76a4d66b576dee44a14c4e73cd2bf18f4d0a812a jcasper Fri Oct 21 12:43:37 2016 -0700 Removing prototypes for previously removed functions, refs #14715 diff --git src/hg/inc/hdb.h src/hg/inc/hdb.h index b8ca57f..72dd2f6 100644 --- src/hg/inc/hdb.h +++ src/hg/inc/hdb.h @@ -86,34 +86,30 @@ char *type; /* A guess at the trackDb type for this. */ }; struct slName *hTrackDbList(void); /* Return list of trackDb tables from the config file. Free list when done. */ void hSetTrackDbName(char *trackDbName); /* Override the hg.conf db.trackDb setting. */ struct slName *hTrackTablesOfType(struct sqlConnection *conn, char *type); /* get list of tables in trackDb list with type */ char *hPdbFromGdb(char *genomeDb); /* 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(int taxon); /* Get database associated with NCBI taxon number if any. */ char *hDbForSciName(char *sciName); /* Get default db for scientific name */ @@ -431,52 +427,39 @@ * names only). See also hDbDbList. */ struct dbDb *hDbDb(char *database); /* Return dbDb entry for a database */ struct dbDb *hDbDbList(void); /* Return list of databases that are actually online. * The list includes the name, description, and where to * find the nib-formatted DNA files. Free this with dbDbFree. */ struct dbDb *hDbDbListMaybeCheck(boolean doCheck); /* Return list of databases in dbDb. If doCheck, check database existence. * The list includes the name, description, and where to * find the nib-formatted DNA files. Free this with dbDbFree. */ -struct dbDb *hArchiveDbDbList(void); -/* Return list of databases in archive central dbDb. - * Free this with dbDbFree. */ - struct hash *hDbDbHash(); /* The hashed-up version of the entire dbDb table, keyed on the db */ -/* this is likely better to use than hArchiveOrganism if it's likely to be */ -/* repeatedly called */ - -struct hash *hDbDbAndArchiveHash(); -/* hDbDbHash() plus the dbDb rows from the archive table */ int hDbDbCmpOrderKey(const void *va, const void *vb); /* Compare to sort based on order key */ char *hDbDbNibPath(char *database); /* return nibPath from dbDb for database */ -struct sqlConnection *hMaybeConnectArchiveCentral(void); -/* Connect to central database for archives. - * Free this up with hDisconnectCentralArchive(). */ - char *hHttpHost(); /* return http host from apache or hostname if run from command line */ boolean hHostHasPrefix(char *prefix); /* Return TRUE if this is running on web-server with host name prefix */ boolean hIsPrivateHost(void); /* Return TRUE if this is running on private (development) web-server. * This was originally genome-test as well as hgwdev, however genome-test * may be repurposed to direct users to the preview site instead of development site. */ boolean hIsBetaHost(void); /* Return TRUE if this is running on beta (QA) web-server. * Use sparingly as behavior on beta should be as close to RR as possible. */ @@ -722,96 +705,75 @@ * fromDb. */ struct hash *hGetDatabaseRank(void); /* Get list of databases and make a hash of order rank * Dispose of this with hashFree. */ struct dbDb *hGetLiftOverFromDatabases(void); /* Get list of databases for which there is at least one liftOver chain file * Dispose of this with dbDbFreeList. */ struct dbDb *hGetLiftOverToDatabases(char *fromDb); /* Get list of databases for which there are liftOver chain files * to convert from the fromDb assembly. * Dispose of this with dbDbFreeList. */ -struct dbDb *hGetAxtInfoDbs(char *db); -/* Get list of db's where we have axt files listed in axtInfo . - * The db's with the same organism as organism go last. - * Dispose of this with dbDbFreeList. */ - -struct axtInfo *hGetAxtAlignments(char *db, char *otherDb); -/* Get list of alignments where we have axt files listed in axtInfo . - * Dispose of this with axtInfoFreeList. */ - -struct axtInfo *hGetAxtAlignmentsChrom(char *db, char *otherDb, char *chrom); -/* Get list of alignments where we have axt files listed in axtInfo for a specified chromosome . - * Dispose of this with axtInfoFreeList. */ - struct dbDb *hGetBlatIndexedDatabases(void); /* Get list of databases for which there is a BLAT index. * Dispose of this with dbDbFreeList. */ boolean hIsBlatIndexedDatabase(char *db); /* Return TRUE if have a BLAT server on sequence corresponding * to give database. */ struct blatServerTable *hFindBlatServer(char *db, boolean isTrans); /* return the blat server information corresponding to the database */ char *hDefaultPos(char *database); /* param database - The database within which to look up this position. return - default chromosome position associated with database. Use freeMem on return value when done. */ char *hOrganism(char *database); /* Return organism associated with database. Use freeMem on * return value when done. */ -char *hArchiveOrganism(char *database); -/* Return organism associated with database. Use freeMem on - * return value when done. This one checks the normal central - * DB first, then the archive dbDb. */ - int hOrganismID(char *database); /* Get organism ID from relational organism table */ /* Return 0 if not found. */ char *hScientificName(char *database); /* Return scientific name for organism represented by this database */ /* 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 * given genome; otherwise return NULL. */ char *hDefaultDbForGenome(char *genome);