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After a bit of a shake down caused by the departure of Simon Kelley from the Acedb team we've decided that we will continue to send out a monthly newsletter and do a monthly build. Although we have cut down enormously on how much we are working on acedb, its still enough to warrant continuing with the builds and newsletters.
This newsletter sees the last contributions to acedb from Simon Kelley and describes a number of changes to support the increasing use of different classes to make virtual sequences for display/annotation via FMap or dumping as GFF. We are moving on to GTK version 2 at long last. And there are a number of bug fixes.
As a parting shot Simon Kelley implemented a mechanism for allowing you to create collections of database classes that can be queried as a unit. You could for example clump all your Smap'd classes into a single composite class to make running queries easier. Here's a brief description of how you do this courtesy of Simon:
"Composite classes" behave in the Query language and the Acedb Main window like a superclass of their members.
They are called "Composite classes" because we already have a concept of superclasses which are the inverse of subclasses.
To make a Composite class:
You need to add the class to subclasses.wrm (I know, I know, it's like using the "Start" menu to shut down the computer.) There is a new tag in Class class called "Composite_of", so to make a Composite class called "Interesting" which is all Sequences and Loci add the following to subclasses.wrm
Class Interesting
Visible
Composite_of Sequence
Composite_of Locus
The new class behaves like a protected class (you can't create objects of that class) but you can query it and select it in the main window.
Unfortunately there will be no AQL support for the foreable future.
If you don't use the Gene finder facility built into FMap then there's probably not much point in reading this.
The introduction of the SMap tags into acedb has meant that it is now possible to construct virtual sequences for display by FMap not just from Sequence class objects, but from any classes the user has embedded the SMap tags in. This has meant changes to Acedb in a number of places to generalise the code to handle any number of classes.
The Gene finder facility allows the user to create new "gene" objects to match the exons/splice site information produced by the Gene Finder code. Previously these objects could only be Sequence class objects, now they could be any one of a number of classes. The "Selected -> temp_gene" menu item now gives a submenu allowing the user to select the class of the temp_gene to be created. To be included in the submenu a class must contain the S_Parent and Source_Exons tags, i.e. the class must be mappable and able to represent exons in the usual acedb style.
The code that fixes and removes temporary genes has also been altered to cope with temp_gene_N objects of different classes.
An earlier attempt to allow different class objects to be created relied on the user setting a USE_CDS_CLASS preference, this is now redundant and has been removed from the preferences list.
GTK has been our underlying widget set (i.e. the library that provides sliders, buttons etc.) for some years now. Up until recently acedb was only compiled with GTK version 1 which is now substantially out of date.
Accordingly we have put some effort (thanks to Simon for getting this all going) into getting acedb to compile with GTK version 2. The newer version has many bug fixes and improvements but has required a number of code and build changes.
The build changes are encapsulated in scripts in w3rdparty/ and the usual wmake/XXXX_DEF files. For now the relevant wmake/XXXX_DEF files contain "GTK2" as part of their file name, e.g. LINUX_GTK2_4_DEF. We have provided DEF files for Linux and Alpha builds.
As users incorporate new classes into their sequence data to replace the old monolithic Sequence class based data there have had to be a number of changes to the FMap. Its likely that these changes will continue for some time to come. Latest changes include:
In response to a frequent user request, fullscreen crosshairs are now the default.
Fixed bug whereby a failed Find didn't give an error message.
Fixed horrible bug in fmap window title, same old dangling text pointer issues. This bug caused window title to sometimes be garbage because pointer that name(key) returned was no longer pointing to the name of the key.
Yet more horrid text pointer stuff, we were passing blixem the pointer returned by name(key), the blixem code then truncated this text directly because it didn't take a copy of the text, this changed the text in the lex thus actually changing the name of the object in the database ! This didn't show up before because most object names were sufficiently short that blixem did not truncate them for display, the Otter/lace system at Sanger creates long object names automatically for its assemblies and this revealed the bug.
Fixed bug in socket layer: I misunderstood how much shutdown() does for you, I thought it closed the file as well as stopping the TCP connection. This turns out not to be true, you need to explicitly close the connection after the shutdown. I think this is fixed but the command that lets you monitor how many files a process has open is su root so I can't check this..sigh.
Simon Kelley says:
For programming, I've added one function
BOOL pickBelongsToComposite(KEY classe, KEY key)
classe can either be a small integer from pickWord2Class or a Key in Class class. The function returns TRUE of key is in classe. It's legal to call it with either composite or ordinary classes.
The introduction of multiple classes has required a number of changes to the smap code, this is a sample of the type of work that's had to be done:
These changes are courtesy of Rob Clack.
Added better support to Aquila for which executable is run, e.g. tace, giface etc.
Aquila requires the Mail package and now warns if its not available.
gff tests added, very important now many different classes are being SMap'd and then dumped.
You can pick up the monthly builds from: