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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@73 60f365c0-8329-0410-b2a4-ec073aeeaa1d

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This commit is contained in:
Eric Coissac
2007-06-20 07:38:54 +00:00
parent dc6e7bba69
commit 433a19fd87
1 changed files with 35 additions and 2 deletions
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37
src/libecoPCR/ecoPCR.h
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@ -80,12 +80,42 @@ typedef struct {
char* label[1]; char* label[1];
} ecorankidx_t; } ecorankidx_t;
/*
*
* Taxonomy name types
*
*/
typedef struct { typedef struct {
int32_t is_scientificname;
int32_t namelength;
int32_t classlength;
int32_t taxid;
char names[1];
} econameformat_t;
typedef struct {
char *name;
char *classname;
int32_t is_scientificname;
struct ecotxnode *taxon;
} econame_t;
typedef struct {
int32_t count;
econame_t names[1];
} econameidx_t;
typedef struct {
ecorankidx_t *ranks; ecorankidx_t *ranks;
econameidx_t *names;
ecotxidx_t *taxons; ecotxidx_t *taxons;
} ecotaxonomy_t; } ecotaxonomy_t;
/***************************************************** /*****************************************************
* *
* Function declarations * Function declarations
@ -175,6 +205,9 @@ ecoseq_t *readnext_ecoseq(FILE *);
ecorankidx_t *read_rankidx(const char *filename); ecorankidx_t *read_rankidx(const char *filename);
econameidx_t *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
/** /**
* Read taxonomy data as formated by the ecoPCRFormat.py script. * Read taxonomy data as formated by the ecoPCRFormat.py script.
@ -189,7 +222,7 @@ ecorankidx_t *read_rankidx(const char *filename);
ecotxidx_t *read_taxonomyidx(const char *filename); ecotxidx_t *read_taxonomyidx(const char *filename);
ecotaxonomy_t *read_taxonomy(const char *prefix); ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName);
ecotx_t *eco_findtaxonbytaxid(ecotaxonomy_t *taxonomy, int32_t taxid); ecotx_t *eco_findtaxonbytaxid(ecotaxonomy_t *taxonomy, int32_t taxid);