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;; 
;; Author: Mark A. Jensen
;; Email : maj -at- fortinbras -dot- us
;;
;; Part of The Documentation Project
;; http://www.bioperl.org/wiki/The_Documentation_Project
;;
;;

;; Copyright (C) 2009 Mark A. Jensen

;; This program 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 of
;; the License, or (at your option) any later version.

;; This program 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 this program; if not, write to the Free
;; Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
;; Boston, MA 02110-1301 USA


(defconst bioperl-init-revision "$Id$"
  "The revision string of bioperl-init.el")


;;
;; menu bar keymaps
;;

(defvar menu-bar-bioperl-doc-menu
  (let (
	(map (make-sparse-keymap "BioPerl Docs"))
	)
    (define-key map [bp-pod-apx]
      '(menu-item "View appendix" bioperl-view-pod-appendix
		  :help "View pod APPENDIX of a module (where most methods are described)"
		  :keys "\\[bioperl-view-pod-appendix]"))
    (define-key map [bp-pod-dsc]
      '(menu-item "View description" bioperl-view-pod-description
		  :help "View pod DESCRIPTION of a module"
		  :keys "\\[bioperl-view-pod-description]"))
    (define-key map [bp-pod-syn]
      '(menu-item "View synopsis" bioperl-view-pod-synopsis
		  :help "View pod SYNOPSIS of a module"
		  :keys "\\[bioperl-view-pod-synopsis]"))
    (define-key map [bp-pod]
      '(menu-item "View pod" bioperl-view-pod
		  :help "Examine entire pod of a module"
		  :keys "\\[bioperl-view-pod]"))
    (define-key map [bp-pod-mth]
      '(menu-item "View method pod" bioperl-view-pod-method
		  :help "View pod (Title:, Usage:, etc) for a single method"
		  :keys "\\[bioperl-view-pod-method]"))
    map)
  "Menu-bar map for doc functions in bioperl-mode.")


(defvar menu-bar-bioperl-ins-menu
  (let (
	(map (make-sparse-keymap "BioPerl Ins"))
	)
    (define-key map [bp-ins-arr]
      '(menu-item "Insert container template" bioperl-insert-array-accessor
		  :help "Insert template functions for an object array"
		  :keys "\\[bioperl-insert-array-accessor]"))
    (define-key map [bp-ins-obj]
      '(menu-item "Insert class/object template" bioperl-insert-class
		  :help "Insert full object template plus std pod"
		  :keys "\\[bioperl-insert-class]"))
    (define-key map [bp-ins-mthpod]
      '(menu-item "Insert method pod template" bioperl-insert-method-pod
		  :help "Insert Bioperl standard method pod template"
		  :keys "\\[bioperl-insert-method-pod]"))
    (define-key map [bp-ins-genpod]
      '(menu-item "Insert generic class pod template" bioperl-insert-generic-class
		  :help "Insert package declaration plus std pod"
		  :keys "\\[bioperl-insert-generic-class]"))
    (define-key map [bp-ins-acc]
      '(menu-item "Insert accessor template" bioperl-insert-accessor
		  :help "Insert accessor (getter/setter) with std pod"
		  :keys "\\[bioperl-insert-accessor]"))
    (define-key map [bp-ins-mod]
      '(menu-item "Insert module identifier" bioperl-insert-module
		  :help "Insert module identifier, with completion"
		  :keys "\\[bioperl-insert-module]"))
    map)
  "Menu-bar map for insertion functions in bioperl-mode")

;;
;; keymap
;;
;; principles: 
;; C-c accesses mode functions
;; meta key commands - documentation reading (pod display, etc.)
;; control key command - documentation writing (template insertions, etc.)
;;


(defvar bioperl-mode-map
  (let ((map (make-sparse-keymap)))
    (define-key map "\C-c\M-p" 'bioperl-view-pod)
    (define-key map "\C-c\M-d" 'bioperl-view-pod-description)
    (define-key map "\C-c\M-s" 'bioperl-view-pod-synopsis)
    (define-key map "\C-c\M-a" 'bioperl-view-pod-appendix)
    (define-key map "\C-c\M-f" 'bioperl-view-pod-method)
    (define-key map "\C-c\M-m" 'bioperl-view-pod-method)
    (define-key map "\C-cm"   'bioperl-insert-module)
    (define-key map "\C-c\C-a" 'bioperl-insert-accessor)
    (define-key map "\C-c\C-v" 'bioperl-insert-accessor)
    (define-key map "\C-c\C-A" 'bioperl-insert-array-accessor)
    (define-key map "\C-c\C-b" 'bioperl-insert-class)
    (define-key map "\C-c\C-M" 'bioperl-insert-class)
    (define-key map "\C-c\C-k" 'bioperl-insert-generic-class)
    (define-key map "\C-c\C-g" 'bioperl-insert-generic-class)
    (define-key map "\C-c\C-p" 'bioperl-insert-method-pod)
    (define-key map [menu-bar] nil)
    (define-key map [menu-bar bp-ins]
      (list 'menu-item "BP Templs" menu-bar-bioperl-ins-menu))
    (define-key map [menu-bar bp-doc] 
      (list 'menu-item "BP Docs" menu-bar-bioperl-doc-menu))
    map)
  "Keymap for Bioperl minor mode")

;;
;; finders
;;


(defun bioperl-find-module-path (&optional symb val)
  "Find path to Bioperl modules and set `bioperl-module-path'.
This path points to the directory containing Bio; same principle
as 'use lib'. SYMB and VAL are dummies allowing `defcustom' to do
initializaton."
  (let (
	(old-exec-path exec-path) 
	(pth) )
    ;; ask BPMODE_PATH first...
    (setq pth (getenv "BPMODE_PATH"))
    ;; try the environment
    (unless pth
      (let (
	    ( plib (concat (getenv "PERL5LIB") path-separator (getenv "PATH")))
	    ( pths )
	    )
	(if plib
	  (progn
	    (setq pths (split-string plib path-separator))