[EMBOSS] please modify two acd files for hmmer package

[jason zhang]

Hi, Peter
Thank you for the suggestion.
> 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.
I planned to hide those advanced options and  they are visible only if 
the end users choose to. But due to the limitation in the web toolkit I 
used, I can not do that easily.
With regards to -sprotein/-snucleotide for antigenic,  the web interface 
can not tell that since there is no such information in ACD. I expect 
the end user has some basic knowledge about the program and will not 
make such mistake.
Not all information in ACD is used. Some information such as variable, 
pattern can not be easily translated to javascript in web page. Again, I 
expect the end user can work it out. Otherwise error will occur at 
execution time.
>
> 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).
This is definitely helpful. I will discuss this with my boss and package 
a parser  if he is ok.
>
> We can do the same for other ACD parsers if there is interest.
>
> regards,
-jason