[EMBOSS] Emma options

[Scott Hazelhurst]

Dear all,

I am not sure if this is a question for this list or the wemboss forum
-- but their site seems down so I'll ask it here.

I have users who want to specify their own penalty matrices. For
example, for nucleotide sequences the options are clustalw, iub or
own. However, if you pick "own" nothing changes: the option to 
specify your own file doesn't appear. I had a look at the acd file --
not that I properly understand it, and it seems 


I had a look at the acd file -- not that I understand acd syntax
properly so it's a like my trying to fix a broken Jumbo engine.
This seems to be the relevant 

    list: dnamatrix  [
      additional: "@(!$(acdprotein))"
      default: "i"
      minimum: "1"
      maximum: "1"
      header: "Nucleotide multiple alignment matrix options"
      values: "i:iub, c:clustalw, o:own"
      delimiter: ","
      codedelimiter: ":"
      information: "Select matrix"
      button: "Y"
      help: "This gives a menu where you are offered amenu where a
             single matrix (not a series) can be selected."
    ]

    variable: umamatrix "@($(dnamatrix) == own)"

    infile: mamatrix  [
      additional: "@($(usermamatrix)?True:$(umamatrix))"
      default: ""
      nullok: "@($(usermamatrix)?@(!$(umamatrix)):True)"
      information: "Filename of user multiple alignment matrix"
      knowntype: "comparison matrix"
    ]

I  changed the "additional" field in mamatrix to be

      additional: "@($(umamatrix))"

and it seems to work in that the file input box now appears when the
"own" option is seleced.



As an aside, does anyone know the format of what the matrix file
should look like. I did some web searching and looked at the clustalw
source code but it's not so easy to re-engineer..

Can anyone help with either of these queries.

Thanks 

Scott