9364b996a1edba88386fa5919e6d5a24a1ff910d angie Tue Feb 2 11:34:23 2016 -0800 Now that dbDb has a taxId field, update hDbForTaxon to use it instead of going throught UniProt. Also added hTaxId() for looking up a db's taxId. diff --git src/hg/inc/hdb.h src/hg/inc/hdb.h index f6c971b..b8ca57f 100644 --- src/hg/inc/hdb.h +++ src/hg/inc/hdb.h @@ -99,31 +99,31 @@ /* return the name of the proteome database given the genome database name */ boolean hArchiveDbExists(char *database); /* Function to check if this is a valid db name in the dbDbArch table of archived databases. */ boolean hDbExists(char *database); /* Function to check if this is a valid db name */ boolean hDbIsActive(char *database); /* Function to check if this is a valid and active db name */ char *hDefaultDb(void); /* Return the default db if all else fails */ -char *hDbForTaxon(struct sqlConnection *conn, int taxon); +char *hDbForTaxon(int taxon); /* Get database associated with NCBI taxon number if any. */ char *hDbForSciName(char *sciName); /* Get default db for scientific name */ char *hDefaultChrom(char *db); /* Return some sequence named in chromInfo from the given db, or NULL if db * has no chromInfo. */ int hChromCount(char *db); /* Return the number of chromosomes (scaffolds etc.) in the given db. */ struct sqlConnection *hAllocConn(char *db); /* Get free connection if possible. If not allocate a new one. */ @@ -782,30 +782,33 @@ /* Return NULL if unknown database */ /* NOTE: must free returned string after use */ char *hHtmlPath(char *database); /* Return /gbdb path name to html description for this database */ /* Return NULL if unknown database */ /* NOTE: must free returned string after use */ char *hFreezeDate(char *database); /* Return freeze date of database. Use freeMem when done. */ char *hFreezeDateOpt(char *database); /* Return freeze date of database or NULL if unknown database * Use freeMem when done. */ +int hTaxId(char *database); +/* Return taxId (NCBI Taxonomy ID) associated with database. */ + char *hGenomeOrArchive(char *database); /* Return genome name associated from the regular or the archive database. */ char *hGenome(char *database); /* Return genome associated with database. Use freeMem on * return value when done. */ char *hPreviousAssembly(char *database); /* Return previous assembly for the genome associated with database. */ boolean hGotClade(void); /* Return TRUE if central db contains clade info tables. */ char *hClade(char *genome); /* If central database has clade tables, return the clade for the