;;; essd-jags.el -- ESS[JAGS] dialect

;; Copyright (C) 2008-2009 Rodney Sparapani

;; Original Author: Rodney Sparapani
;; Created: 13 March 2008
;; Maintainers: ESS-help <ess-help@stat.math.ethz.ch>

;; This file is part of ESS

;; This file is free software; you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation; either version 2, or (at your option)
;; any later version.
;;
;; This file is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;; GNU General Public License for more details.
;;
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs; see the file COPYING.  If not, write to
;; the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.
;;
;; In short: you may use this code any way you like, as long as you
;; don't charge money for it, remove this notice, or hold anyone liable
;; for its results.

;; Code:

(require 'essl-bugs)
(require 'ess-utils)
(require 'ess-inf)

(setq auto-mode-alist
    (delete '("\\.[bB][uU][gG]\\'" . ess-bugs-mode) auto-mode-alist))

(setq auto-mode-alist
    (append '(("\\.[bB][uU][gG]\\'" . ess-jags-mode)) auto-mode-alist))

(defvar ess-jags-command "jags" "Default JAGS program in PATH.")
(make-local-variable 'ess-jags-command)

(defvar ess-jags-monitor '("") "Default list of variables to monitor.")
(make-local-variable 'ess-jags-monitor)

(defvar ess-jags-thin 1 "Default thinning parameter.")
(make-local-variable 'ess-jags-thin)

(defvar ess-jags-chains 1 "Default number of chains.")
(make-local-variable 'ess-jags-chains)

(defvar ess-jags-burnin 10000 "Default burn-in.")
(make-local-variable 'ess-jags-burnin)

(defvar ess-jags-update 10000 "Default number of updates after burnin.")
(make-local-variable 'ess-jags-update)

(defvar ess-jags-system t "Default whether JAGS recognizes the system command.")

(defvar ess-jags-font-lock-keywords
    (list
	;; .bug files
	(cons "#.*\n"			font-lock-comment-face)

	(cons "^[ \t]*\\(model\\|var\\)\\>"
					font-lock-keyword-face)

	(cons (concat "\\<d\\(bern\\|beta\\|bin\\|cat\\|chisq\\|"
		"dexp\\|dirch\\|exp\\|\\(gen[.]\\)?gamma\\|hyper\\|"
		"interval\\|lnorm\\|logis\\|mnorm\\|mt\\|multi\\|"
		"negbin\\|norm\\(mix\\)?\\|par\\|pois\\|sum\\|t\\|"
		"unif\\|weib\\|wish\\)[ \t\n]*(")
					font-lock-constant-face)

	(cons (concat "\\<\\(abs\\|cos\\|dim\\|\\(i\\)?cloglog\\|equals\\|"
		"exp\\|for\\|inprod\\|interp[.]line\\|inverse\\|length\\|"
		"\\(i\\)?logit\\|logdet\\|logfact\\|loggam\\|max\\|mean\\|"
		"mexp\\|min\\|phi\\|pow\\|probit\\|prod\\|rank\\|round\\|"
		"sd\\|sin\\|sort\\|sqrt\\|step\\|sum\\|t\\|trunc\\|T\\)[ \t\n]*(")
					font-lock-function-name-face)

	;; .jmd files
	(cons (concat "\\<\\(adapt\\|cd\\|clear\\|coda\\|data\\|dir\\|"
		"exit\\|in\\(itialize\\)?\\|load\\|model\\|monitors\\|parameters\\|"
		"pwd\\|run\\|s\\(amplers\\|ystem\\)\\|to\\|update\\)[ \t\n]")
					font-lock-keyword-face)

	(cons "\\<\\(compile\\|monitor\\)[, \t\n]"
					font-lock-keyword-face)

	(cons "[, \t\n]\\(by\\|chain\\|nchains\\|stem\\|thin\\|type\\)[ \t\n]*("
					font-lock-function-name-face)
    )
    "ESS[JAGS]: Font lock keywords."
)

(defun ess-jags-switch-to-suffix (suffix &optional jags-chains jags-monitor jags-thin
   jags-burnin jags-update)
   "ESS[JAGS]: Switch to file with suffix."
   (find-file (concat ess-bugs-file-dir ess-bugs-file-root suffix))

   (if (equal 0 (buffer-size)) (progn
	(if (equal ".bug" suffix) (progn
	    (insert "var ;\n")
	    (insert "model {\n")
            (insert "    for (i in 1:N) {\n    \n")
            (insert "    }\n")
            (insert "}\n")
	    (insert "#Local Variables" ":\n")
	    (insert "#ess-jags-chains:1\n")
	    (insert "#ess-jags-monitor:(\"\")\n")
	    (insert "#ess-jags-thin:1\n")
	    (insert "#ess-jags-burnin:10000\n")
	    (insert "#ess-jags-update:10000\n")
	    (insert "#End:\n")
	))

	(if (equal ".jmd" suffix) (let
	    ((ess-jags-temp-chains "") (ess-jags-temp-monitor "") (ess-jags-temp-chain ""))

	    (if jags-chains (setq ess-jags-chains jags-chains))
	    (if jags-monitor (setq ess-jags-monitor jags-monitor))
	    (if jags-thin (setq ess-jags-thin jags-thin))

	    (setq ess-jags-temp-chains
		(concat "compile, nchains(" (format "%d" ess-jags-chains) ")\n"))

	    (setq jags-chains ess-jags-chains)

	    (while (< 0 jags-chains)
		(setq ess-jags-temp-chains
		    (concat ess-jags-temp-chains
			"parameters ## \"" ess-bugs-file-root
			".##" (format "%d" jags-chains) "\", chain("
			(format "%d" jags-chains) ")\n"))
		(setq jags-chains (- jags-chains 1)))

	    (setq ess-jags-temp-monitor "")

		(while (and (listp ess-jags-monitor) (consp ess-jags-monitor))
		    (if (not (string-equal "" (car ess-jags-monitor)))
			(setq ess-jags-temp-monitor
			    (concat ess-jags-temp-monitor "monitor "
				(car ess-jags-monitor) ", thin(" (format "%d" ess-jags-thin) ")\n")))
		    (setq ess-jags-monitor (cdr ess-jags-monitor)))

	    (insert "model in \"" ess-bugs-file-root ".bug\"\n")
	    (insert "data in \"" ess-bugs-file-root ".txt\"\n")
	    (insert (ess-replace-in-string ess-jags-temp-chains "##" "in"))
	    (insert "initialize\n")
	    (insert "update " (format "%d" (* jags-thin jags-burnin)) "\n")
	    (insert ess-jags-temp-monitor)
	    (insert "update " (format "%d" (* jags-thin jags-update)) "\n")
	    (insert (ess-replace-in-string
		(ess-replace-in-string ess-jags-temp-chains
		    "compile, nchains([0-9]+)" "#") "##" "to"))
	    (insert "coda "
		(if ess-microsoft-p (if (w32-shell-dos-semantics) "*" "\\*") "\\*")
		", stem(\"" ess-bugs-file-root "\")\n")

	    (if ess-jags-system (progn
		(insert "system rm -f " ess-bugs-file-root ".ind\n")
		(insert "system ln -s " ess-bugs-file-root "index.txt " ess-bugs-file-root ".ind\n")

		(setq jags-chains ess-jags-chains)

		(while (< 0 jags-chains)
		    (setq ess-jags-temp-chain (format "%d" jags-chains))

		    ;.txt not recognized by BOA and impractical to over-ride
		    (insert "system rm -f " ess-bugs-file-root ess-jags-temp-chain ".out\n")
		    (insert "system ln -s " ess-bugs-file-root "chain" ess-jags-temp-chain ".txt "
			ess-bugs-file-root ess-jags-temp-chain ".out\n")
		    (setq jags-chains (- jags-chains 1)))))

	    (insert "exit\n")
	    (insert "Local Variables" ":\n")
	    (insert "ess-jags-chains:" (format "%d" ess-jags-chains) "\n")
	    (insert "ess-jags-command:\"jags\"\n")
	    (insert "End:\n")
	))
    ))
)

(defun ess-bugs-next-action ()
   "ESS[JAGS]: Perform the appropriate next action."
   (interactive)
   (ess-bugs-file)

   (if (equal ".bug" ess-bugs-file-suffix) (ess-jags-na-bug)
   ;;else
   (if (equal ".jmd" ess-bugs-file-suffix) (progn
	(ess-save-and-set-local-variables)
	(ess-jags-na-jmd ess-jags-command ess-jags-chains))))
)

(defun ess-jags-na-jmd (jags-command jags-chains)
    "ESS[JAGS]: Perform the Next-Action for .jmd."
    ;(ess-save-and-set-local-variables)
(if (equal 0 (buffer-size)) (ess-jags-switch-to-suffix ".jmd")
;else
    (shell)

    (if (w32-shell-dos-semantics)
	(if (string-equal ":" (substring ess-bugs-file 1 2))
	    (progn
		(insert (substring ess-bugs-file 0 2))
		(comint-send-input)
	    )
	)
    )

	(insert "cd \"" ess-bugs-file-dir "\"")
	(comint-send-input)

;    (let ((ess-jags-temp-chains ""))
;
;	(while (< 0 jags-chains)
;	    (setq ess-jags-temp-chains
;		(concat (format "%d " jags-chains) ess-jags-temp-chains))
;	    (setq jags-chains (- jags-chains 1)))

	(insert ess-bugs-batch-pre-command " " jags-command " "
		ess-bugs-file-root ".jmd "

		(if (or (equal shell-file-name "/bin/csh")
			(equal shell-file-name "/bin/tcsh")
			(equal shell-file-name "/bin/zsh"))
			    (concat ">& " ess-bugs-file-root ".jog ")
		;else
			    "> " ess-bugs-file-root ".jog 2>&1 ")

;		;.txt not recognized by BOA and impractical to over-ride
;		"&& (rm -f " ess-bugs-file-root ".ind; "
;		"ln -s " ess-bugs-file-root "index.txt " ess-bugs-file-root ".ind; "
;		"for i in " ess-jags-temp-chains "; do; "
;		"rm -f " ess-bugs-file-root "$i.out; "
;		"ln -s " ess-bugs-file-root "chain$i.txt " ess-bugs-file-root "$i.out; done) "

		ess-bugs-batch-post-command)

	(comint-send-input)
));)

(defun ess-jags-na-bug ()
    "ESS[JAGS]: Perform Next-Action for .bug"

	(if (equal 0 (buffer-size)) (ess-jags-switch-to-suffix ".bug")
	;else
	    (ess-save-and-set-local-variables)
	    (ess-jags-switch-to-suffix ".jmd"
		ess-jags-chains ess-jags-monitor ess-jags-thin ess-jags-burnin ess-jags-update))
)

(defun ess-jags-mode ()
   "ESS[JAGS]: Major mode for JAGS."
   (interactive)
   (kill-all-local-variables)
   (ess-setq-vars-local '((comment-start . "#")))
   (setq major-mode 'ess-jags-mode)
   (setq mode-name "ESS[JAGS]")
   (use-local-map ess-bugs-mode-map)
   (setq font-lock-auto-fontify t)
   (make-local-variable 'font-lock-defaults)
   (setq font-lock-defaults '(ess-jags-font-lock-keywords nil t))
   (run-hooks 'ess-bugs-mode-hook)

   (if (not (w32-shell-dos-semantics))
	(add-hook 'comint-output-filter-functions 'ess-bugs-exit-notify-sh))
)

(setq features (delete 'essd-bugs features))
(provide 'essd-jags)