[EMBOSS] Seqall Datatype

Peter Robinson peter.robinson at t-online.de
Thu Dec 20 15:08:59 UTC 2007


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");

I have seen

AjPSeq seq;
while(ajSeqallNext(seqs, &seq)) {


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 

By the way, in http://emboss.sourceforge.net/developers/program.html

*17.2 Getting information from a sequence*

*ajSeqGetName* get the name. This is a pointer to the internal AjPStr

*ajSeqName* get the name. This is a pointer to the internal char*

these datatypes are flagged as obsolete by the compiler, so the document 
may need revision here?

Peter Robinson

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