Patten lists ajax header, dirst draft

Henrikki Almusa henrikki.almusa at
Mon Jun 28 11:46:31 UTC 2004

On Monday 28 June 2004 11:20, Henrikki Almusa wrote:
> typedef struct AjSPattern {
>         AjPStr name;
>         AjPStr origpat;
>         AjPStr propat;
>         AjPRegex regexpat;
>         ajint mismatch;
> } AjOPattern;

One question to those, that might know more about the workings of prosite 
pattern searching (fuzz*).

There are functions (in nucleus/embpat.c):

void embPatCompile(ajint type, AjPStr pattern, AjPStr opattern, ajint* plen,
                   ajint** buf, EmbOPatBYPNode* off, ajuint** sotable,
                   ajuint* solimit, ajint* m, AjPStr* regexp, ajint*** skipm,
                   ajint mismatch);

void            embPatFuzzSearch(ajint type, ajint begin, AjPStr pattern,
                                 AjPStr opattern, AjPStr name,
                                 AjPStr text, AjPList *l,
                                 ajint plen, ajint mismatch,
                                 AjBool left, AjBool right,
                                 ajint *buf, EmbOPatBYPNode *off,
                                 ajuint *sotable,
                                 ajint solimit, AjPStr regexp, ajint **skipm,
                                 ajint *hits, ajint m, void **tidy);

Now in fuzznuc they both use the same values for pretty much everything. So 
does this mean that all of those (f.ex. *off, *sotable, solimit) are 
something that should be saved? Because in that case, the above struct for 
pattern won't work. There should be additional stucture to compas everything 
that is needed from complile function to search.

Henrikki Almusa

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