.emacs file

;; Are we running XEmacs or Emacs?
(defvar running-xemacs (string-match "XEmacs\\|Lucid" emacs-version))

;; disable menu bar when running in terminal
(when (not (display-graphic-p))
  (menu-bar-mode -1))

;;My libraries, ebib, wordcount etc
(add-to-list 'load-path "~/.emacs-lisp/")


;;;;;;;;;;;;;;;
;; emacs IDE ;;
;;;;;;;;;;;;;;;
;;  (package-initialize)
;;  (eide-start)

(add-to-list 'load-path "/home/terdon/.emacs-lisp/Emacs-PDE-0.2.16/lisp")
;;(load "pde-load")
(load "imenu-tree")
;; (setq pde-extra-setting t)


;; ;; Load imenu automatically in CPerl mode
;; (add-hook 'cperl-mode-hook 'imenu-tree)


;; (add-to-list 'load-path "~/.emacs.d/elpa/archives")
;; (add-to-list 'load-path "~/.emacs.d/elpa/auto-complete-20160310.2248")
;; (add-to-list 'load-path "~/.emacs.d/elpa/eide-2.1.1")
;; (add-to-list 'load-path "~/.emacs.d/elpa/gnupg")
;; (add-to-list 'load-path "~/.emacs.d/elpa/log4e-20150105.505")
;; (add-to-list 'load-path "~/.emacs.d/elpa/plsense-20151104.645")
;; (add-to-list 'load-path "~/.emacs.d/elpa/popup-20151222.1339")
;; (add-to-list 'load-path "~/.emacs.d/elpa/yaxception-20150105.652")

;; (require 'plsense)
;; (require 'auto-complete-config)
;; (ac-config-default)


;; ;; Key binding
;; (setq plsense-popup-help-key "C-:")
;; (setq plsense-display-help-buffer-key "M-:")
;; (setq plsense-jump-to-definition-key "C->")

;; ;; Make config suit for you. About the config item, eval the following sexp.
;; ;; (customize-group "plsense")

;; ;; Do setting recommemded configuration
;; (plsense-config-default)


;;;;;;;;;;;;;;;;;;;;;
;; Disable toolbar ;;
;;;;;;;;;;;;;;;;;;;;;
(tool-bar-mode -1)

;;;;;;;;;;;;;;;;;;;;;;
;; Disable the bell ;;
;;;;;;;;;;;;;;;;;;;;;;
(setq ring-bell-function 'ignore)

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Set the autosave interval to 30 minutes ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(setq auto-save-timeout 1800)

;;;;;;;;;;;;;;;;;;;;
;; Start a server ;;
;;;;;;;;;;;;;;;;;;;;
;;(server-start)


;; use Shift+arrow_keys to move cursor around split panes
(windmove-default-keybindings)

;; when cursor is on edge, move to the other side, as in a torus space
(setq windmove-wrap-around t )


;;;;;;;;;;;;;;;;;;;;;
;; Tabs or spaces? ;;
;;;;;;;;;;;;;;;;;;;;;
(setq-default tab-width 2)
(setq-default indent-tabs-mode t)
(defvaralias 'c-basic-offset 'tab-width)
(defvaralias 'cperl-indent-level 'tab-width)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Enable installing packages from melpa.org ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(require 'package) ;; You might already have this line
(add-to-list 'package-archives
             '("melpa" . "http://melpa.org/packages/") t)
(when (< emacs-major-version 24)
  ;; For important compatibility libraries like cl-lib
  (add-to-list 'package-archives '("gnu" . "http://elpa.gnu.org/packages/")))
(package-initialize) ;; You might already have this line


;; ===== Make Text mode the default mode for new buffers =====
;;(setq major-mode 'text-mode)
;; ===== Make markdown mode the default mode for new buffers =====
(setq major-mode 'markdown-mode)

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

(define-key global-map "\C-cl" 'org-store-link)
(define-key global-map "\C-ca" 'org-agenda)
(setq org-log-done t)



;; disable blinking cursor
(blink-cursor-mode 0)

;; Interpret ANSI color escape codes
(add-hook 'shell-mode-hook 'ansi-color-for-comint-mode-on)

;; Set up the keyboard so the delete key on both the regular keyboard
;; and the keypad delete the character under the cursor and to the right
;; under X, instead of the default, backspace behavior.
(global-set-key [delete] 'delete-char)
(global-set-key [kp-delete] 'delete-char)
(global-set-key "\C-cc" 'comment-region)
(global-set-key "\C-cb" 'comment-box)
(global-set-key "\C-cu" 'uncomment-region)
(global-set-key "\C-cr" 'query-replace)
(global-set-key "\M-gg" 'goto-line)
(global-set-key "\C-ci" 'ebib-insert-bibtex-key)
;; (global-set-key "\C-ce" 'ecb-activate)

;;; Compare windows
(global-set-key "\C-cw" 'compare-windows)
;;; Rebind `C-x C-b' for `buffer-menu'
(global-set-key "\C-x\C-b" 'buffer-menu)
;; Turn on font-lock mode for Emacs
(cond ((not running-xemacs)
       (global-font-lock-mode t)
))
;; use all spaces, no tabs for indentation
;;(setq-default indent-tabs-mode nil)

;; delete with backspace and delete
(delete-selection-mode t)
(add-hook 'LaTeX-mode-hook 'flyspell-mode)

;; make flyspell mode ignore latex commands
(setq ispell-extra-args '("--dont-tex-check-comments"))

;;(set-default-font "-apple-Monaco-normal-normal-normal-*-14-*-*-*-*-0-iso10646-1")
(set-default-font "Monaco")
;; set font size
(set-face-attribute 'default nil :height 110)
;;(set-default-font "monaco")

;;-*-Monaco-normal-r-*-*-16-*-*-*-*-*-*-*")
;;;;                   -*-Monaco-medium-r-*-*-10-*-*-*-*-*-*-*
;; Visual feedback on selections
(setq-default transient-mark-mode t)

;; Always end a file with a newline
(setq require-final-newline t)

;; Stop at the end of the file, not just add lines
(setq next-line-add-newlines nil)


;; highlight paired parentheses
(show-paren-mode t )



;; Pretty parentheses
(when (require 'rainbow-delimiters nil 'noerror)
  (add-hook 'cperl-mode-hook 'rainbow-delimiters-mode))

;;;;;;;;;;;;;;;;;;;;;
;; auto-install.el ;;
;;;;;;;;;;;;;;;;;;;;;
;; (require 'auto-install)
;; (auto-install-update-emacswiki-package-name t)


;;;;;;;;;;;;;;;;;;;;;
;; perl completion ;;
;;;;;;;;;;;;;;;;;;;;;
(add-hook 'cperl-mode-hook
          (lambda()
            (require 'perl-completion)
            (perl-completion-mode t)))



;;;;;;;;;;;;;;;;;;;;
;; ----- ECB ---- ;;
;;;;;;;;;;;;;;;;;;;;
;; (add-to-list 'load-path
;;              "~/.emacs-lisp/ecb/");;"/usr/share/emacs23/site-lisp/ecb/")
;; (require 'ecb)
;;;; activate ecb for the following modes
;; (dolist (hook '(
;;      c-mode-hook
;;      cperl-mode-hook
;;      perl-mode-hook
;;      php-mode-hook
;;      js-mode-hook
;;      python-mode
;;      sh-mode-hook
;;      ))
;;   (add-hook hook 'ecb-activate))

;;; Modify the variable ecb-layout-name to use change the layout
;;; then C-c . l to refresh the ecb screen
;;; or just use the function ecb-change-layout
;;(setq ecb-layout-name "terdon1")
;;(setq ecb-layout-name "terdon2")
;(setq initial-buffer-choice user-init-file)

;;; use the icons in the tree displays (t)
;;(setq ecb-tree-use-image-icons t)


;; Enable wheelmouse support by default
(cond (window-system
       (mwheel-install)
))
(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.
 '(case-fold-search t)
 '(current-language-environment "English")
 '(custom-enabled-themes (quote (tango-dark)))
 '(custom-safe-themes
     (quote
        ("38908037082b9fc2e6762961026299d026963e57c726c3bc0b9e66cd0def0926" default)))
 '(default-input-method "latin-9-prefix")
 '(ebib-preload-bib-files (quote ("~/doc/Papers/moonlighting.bib")))
 '(global-font-lock-mode t nil (font-lock))
 '(inhibit-startup-screen t)
 '(safe-local-variable-values (quote ((Local . "american"))))
 '(save-place t nil (saveplace))
 '(show-paren-mode t nil (paren))
 '(tex-dvi-view-command
     (quote
        (cond
         ((eq window-system
                    (quote x))
            "evince")
         ((eq window-system
                    (quote w32))
            "yap")
         (t "dvi2tty * | cat -s"))))
 '(transient-mark-mode t))
(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.
 '(cperl-array-face ((((class color) (background light)) (:foreground "OrangeRed"))))
 '(cperl-hash-face ((((class color) (background light)) (:foreground "coral4"))))
 '(cperl-nonoverridable-face ((t (:foreground "RoyalBlue"))))
 '(font-lock-comment-face ((t (:foreground "SlateGray"))))
 '(markdown-header-face-1 ((t (:inherit markdown-header-face :height 1.1))))
 '(markdown-header-face-2 ((t (:inherit markdown-header-face :height 1.05))))
 '(markdown-header-face-3 ((t (:inherit markdown-header-face :height 1.03))))
 '(markdown-header-face-4 ((t (:inherit markdown-header-face :height 1.01)))))




;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; enable highlighting regions from the keyboard ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(setq transient-mark-mode t)


;; Load Ebib mode
(autoload 'ebib "ebib" "Ebib, a BibTeX database manager." t)

;; Load wc mode
(autoload 'wc "wc" "Word Count" t)


;; enable wordcount for LaTex
;; http://superuser.com/questions/125027/word-count-for-latex-within-emacs
(defun latex-word-count ()
  (interactive)
  (shell-command (concat "~/scripts/texcount.pl "
                         ; "uncomment then options go here "
                         (buffer-file-name))))

;; save history across sessions
(require 'recentf)
(recentf-mode 1)
(setq recentf-max-menu-items 50)

;; ralee mode is good for RNA alignment editing
;; (add-to-list 'load-path "~/.ralee/")
;; (autoload 'ralee-mode "ralee-mode" "Yay! RNA things" t)
;; (setq auto-mode-alist (cons '("\\.stk$" . ralee-mode) auto-mode-alist))

;; Show current line and column number
(setq-default column-number-mode t)
(line-number-mode t)

;; Set encoding
(prefer-coding-system 'utf-8)
(setq coding-system-for-read 'utf-8)
(setq coding-system-for-write 'utf-8)

;; tramp for remote file editing
(setq tramp-default-method "sshx")
(setq tramp-verbose 10)



;;/lacoloc@badabing:/home/lacoloc/foo1
;;; Buffer tricks for C-x C-b
(require 'ibuffer)
(setq ibuffer-saved-filter-groups
  (quote (("default"

            ("Coding" ;; prog stuff not already in MyProjectX
              (or
                (mode . c-mode)
                (mode . perl-mode)
        (mode . cperl-mode)
                (mode . python-mode)
                (mode . emacs-lisp-mode)
        (mode . php-mode)
        (mode . js-mode)
        (mode . shell-script\[sh\]-mode)
        (mode . shell-script\[bash\]-mode)
        (mode . shell-script-mode)
        (mode . shell-script-mode)
        (mode . shell-script-mode)
        (mode . shell-script-mode)
        (name . "\\.sh$")


                )
          )
        ("HTML/CSS"

          (or
           (mode . myhtml-mode)
           (mode . html-mode)
           (mode . htm-mode)
           (mode . css-mode)

          )

         )
        ("PlainText"  (mode . text-mode))
        ))))

     (add-hook 'ibuffer-mode-hook
           (lambda ()
             (ibuffer-switch-to-saved-filter-groups "default")))
(global-set-key (kbd "C-x C-b") 'ibuffer)



;;;;;; HTML stuff  ;;;;;;;;;;;
;;;;;;; Color colors in css and html files
(autoload 'myhtml-mode "myhtml-mode" "My HTML mode." t)
(autoload 'rainbow-mode "rainbow-mode" "Color stuff" t)

;;; set myHTML as default mode
(setq auto-mode-alist (cons '("\\.html$" . myhtml-mode) auto-mode-alist))

;;;  web-mode single mode for web docs
(require 'web-mode)
(add-to-list 'auto-mode-alist '("\\.phtml\\'" . web-mode))
(add-to-list 'auto-mode-alist '("\\.php\\'" . web-mode))
(add-to-list 'auto-mode-alist '("\\.css\\'" . web-mode))
(add-to-list 'auto-mode-alist '("\\.html\\'" . web-mode))
(add-to-list 'auto-mode-alist '("\\.htm\\'" . web-mode))

(add-hook 'css-mode-hook 'rainbow-mode)

;;;;;;;;;; HTML keybindings ;;;;;;;;

;;; Ctrl+c Ctrl+d :Delete matching tags. WARNING: if your HTML tags
;;; are not always matched, it might delete the wrong starting/ending tag


(add-hook 'myhtml-mode-hook
      (lambda ()
 ;;; sgml-delete-tag function

        (local-set-key (kbd "C-c b") 'bold-word)
        (local-set-key (kbd "C-c p") 'insert-p)
        (local-set-key (kbd "M-4") 'tag-image)
        (local-set-key (kbd "M-5") 'wrap-url)
        (local-set-key (kbd "C-c C-d") 'sgml-delete-tag)

        )
      )



;;; Idle highlight stuff
;; (defun my-coding-hook () (make-local-variable 'column-number-mode) (column-number-mode t)  (idle-highlight t))

;; (add-hook 'emacs-lisp-mode-hook 'my-coding-hook) (add-hook 'ruby-mode-hook 'my-coding-hook) (add-hook 'js2-mode-hook 'my-coding-hook) (add-hook 'perl-mode-hook 'my-coding-hook) (add-hook 'python-mode-hook 'my-coding-hook) (add-hook 'php-mode-hook 'my-coding-hook) (add-hook 'js-mode-hook 'my-coding-hook)

;;; 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))


;;
(define-key isearch-mode-map (kbd "C-o")
  (lambda ()
    (interactive)
    (let ((case-fold-search isearch-case-fold-search))
      (occur (if isearch-regexp isearch-string
               (regexp-quote isearch-string))))))


;;; yasnippet for tab autocomplete
;;; https://github.com/capitaomorte/yasnippet

(add-to-list 'load-path
              "~/.emacs.d/plugins/yasnippet")
(require 'yasnippet)
(yas/global-mode 1)


;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Customize cperl-mode ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;

;; make cperl-mode always highlight scalar variables
 (setq cperl-highlight-variables-indiscriminately t)

;; Disable whitespace underline
(setq cperl-invalid-face (quote off))

;; Set as default for perl files
(require 'cperl-mode)
;; Perl file extension associations
(add-to-list 'auto-mode-alist '("\\.pl$" . cperl-mode))
(add-to-list 'auto-mode-alist '("\\.ph$" . cperl-mode))
(add-to-list 'auto-mode-alist '("\\.cgi$" . cperl-mode))
(add-to-list 'auto-mode-alist '("\\.pm$" . cperl-mode))
(add-to-list 'interpreter-mode-alist '("perl" . cperl-mode))
(add-to-list 'auto-mode-alist '("\\.pl$" . cperl-mode))
(add-to-list 'auto-mode-alist '("\\.cgi$" . cperl-mode))
(add-to-list 'auto-mode-alist '("\\.pm$" . cperl-mode))
(add-to-list 'interpreter-mode-alist '("perl" . cperl-mode))
(add-to-list 'auto-mode-alist '("\\.pm$" . cperl-mode))
;; BSD/Allman indentation style using cperl-mode
(cperl-set-style "BSD")
(setq cperl-electric-keywords t) ;; expands for keywords such as
                                     ;; foreach, while, etc...
;; Load README files with markdown-mode
(add-to-list 'auto-mode-alist '(".*README.*" . markdown-mode))

; Outline-minor-mode key map
 (define-prefix-command 'cm-map nil "Outline-")
 ; HIDE
 (define-key cm-map "q" 'hide-sublevels)    ; Hide everything but the top-level headings
 (define-key cm-map "t" 'hide-body)         ; Hide everything but headings (all body lines)
 (define-key cm-map "o" 'hide-other)        ; Hide other branches
 (define-key cm-map "c" 'hide-entry)        ; Hide this entry's body
 (define-key cm-map "l" 'hide-leaves)       ; Hide body lines in this entry and sub-entries
 (define-key cm-map "d" 'hide-subtree)      ; Hide everything in this entry and sub-entries
 ; SHOW
 (define-key cm-map "a" 'show-all)          ; Show (expand) everything
 (define-key cm-map "e" 'show-entry)        ; Show this heading's body
 (define-key cm-map "i" 'show-children)     ; Show this heading's immediate child sub-headings
 (define-key cm-map "k" 'show-branches)     ; Show all sub-headings under this heading
 (define-key cm-map "s" 'show-subtree)      ; Show (expand) everything in this heading & below
 ; MOVE
 (define-key cm-map "u" 'outline-up-heading)                ; Up
 (define-key cm-map "n" 'outline-next-visible-heading)      ; Next
 (define-key cm-map "p" 'outline-previous-visible-heading)  ; Previous
 (define-key cm-map "f" 'outline-forward-same-level)        ; Forward - same level
 (define-key cm-map "b" 'outline-backward-same-level)       ; Backward - same level
 (global-set-key "\M-o" cm-map)



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Make TAB expand words. Source:                 ;;
;; http://emacsblog.org/2007/03/12/tab-completion-everywhere/ ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(defun my-tab-fix ()
  (local-set-key [tab] 'indent-or-expand))

(add-hook 'c-mode-hook          'my-tab-fix)
(add-hook 'cperl-mode-hook          'my-tab-fix)
(add-hook 'php-mode-hook          'my-tab-fix)
(add-hook 'js-mode-hook          'my-tab-fix)
(add-hook 'python-mode          'my-tab-fix)
(add-hook 'sh-mode-hook         'my-tab-fix)
(add-hook 'emacs-lisp-mode-hook 'my-tab-fix)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Define the indent-or-expand function we ;;
;; just mapped to TAB              ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(defun indent-or-expand (arg)
  "Either indent according to mode, or expand the word preceding
point."
  (interactive "*P")
  (if (and
       (or (bobp) (= ?w (char-syntax (char-before))))
       (or (eobp) (not (= ?w (char-syntax (char-after))))))
      (dabbrev-expand arg)
    (indent-according-to-mode)))

;;; Stop emacs from showing buffer menu when >=3 files opened
(setq inhibit-startup-buffer-menu t)


;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Bury unwanted buffers ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;

; necessary support function for buffer burial
(defun crs-delete-these (delete-these from-this-list)
  "Delete DELETE-THESE FROM-THIS-LIST."
  (cond
   ((car delete-these)
    (if (member (car delete-these) from-this-list)
        (crs-delete-these (cdr delete-these) (delete (car delete-these)
                             from-this-list))
      (crs-delete-these (cdr delete-these) from-this-list)))
   (t from-this-list)))
                    ; this is the list of buffers I never want to see
(defvar crs-hated-buffers
  '("KILL" "*Compile-Log*" "*Messages*" "*scratch*" "*auto-install"))
                    ; might as well use this for both
(setq iswitchb-buffer-ignore (append '("^ " "*Buffer") crs-hated-buffers))
(defun crs-hated-buffers ()
  "List of buffers I never want to see, converted from names to buffers."
  (delete nil
          (append
           (mapcar 'get-buffer crs-hated-buffers)
           (mapcar (lambda (this-buffer)
                     (if (string-match "^ " (buffer-name this-buffer))
                         this-buffer))
                   (buffer-list)))))
; I'm sick of switching buffers only to find KILL right in front of me
(defun crs-bury-buffer (&optional n)
  (interactive)
  (unless n
    (setq n 1))
  (let ((my-buffer-list (crs-delete-these (crs-hated-buffers)
                                          (buffer-list (selected-frame)))))
    (switch-to-buffer
     (if (< n 0)
         (nth (+ (length my-buffer-list) n)
              my-buffer-list)
       (bury-buffer)
       (nth n my-buffer-list)))))
(global-set-key [(control tab)] 'crs-bury-buffer)
(global-set-key [(control meta tab)] (lambda ()
                                       (interactive)
                                       (crs-bury-buffer -1)))



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;                  ETAGS                 ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
  (defun create-tags (dir-name)
     "Create tags file."
     (interactive "DDirectory: ")
     (eshell-command
      (format "find %s -type f -name \"*.[ch]\" | etags -L -" dir-name)))


  ;;;  Jonas.Jarnestrom<at>ki.ericsson.se A smarter
  ;;;  find-tag that automagically reruns etags when it cant find a
  ;;;  requested item and then makes a new try to locate it.
  ;;;  Fri Mar 15 09:52:14 2002

  (defadvice find-tag (around refresh-etags activate)
   "Rerun etags and reload tags if tag not found and redo find-tag.
   If buffer is modified, ask about save before running etags."
  (let ((extension (file-name-extension (buffer-file-name))))
    (condition-case err
    ad-do-it
      (error (and (buffer-modified-p)
          (not (ding))
          (y-or-n-p "Buffer is modified, save it? ")
          (save-buffer))
         (er-refresh-etags extension)
         ad-do-it))))

  (defun er-refresh-etags (&optional extension)
  "Run etags on all peer files in current dir and reload them silently."
  (interactive)
  (shell-command (format "etags *.%s" (or extension "el")))
  (let ((tags-revert-without-query t))  ; don't query, revert silently
    (visit-tags-table default-directory nil)))


(global-set-key "\M-s" 'tags-search)


;;; Delete  buffer
;;(kill-buffer "*Completions*")



;;;;;;;; Color theme ;;;;;;;;;;;;;;

(defun color-theme-djcb-dark ()
  "dark color theme created by djcb, Jan. 2009."
  (interactive)
  (color-theme-install
    '(color-theme-djcb-dark
       ((foreground-color . "#a9eadf")
         (background-color . "black")
         (background-mode . dark))
       (bold ((t (:bold t))))
       (bold-italic ((t (:italic t :bold t))))
       (default ((t (nil))))

       (font-lock-builtin-face ((t (:italic t :foreground "#a96da0"))))
       (font-lock-comment-face ((t (:italic t :foreground "#bbbbbb"))))
       (font-lock-comment-delimiter-face ((t (:foreground "#666666"))))
       (font-lock-constant-face ((t (:bold t :foreground "#197b6e"))))
       (font-lock-doc-string-face ((t (:foreground "#3041c4"))))
       (font-lock-doc-face ((t (:foreground "gray"))))
       (font-lock-reference-face ((t (:foreground "white"))))
       (font-lock-function-name-face ((t (:foreground "#356da0"))))
       (font-lock-keyword-face ((t (:bold t :foreground "#bcf0f1"))))
       (font-lock-preprocessor-face ((t (:foreground "#e3ea94"))))
       (font-lock-string-face ((t (:foreground "#ffffff"))))
       (font-lock-type-face ((t (:bold t :foreground "#364498"))))
       (font-lock-variable-name-face ((t (:foreground "#7685de"))))
       (font-lock-warning-face ((t (:bold t :italic nil :underline nil
                                     :foreground "yellow"))))
       (hl-line ((t (:background "#112233"))))
       (mode-line ((t (:foreground "#ffffff" :background "#333333"))))
       (region ((t (:foreground nil :background "#555555"))))
       (show-paren-match-face ((t (:bold t :foreground "#ffffff"
                                    :background "#050505")))))))



(add-to-list 'process-coding-system-alist '("zsh" . utf-8))

(put 'upcase-region 'disabled nil)


;; Informative comments,
;; comments that I want to keep or whatever
(add-hook 'tex-mode-hook
  (lambda ()
    (font-lock-add-keywords nil
      ;;'(("\\<\\(FIXME\\|TODO\\|HACK\\|fixme\\|todo\\|hack\\)" 1
                '(("\\(%#.*\\)" 1
        font-lock-warning-face t)))))
(add-hook 'cperl-mode-hook
  (lambda ()
    (font-lock-add-keywords nil
                '(("\\(#%.*\\)" 1
        font-lock-warning-face t)))))

;;;;;;;;;;;;;;;;;;;;
;; Enable tabbar  ;;
;;;;;;;;;;;;;;;;;;;;
;(tabbar-mode t)


;;; Markdown mode
(autoload 'markdown-mode "markdown-mode.el" "Major mode for editing Markdown files" t)
(setq auto-mode-alist (cons '("\\.text$" . markdown-mode) auto-mode-alist))
(setq auto-mode-alist (cons '("\\.md$" . markdown-mode) auto-mode-alist))
(setq auto-mode-alist (cons '("\\.mdown$" . markdown-mode) auto-mode-alist))
(setq auto-mode-alist (cons '("\\.mdt$" . markdown-mode) auto-mode-alist))
(setq auto-mode-alist (cons '("\\.markdown$" . markdown-mode) auto-mode-alist))


;;;;;;;;;;;;;;;;;;
;; Color themes ;;
;;;;;;;;;;;;;;;;;;

(add-to-list 'load-path "~/.emacs-lisp/emacs-color-theme-solarized")
 (load-theme 'tango-dark)

;;;;;;;;;;;;;;;;;
;; LaTeX stuff ;;
;;;;;;;;;;;;;;;;;
(setq TeX-PDF-mode t)

(setq TeX-auto-save t)
(setq TeX-parse-self t)
(setq-default TeX-master nil)

(add-hook 'LaTeX-mode-hook 'visual-line-mode)
(add-hook 'LaTeX-mode-hook 'flyspell-mode)
(add-hook 'LaTeX-mode-hook 'LaTeX-math-mode)

(add-hook 'LaTeX-mode-hook 'turn-on-reftex)
(setq reftex-plug-into-AUCTeX t)

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Chrome edit with emacs extension ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(add-to-list 'load-path "~/.emacs.d/plugins")
(require 'edit-server)
(edit-server-start)

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Enable markdown mode for editing SE posts ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Integrate Emacs with Stack Exchange http://stackoverflow.com/a/10386560/789593
(add-to-list 'auto-mode-alist '("stack\\(exchange\\|overflow\\)\\.com\\.[a-z0-9]+\\.txt" . markdown-mode))
(add-to-list 'auto-mode-alist '("superuser\\.com\\.[a-z0-9]+\\.txt" . markdown-mode))



;; Insert text around a region. In this case, it's
;; the LaTeX code environment from the listings package
(defun wrap-code (start end)
  "Insert a \begin{code} and \end{code} around a region."
  (interactive "r")

  (save-excursion
    (goto-char end) (insert "\\end{code}")
    (goto-char start)(insert "\\begin{code}") (newline-and-indent)
    ))
;; Assign its shortcut
(global-set-key (kbd "C-c p") 'wrap-code)



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; SE Markdown: http://emacs.stackexchange.com/questions/723/how-can-i-use-the-se-flavor-of-markdown-in-emacs ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; This variable controls how you want lists to look. It adds some space  ;;
;; to indent the list, and uses a pretty bullet-point.                    ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(defvar endless/bullet-appearance
  (propertize (if (char-displayable-p ?•) "  •" "  *")
              'face 'markdown-list-face)
  "String to be displayed as the bullet of markdown list items.")


;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; This is the command that actually adds the rules. There is one for lists and one for links. ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(font-lock-add-keywords
 'markdown-mode
 '(("^ *\\(\\*\\|\\+\\|-\\|\\) "
    1 `(face nil display ,endless/bullet-appearance) prepend)
   ("\\[[^]]*\\]\\(([^)]*)\\|\\[[^]]*\\]\\)"
    1 '(face nil display "") prepend))
 'append)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Because we’re using the display property to hide part of the link,     ;;
;; we need to tell font-lock that it should erase that property whenever  ;;
;; you delete part of the link (that way we can still edit it).           ;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(add-hook 'markdown-mode-hook #'endless/markdown-font-lock)

(defun endless/markdown-font-lock ()
  "Configure aggressive font-locking of `markdown-mode'."
  (add-to-list (make-local-variable 'font-lock-extra-managed-props) 'display))

;; Faces



;; Insert links and make them editable

(add-hook 'markdown-mode-hook #'endless/markdown-font-lock)

(defun endless/markdown-font-lock ()
  "Configure aggressive font-locking of `markdown-mode'."
  (define-key markdown-mode-map "\C-c\C-l" #'endless/markdown-insert-link)
  (add-to-list (make-local-variable 'font-lock-extra-managed-props) 'display))
(defun endless/markdown-insert-link ()
  "Insert or edit link at point."
  (interactive)
  (if (or (looking-at endless/markdown-link-regexp)
          (and (ignore-errors (backward-up-list) t)
               (or (looking-at endless/markdown-link-regexp)
                   (and (forward-sexp -1)
                        (looking-at endless/markdown-link-regexp)))))
      (let ((data (endless/ask-for-link
                   (match-string-no-properties 1)
                   (or (match-string-no-properties 2)
                       (match-string-no-properties 3)))))
        (if (match-string-no-properties 2)
            (replace-match (cdr data) :fixedcase :literal nil 2)
          (replace-match (cdr data) :fixedcase :literal nil 3))
        (replace-match (car data) :fixedcase :literal nil 1))
    (let ((data (endless/ask-for-link)))
      (insert "[" (car data) "](" (cdr data) ")"))))

(defun endless/ask-for-link (&optional name link)
  (cons (read-string "Text of the link: " name)
        (read-string "URL of the link: " link)))