[EMBOSS] please modify two acd files for hmmer package

[Peter Rice]

jason zhang wrote:
> Hi, peter
> Peter Rice wrote:
>> I am curious ... what does your parser do? We have a few changes in 
>> the new release (extra attributes).
>>
> I am coding an application which provides web interface and web service 
> interface to a set of applications including EMBOSS.  If you are 
> interested, the web interface is here: 
> http://174.129.249.18:8080/appweb.

Thanks. I gave it a try. looks like a good start.

> The application is currently at beta stage.  The application parses ACD 
> file and generates Web interface and Web Service (WSDL).   Are the extra 
> attributes in the new release documented somewhere? I will support them 
> in my parser if web interface or Web Service are impacted.

There is updated documentation at 
http://emboss.sourceforge.net/developers/acd/syntax.html which we 
automatically update with new datatypes and attributes (though I now 
notice it says version 3.0.0 - I will fix that!)

I see your web interface includes every option ... rather like we do 
with the SoapLab web services. A few are not valid in all cases ... for 
example, when I run "antigenic" which only accepts protein sequences the 
-snucleotide option will break the run and -sprotein is unnecessary. On 
balance I find users are happiest when the options are always the same 
... but you could consider hiding the less useful ones (sequence input 
options, anything in the "advanced" section of ACD ... with some way for 
the user to find them and use them. This is in line with the command 
line philosophy - even with -option on the command line these are never 
prompted for, but they can be used if the user reads the documentation 
or studies the -help options.

Let us know if there is anything we can do to help ... for example, 
could we run your parser on each new release and send you the results 
(that implies running it aftre significant ACD changes and informing you 
if we see any problems at that stage).

We can do the same for other ACD parsers if there is interest.

regards,

Peter Rice