;;; org-cite --- format Org-mode bibliographic references

;; Copyright (C) 2011 Christian Moe

;; Author: Christian Moe <mail at christianmoe dot com>
;; Keywords: citations, references, bibliography, wp
;; Version: 0.1 alpha

;; This file is not part of GNU Emacs.

;; Org-cite 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 3, or (at your option)
;; any later version.

;; Org-cite 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.  If not, see <http://www.gnu.org/licenses/>.

;;; Commentary:

;;; Code:


(defun org-cite-format ()
  "Dispatch formatting if there is at least one cite, and the
export target is not LaTeX."
  (goto-char (point-min))
  (when (re-search-forward org-cite-latex-cite-re nil t)
    (unless (equal org-export-current-backend 'latex)
      (org-cite-format-with-bibtex))))

(defun org-cite-toggle ()
  "Toggle use of org-cite-format on export."
  (interactive)
  (if (member 'org-cite-format org-export-preprocess-hook)
      (remove-hook 'org-export-preprocess-hook 'org-cite-format)
    (add-hook 'org-export-preprocess-hook 'org-cite-format)))

(defvar org-cite-strings
  ()
  "Plist of strings, returned by org-cite-str. Set at runtime
depending on how we're formatting.")

(defvar org-cite-default-strings
  '(:loc-sep ", "
    :nobreak  " "             ; (char-to-string ?\240)	     
    :and "and"                ; e.g. before last author name
    :et-al "et al."    ; in place of full list of co-authors
    :number "no."
    :p "p."
    :pp "pp."
    :in "in"
    :ed "ed."
    :eds "eds."
    :ed-by "ed."
    :edn "ed."       ; abbreviation for edition, e.g. in "(2nd ed.)"
    :no-date "n.d."
    )
  "Default strings to use when formatting citations and bibliographies.")

(defun org-cite-str (key)
  "Gettext function for org-cite. Looks up org-cite-strings for the
 string corresponding to KEY."
  (plist-get org-cite-strings key))

(defvar org-cite-alphabet
  "abcdefghijklmnopqrstuvwxyz"
  "String containing the alphabet in lower-case letters. You can
customize this if you need a different alphabet, default is
English.")

(defvar org-cite-months
  '("January" "February" "March" "April" "May" "June" 
    "July" "August" "September" "October" "November" "December"))

(defvar org-cite-months-abbrev
  '("Jan" "Feb" "Mar" "Apr" "May" "Jun" 
    "Jul" "Aug" "Sep" "Oct" "Nov" "Dec"))

(defun org-cite-num-to-letter (num)
  "Helper function that returns letter number NUM from the list
a, b, c... NUM can be numeric or string; if NUM is nil, the empty
string is returned."
  (when (stringp num) (setq num (string-to-number num)))
  (if num
      (char-to-string (aref (vconcat org-cite-alphabet) (1- num)))
    ""))

(defvar org-cite-method 'numeric
  "The basic reference method to use. Possible values: 

- author-date: e.g. citations formatted as `(Brown, 2006)', 
  with alphabetically ordered reference list at end
- numeric: numeric references, e.g. citations like (1), and
  reference list with items prefixed in same way.
- notes: inserted as Org footnotes. Note that locator
  information is currently lost.
- text: inserted as full text.")

(defvar org-cite-formatter 'bibtex
  "The reference-formatting backend to use. Currently bibtex is
the only option.")

(defun org-cite-replace-in-buffer (subst)
  "Make simple substitutions in the buffer. SUBST is an alist of
regexps matched to replacements. Goes beyond
format-replace-strings in that replacements can be strings,
symbols, or expressions."
  (let (rep)
    (while subst
      (goto-char (point-min))
      (while (re-search-forward (car (car subst)) nil t)
	(setq rep (cdr (car subst)))
	(replace-match 
	 (cond 
	  ((symbolp rep) ; replacement is a symbol, get value
	   (symbol-value rep))
	  ((and (listp rep) (functionp (car rep))) ; replacement is a function,
	   (eval rep))                             ; evaluate it
	  ((stringp rep) rep)) ; replacement is a string, return it
	 t)) ; replace with fixed-case
      (setq subst (cdr subst)))))


(defvar org-cite-final-substitutions
  '(
    ;; (" ()" . "") ; empty parens, e.g. because of missing journal number
    ;; (", )" . ")") ; nothing after comma, e.g. missing month info
    ("/(" . "/ (")) ; give italics space to breathe before issue number
"These are just dirty fixes to problems left by other dirty fixes.
TODO: clean fixes.")


;;;;;;;;;;;;;;;;;;;;;;;
;;; BibTeX-specific ;;;
;;;;;;;;;;;;;;;;;;;;;;;

;; A note on LaTeX regexps
;;
;; To match LaTeX command arguments, I have used
;; "{\\([^}]+\\)}". That's fine e.g. in org-cite-latex-cite-re and
;; bibitem searches, which only look for a citekey. However, this
;; fails if the argument itself contains curly braces. org-cite relies
;; on cleaning those up first. It will not always succeed. A better
;; approach is needed.


(defvar org-cite-latex-cite-re  
  "\\\\\\(.*?cite.*?\\)\\(\\[\\(.+?\\)\\]\\)?\\(\\[\\(.+?\\)\\]\\)?{\\([^}]+\\)}"
  "Regular expression to search and parse latex cites.  
The match-strings are: 
1 - the cite macro (cite, citet, etc.), 
2 - the pre-note option (if any); 
3 - its contents (e.g. `see'); 
4 - the post-note option (if any); 
5 - its contents, usually a locator, e.g. page number; 
6 - the citekey(s). 
TODO: May break if there's a line-break in an option.")

(defvar org-cite-apacite-cite-re 
   "\\\\\\(.*?cite.*?\\)\\(<\\([^>]+\\)>\\)?\\(\\[\\([^]]+\\)\\]\\)?{\\([^}]+\\)}"
  ;; WAS: "\\\\\\(.*?cite.*?\\)\\(<\\(.+?\\)>\\)?\\(\\[\\(.+?\\)\\]\\)?{\\([^}]+\\)}"
  "Regular expression to search and parse latex cites.  
The match-strings are as for org-cite-latex-cite-re.")

(defvar org-cite-apacite-strings
  '(:loc-sep ", "
    :nobreak  " "             ; (char-to-string ?\240)	     
    :and "&"
    :et-al "et al."
    :number "No."
    :p "p."
    :pp "pp."
    :in "In"
    :ed "Ed."
    :eds "Eds."
    :ed-by "ed."
    :edn "ed."
    :no-date "n.d.")
  "Default strings to use with apacite.")

(defvar org-cite-bibtex-package nil
"A symbol representing the BibTeX package used. Currently
supported options are 'natbib and 'apacite.")

(defvar org-cite-bibcite-re "\\\\bibcite{\\([^}]+\\)}{\\([^}]+\\)}"
"Analytic regexp for a default bibcite.
Match-strings: 1 citekey, 2 numbering,
e.g. \\bibcite{Smith2000}{1}")

(defvar org-cite-natbib-bibcite-re 
  "\\\\bibcite{\\([^}]+\\)}{{\\([^}]+\\)}{\\([^}]+\\)}{{\\([^}]+\\)}}{{\\([^}]+\\)}}}"
"Analytic regexp for bibcites when using natbib. 
Match-strings: 1 citekey, 2 numbering, 3 year, 4 shortened
authorlist, 5 full authorlist, e.g.
\\bibcite{Smith2000}{{1}{2000}{{Smith et al}}{{Smith, Jones and Black}}}")

(defvar org-cite-apacite-bibcite-re 
  "\\\\bibcite{\\([^}]+\\)}{\\\\citeauthoryear {\\(.+?\\)}{\\(.+?\\)}{{\\(.+?\\)}\\({\\\\APACexlab {{\\\\BCnt {\\([0-9]\\)}}}}\\)?}}"
;; WAS: "\\\\bibcite{\\([^}]+\\)}{\\\\citeauthoryear {\\(.+?\\)}{\\(.+?\\)}{{\\\\APACyear {\\([0-9]+\\)}}\\({\\\\APACexlab {{\\\\BCnt {\\([0-9]\\)}}}}\\)?}}"
"Analytic regexp for bibcites when using apacite.
Match-strings:
 1) citekey
 2) authorslong
 3) authors
 4) year (or no date)
 5) Maybe a section with same-author-same-year distinguisher
 6) Maybe a same-author-same-year distinguisher")

(defun org-cite-get-bibcites (file)
  (let ((package org-cite-bibtex-package)
	path bibcites bibstyle bibcite-re year key-citation)
    (with-temp-buffer
      (unless (file-exists-p (setq path (concat "./" file ".aux")))
	(error (format "org-cite could not find %s" path)))
      (insert-file-contents path)
      ;; Convert special characters to utf-8 representation
      (setq case-fold-search nil)
      (org-cite-replace-in-buffer org-cite-latex-chars-utf8)
      ;; Find the bibstyle
      (goto-char (point-min))
      (re-search-forward "\\\\bibstyle{\\([^}]+\\)}" nil t)
      (setq bibstyle (match-string 1))
      (when (equal package 'apacite)
	;; cleanup apacite crud
	(org-cite-replace-in-buffer org-cite-apacite-substitutions))
      (setq bibcite-re
	    (cond
	     ((equal package 'natbib) 
	      org-cite-natbib-bibcite-re) 
	     ((equal package 'apacite)
	      org-cite-apacite-bibcite-re)
	     (t org-cite-bibcite-re))) ; close setq
      (goto-char (point-min))
      (while (re-search-forward bibcite-re nil t)
	(setq year
	      (cond 
	       ((equal package 'apacite) (match-string 4))
	       (t (match-string 3)))) ; natbib
	;; (unless (and year (string-match "[0-9]+" year)) ; FIXME - not working
	;;   (setq year (org-cite-str :no-date)))
	(setq key-citation
	      (cond
	       ;; natbib
	       ((equal package 'natbib) ; natbib
		(cons (match-string 1) 
		      (list :num (match-string 2)
			    :year year
			    :authors (match-string 4) 
			    :authorslong (match-string 5))))
	       ;; apacite
	       ((equal package 'apacite) 
		(cons (match-string 1)
		      (list :authorslong (match-string 2)
			    :authors (match-string 3)
			    :year 
			    (concat year
			     ;; with letter marker, if any
			     (if (match-string 6)
				 (org-cite-num-to-letter (match-string 6)))))))
	       ;; plain
	       (t (cons (match-string 1) (match-string 2))))) ; close setq 
	(setq bibcites (cons key-citation bibcites))) ; close while
      bibcites)))

(defun org-cite-format-natbib-citation (citetype citekey bibcite &optional loc pre)
  "Format a citation as if using the BibTeX natbib
package. CITETYPE can be one of the following symbols: cite,
citet, citet*, citep, citep*, citealt, citealt*, citealp,
citealp*, citeauthor, citeauthor*, citeyear, citeyearpar,
nocite. BIBCITE should be a plist including :year, :authors
and :authorslong; if there are multiple citekeys, the value of
this argument is ignored and each bibcite is looked up
afresh. LOC is a note to appear at the end of the citation (aka a
post-note), usually referencing a location within the work,
e.g. page number. PRE is a note to appear before the citation,
e.g. `see'. The logical order of LOC and PRE is reversed in the
argument list because LOC is far more frequent."
  (let ((citekeys (split-string citekey " ?, ?")) ; allows a single space
	(locs (when loc (split-string loc " ?, ?")))
	previous-authors ; lets us check if current authors same as last
	citet-parens-open ; flag if we have a citet parenthesis open for more works by same authors
	citation)
    (setq pre (if pre (concat pre " ") ""))

    ;; If there are multiple works in one cite, loop through them
    (while citekeys
      (setq citekey (car citekeys))
      (setq loc (car locs))
      (setq bibcite (cdr (assoc citekey bibcites)))
      (let ((authors (if (string-match "[*]" citetype)
			 (plist-get bibcite :authorslong)
		       (plist-get bibcite :authors)))
	    (year (plist-get bibcite :year))
	    (locstring (format "%s%s"  
			       (if loc (org-cite-str :loc-sep) "")
			       (or loc ""))))
	;; If this is not the first work, add a separator, keeping
	;; track of whether we're in an open citet parenthesis
	(when previous-authors
	  (when citet-parens-open
	    (unless (string= authors previous-authors)
	      (setq citation (concat citation ")"))
	      (setq citet-parens-open nil)))
	  (setq citation (concat citation "; ")))
	;; add this work
	(setq 
	 citation
	 (concat
	  citation	  
	  (if (string= authors previous-authors)
	      ;; if this is another work by authors already named in this citation
	      ;; TODO Find a less extensive way to do the following!
		  (cond
		   ((string-match "citet" citetype) ; matches citet and citet*
		    (format "[[%s][%s]]%s" citekey year locstring))
		   ((string-match "citeauthor" citetype) ; this shouldn't happen
		    (format "[[%s][%s]]%s" citekey authors locstring))
		   ((string-match "citeyearpar" citetype)
		    (format "[[%s][%s]]%s" citekey year locstring))
		   ((string-match "citeyear" citetype)
		    (format "[[%s][%s]]%s" citekey year locstring))
		   ((string-match "citealt" citetype)
		    (format "[[%s][%s]]%s" citekey year locstring))
		   ((string-match "citealp" citetype)
		    (format "[[%s][%s]]%s" authors citekey year locstring))
		   ((string-match "nocite" citetype)
		    "")
		   ((string-match "cite" citetype) ; cite or citep
		    (format "[[%s][%s]]%s" citekey year locstring))
		   (t 
		    (format "*[org-cite failed to format =%s= citation]*" citetype)))
	    ;; else (when authors are not already named in this citation)
	    (cond
	     ((string-match "citet" citetype)
	      (format "%s ([[%s][%s]]%s" authors citekey year locstring))
	     ((string-match "citeauthor" citetype)
	      (format "[[%s][%s]]%s" citekey authors locstring))
	     ((string-match "citeyearpar" citetype)
	      (format "[[%s][%s]]%s" citekey year locstring))
	     ((string-match "citeyear" citetype)
	      (format "[[%s][%s]]%s" citekey year locstring))
	     ((string-match "citealt" citetype)
	      (format "%s [[%s][%s]]%s" authors citekey year locstring))
	     ((string-match "citealp" citetype)
	      (format "%s, [[%s][%s]]%s" authors citekey year locstring))
	     ((string-match "nocite" citetype)
	      "")
	     ((string-match "cite" citetype) ; other alternatives eliminated, this leaves "cite" or "citep", both bracketed
	      (format "[[%s][%s, %s]]%s" citekey authors year locstring))
	     (t 
	      (format "*[org-cite failed to format =%s= citation]*" citetype)))))) ; end setq citation
	;; Keep track of whether we might be adding to an open citet parenthesis
	(when (string-match "citet" citetype) (setq citet-parens-open t))	
	;; Loop round
	(setq previous-authors authors)
	(setq locs (cdr locs))
	(setq citekeys (cdr citekeys)))) ; end while citekeys

    ;; Close citet bracket if necessary
    (when citet-parens-open
      (setq citation (concat citation ")")))
    ;; Add pre-note
    (setq citation (concat pre citation))
    ;; Bracket whole citation, if it's one of those types
    (when (member citetype 
		  '("citeauthor" "citeauthor*" "citeyearpar" 
		   "cite" "cite*" "citep" "citep*"))
      (setq citation (concat "(" citation ")")))
    ;; Tidy up
    (setq citation (replace-regexp-in-string "~" (org-cite-str :nobreak) citation))
    (setq citation (replace-regexp-in-string "[{}]" "" citation)) ;; FIXME this may hide debugging info
    ;; Return citation
    citation))

(defun org-cite-format-with-bibtex ()
  (interactive)
  (let* ((package org-cite-bibtex-package) ; natbib, apacite, nil=plain...
	 (cite-re (if (equal package 'apacite) 
		      org-cite-apacite-cite-re 
		    org-cite-latex-cite-re))
	 (loc-sep (org-cite-str :loc-sep))
	 method file 
	 bibcites bibcite 
	 biblist ; if method is 'text, biblist holds the formatted bibliography
	 cited ; list of already cited works
	 citetype pre loc citekey citation)
    ;; Set default method
    (unless method (setq method org-cite-method))
    ;; Set the strings to use
    (cond 
     ((equal package 'apacite)
      (setq org-cite-strings org-cite-apacite-strings))
     (t
      (setq org-cite-strings org-cite-default-strings)))
    ;; Get file
    (setq file (file-name-sans-extension 
		(file-name-nondirectory 
		 (or
		  org-current-export-file
		  (buffer-file-name)))))					 
    ;; Get bibcites
    (setq bibcites (org-cite-get-bibcites file))
    ;; If using references in text, get the references now
    (when (equal method 'text)
      (let (parts tmplist)
	(setq biblist (split-string (org-cite-get-bbl file method bibcites) "\n\n" t))
	(while biblist
	   (setq parts (split-string (car biblist) "::::"))
	   (setq tmplist
		 (cons (cons 
			(org-trim (car parts)) ; TODO a better way to trim newlines than:
			(replace-regexp-in-string "\n" " " (org-trim (car (cdr parts)))))
		       tmplist))
	   (setq biblist (cdr biblist)))
	(setq biblist tmplist)))
    ;;; Format citations
    ;;;
    (goto-char (point-min))
    ;; Analyse cite macros
    (while (re-search-forward cite-re nil t)
      (if (equal package 'apacite)
	  (setq citetype (match-string 1) ; see org-cite-latex-cite-re
		pre (match-string 3)
		loc (match-string 5)
		citekey (match-string 6))		
	;; else (natbib or plain)
	(setq citetype (match-string 1) ; see org-cite-latex-cite-re
	      pre (and (match-string 4) (match-string 3)) ; only if there is a second, perhaps empty, option
	      loc (or (match-string 5) (match-string 3))
	      citekey (match-string 6)))
      (setq bibcite (cdr (assoc citekey bibcites)))

	;; (setq citetype (match-string 1) ; see org-cite-latex-cite-re
	;; 	    pre (if (and (match-string 2)
	;; 			 (string= "<" (substring (match-string 2) 0)))
	;; 		    ;; if apacite, the pre-note is in sharp brackets
	;; 		    (match-string 3)
	;; 		  ;; else (natbib), make first option pre only if there is a second
	;; 		  (and (match-string 4) (match-string 3)))
	;; 	    loc (or (match-string 5) (match-string 3))
	;; 	    citekey (match-string 6)
	;; 	    bibcite (cdr (assoc citekey bibcites)))

      (cond

       ;; Author-date or numerical references
       ((or (equal method 'author-date) (equal method 'numeric))
	(replace-match
	 (cond
	  ;; natbib
	  ((equal package 'natbib)
	   (save-match-data
	     (org-cite-format-natbib-citation citetype citekey bibcite loc pre)))
	  ;; apacite 	  
	  ((equal package 'apacite)
	   (save-match-data
	     ;; TODO - implement org-cite-format-apacite-citation if needed
	     ;;        but for now, rely on natbib
	     (when (string-match "^cite\\($\\|[^y]\\)" citetype)
	       ;; apacite commands that begin with "cite", except
	       ;; those that begin with "citeyear", map to "fullcite"
	       ;; the first time they appear, "shortcite" thereafter
	       (setq citetype
		     (concat
		      (if (member citekey cited) "short" "full")
		      citetype)))
	     ;; Map the apacite cite to a natbib citetype and do the natbib formatting
	     (if (assoc citetype org-cite-apacite-citetypes)
		 (setq citetype (cdr (assoc citetype org-cite-apacite-citetypes)))
	       (setq citetype "unknown")) ; TODO improve error handling
	     (org-cite-format-natbib-citation citetype citekey bibcite loc pre))) 
	  ;; plain
	  (t (format " ([[%s][%s%s%s]])"
		   citekey 
		   bibcite
		   (if loc loc-sep "")
		   (or loc "")))))) ; close cond, replace-match, or

       ;; Full-text reference
       ((equal method 'text)
	(replace-match
	 (format "%s%s%s"
		 (cdr (assoc citekey biblist)) ; biblist item, not bibcite
		 (if loc loc-sep "")
		 (or loc ""))))

       ;; Footnote reference
       ((equal method 'notes)
	(replace-match (format "[fn:%s]" citekey)))) ; end cond
      ;; Add this to list of already cited works
      (setq cited (cons citekey cited))) ; end while

  ;; Insert bibliography/references unless we have full references in
  ;; text. If there is a \bibliography command, place it there, after
  ;; the surrounding latex block if there is one. Else place at end of
  ;; buffer.
  (unless (equal method 'text)
    (goto-char (point-min))
    (if (search-forward "\\bibliography" nil t)
	(when (org-in-block-p '("latex"))
	    (search-forward "#+end_latex" nil t))
      (goto-char (point-max)))
    (insert (org-cite-get-bbl file method bibcites))))
  (goto-char (point-min))
  (if (called-interactively-p)
      (message "Your original document has changed. Kill without saving or undo (C-c /) to avoid losing data.")
    (message "Done formatting bibliographic references")))

(defun org-cite-get-bbl (file method bibcites)
  "Return the contents of a .bbl file output by Bibtex as a
string in Org format."
  (let ((package org-cite-bibtex-package)
	citekey
	returnvalue)
    ;; Get the .bbl contents and reformat them 
    ;;
    ;; We're using a named buffer for debugging purposes -- if bbl
    ;; cleanup fails (as it often will), inspecting the contents of
    ;; org-cite-temp-bbl will show what org-cite choked on. With luck,
    ;; there'll be some superfluous braces that can be removed from
    ;; the BibTeX.
    (with-current-buffer (get-buffer-create "org-cite-temp-bbl")
      (latex-mode)
      (insert-file-contents (concat "./" file ".bbl"))
      (goto-char (point-min))
      ;; Remove thebibliography environment
      (while (search-forward "{thebibliography}" nil t)
	(move-beginning-of-line nil)
	(kill-whole-line))
      ;; Replace bibitem macros with link/footnote targets
      (goto-char (point-min))
      (while (re-search-forward "\\\\bibitem\\(\\[[^]]+\\]\\)?{\\([^}]+\\)}" nil t)
	;; WAS:    (re-search-forward "\\\\bibitem{\\([^}]+\\)}" nil t)
	(setq citekey (match-string 2))
	(cond
	 ((equal method 'author-date)
	  (replace-match (format "# <<%s>>" citekey)))
	 ((equal method 'numeric)
	  (replace-match 
	   (format "# <<%s>>\n(%s)" 
		   citekey 
		   (cdr (assoc citekey bibcites)))))
	 ((equal method 'text)
	  (replace-match (format "%s::::" citekey)))
	 ((equal method 'notes)
	  (replace-match (format "[fn:%s]" citekey)))))
      ;; Replace special characters with utf8 representation
      (setq case-fold-search nil)
      (org-cite-replace-in-buffer org-cite-latex-chars-utf8)
      ;; Replace {\e ...} with /.../, _{...}, ^{...} and [space]{...} with nothing
      ;; - TODO could this be done by org-cite-replace-in-buffer?
      (org-cite-latex-clean-braces)
      ;; Do a couple more substitutions before tackling apacite
      (org-cite-replace-in-buffer
       '(("\\\\textit{\\([^}]+\\)}" . "/\\1/")
	 ("\\\\textbf{\\([^}]+\\)}" . "*\\1*")))
      ;; Remove APACITE crud
      (when (equal package 'apacite)
	(org-cite-replace-in-buffer org-cite-apacite-substitutions))
      ;; Remove ordinary NATBIB crud
      (org-cite-replace-in-buffer
       '(("\\\\newblock" . "") 
	 ("~" . (org-cite-str :nobreak))
	 ("\\\\/" . "") ; weird \/ sequences
	 ("\\\\" . ""))) ; all remaining backslashes
      ;; If apacite, remove single empty newlines if not followed by
      ;; link target)
      (when (equal package 'apacite)
	(org-cite-replace-in-buffer '(("\n\n\\([^#]\\)" . " \\1"))))
      ;; Tidy up
      (org-cite-replace-in-buffer org-cite-final-substitutions)
      ;; Fill as org-mode
      (org-mode)
      (fill-region (point-min) (point-max))
      ;; Return as string
      (setq returnvalue (buffer-string))
      ;; Close buffer
      (kill-buffer))
    returnvalue))

(defun org-cite-latex-clean-braces ()
  "Clean up various formatting in curly braces within the main macros."
  (let (opentag closetag at-closing-brace)
    (goto-char (point-min))
    (while (re-search-forward "\\([{[:space:]~_^\n\"'-]\\){\\(\\\\em\\)?\\( \\)?" nil t)
      (setq at-closing-brace nil)
      (cond 
       ((string= (match-string 2) "\\em")
	(setq opentag " /" closetag "/"))
       ((string= (match-string 1) "^")
	;;(setq opentag "@<sup>" closetag "@</sup>"))
	(setq opentag " " closetag ""))
       ((string= (match-string 1) "_")
	;;(setq opentag "@<sub>" closetag "@</sub>"))
	(setq opentag " " closetag ""))
       ((string= (match-string 1) "~")
	(setq opentag "~" closetag " "))
       ((string= (match-string 1) "\"") 
	(setq opentag "\"" closetag " "))
       ((string= (match-string 1) "'") 
	(setq opentag "'" closetag " "))
       ((string= (match-string 1) "{")
	(setq opentag "{" closetag ""))
       ((string= (match-string 1) "\n")
	(setq opentag "\n" closetag ""))
       (t
	(setq opentag " " closetag "")))
      (goto-char (match-beginning 0))
      (if (or (string= (match-string 1) "{")  
	      (string= (match-string 1) "\n"))
	  ;; if the opening curly brace is right after a brace or
	  ;; a newline, move forward to the brace we want
	  (forward-char))                
      (while (not at-closing-brace)
	(forward-sexp)
	(if (= 125 (char-before)) (setq at-closing-brace t)))
      (delete-char -1)
      (insert closetag)
      (replace-match opentag))))

(defvar org-cite-apacite-citetypes
  '(("fullcite" . "citep*") ; (Black, Green and Brown, 2011)
    ("shortcite" . "citep") ; (Black et al., 2011)
    ("fullciteNP" . "citealp*") ; Black, Green and Brown, 2011
    ("shortciteNP" . "citealp") ; Black et al., 2011
    ;; there's no apacite equivalent of natbib citealt(*)
    ("fullciteA" . "citet*") ; Black, Green and Brown (2011)
    ("shortciteA" . "citet") ; Black et al. (2011)
    ("fullciteauthor" . "citeauthor*") ; (Black, Green and Brown) NO - natbib doesn't have a "citeauthorpar*"
    ("shortciteauthor" . "citeauthor") ; (Black et al.) NO - ditto
    ("fullciteauthorNP" . "citeauthor*") ; Black, Green and Brown
    ("shortciteauthorNP" . "citeauthor") ; Black et al.
    ("citeyear" . "citeyearpar") ; (2011)
    ("citeyearNP" . "citeyear") ; 2011
    ("nocite" . "nocite") ; 
    ("nocitemeta" . "nocite")) ; NOT QUITE - natbib doesn't have this
"Maps apacite cite commands to the corresponding natbib
commands. The apacite commands beginning with `cite' are not
included, as they are mapped to the corresponding commands
beginning with `full' or `short' before this table is looked up.

MAYBE TODO: For full APA support, it may be necessary to define a
separate citation-formatting function for apacites, but for now
we try cheating.")

(defvar org-cite-apacite-substitutions
  '(("%\n" . "")
    ("\\\\nobreakspace " . (org-cite-str :nobreak))
    ;; I have no idea if these complicated expressions are necessary.
    ;; Will have to look more into apacite.
    ("\\\\BAstyle\\({\\([^}]*\\)}\\)?" . "")
    ("\\\\BAastyle\\({\\([^}]*\\)}\\)?" . "")
    ("\\\\BAnd\\({\\([^}]*\\)}\\)?" . (org-cite-str :and)) ; ed. AND trans.
    ("\\\\BBOP\\({\\([^}]*\\)}\\)?" . "(")
    ("\\\\BBCP\\({\\([^}]*\\)}\\)?" . ")")
    ("\\\\BAP\\({\\([^}]*\\)}\\)?" . " ")
    ("\\\\BBAA\\({\\([^}]*\\)}\\)?" . (org-cite-str :and))
    ("\\\\BBA\\({\\([^}]*\\)}\\)?" . (org-cite-str :and))
    ("\\\\BBAA\\({\\([^}]*\\)}\\)?" . (org-cite-str :and))
    ("\\\\BOthers\\(Period\\| \\){.}" . (org-cite-str :et-al))
    ("\\\\BBAY\\({\\([^}]*\\)}\\)?" . ", ") ; between author and year
    ("\\\\BBYY\\({\\([^}]*\\)}\\)?" . ", ") ; between subsequent years   
    ("\\\\BBN\\({\\([^}]*\\)}\\)?" . ", ")  ; before a postfix note (locator)  
    ("\\\\BBOQ\\({\\([^}]*\\)}\\)?" . "") ; TODO opening quote in title
    ("\\\\BBCQ\\({\\([^}]*\\)}\\)?" . "") ; TODO closing quote in title
    ("\\\\BBC\\({\\([^}]*\\)}\\)?" . "; ")  ; between multiple cites
    ("\\\\BPBI\\({\\([^}]*\\)}\\)?" . ".~") ; Period between initial
    ("\\\\BHBI\\({\\([^}]*\\)}\\)?" . ".-") ; Hyphen between initials
    ("\\\\BCBL\\({\\([^}]*\\)}\\)?" . ",") ; comma before last author
    ("\\\\BCBT\\({\\([^}]*\\)}\\)?" . ",") ; comma between author
    ("\\\\BIn\\({\\([^}]*\\)}\\)?" . (org-cite-str :in)) ; part of other work
    ("\\\\BEDS\\({\\([^}]*\\)}\\)?" . (org-cite-str :eds)) ; Book editors
    ("\\\\BED\\({\\([^}]*\\)}\\)?" . (org-cite-str :ed)) ; Book editor
    ("\\\\BEd" . (org-cite-str :edn))  ; abbreviation for "edition"
    ("\\\\BTR\\({\\([^}]*\\)}\\)?" . "Tech. Rep.") 
    ("\\\\BPGS\\({\\([^}]*\\)}\\)?" . (org-cite-str :pp)) ; between pages
    ("\\\\BNUM\\({\\([^}]*\\)}\\)?" . (org-cite-str :number)) ; Non-journal-issue number, e.g. Report No.
    ;; The followig three are important for cleaning up no-date bibcites 
    ("\\\\bibnodate{}" . (org-cite-str :no-date)) ; TODO check format
    ("{\\\\bibnodate {}}" . (org-cite-str :no-date)) ; NOTE this is some weirdness that crops up in .aux files
    ("\\\\APACyear {\\([^}]+\\)}" . "\\1")
    ("\\\\bibcomputersoftwaremanual" . "computer software manual") ; TODO check format
    ("\\\\unskip" . "")
    ("\\\\protect" . "")
    ("\\\\&" . "&")
    ("{\\\\BCnt{\\([0-9]\\)}}" . (org-cite-num-to-letter (match-string 1))) ; year letter
    (" {}" . "")
    ("\\\\ " . " ")
    ("\\\\APACinsertmetastar{\\([^}]+\\)}" . "\n") ; Before the authorlist
    ("\\\\APACciteatitle{\\([^}]+\\)}" . "“\\1”") ; Cite article title in text
    ("\\\\APACcitebtitle{\\([^}]+\\)}" . "/\\1/") ; Cite book title in text
    ("\\\\APACmonth{\\([0-9]+\\)}" . (nth (1- (string-to-number (match-string 1))) org-cite-months)) ;
    ("\\\\APACrefYearMonthDay{\\([^}]*\\)}{\\([^}]+\\)?}{\\([^}]+\\)?}" . ;; "(\\1, \\2)")
     (concat "(\\1"
     	     (when (match-string 2) ", \\2")
	     (when (match-string 3) " \\3")
	     ")"))
    ("\\\\APACrefYear{\\([^}]+\\)}" . "(\\1)")
    ("\\\\APACrefatitle{\\([^}]+\\)}{\\([^}]+\\)}" . "\\1") ; article title (\\1 is lowercased)
    ("\\\\APACrefbtitle{\\([^}]+\\)}{\\([^}]+\\)}" . "/\\1/") ; book title (\\1 is lowercased)
    ("\\\\APACrefnote{\\([^}]+\\)}" . "(\\1)") ; TODO check formatting (brackets?)
    ("\\\\APACjournalVolNumPages{\\([^}]*\\)}{\\([^}]+\\)?}{\\([^}]+\\)?}{\\([^}]+\\)?}" . 
     (concat "/\\1"
	     (if (match-string 2) ", \\2/ " "/ ")
	     (when (match-string 3) "(\\3)")
	     (when (match-string 4) ", \\4")))
    ("\\\\APACbVolEdTR{\\([^}]*\\)}{\\([^}]*\\)}" . "\\1 \\2") ; not sure about this one
    ("\\\\APACaddressPublisher{\\([^}]+\\)?}{\\([^}]+\\)?}" . 
     (concat (match-string 1) 
	     (when (and (match-string 1) (match-string 2)) ": ") 
	     (match-string 2)))
    ("\\\\APACaddressPublisherEqAuth{\\([^}]+\\)}{\\([^}]+\\)}" . "\\1: \\2")
    ("\\\\APACaddressInstitution{\\([^}]+\\)}{\\([^}]+\\)}" . "\\1: \\2")
    ("\\\\APAChowpublished{\\([^}]+\\)}" . "\\1")
    ("\\\\begin{APACrefURL}" . "Available from ")
    ("\\\\url{\\([^}]+\\)}" . "\\1")
    ("\\\\end{APACrefURL}" . "")
    ("\\\\PrintBackRefs{\\([^}]+\\)}" . "\n")
    ("\\\\PrintOrdinal{\\([^}]+\\)}" . "\\1"))
"Substitutions for the semantic crud left in LaTeX aux and bbl
files by apacite.")


(defun org-cite-map-chars (&optional source target include-math to-string)
  "Utility to extract from org-entities an alist of special
characters/markup in the SOURCE encoding and their equivalents in
the TARGET encoding (for an example, see
org-cite-latex-chars-utf8). SOURCE and TARGET default to latex
and utf8 respectively. Other options are org, html, ascii and
latin1. The list is extracted from org-entities. If INCLUDE-MATH
is non-nil, characters that need to be in math-mode in LaTeX are
also included. If TO-STRING is non-nil, results are returned as a
string of elisp rather than as a list."
  (let ((entities (reverse org-entities))
	(fields '((org . 0) (latex . 1) (mathp . 2) (html . 3) 
		  (ascii . 4) (latin1 . 5) (utf8 . 6)))
	charmap
	record sourcechar targetchar)
    (unless source
      (setq source 'latex
	    target 'utf8))
    (while entities
      (setq record (car entities))
      (when (and (listp record)  ; this is an entry in org-entities
		 (or (not (nth 2 record)) ; and it either is not math-only
		     include-math))  ; or we include math
	(setq sourcechar (nth (cdr (assoc source fields)) record)
	      targetchar (nth (cdr (assoc target fields)) record))
	(when (eq source 'latex)
	  ;; Don't include it if it doesn't start with a "\"
	  (unless (string-match "\\\\" sourcechar) (setq sourcechar ""))
	  ;; Add matchsticks for matching rather than replacing
	  (setq sourcechar (replace-regexp-in-string "\\\\" "\\\\\\\\\\\\\\\\" sourcechar)))
	(unless (string= sourcechar "")
	  (setq charmap 
		(if to-string 
		    (concat "\n(\"" sourcechar "\" . \"" targetchar "\")" charmap)
		  (cons (cons sourcechar targetchar) charmap)))))
	(setq entities (cdr entities)))
    charmap))

(org-cite-map-chars 'latex 'utf8)

(defvar org-cite-latex-chars-utf8
      '(("\\\\`{A}" . "À")
	("\\\\`{a}" . "à")
	("\\\\'{A}" . "Á")
	("\\\\'{a}" . "á")
	("\\\\^{A}" . "Â")
	("\\\\^{a}" . "â")
	("\\\\~{A}" . "Ã")
	("\\\\~{a}" . "ã")
	("\\\\\"{A}" . "Ä")
	("\\\\\"{a}" . "ä")
	("\\\\AA{}" . "Å")
	("\\\\AA{}" . "Å")
	("\\\\aa{}" . "å")
	("\\\\AE{}" . "Æ")
	("\\\\ae{}" . "æ")
	("\\\\c{C}" . "Ç")
	("\\\\c{c}" . "ç")
	("\\\\'{C}" . "Ć") ; lat2: Cacute 
	("\\\\'{c}" . "ć") ; lat2: cacute 
	("\\\\v{C}" . "Č") ; lat2: Ccaron 
	("\\\\v{c}" . "č") ; lat2: ccaron 
	("\\\\^{C}" . "Ĉ") ; lat2: Ccirc
	("\\\\^{c}" . "ĉ") ; lat2: ccirc 
	("\\\\DJ" . "Đ")   ; lat2: Dstrok
	("\\\\dj" . "đ")   ; lat2: dstrok 
	("\\\\`{E}" . "È")
	("\\\\`{e}" . "è")
	("\\\\'{E}" . "É")
	("\\\\'{e}" . "é")
	("\\\\^{E}" . "Ê")
	("\\\\^{e}" . "ê")
	("\\\\\"{E}" . "Ë")
	("\\\\\"{e}" . "ë")
	("\\\\^{G}" . "Ĝ") ; lat2: Gcirc
	("\\\\^{g}" . "ĝ") ; lat2: gcirc 
	("\\\\^{H}" . "Ĥ") ; lat2: Hcirc
	("\\\\^{h}" . "ĥ") ; lat2: hcirc 
	("\\\\`{I}" . "Ì")
	("\\\\`{i}" . "ì")
	("\\\\'{I}" . "Í")
	("\\\\'{i}" . "í")
	("\\\\^{I}" . "Î")
	("\\\\^{i}" . "î")
	("\\\\\"{I}" . "Ï")
	("\\\\\"{i}" . "ï")
	("\\\\^{J}" . "Ĵ") ; lat2: Jcirc
	("\\\\^{j}" . "ĵ") ; lat2: jcirc 
	("\\\\~{N}" . "Ñ")
	("\\\\~{n}" . "ñ")
	("\\\\`{O}" . "Ò")
	("\\\\`{o}" . "ò")
	("\\\\'{O}" . "Ó")
	("\\\\'{o}" . "ó")
	("\\\\^{O}" . "Ô")
	("\\\\^{o}" . "ô")
	("\\\\~{O}" . "Õ")
	("\\\\~{o}" . "õ")
	("\\\\\"{O}" . "Ö")
	("\\\\\"{o}" . "ö")
	("\\\\O" . "Ø")
	("\\\\o{}" . "ø")
	("\\\\OE{}" . "Œ")
	("\\\\oe{}" . "œ")
	("\\\\v{S}" . "Š")
	("\\\\v{s}" . "š")
	("\\\\^{S}" . "Ŝ") ; lat2: Scirc
	("\\\\^{s}" . "ŝ") ; lat2: scirc 
	("\\\\ss{}" . "ß")
	("\\\\`{U}" . "Ù")
	("\\\\`{u}" . "ù")
	("\\\\'{U}" . "Ú")
	("\\\\'{u}" . "ú")
	("\\\\^{U}" . "Û")
	("\\\\^{u}" . "û")
	("\\\\\"{U}" . "Ü")
	("\\\\\"{u}" . "ü")
	("\\\\u{U}" . "Ŭ") ; lat2: Ubreve
	("\\\\u{u}" . "ŭ") ; lat2: ubreve
	("\\\\'{Y}" . "Ý")
	("\\\\'{y}" . "ý")
	("\\\\\"{Y}" . "Ÿ")
	("\\\\\"{y}" . "ÿ")
	("\\\\v{Z}" . "Ž") ; lat2
	("\\\\v{z}" . "ž") ; lat2
	("\\\\DH{}" . "Ð")
	("\\\\dh{}" . "ð")
	("\\\\TH{}" . "Þ")
	("\\\\th{}" . "þ")
	("\\\\dots{}" . "…")
	("\\\\dots{}" . "…")
	("\\\\textperiodcentered{}" . "·")
	("\\\\-" . "")
	("\\\\textquotedbl{}" . "\"")
	("\\\\textasciiacute{}" . "´")
	("\\\\textquotedblleft{}" . "“")
	("\\\\textquotedblright{}" . "”")
	("\\\\quotedblbase{}" . "„")
	("\\\\textquoteleft{}" . "‘")
	("\\\\textquoteright{}" . "’")
	("\\\\quotesinglbase{}" . "‚")
	("\\\\guillemotleft{}" . "«")
	("\\\\guillemotright{}" . "»")
	("\\\\guilsinglleft{}" . "‹")
	("\\\\guilsinglright{}" . "›")
	("\\\\textbrokenbar{}" . "¦")
	("\\\\S" . "§")
	("\\\\&" . "&")
	("\\\\textless{}" . "<")
	("\\\\textgreater{}" . ">")
	("\\\\~{}" . "~")
	("\\\\textdagger{}" . "†")
	("\\\\textdaggerdbl{}" . "‡")
	("\\\\hspace*{.5em}" . " ")
	("\\\\hspace*{1em}" . " ")
	("\\\\hspace*{.2em}" . " ")
	("\\\\textcurrency{}" . "¤")
	("\\\\textcent{}" . "¢")
	("\\\\pounds{}" . "£")
	("\\\\textyen{}" . "¥")
	("\\\\texteuro{}" . "€")
	("\\\\EUR{}" . "€")
	("\\\\EURdig{}" . "€")
	("\\\\EURhv{}" . "€")
	("\\\\EURcr{}" . "€")
	("\\\\EURtm{}" . "€")
	("\\\\textcopyright{}" . "©")
	("\\\\textregistered{}" . "®")
	("\\\\texttrademark{}" . "™")
	("\\\\textpm{}" . "±")
	("\\\\textpm{}" . "±")
	("\\\\texttimes{}" . "×")
	("\\\\textdiv{}" . "÷")
	("\\\\textonehalf{}" . "½")
	("\\\\textonequarter{}" . "¼")
	("\\\\textthreequarters{}" . "¾")
	("\\\\textperthousand{}" . "‰")
	("\\\\textonesuperior{}" . "¹")
	("\\\\texttwosuperior{}" . "²")
	("\\\\textthreesuperior{}" . "³")
	("\\\\textmu{}" . "µ")
	("\\\\textasciimacron{}" . "¯")
	("\\\\textdegree{}" . "°")
	("\\\\textlnot{}" . "¬")
	("\\\\textbullet{}" . "•")
	("\\\\textbullet{}" . "•")
	("\\\\P{}" . "¶")
	("\\\\textordfeminine{}" . "ª")
	("\\\\textordmasculine{}" . "º")
	("\\\\c{}" . "¸")
	("\\\\textasciidieresis{}" . "¨")
	("\\\\/{}" . "‌")
	("\\\\smiley{}" . "☺")
	("\\\\blacksmiley{}" . "☻")
	("\\\\frownie{}" . "☹"))
"Maps LaTeX special characters to utf-8. Based on org-entities,
with additions.")
			   
(provide 'org-cite)