Prophet & profit

[Henrikki Almusa]

Hello,

I was watching the outputs of prophet and profit and noticed that they seem to 
have their own respective outputs. After some check in code I noticed that 
Profit has its own function 'profit_printHits' and prophet uses some basic 
function 'embAlignPrintProfile'.

Now to question. Is there some reason why they don't use AjPAlign and its 
functions (other than that it was created before the standard formats)? Would 
it be a good thing to try to make them use AjPAlign?

Mainly i'm after the idea that one could use '-aformat' with prophet and 
profit. I might have time to take a look and see if I can fix this.

I did some reading on code and noticed that embAlignReportProfile uses seqset 
and prophet doesn't read this in. So what is that seqset and why it is 
embAlingReportProfile and not in embAlingReport(Local|Global)? Can seqset be 
made, instead of read from file or would if be better to use 
embAlingReportLocal instead of embAlingReportProfile?

Thanks,
-- 
Henrikki Almusa