Howdo, Brian - I didn't notice your email till just now.
Brian Smith wrote:
As a 1.x user I really like the look of 2.3 - will be a great tool.
I am having some troubles with certain features (using webstarted 2.3 on WinXP):
Fetch sequences doesn't seem to work for me. Selecting Uniprot or PDB and entering known accession numbers/ids just gives me an "Error retrieving..." dialogue each time. I think I have my proxy setting correct (bare hostname & port and the web services are working now). Does this service depend on particular servers? Is there a way to get more informative debug info?
There is.
Jalview creates a .jalview_properties file in the directory above the 'My Documents' folder. If you close Jalview, and add the line :
logs.Jalview.level=DEBUG
(and make sure there's a new line at the end)
then much more debugging info will be generated.
logs.Axis.level=INFO
can also be changed to get debug information out of the SOAP services,
and
logs.Castor.level=INFO
can be changed to DEBUG if you want excessive info on XML serialization and deserialization.
You also need to have the Java Console displayed though. If you open up the Java settings control panel (you can do this by running the command javaws -viewer) and look under the Java Console settings in the 'Advanced' tab.
I'd be interested to see what the errors that you observe are. I have two independent occurences of Jalview runnng on XP boxes not being able to access either the EBI services or the Jalview questionnaire service. One of these was due to an issue at the EBI - this might be occuring for you, too.
Add Sequence -> URL option. Is there a way to read sequences from SRS or NCBI via this route in a format that is recognised, or is it intended more for accessing e.g. a ready formatted file on a local server?
In principle you should be able to construct a URL query for both SRS and NCBI that returns a sequence file in a recognised format. Try copying the URL associated with a link on the server for viewing a sequence as fasta, for instance.
At the moment, jalview doesn't discard the html tags that certain servers present the flatfiles in though - so that might be the problem. You could try cut'n'paste in that case (directly into the alignment window).
NCBI
URLs complain about the format while EBI SRS URLs load garbage composed of the characters in the URL itself which seems fair enough if you're not parsing the html stuff.
You'll have to be a bit more specific with this - can you provide some urls which were giving problems ?
Web Services: was the server really down for a while this afternoon? I was getting errors on submission but seems to be working now.
There was no downtime as far as I know. Looking at the logs, there were no errors - except for some jobs that were killed because they ran for more than an hour. If these were yours then sorry - this is the policy with public jobs. What submission errors did you get ?
cheers.
Jim.