Bibus

Download

Or You can download all file here: http://learn.tsinghua.edu.cn:8080/2005211356/src/bibus.zip

Installation

 $ mysql -u user -p -e "CREATE DATABASE biblio"
 $ mysql -u user -p biblio < mysql.sql
  If you want have a try, you can import example data as well.
 $ mysql -u user -p biblio < biblio.sql
 (add-to-list 'load-path "/path/to/bibus")
 (require 'bibus)

That’s all! Let’s begin.

Start up

bibus invoke by M-x bibus. When it start up, three windows will show in current frame. Typically it will like as following:

         +-----+----------+
         | key |  ref     |
         |     |          |
         |     |          |
         |     |          |
         |     |          |
         |     +----------+
         |     |  entry   |
         +-----+----------+

When you in other buffer, you can back to the bibus by use M-x bibus, too.

In KEY buffer

In “key” buffer, there is a tree widget like this:

[-] Bibus
 |-[-] References
 |  |-  RNA2ndStruct
 |  |-  Database
 |  `-  Junk
 |-  Tagged
 |-  All
 |-[+] Query
 |-  Online
 |-  Import
 `-  Cited

The first node “References” contain several keys. In bibus, a reference can associate with one or more keys. When put button of the keys, the references associate with this key will be displayed in ref buffer. So when you move the TextCursor to the word “RNA2ndStruct”, and press key RET, the reference related with RNA second struct will be displayed. You can use TAB to navigate from one widget to other. You can use key “a” and “d” to add a new key or delete key at current line.

The “Tagged” is a special key, which you can’t temporarily tagged some references. The “All” key contain all references in the database. You can’t delete this keys.

The subtree “Query” contain some query items. When press RET when cursor on the icon before Query, the items will be show. You can use key “s” to view the query sql. Edit the sql with key “e”, and delete with key “d”. To add new query, use key “A”. For a temporary query, you can use C-c C-s which also work in ref or entry buffer. If you want save the temporary query, use key “R” to name the query.

To move to REF buffer, use key sequence C-c C-r, C-c C-e to move to ENTRY buffer, and C-c C-k to move back to KEY buffer. This command is common to REF and ENTRY buffer.

Summary:

Key mode:
 key             binding
---             -------

A               bibus-add-query
R               bibus-name-last-query
a               bibus-add-key
d               bibus-delete-key
e               bibus-edit-query
r               bibus-rename-key
s               bibus-show-key

C-c C-e         bibus-switch-to-entry
C-c C-k         bibus-switch-to-key
C-c C-n         bibus-name-last-query
C-c C-r         bibus-switch-to-ref
C-c C-s         bibus-query

In REF buffer

When you select a key to display, a table like this will display REF buffer:

 Identifier      Author               Year  Title                                   
 Bernhart2006#7> Bernhart, Stephan H> 2006  Local RNA base pairing probabilities in>
 Fekete2000      Fekete, M;Hofacker,> 2000  Prediction of RNA base pairing probabil>
 Flamm2000       Flamm, C;Fontana, W> 2000  RNA folding at elementary step resoluti>
 Flamm2001       Flamm, C;Hofacker, > 2001  Design of multistable RNA molecules     
 Fontana1993     Fontana, W;Stadler,> 1993  RNA folding and combinatory landscapes  
 Hofacker2006    Hofacker, Ivo L;Sta> 2006  Memory efficient folding algorithms for>
 Kidd-Ljunggren> Kidd-Ljunggren, K;Z> 2000  The hepatitis B virus pregenome: predic>
 Muckstein2006   Muckstein, Ulrike;T> 2006  Thermodynamics of RNA-RNA binding       

You can use TAB and BACKTAB to move between columns. You can widen the current column by key “>” and “<” to narrow it. This is only take effect in this section. If you want to save it, you should modify the variable ‘bibus-formats’ and save it in you .emacs. The table can be sort use key “S”. “C-u S” mean sort the table by ascent.

If you want to see the full content of current field, you can press key “s”. And “w” can add the content to kill ring, which you can paste to other place.

To tag the reference to other key, use key “t”. You can tag several reference by marked it first. Mark a reference by use key “m”. After mark the reference, you can do some command with the marked reference, such as associate with other key, add to “Tagged” key, delete them from current key, and delete them from database. Note that, when you delete the reference from current key when press key “d”, the reference is not delete from database. You can delete the reference from database in “All” key using key “D”. When you has some references marked, and you want add a new key name to current reference, you can use key “C-t” to set key for reference of current line. C-c C-o to open the “URL” of the reference, and C-c C-f to open the file. The reference table bibref doesn’t contain a field “File”, so you have to save the file name to a custom field, such as “Custom5”. To change the file name, press key “R”.

Summary:

 key             binding
---             -------
TAB             bibus-next-field
C-t             bibus-set-current-ref-key
C-v             bibus-scroll-up
<               bibus-narrow-column
>               bibus-widen-column
D               bibus-delete-ref
K               bibus-ref-assoc-keys
M               bibus-mark-ref-all
R               bibus-relocate-ref-file
S               bibus-sort-ref
T               bibus-tag-ref
U               bibus-unmark-ref-all
d               bibus-delete-key-ref
j               next-line
k               previous-line
m               bibus-mark-ref-forward
s               bibus-show-field-at-point
t               bibus-set-ref-key
u               bibus-unmark-ref-forward
w               bibus-copy-field-at-point
<backtab>       bibus-prev-field

C-c C-e         bibus-switch-to-entry
C-c C-f         bibus-open-ref-file
C-c C-k         bibus-switch-to-key
C-c C-n         bibus-name-last-query
C-c C-o         bibus-browse-ref-url
C-c C-r         bibus-switch-to-ref
C-c C-s         bibus-query

M->             bibus-end-of-buffer
M-v             bibus-scroll-down

In ENTRY buffer

ENTRY buffer is to show the detail information for the reference. When you move to difference line in REF buffer, the ENTRY will change accord to the line of you cursor. This may take sometime to update, because it is done by a timer which repeat after a delay of certain seconds. The content to show in ENTRY buffer can be customize by modify the variable ‘bibus-entry-list-fields’ which may require to familar with elisp.

When press key “E” in ENTRY buffer, a form will display, you can set the field, and submit by press button in the last line or press key “C-c C-c” outside the text field(I don’t know how to modify keymap in the text field). Quit without change can use key C-u C-c C-c. Reset all field by use key “E”.

Summary:

TAB             widget-forward
RET             widget-button-press
E               bibus-entry-edit
<S-tab>         advertised-widget-backward
<backtab>       widget-backward

C-c C-c         bibus-entry-edit-submit
C-c C-e         bibus-switch-to-entry
C-c C-k         bibus-switch-to-key
C-c C-n         bibus-name-last-query
C-c C-r         bibus-switch-to-ref
C-c C-s         bibus-query

More about customize

Change the buffer name of ref, key, entry

Set bibus-buffer-names in the form of its definition.

Change the window config

Set bibus-window-configuration as the docstring, And Type M-x bibus-erase-window-config, then M-x bibus.

To explain how to work out a setting of bibus-window-configuration, take the setting (key (vertical 0.8 (entry)) (horizontal 0.35 (ref))) as an example.

Let us start at one window, the CAR part of bibus-window-configuration is key, that told set the window associate with the buffer key. the second slot of bibus-window-configuration is (vertical 0.8 (entry)). It tell emacs to split current window vertically with portion 0.8. The third slot is (entry), this is mean set the other window, the below one, as with config (entry), which just set the window associate with entry buffer.

Then we get the windows like this, and current selected window still in key, the above one:

      +--------------------+
      | key                |
      |                    |
      |                    |
      |                    |
      |                    |
      |                    |
      +--------------------+
      | entry              |
      |                    |        
      +--------------------+        

The third slot is (horizontal 0.35 (ref)). It tell emacs to split current window horizontally with poition 0.35 and set the other window with config (ref).

At last we get windows like this:

      +-----+--------------+
      | key | ref          |
      |     |              |
      |     |              |
      |     |              |
      |     |              |
      |     |              |
      +-----+--------------+
      | entry              |
      |                    |        
      +--------------------+        

The setting is done recursively. Before set up a configuration, draw it out and split the window step by step, you can easily make it.

key binding

There is a common map bibus-common-map. Modify this map will take effect in the three buffer. But certain command only can be preformed in one buffer, be careful.

elide string

You can set your elide string in ref buffer, such as “…”. But I don’t think it is a good idea.

reference table formats

You can set the table fields to display in ref buffer. Take the default as example:

(setq bibus-formats
  '(("Author" 20) " " ("Year" 5) " " ("Journal" 10) " " ("Title" 40)))

If the element is a string, this will insert to every line. If it is a list, the CAR part is field name, the CDR part is widen of the column. After change the format, you should compile it by M-x bibus-compile-format.