(setq active-length (pop result))
(setq position (1+ position))
(setq character (ignore-error 'error (aref str position))))
tree))
;;;###autoload
(defun st-print-tree-for-str (str)
"Print the suffix tree for STR."
(let* ((symbol (make-symbol "test")))
(set symbol (st-build-for-str str))
(insert "suffix tree for \"" str "\"" "\n")
(st-print-tree (symbol-value symbol) str)))
;;;###autoload
(defun st-print-tree (tree str)
"Print TREE with the aid of STR."
(let* ((symbol-tree (make-symbol "test-tree")))
(set symbol-tree (hierarchy-new))
(maphash
(lambda (key value)
(hierarchy-add-tree
(symbol-value symbol-tree) key nil
(lambda (item)
(hash-table-values (cadr (cdr (cdr (gethash item tree))))))))
tree)
(hierarchy-print (symbol-value symbol-tree)
(lambda (item)
(cond ((= item 1) "root")
(t (let ((node (gethash item tree)))
(substring str (car node) (cond ((integerp (cadr node)) (cadr node)))))))))))
;;; Some printing functions
(use-package "hierarchy" 'hierarchy)
;; ;;;###autoload
;; (defvar st-output-buffer-name "*suffix-tree*"
;; "The name of the buffer that contains the output.")
;; ;;;###autoload
;; (defun st-print-tree (tree node str prefix)
;; "Print TREE in the dedicated output buffer starting at NODE.
;; PREFIX is used to recursively call this function.
;; We need STR since the information we stored in the tree
;; only contains the index into STR,
;; for the sake of optimizations."
;; (with-temp-buffer-window st-output-buffer-name '((display-buffer-at-bottom)) nil
;; (st-print-tree-internal tree node str prefix)))
;; ;;;###autoload
;; (defun st-print-tree-internal (tree node str prefix)
;; "The function that really prints out the data."
;; (let* ((node-data (gethash node tree))
;; (start (car node-data))
;; (end (cadr node-data))
;; (edges (cdddr node-data))
;; (node-num (format "(%d)" node))
;; (node-label (format "%s-%s-%s"
;; prefix node-num
;; (substring str start end))))
;; (prin1 node-label)
;; ;; print the first edge
;; (let* ((prefix-base (concat
;; prefix
;; (make-string (length node-label) 32)))
;; ;; TODO
;; ))))
(provide 'suffix-tree)
;;; suffiex-tree.el ends here.
;;; archive
;; ;;;###autoload
;; (defvar st-root nil
;; "The root of the suffix tree.")
;; ;;;###autoload
;; (defvar st-position nil
;; "The current position in the string.")
;; ;;;###autoload
;; (defvar st-wait-for-link nil
;; "The node that is waiting to have a suffix link.")
;; ;;;###autoload
;; (defvar st-remain nil
;; "The number of remaining suffixes to insert.")
;; ;;;###autoload
;; (defvar st-active-node nil
;; "Where to insert a new suffix.")
;; ;;;###autoload
;; (defvar st-active-edge-index nil
;; "The index of the active edge.")
;; ;;;###autoload
;; (defvar st-active-length nil
;; "How far down is the active point down the active edge.")
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