[EMBOSS] Seqall Datatype

[Peter Robinson]

Peter Rice wrote:
> Dear Peter,
>
>> I am trying my hand at an EMBOSS program and would like to read in a 
>> list of sequences from a FASTA file and make pairwise comparisons 
>> between each sequence.  If I startwith a AjPSeqall object
>>
>> AjPSeqall seqs=NULL;
>> seqs = ajAcdGetSeqall ("seqs");
>
> You want all the sequences in memory so you can work through the pairs 
> - better to use AjPSeqset and ajAcdGetSeqset
>
>> in the documentation, but I would like to do something like a double 
>> for loop to get all pairwise comparisons. What is the best way of 
>> doing this? I have been searching in the online docs but did not yet 
>> find anything.
>
> distmat has the kind of loop you are looking for (except it does self 
> matches too)
>
>
>> By the way, in http://emboss.sourceforge.net/developers/program.html
>>
>> these datatypes are flagged as obsolete by the compiler, so the 
>> document may need revision here?
>
> Yes, all being revised for the books we are preparing ... we will take 
> a look through program.html and make some basic updates to correct 
> these things.
>
> regards,
>
> Peter
>
Dear Peter,
thanks for the tip, that was just what I needed!
best wishes for the holidays!
Peter