Pattern lists

[Henrikki Almusa]

Hello,

I can finally report that I have succesfully tested the pattern list with dreg 
and fuzznuc. I will attach four files. Current version of ajpat.c and ajpat.h 
with comments. Patch which I used to test both dreg and fuzznuc. And patch to 
change 'nucleus/embpat.c' and 'nucleus/empat.h', which I have modified to 
allow prosite patterns to run as well. Now I have few questions about next 
part.

1. How to do the acd overloading. In my patch to dreg and fuzznuc, I used 
string and then did what was needed in program. This is not probably the 
correct way, but ok for testing.

2. Should I add a search function into pattern lists? This would allow 
fuzz(nuc|pro|tran) to run regular expression pattern as well (thus obsoleting 
dreg and preg). This change would also mean that patterns in files would need 
a <type=[value]> attribute as well (value might a number or string). But this 
might cause confusion as mismatch values don't work with regexes (even though 
it would be there).

3. Is it ok to use '#include ../nucleus/emboss.h' in 'ajpat.c'? This was done 
as I needed functions from 'nucleus/embpat.h'. If not how this should be done 
then?

4. Any thing else that needs to be fixed for inclusion into emboss? Any 
namings or such? 

Note that to make the patches smaller, I didn't add whitespaces properly in 
front of the lines in dreg and fuzznuc patch.

Thanks,
-- 
Henrikki Almusa
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