color coding in emacs

color coding in emacs

[Inge]

hi
i frequently use a text editor to view some files containing DNA info.
These are just simply a great number of lines of characters, the
characters can be A,C,G or T. At the moment I would like to have the
text color coded, so that each A has one color, each C has another
color, etc. Since emacs is my favorite editor I wanted to start and see
if emacs could do it for me.
However, I am having some difficulties. I thought about creating a new
major mode and use font-lock. But somehow this doesn't work. The mode
is recognised, but there is no highlighting or coloring. It does work
when I manually use hi-lock, but I want the coloring pattern saved
outside of the file.
Can anyone tell me if this is at all doable with emacs?


To my .emacs (init) file I added the lines:
;; load mode file for fasta mode
(require 'fasta-mode "/home/ivdberg/customize/fasta-mode.el")

(add-to-list 'auto-mode-alist '("\\.fa\\'" . fasta-mode))
(add-to-list 'auto-mode-alist '("\\.fasta\\'" . fasta-mode))

Fasta-mode.el looks like this:
;; fasta-mode.el
;; mode inteded for automatic highlighting of fasta files

(defvar fasta-mode-hook nil)

(defconst fasta-font-lock-keywords
  (list
   '("A" . "Yellow")
   '("C" . "Green")
   '("G" . "Blue")
   '("T" . "Pink"))
)

(defun fasta-mode ()
  "Major mode for highlighting fasta files"
  (interactive)
  (kill-all-local-variables)

  (set (make-local-variable 'font-lock-defaults)
'(fasta-font-lock-keywords))

  (setq major-mode 'fasta-mode)
  (setq mode-name "Fasta")
  (run-hooks 'fasta-mode-hook)
)

(provide 'fasta-mode)

Re: color coding in emacs

[Kevin Rodgers]

Inge wrote:
> hi
> i frequently use a text editor to view some files containing DNA info.
> These are just simply a great number of lines of characters, the
> characters can be A,C,G or T. At the moment I would like to have the
> text color coded, so that each A has one color, each C has another
> color, etc. Since emacs is my favorite editor I wanted to start and see
> if emacs could do it for me.
> However, I am having some difficulties. I thought about creating a new
> major mode and use font-lock. But somehow this doesn't work. The mode
> is recognised, but there is no highlighting or coloring. It does work
> when I manually use hi-lock, but I want the coloring pattern saved
> outside of the file.
> Can anyone tell me if this is at all doable with emacs?

Googling for emacs and dna yields many results, including
http://www.mahalito.net/~harley/elisp/dna-mode.el

> To my .emacs (init) file I added the lines:
> ;; load mode file for fasta mode
> (require 'fasta-mode "/home/ivdberg/customize/fasta-mode.el")
> 
> (add-to-list 'auto-mode-alist '("\\.fa\\'" . fasta-mode))
> (add-to-list 'auto-mode-alist '("\\.fasta\\'" . fasta-mode))
> 
> Fasta-mode.el looks like this:
> ;; fasta-mode.el
> ;; mode inteded for automatic highlighting of fasta files
> 
> (defvar fasta-mode-hook nil)
> 
> (defconst fasta-font-lock-keywords
>   (list
>    '("A" . "Yellow")
>    '("C" . "Green")
>    '("G" . "Blue")
>    '("T" . "Pink"))
> )
> 
> (defun fasta-mode ()
>   "Major mode for highlighting fasta files"
>   (interactive)
>   (kill-all-local-variables)
> 
>   (set (make-local-variable 'font-lock-defaults)
> '(fasta-font-lock-keywords))
> 
>   (setq major-mode 'fasta-mode)
>   (setq mode-name "Fasta")
>   (run-hooks 'fasta-mode-hook)
> )
> 
> (provide 'fasta-mode)

If you want to roll your own, see
http://www.emacswiki.org/cgi-bin/wiki/CreateNewMajorMode

-- 
Kevin Rodgers

Re: color coding in emacs

[Inge]

thank you!
somehow I only did google searches for emacs and coloring/highlighting,
not thinking of the more obvious emacs and dna.

cheers,
Inge