IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

November newsletter

Ed Griffiths edgrif at sanger.ac.uk
Fri Dec 1 08:20:22 EST 2000

and the November newsletter....

the next one should be out around mid-December....

| Ed Griffiths, Acedb development, Informatics Group,                    |
|               The Sanger Centre, Wellcome Trust Genome Campus,         |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif at sanger.ac.uk   URL: http://www.sanger.ac.uk/Users/edgrif |
|   Tel: +44-1223-494780       Fax: +44 1223 494919                      |


ACEDB User Group Newsletter - November 2000

If you want to have this newsletter mailed to you _or_ you want to make
comments/suggestions about the format/content then send an email to
acedb at sanger.ac.uk.

A new acedb developer joins the team, a number of new features for users and
a number of bug fixes.

General News

New acedb developer

After a hiatus of some months following the departure of Fred Wobus from our
team (now pursuing his hobby of scuba diving in Thailand !), we have been
joined by John Sturdy (jcgs at sanger.ac.uk). John is a Computer Science Ph.D.
and has worked for various software companies locally for some years.
Initially he will be working on improving the acedb web site so you should
see quite a few improvements there over the next few weeks.

New Features

"Tree/Text" view and "update" mode

An irritating feature of using "update" mode in the "Tree" window has been
that the window is repositioned at the top when the mode is selected, thus
losing the users place each time an update is performed. This has now been
fixed: select a tag by clicking on it, then select "update" from the right
button menu and the tag will stay visible in the window.

"Tree/Text" view and "Tag search" menu item

Searching for a particular tag in a large object in the tree window can be
tedious, especially when this involves opening collapsed nodes to find the
tag. The right button menu now has an additional "Find tag" item that allows
you to search for a tag (it will find the tag whether the tag is within a
collapsed node or not).

Fmap Horizontal Scrolling

A horizontal scroll bar has been added to the fmap display so its no longer
necessary to turn columns off to see whats displayed over to the right of
the display. Headings/Titles/Column buttons are not redrawn as you scroll
because this slows scrolling down too much.

Support for 2-button mouse users

Most MS-Windows users have 2-button mice which means they have not been able
to use functions that were linked to the middle button on Xwindows/Unix
machines. This has now been fixed by making shift-leftmousebutton do the
same job as the middle button for 2-button users.

Change to help in tace

The _"?"_ command to get help in tace has changed in the way it works. If
there is only one command matching the string following "?" then the syntax
for that one command will be printed, if there is more than one, then syntax
for all matching commands will be printed, e.g.

     gives a list of all available commands
"? d"
     will give a list of all command beginning with "d"
"? du"
     will list the "dump" command because it's the only command that matches

New "spick" addtion to keyset manipulating commands in tace.

If you use the spush, spop etc. commands for manipulating keysets in tace
then you should note a useful addition to these of spick (courtesy of
Lincoln Stein). spick allows you to choose one of the stacked keysets and
make it the active keyset without having to spop the stack to get to the one
you want.

Bugs Fixed

Two Acedb MS-Windows bug fixes

Printing acedb windows now works from Windows 95 in the same way as for
acedb on Unix machines.

You can now use the up and down arrows to scroll through the items in the
keyset window.

xace/tace hang when trying to get write access

Oh dear, while I'd love to say this bug was fixed, its not and can't be for
the foreseeable future. The cause of the bug is based in NFS/lockmanager
problems which arise from time to time on the Sanger network. Acedb uses
lock files to make sure that only one user can have write access to a
database at a time, this works well most of the time. There can be problems
in two situations however: when the network is heavily loaded so that NFS
starts to time out meaning that requests to create/write lockfiles stall and
when lock managers on machines remote from yours on the network begin to
hang (usually because of the NFS problems) meaning that acedb will be unable
to lock its lock files. In either case xace or tace will simply hang, i.e.
not respond to mouse clicks etc.. When this happens, all you can do is kill
the program using the Unix "kill" command, you will need to use "ps" to find
out the process id of the hung program and then type "kill -9 xxxxx" where
xxxxx is the process id. The acedb code cannot detect that this problem has
occurred because it cannot run while waiting to create/lock the lockfile.
Sadly there is nothing we can do to solve this problem.

gene finder bug

There is a bug in the November code which may cause the "Gene finder" button
in fmap to crash the xace program. The problem happens when the definition
of the ?Method class in the models.wrm file in the users database does not
match the definition in the models.wrm file distributed with the code.
Previous versions of acedb did not detect this mismatch and continued to
run, probably with some errors in display of some fmap information.
Detection of this sort of parse error was tightened up recently to support
new function in AcePerl, hence the reason for the code failing now. Database
administrators should check that the definition of the ?Method class in
their models.wrm files matches that distributed with the code level they are

We hope to make the code more tolerant of this problem in the future by
altering the code to check the model of the database against its method own
object and decide if it can continue if there is a difference. This will
probably not happen until the New Year.

Tab key:

There was a bug whereby if the user pressed the Tab key while inputting
text, the window would then no longer accept input. This has now been fixed
and tabs can be used as input to text boxes.

November monthly build now available.

You can pick up the monthly builds from:

_Sanger users_
_External users_

Next User Group Meeting - D213, 2.30pm, Thursday, 9th November

Ed Griffiths <edgrif at sanger.ac.uk>
Last modified: Thu Nov 30 15:53:27 GMT 2000

More information about the Acedb mailing list

Send comments to us at archive@iubioarchive.bio.net