Patterns, patternlists and nucleus/embpat.h

[Henrikki Almusa]

Hello,

I've been checking more on how I could make patterns and patternlist system 
(some patches sent month ago) to work with fuzz(nuc|pro|tran). Only way that 
i could think of is making a new stucture in 'nucleus/embpat.h', which would 
hold almost all the variables needed to run embPatGetType (), 
embPatCompile(), embPatFuzzSearch().

So heres the proposition:

/* @data EmbPPatComp 
**********************************************************
**
** NUCLEUS data structure that holds all needed datas for compiling and
** searching. Not including mismatch number.
**
** @attr pattern [AjPStr] Prosite pattern string
** @attr type [ajint] Prosite pattern compile type
** @attr plen [ajint] Prosite pattern length
** @attr buf [ajint*] Buffer for BMH search
** @attr off [struct EmbSPatBYPNode] Offset buffer for B-Y/P search
** @attr sotable [ajuint*] Buffer for SHIFT-OR
** @attr solimit [ajint] Limit for BMH search
** @attr m [ajint] Real length of pattern (from embPatGetType)
** @attr regex [AjPStr] PCRE regexp string
** @attr skipm [ajint**] Skip buffer for Tarhio-Ukkonen
** @attr amino [AjPBool] Must match left begin
** @attr carboxyl [AjPBool] Must match right
** @@
******************************************************************************/

typedef struct EmbSPatComp
{
    AjPStr pattern;
    ajint type;
    ajint plen;
    ajint* buf;
    EmbOPatBYPNode off[AJALPHA];
    ajuint* sotable;
    ajuint solimit;
    ajint m;
    AjPStr regex;
    ajint** skipm;
    AjPBool amino;
    AjPBool carboxyl;
} EmbOPatComp;
#define EmbPPatComp EmbOPatComp*

And functions for this would be:

void embPatCompileII (EmbPPatComp thys);
void embPatFuzzSearchII (EmbPPATComp thys, ajint begin, const AjPStr name,
			 const AjPStr text, AjPList l, ajint mismatch,
			 void** tidy);
void embPatGetTypeII (EmbPPatComp thys, const AjPStr pattern, ajint mismatch,
		      AjPBool protein);


Any comments?
Thanks,
-- 
Henrikki Almusa