# ACEDB User Group Newsletter - January 2004

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@sanger.ac.uk.

A very brief (and late) newsletter for January as both Rob and I have been working mostly on ZMap or DAS 2 issues. There will be a report of progress on ZMap next month.

## New Features

### Some New Query Features

Jean has added further optimisations to the Query language to improve the performance when using COUT.

He has also added webQuery, a registered acembly uitility for users of acembly, please contact Jean Thierry-Mieg for details.

## Articles

### More SMap Related Changes

A number of changes have been made to support the introduction of new classes for sequence annotation in worm base:

In the Sequence class the Source_Exons tag was preceded by a "From" tag:

    	  Structure  From	Source UNIQUE ?Sequence
    				Source_Exons Int UNIQUE Int // start at 1

A dependency in the Temporary Gene code of FMap on the "From" tag has been removed allowing embedding of just the "Source_Exons" tag set into any SMappable class.

The temporary gene code now copies the "CDS", "Start_not_found" and "End_not_found" tags into the temporary gene in a more consistent way.

Any class that contains "Source_Exon" and/or "CDS" tags will now behave like a Sequence class objects for display, dumping etc. giving a consistent look/feel to the way such objects can be annotated. Note that the code now prints a warning if you have a "CDS" tag in an object but no defined "Source_exons". Previously the code manufactured a source exon for dumping/display if one did not exist, but a discussion with the worm group suggested that this sort of implicit production of features was leading to undetected data inconsistencies.

## Bugs Fixed

### Tree Display Update Bug

A bug which meant that text editting was broken in the Update Tree Display mode after a mouse click in the window has been fixed.

### DNA exporting coordinate bug in FMap

A woeful bug in the code that reports DNA assuming it begins at zero instead of 1 has been fixed. This was resulting in the start/end coords in the FASTA file being one less than they should have been.

## Developers Corner

### GTK version 2 is coming

The next monthly build will see wmake/XXXXX_DEF files for compiling acedb with GTK version 2 for both the Alpha and Linux. This will be an important move as the newer version of GTK fixes many bugs and has some good new features. We also need to move versions because the previous GTK version is no longer supported.

### xacez, xace + ZMap

The acedb makefile system now includes an "xacez" target which builds an xace execuatable which includes the display part of the new ZMap code. This is completely experimental so please don't report bugs on it yet. The intention is to allow part of the ZMap code to be embedded in xace so annotators here at Sanger can try out the display as early as possible.

## January monthly build now available.

You can pick up the monthly builds from:

Sanger users
  ~acedb/RELEASE.DEVELOPMENT
External users
  http://www.acedb.org/Software/Downloads/monthly.shtml

Last modified: Tue Feb 24 10:23:37 GMT 2004