# ACEDB User Group Newsletter - February 2003

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.

Some enhancements to existing commands and some completely new features such as DAS support and a the prototype of a new FMap like display which will form the basis of a client/server version of FMap.

## New Features

### Message window changes in xace and the stand-alone blixem

If you are used to using the "Message window" which contains a scrolled list of information messages from acedb then you will see that the menu for this window contains a new "Close" button. This allows you to "Close" the message window to get rid of it from the screen temporarily but it will reappear next time there is a message. If you select the "Quit" button then the message window will be closed permanently and acedb will switch back to using individual popup windows for each message.

This change has been made so that the message window can be used in the same way from both xace and the stand-alone blixem program. If you use blixem as a separate/stand-alone program, rather than as part of xace, then you may have been irritated to find that you could not use the scrolled message window, now you can. When the first individual popup window comes up then select the "Switch to Scrolled Message Window" button, all future messages will appear in the single message window. If you want to swop back to the individual popup window, then select "Quit" from the scrolled message window menu.

### "Time_Stamps" command now prints out current time stamp status

A small enhancement to the `Time_Stamps` command (available in tace, giface or the server) means that you can now use the command without options to check what the current status of time stamp setting for the database:

    acedb> ? time
    // ACEDB command: time
    Time_Stamps {on | off} : Show current setting or toggle time stamps creation
    // 0 Active Objects
    acedb> time_stamps
    // Time-stamps currently ON
    // 0 Active Objects
    acedb> time_stamps off
    // Time-stamps now OFF
    // 0 Active Objects
    acedb> time_stamps
    // Time-stamps currently OFF
    // 0 Active Objects
    acedb>

### DAS dumping from acedb

(Note that this is work still under development.

Acedb now supports some of the DAS 1.0 protocol and is able to dump both DASDNA and DASGFF format.

New "dasdna" and "dasgff" commands can be found in the "gif" submenu in giface or the giface version of the server. You could issue the following commands to get dna and gff in DAS format:

    acedb> gif seqget myclone ; dasdna -file my.das

    acedb> gif seqget myclone ; dasgff -file my.das

More DAS support will be added soon and in particular support will be provided for the DAS 2.0 protocol when it comes out.

### Status command now reports last database save date

You can now use the "status" command in any acedb program to find out when the database was last saved. The "database" section of the status output now gives this date in the "Last Save" field:

    acedb> status -database
     // ************************************************
     // AceDB status at 2003-03-06_16:20:59
     //
     // - Database
     //               Title: You complete Wally
     //                Name:
     //             Release: 4_0
     //           Directory: /nfs/team71/acedb/edgrif/acedb/databases/bA404F10
     //             Session: 19
     //                User: edgrif
     //           Last Save: 2002-06-12_14:32:07      <<<<<<<< last database save
     //        Write Access: No
     //      Global Address: 1890
     //
     // ************************************************

    // 0 Active Objects
    acedb>

### AceDB on the HP Itanium

If you build your own AceDB programs from the source code then you can now build on the HP Itanium based machines by setting `ACEDB_MACHINE` to "`HP_4_GCC`". Please send any problems/updates to the make files to acedb@sanger.ac.uk.

## Bugs Fixed

### Temp Gene on reverse strand off by 2

If you use the Gene Finder package from within FMap, there was a horrible bug that led to just the first temporary gene made on the reverse strand being off by 2 in position. This is now fixed, as a side effect the initial double recaculation that acedb was doing the first time an FMap was shown has also been fixed.

### Huge block files

(This article is courtesy of Jean Thierry-Mieg mieg@ray.nlm.nih.gov)

Jean fixed a very old problem that sometimes meant blocks were created that were well over the limit given in database.wrm. There is now a hard limit of 1.8 Gb otherwise the database can end up with blocks that are too big to be read for 32-bit machines which have a hard limit at 2Gb for any disk file.

### Bug in sMapDNA

Fixed bug in sMapDNA(), the function truncates the dna array at wherever it gets up to in inserting the dna found in the database, this is incorrect. The function should reset arrayMax for the dna array to be the maximum size of the array otherwise this causes all sorts of problems not only in FMap but also in the interface presented by the dna exporting functions in tace and giface which end up outputting dna arrays that are clipped in length.

## Future Plans

### Client/server version of FMap

Simon Kelley has been working hard on the graphical part of the new proposed client/server version of FMap. So far the code can display crude sequences and allows multiple windows onto the same sequence and has much improved navigation. The column mechanism will remain much the same except that the special code that displayed alleles and other features will gradually be migrated to use methods.

Ask Simon if you want an early view of what the new FMap will look like.

## Developers Corner

If you wish to make comments/suggestions about any of the below, please mail them to acedb@sanger.ac.uk

### Glib usage

Now that we make link in Glib it makes sense to use its many good functions, I recently made use of the string functions that provide dynamically growing and appendable strings for DAS-GFF dumping code.

Glib also provides very portable functions for getting hold of the program name, the strings corresponding to signal values and much else.

It's worth taking a look at what's available on the Glib pages.

### Change to GFF dumping code in acedb

To support both standard GFF and DASGFF output the dumping code in fmapcontrol.c has been rearranged. The main "`SEG -> GFF`" code still remains in just one routine, but both the standard GFF and the DASGFF dumping routines register callbacks with this main routine. The main routine then calls the callbacks to output each GFF feature in the style of their respective formats.

The rationale for adding DAS support is to allow us to test the new FMap client using DAS format as soon as possible. Lincoln Stein has kindly offered to write some bridge code to translate DAS requests into corresponding acedb commands allowing acedb to act as a DAS server.

## February 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

## Next User Group Meeting - D319, 3.00pm, Thursday, 13th March, 2003

Last modified: Thu Mar 6 17:39:38 GMT 2003