(if (functionp 'tool-bar-mode) (tool-bar-mode 0))
(if (functionp 'scroll-bar-mode) (scroll-bar-mode -1))
(menu-bar-mode 0)
(setq inhibit-startup-screen t)
(show-paren-mode 1)
;;c-mode indentation
(add-hook 'c-mode-hook
	  (lambda () 
	    (c-set-style "bsd")
	    (setq c-basic-offset 4)))
(add-to-list 'load-path "~/share/emacs/site-lisp")
(autoload #'espresso-mode "espresso" "Start espresso-mode" t)
(add-to-list 'auto-mode-alist '("\\.js$" . espresso-mode))
(add-to-list 'auto-mode-alist '("\\.json$" . espresso-mode))
;; TeX
;(autoload 'tex-mode "tex-site.el" "AucTeX" t)
;(autoload 'tex-mode "preview-latex.el" "preview-LaTeX" t)
(setq TeX-PDF-mode t)
(load "auctex" t)
(if (load "auctex/tex" t)
    (add-to-list 'TeX-output-view-style '("^pdf$" "." "evince %o")))
(load "preview-latex" t)
(defun evince-pdf ()
  "homebrew view pdf, convenient from latex"
  (interactive)
  ;;(expand-file-name "~/foo")
  ;;(shell-quote-argument "some file with spaces")
  (shell-command
   (concat "okular " (file-name-sans-extension (buffer-file-name)) ".pdf &"))
)
(global-set-key [f10] 'evince-pdf)

;;read local config first
(setq my-local-config "~/local.el")
(if (file-readable-p my-local-config) (load my-local-config))

(setq TeX-auto-save t)
(setq TeX-parse-self t)
;; add to local inria config:
;; (add-to-list 'TeX-expand-list 
;;   '("%(mode)" (lambda nil (if TeX-interactive-mode ""
;;      " -interaction nonstopmode -file-line-error "))))
;;(setq-default TeX-master nil)

(defun translate ()
  "Translate the word at point using WordReference."
  (interactive)
  (browse-url (concat "http://www.wordreference.com/fren/" 
		      (thing-at-point 'word)))
)
(setq c-auto-newline nil)
(global-set-key [f9] 'compile)
(setq compilation-scroll-output t)
(setq compile-command "make ")
(setq compilation-read-command nil)
(global-set-key "\C-x\C-m" 'translate)
(global-set-key "\M-s" 'isearch-forward-regexp)
(global-set-key "\M-r" 'isearch-backward-regexp)

(defalias 'qrr 'query-replace-regexp)
;;(load "gnuserv")
;;(gnuserv-start)
;;(setq gnuserv-frame (car (frame-list)))
;; mozex docs: http://mozex.mozdev.org/arguments.html

;;; uncomment this line to disable loading of "default.el" at startup
;; (setq inhibit-default-init t)

;; turn on font-lock mode
(when (fboundp 'global-font-lock-mode)
  (global-font-lock-mode t))

;; default to better frame titles
(setq frame-title-format
      (concat  "%b - emacs@" system-name))

;; default to unified diffs
(setq diff-switches "-u")

;;orgmode
(add-to-list 'auto-mode-alist '("\\.org$" . org-mode))

;;ess-mode NOTE: if site-wide file is present, it is read first, and
;;if it loads ess, then the following code will not do anything!
;;Furthermore, if we need to load user-specific ESS, then we need to
;;start emacs with --no-site-file or (unload-feature ...) here
(autoload 'R "ess-site.el" "ESS" t)
(autoload 'R-mode "ess-site.el" "ESS" t)
(autoload 'r-mode "ess-site.el" "ESS" t)
(autoload 'Rd-mode "ess-site.el" "ESS" t)
(autoload 'noweb-mode "ess-site.el" "ESS" t)
(add-to-list 'auto-mode-alist '("\\.R$" . R-mode))
(add-to-list 'auto-mode-alist '("\\.r$" . R-mode))
(add-to-list 'auto-mode-alist '("\\.Rd$" . Rd-mode))
(add-to-list 'auto-mode-alist '("\\.Rnw$" . noweb-mode))
(setq ess-eval-visibly-p nil)
(setq ess-ask-for-ess-directory nil)
(require 'ess-eldoc "ess-eldoc" t)
; as defined in install-r-dev.sh, we install ESS to ~/R/ess-svn
(add-to-list 'load-path "~/R/ess-svn/lisp")
;(require 'ess-tracebug "ess-tracebug" t)
;(add-hook 'ess-post-run-hook 'ess-tracebug t)

;;ruby
(autoload 'ruby-mode "ruby-mode")
(load "inf-ruby" t)
(add-to-list 'auto-mode-alist '("\\.rb$" . ruby-mode))
(defun inf-ruby-keys ()
  "Set local key defs for inf-ruby in ruby-mode"
  (define-key ruby-mode-map "\M-\C-x" 'ruby-send-definition)
;  (define-key ruby-mode-map "\C-x\C-e" 'ruby-send-last-sexp)
  (define-key ruby-mode-map "\C-c\C-b" 'ruby-send-block)
  (define-key ruby-mode-map "\C-c\M-b" 'ruby-send-block-and-go)
  (define-key ruby-mode-map "\C-c\C-x" 'ruby-send-definition)
  (define-key ruby-mode-map "\C-c\M-x" 'ruby-send-definition-and-go)
  (define-key ruby-mode-map "\C-c\C-r" 'ruby-send-region)
  (define-key ruby-mode-map "\C-c\M-r" 'ruby-send-region-and-go)
  (define-key ruby-mode-map "\C-c\C-z" 'switch-to-ruby)
  (define-key ruby-mode-map "\C-c\C-l" 'ruby-load-file)
  (define-key ruby-mode-map "\C-c\C-s" 'run-ruby)
)
   (add-hook 'ruby-mode-hook
         '(lambda ()
            (inf-ruby-keys)
   ))

;; opa web application language
(autoload 'opa-js-mode "opa-js-mode.el" "OPA JS editing mode." t)
(autoload 'opa-classic-mode "opa-mode.el" "OPA CLASSIC editing mode." t)
(add-to-list 'auto-mode-alist '("\\.opa$" . opa-js-mode))
(add-to-list 'auto-mode-alist '("\\.js\\.opa$" . opa-js-mode))
(add-to-list 'auto-mode-alist '("\\.classic\\.opa$" . opa-classic-mode))

;;matlab
(autoload 'matlab-mode "matlab" "Enter MATLAB mode." t)
(setq auto-mode-alist (cons '("\\.m\\'" . matlab-mode) auto-mode-alist))
(autoload 'matlab-shell "matlab" "Interactive MATLAB mode." t)

;;mew
(setq mew-search-method 'est)
(autoload 'mew "mew" nil t)

;;diary and calendar
(setq mark-diary-entries-in-calendar t)
(defun getcal (url)
  "Download ics file and add to diary"
  (let ((tmpfile (url-file-local-copy url)))
    (icalendar-import-file tmpfile "~/diary" t)
    (kill-buffer (car (last (split-string tmpfile "/"))))
    )
)
(setq google-calendars '(
"http://www.google.com/calendar/ical/1bdkfnl39jd0a10vodi28801no%40group.calendar.google.com/public/basic.ics" ;the biology of cancer reading group
"http://www.google.com/calendar/ical/5gonmk23vveccgfg28gqn9bq1g%40group.calendar.google.com/private-b37faa7b9f13bcac7f62eeaaaf3d0dbb/basic.ics" ;u900 life
"http://www.google.com/calendar/ical/po457fh71hehgk6ocl8jpbc5g4%40group.calendar.google.com/private-a40c97623a08cdeb2fbbc4d1c44f415f/basic.ics" ;machine learning reading group
"http://www.google.com/calendar/ical/096brb9u34b3afdkbk2op85828%40group.calendar.google.com/private-a57e4a937d7060b0d1c955b3393849a3/basic.ics" ;biostat meeting
"http://www.google.com/calendar/ical/ni4a8ikjnom3m1islsi1agtqdg%40group.calendar.google.com/private-2f7dd4195942d2af7f86865d7f373906/basic.ics" ;NGS bioinfo
"http://www.google.com/calendar/ical/bb4sp61sjut180j51lmei5jen4%40group.calendar.google.com/private-ced8869a44be5b733e124a47a9007511/basic.ics" ;sysbio meeting
"http://www.google.com/calendar/ical/g46ao0ssoj9pcqaua0b1rgj2ho%40group.calendar.google.com/private-d122ef801a26afe52a8c9816883e84d1/basic.ics" ;BioIT
"http://www.google.com/calendar/ical/1jd8unhc4fr2a799nb46cdfdrk%40group.calendar.google.com/private-73065e313dc01f9e614ffb250a8898c9/basic.ics" ;Biostat tech watch
"http://www.google.com/calendar/ical/j2nqdnhmvr7km16hcup4t39n78%40group.calendar.google.com/private-ad05f94be827208e25089ff488ca6756/basic.ics" ;RPPA platform meetings
"http://www.google.com/calendar/ical/vm0nrt08bce35rks0qa77kfboc%40group.calendar.google.com/private-b87d1d8db9fa5c6808dadc47d7e10650/basic.ics" ;Affy transfert meetings
"http://www.google.com/calendar/ical/u8ogks4el7tch7t1t2mvhgf9cc%40group.calendar.google.com/private-0ee6269194300afcce520781e4f377a4/basic.ics" ;UGS
"http://www.google.com/calendar/ical/cpu6pkijm0umfptb3iq406h3gk%40group.calendar.google.com/private-bd69bf896d14c3f0aa17f97616c1aa90/basic.ics" ;confs
))
(defun getcals ()
  (find-file "~/diary")
  (flush-lines "^[& ]")
  (dolist (url google-calendars) (getcal url))
  (kill-buffer "diary"))
;;(getcals)

;;super-python mode
;(if (require 'pymacs "pymacs" t)
;    (pymacs-load "ropemacs" "rope-"))

;;svn-in-emacs mode
(load "psvn" t)
(setq vc-follow-symlinks t)

;;common lisp setup assumes you have slime from cvs here:
(add-to-list 'load-path "~/lisp/slime")
;cvs -d :pserver:anonymous:anonymous@common-lisp.net:/project/slime/cvsroot co slime
(setq inferior-lisp-program "clisp")
(if (require 'slime "slime" t)
    (slime-setup '(slime-fancy)))

;;experimental stuff
(message "Start clojure-mode code")
(add-to-list 'load-path "~/lisp/clojure-mode")
(load "clojure-mode" t)
;(add-hook 'slime-repl-mode-hook 'clojure-mode-font-lock-setup)
;(setq inferior-lisp "clojure")
;(load "lush/lush" t)
;;adds dev version to the path, sometimes autoloaded
;(slime-setup '(slime-repl))
;(add-hook 'slime-repl-mode-hook 'clojure-mode-font-lock-setup)
(message "End clojure-mode code")

;elisp
(add-hook 'emacs-lisp-mode-hook 'turn-on-eldoc-mode)
(custom-set-variables
  ;; custom-set-variables was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
 '(org-agenda-files (quote ("/nas/home1/h/hocking/bioviz/test.org")))
 '(safe-local-variable-values (quote ((noweb-code-mode . R-mode) (noweb-default-code-mode . R-node) (noweb-default-code-mode . R) (TeX-master . 2011-06-09-HOCKING-development) (TeX-master . 2011-06-09-HOCKING-development\.tex) (noweb-default-code-mode . R-mode) (gdb-many-windows . 1)))))
(custom-set-faces
  ;; custom-set-faces was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
 )

(put 'downcase-region 'disabled nil)


;;; This was installed by package-install.el.
;;; This provides support for the package system and
;;; interfacing with ELPA, the package archive.
;;; Move this code earlier if you want to reference
;;; packages in your .emacs.
;(when
;    (load
;     (expand-file-name "~/.emacs.d/elpa/package.el"))
;  (package-initialize))


;;sweave mode auto make
;; (defun pgfsweave ()
;;   "Run pgfsweave on the file of the current buffer"
;;   (interactive)
;;   (compile
;;    (concat "R CMD pgfsweave "
;; 	   (file-name-sans-extension buffer-file-name))
;;    t))
;; ; hit f11 to compile a pgfsweave file
;; (global-set-key [f11] 'pgfsweave)
; compilation buffer scrolling
(put 'narrow-to-region 'disabled nil)