4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/inc/hdb.h src/hg/inc/hdb.h index 655d358..488090a 100644 --- src/hg/inc/hdb.h +++ src/hg/inc/hdb.h @@ -1,1082 +1,1082 @@ /* hdb - human genome browser database. */ /* Copyright (C) 2014 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef HDB_H #define HDB_H #ifndef DNAUTIL_H #include "dnautil.h" #endif #ifndef DNASEQ_H #include "dnaseq.h" #endif #ifndef DYSTRING_H #include "dystring.h" #endif #ifndef JKSQL_H #include "jksql.h" #endif #ifndef TRACKDB_H #include "trackDb.h" #endif #ifndef HGRELATE_H #include "hgRelate.h" #endif #ifndef BED_H #include "bed.h" #endif #ifndef CUSTOMTRACK_H #include "customTrack.h" #endif struct chromInfo; /* At or below this number of sequences, allow split tables: */ #define HDB_MAX_SEQS_FOR_SPLIT 100 /* Statically-allocated string lengths (max supported len incl. final \0): */ #define HDB_MAX_CHROM_STRING 255 #define HDB_MAX_BAND_STRING 64 #define HDB_MAX_FIELD_STRING 32 #define HDB_MAX_TABLE_STRING 128 #define HDB_MAX_PATH_STRING 512 struct blatServerTable /* Information about a BLAT server. */ { char *db; /* Database name. */ char *genome; /* Genome name. */ boolean isTrans; /* Is tranlated to protein? */ char *host; /* Name of machine hosting server. */ char *port; /* Port that hosts server. */ char *nibDir; /* Directory of sequence files. */ }; struct hTableInfo /* Some info on a track table, extracted from its field names. */ { struct hTableInfo *next; /* Next in list. */ char *rootName; /* Name without chrN_. */ boolean isPos; /* True if table is positional. */ boolean isSplit; /* True if table is split. */ boolean hasBin; /* True if table starts with field. */ char chromField[HDB_MAX_FIELD_STRING]; /* Name of chromosome field. */ char startField[HDB_MAX_FIELD_STRING]; /* Name of chromosome start field. */ char endField[HDB_MAX_FIELD_STRING]; /* Name of chromosome end field. */ char nameField[HDB_MAX_FIELD_STRING]; /* Name of item name field. */ char scoreField[HDB_MAX_FIELD_STRING]; /* Name of score field. */ char strandField[HDB_MAX_FIELD_STRING]; /* Name of strand field. */ char cdsStartField[HDB_MAX_FIELD_STRING]; /* Name of cds(thick)Start field. */ char cdsEndField[HDB_MAX_FIELD_STRING]; /* Name of cds(thick)End field. */ char countField[HDB_MAX_FIELD_STRING]; /* Name of exon(block)Count field. */ char startsField[HDB_MAX_FIELD_STRING]; /* Name of exon(block)Starts field. */ char endsSizesField[HDB_MAX_FIELD_STRING]; /* Name of exon(block)Ends(Sizes) field. */ char spanField[HDB_MAX_FIELD_STRING]; /* Name of span field. (wiggle) */ boolean hasCDS; /* True if it has cdsStart,cdsEnd fields. */ boolean hasBlocks; /* True if it has count,starts,endsSizes. */ 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 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 */ 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. */ char *hNcbiGcfId(char *db); /* Return the NCBI RefSeq assembly+annotations ID (GCF_...) for db, or NULL if we don't know it. */ char *hNcbiGcaId(char *db); /* Return the NCBI GenBank assembly id (GCA_...) for db, or NULL if we don't know it. */ struct sqlConnection *hAllocConn(char *db); /* Get free connection if possible. If not allocate a new one. */ struct sqlConnection *hAllocConnMaybe(char *db); /* Get free connection if possible. If not allocate a new one. Return * NULL if db doesn't exist or can't be connected to. */ char *getTrackProfileName(struct trackDb *tdb); /* get profile is associated with a track, return it, otherwise NULL */ struct sqlConnection *hAllocConnProfile(char *profileName, char *db); /* Get free connection, specifying a profile and/or a database. If none * is available, allocate a new one. */ struct sqlConnection *hAllocConnProfileMaybe(char *profileName, char *db); /* Get free connection, specifying a profile and/or a database. If none is * available, allocate a new one. Return NULL if database doesn't exist. */ struct sqlConnection *hAllocConnTrack(char *db, struct trackDb *tdb); /* Get free connection for accessing tables associated with the specified * track and database. If none is available, allocate a new one. */ struct sqlConnection *hAllocConnProfileTbl(char *db, char *spec, char **tableRet); /* Allocate a connection to db, spec can either be in the form `table' or * `profile:table'. If it contains profile, connect via that profile. Also * returns pointer to table in spec string. */ struct sqlConnection *hAllocConnProfileTblMaybe(char *db, char *spec, char **tableRet); /* Allocate a connection to db, spec can either be in the form `table' or * `profile:table'. If it contains profile, connect via that profile. Also * returns pointer to table in spec string. Return NULL if database doesn't exist */ struct sqlConnection *hAllocConnDbTbl(char *spec, char **tableRet, char *defaultDb); /* Allocate a connection to db and table, spec is in form `db.table'; if * defaultDb is not NULL, 'table' can also be used. Also returns pointer to * table in spec string. */ void hFreeConn(struct sqlConnection **pConn); /* Put back connection for reuse. */ struct sqlConnection *hConnectCentral(void); /* Connect to central database where user info and other info * not specific to a particular genome lives. Free this up * with hDisconnectCentral(). */ void hDisconnectCentral(struct sqlConnection **pConn); /* Put back connection for reuse. */ struct sqlConnection *hConnectCart(void); /* Connect to cart database. Defaults to the central connection * unless cart.db or cart.host are configured. Free this * up with hDisconnectCart(). */ void hDisconnectCart(struct sqlConnection **pConn); /* Put back connection for reuse. */ char *hgOfficialChromName(char *db, char *name); /* Returns "cannonical" name of chromosome or NULL * if not a chromosome. */ boolean hgIsOfficialChromName(char *db, char *name); /* Determine if name is exact (case-sensitive) match with * a chromosome in the current assembly */ boolean hgPdbOk(char *database); /* Return TRUE if hgPdbOk is on in dbDb * on this database. */ boolean hgNearOk(char *database); /* Return TRUE if ok to put up familyBrowser (hgNear) * on this database. */ boolean hgPcrOk(char *database); /* Return TRUE if ok to put up hgPcr on this database. */ boolean hTableExists(char *db, char *table); /* Return TRUE if a table exists in database. */ boolean hTableOrSplitExists(char *db, char *table); /* Return TRUE if table (or a chrN_table) exists in database. */ char *hTableForTrack(char *db, char *trackName); /* Return a table for a track in db. Returns one of the split * tables, or main table if not split */ char *hReplaceGbdbLocal(char* fileName); /* Returns a gbdb filename, potentially rewriting it according to hg.conf's gbdbLoc1 */ /* Result has to be freed */ char *hReplaceGbdb(char* fileName); /* clone and change a filename that can be located in /gbdb to somewhere else * according to hg.conf's "gbdbLoc1" and "gbdbLoc2". Result has to be freed. */ char *hReplaceGbdbSeqDir(char *path, char *db); /* similar to hReplaceGbdb, but accepts a nib or 2bit "directory" (basename) under * gbdb, like /gbdb/hg19 (for jkLib that means /gbdb/hg19/hg19.2bit). */ char* hReplaceGbdbMustDownload(char* path); /* given a location in /gbdb, rewrite it to the new location using gbdbLoc1 and download it * if needed from gbdbLoc2. */ void hParseTableName(char *db, char *table, char trackName[HDB_MAX_TABLE_STRING], char chrom[HDB_MAX_CHROM_STRING]); /* Parse an actual table name like "chr17_random_blastzWhatever" into * the track name (blastzWhatever) and chrom (chr17_random). */ void hParseDbDotTable(char *dbIn, char *dbDotTable, char *dbOut, size_t dbOutSize, char *tableOut, size_t tableOutSize); /* If dbDotTable contains a '.', then assume it is db.table and parse out into dbOut and tableOut. * If not, then it's just a table; copy dbIn into dbOut and dbDotTable into tableOut. */ int hChromSize(char *db, char *chromName); /* Return size of chromosome. */ struct chromInfo *hGetChromInfo(char *db, char *chrom); /* Get chromInfo for named chromosome (case-insens.) from db. * Return NULL if no such chrom. */ struct dnaSeq *hFetchSeq(char *fileName, char *seqName, int start, int end); /* Fetch sequence from file. If it is a .2bit file then fetch the named sequence. If it is .nib then just ignore seqName. */ struct dnaSeq *hFetchSeqMixed(char *fileName, char *seqName, int start, int end); /* Fetch mixed case sequence. */ struct dnaSeq *hChromSeq(char *db, char *chrom, int start, int end); /* Return lower case DNA from chromosome. */ struct dnaSeq *hChromSeqFromPath(char *nibPath, char *db, char *chrom, int start, int end); /* Return lower case DNA from chromosome. */ struct dnaSeq *hChromSeqMixed(char *db, char *chrom, int start, int end); /* Return mixed case (repeats in lower case) DNA from chromosome. */ struct dnaSeq *hChromSeqMixedFromPath(char *nibPath, char *db, char *chrom, int start, int end); /* Return mixed case (repeats in lower case) DNA from chromosome, given an * input nib path. */ struct dnaSeq *hSeqForBed(char *db, struct bed *bed); /* Get the sequence associated with a particular bed concatenated together. */ boolean hChromBand(char *db, char *chrom, int pos, char retBand[HDB_MAX_BAND_STRING]); /* Fill in text string that says what band pos is on. * Return FALSE if not on any band, or table missing. */ boolean hChromBandConn(struct sqlConnection *conn, char *chrom, int pos, char retBand[HDB_MAX_BAND_STRING]); /* Fill in text string that says what band pos is on. * Return FALSE if not on any band, or table missing. */ boolean hScaffoldPos(char *db, char *chrom, int start, int end, char **retScaffold, int *retStart, int *retEnd); /* Return the scaffold, and start end coordinates on a scaffold, for * a chromosome range. If the range extends past end of a scaffold, * it is truncated to the scaffold end. * Return FALSE if unable to convert */ struct dnaSeq *hDnaFromSeq(char *db, char *seqName, int start, int end, enum dnaCase dnaCase); /* Fetch DNA in a variety of cases. */ struct dnaSeq *hLoadChrom(char *db, char *chromName); /* Fetch entire chromosome into memory. */ void hNibForChrom(char *db, char *chromName, char retNibName[HDB_MAX_PATH_STRING]); /* Get .nib file associated with chromosome. */ void hNibForChromFromPath(char *nibPath, char *db, char *chromName, char retNibName[HDB_MAX_PATH_STRING]); /* Get .nib file associated with chromosome, given a nib file path. */ struct slName *hAllChromNames(char *db); /* Get list of all chromosomes in database. */ char *hExtFileNameC(struct sqlConnection *conn, char *extFileTable, unsigned extFileId); /* Get external file name from table and ID. Typically * extFile table will be 'extFile' or 'gbExtFile' * Abort if the id is not in the table or if the file * fails size check. Please freeMem the result when you * are done with it. (requires conn passed in) */ char *hExtFileName(char *db, char *extFileTable, unsigned extFileId); /* Get external file name from table and ID. Typically * extFile table will be 'extFile' or 'gbExtFile' * Abort if the id is not in the table or if the file * fails size check. Please freeMem the result when you * are done with it. */ struct dnaSeq *hDnaSeqGet(char *db, char *acc, char *seqTbl, char *extFileTbl); /* Get a cDNA or DNA sequence from the specified seq and extFile tables. The * seqTbl/extFileTbl arguments may include the database, in which case they * override what is in db (which could even be NULL). Return NULL if not * found. */ struct dnaSeq *hDnaSeqMustGet(char *db, char *acc, char *seqTbl, char *extFileTbl); /* Get a cDNA or DNA sequence from the specified seq and extFile tables. The * seqTbl/extFileTbl arguments may include the database, in which case they * override what is in db (which could even be NULL). * Abort if not found. */ struct dnaSeq *hDnaSeqGetConn(struct sqlConnection *conn, char *acc, char *seqTbl, char *extFileTbl); /* Get a cDNA or DNA sequence from the specified seq and extFile tables. Return NULL if not * found. */ struct dnaSeq *hDnaSeqMustGetConn(struct sqlConnection *conn, char *acc, char *seqTbl, char *extFileTbl); /* Get a cDNA or DNA sequence from the specified seq and extFile tables. * Abort if not found. */ aaSeq *hPepSeqGet(char *db, char *acc, char *seqTbl, char *extFileTbl); /* Get a peptide sequence from the specified seq and extFile tables. The * seqTbl/extFileTbl arguments may include the database, in which case they * override what is in db (which could even be NULL). Return * NULL if not found. */ aaSeq *hPepSeqMustGet(char *db, char *acc, char *seqTbl, char *extFileTbl); /* Get a peptide sequence from the specified seq and extFile tables. Abort if * not found. */ int hRnaSeqAndIdx(char *acc, struct dnaSeq **retSeq, HGID *retId, struct sqlConnection *conn); /* Return sequence for RNA and it's database ID. Return -1 if not found. */ char* hGetSeqAndId(struct sqlConnection *conn, char *acc, HGID *retId); /* Return sequence as a fasta record in a string and it's database ID, or * NULL if not found. */ struct dnaSeq *hExtSeq(char *db, char *acc); /* Return sequence for external seq. */ struct dnaSeq *hExtSeqPart(char *db, char *acc, int start, int end); /* Return part of external sequence. */ struct dnaSeq *hRnaSeq(char *db, char *acc); /* Return sequence for RNA. */ aaSeq *hPepSeq(char *db, char *acc); /* Return sequence for a peptide. */ boolean hGenBankHaveSeq(char *db, char *acc, char *compatTable); /* Get a GenBank or RefSeq mRNA or EST sequence or NULL if it doesn't exist. * This handles compatibility between pre-incremental genbank databases where * refSeq sequences were stored in tables and the newer scheme that keeps all * sequences in external files. If compatTable is not NULL and the table * exists, it is used to obtain the sequence. Otherwise the seq and gbSeq * tables are checked. */ struct dnaSeq *hGenBankGetMrna(char *db, char *acc, char *compatTable); /* Get a GenBank or RefSeq mRNA or EST sequence or NULL if it doesn't exist. * This handles compatibility between pre-incremental genbank databases where * refSeq sequences were stored in tables and the newer scheme that keeps all * sequences in external files. If compatTable is not NULL and the table * exists, it is used to obtain the sequence. Otherwise the seq and gbSeq * tables are checked. */ struct dnaSeq *hGenBankGetMrnaC(struct sqlConnection *conn, char *acc, char *compatTable); /* Same as above, but can pass in connection to any db */ aaSeq *hGenBankGetPep(char *db, char *acc, char *compatTable); /* Get a RefSeq peptide sequence or NULL if it doesn't exist. This handles * compatibility between pre-incremental genbank databases where refSeq * sequences were stored in tables and the newer scheme that keeps all * sequences in external files. If compatTable is not NULL and the table * exists, it is used to obtain the sequence. Otherwise the seq and gbSeq * tables are checked. */ aaSeq *hGenBankGetPepC(struct sqlConnection *conn, char *acc, char *compatTable); /* Same as above, but can pass in connection to any db */ char *hGenBankGetDesc(char *db, char *acc, boolean native); /* Get a description for a genbank or refseq mRNA. If native is TRUE, an * attempt is made to get a more compact description that doesn't include * species name. Acc may optionally include the version. NULL is returned if * a description isn't available. Free string when done. */ struct bed *hGetCtBedRange(char *db, char *browserDb, char *table, char *chrom, int chromStart, int chromEnd, char *sqlConstraints); /* Return a bed list of all items (that match sqlConstraints, if nonNULL) * in the given range in table. If chromEnd is 0, omit the range (whole chrom). * WARNING: this does not use the bin column and maybe slower than you would like. */ struct bed *hGetBedRange(char *db, char *table, char *chrom, int chromStart, int chromEnd, char *sqlConstraints); /* Return a bed list of all items (that match sqlConstraints, if nonNULL) * in the given range in table. If chromEnd is 0, omit the range (whole chrom). * WARNING: this does not use the bin column and maybe slower than you would like.*/ int hGetBedRangeCount(char *db, char *table, char *chrom, int chromStart, int chromEnd, char *sqlConstraints); /* Return a count of all the items (that match sqlConstraints, if nonNULL) * in the given range in table. If chromEnd is 0, omit the range (whole chrom). * WARNING: this does not use the bin column and maybe slower than you would like. * C.f. hGetBedRange() but returns only the result of SELECT COUNT(*) FROM ... */ struct bed *hGetFullBed(char *db, char *table); /* Return a genome-wide bed list of the table. */ /* WARNING: This isn't designed for CGI use. It's a looped call to */ /* hGetBedRange() which has its own warning. */ struct hash *hCtgPosHash(void); /* Return hash of ctgPos from current database keyed by contig name. */ char *hFreezeFromDb(char *database); /* return the freeze for the database version. For example: "hg6" returns "Dec 12, 2000". If database not recognized returns NULL */ char *hDbFromFreeze(char *freeze); /* Return database version from freeze name. */ struct slName *hDbList(void); /* List of all database versions that are online (database * 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 hash *hDbDbHash(); /* The hashed-up version of the entire dbDb table, keyed on the db */ 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 */ char *hHttpHost(); /* return http host from apache or hostname if run from command line */ char *hLocalHostCgiBinUrl(); /* Return the current full absolute URL of the cgi-bin directory of the local * server in the format http(s)://<host>/<cgiBinDir>, e.g. * https://genome.ucsc.edu/cgi-bin/. * The <host> is coming from the SERVER_NAME variable, which is * the ServerName setting in the Apache config file. * The cgi-bin directory is coming from the SCRIPT_NAME variable, the relative * location of the cgi program relative to Apache's DOCUMENT_ROOT. * Https is used if the variable HTTPS is set by Apache. * * If login.relativeLink=on is set, return only the empty string. * (This is used on the CIRM server, as it has no way of knowing what its * actual server name is, it is behind a reverse proxy) * Result has to be free'd. */ char *hLoginHostCgiBinUrl(); /* Return the current full absolute URL of the cgi-bin directory of the host * used for logins. Genome-euro/genome-asia use genome.ucsc.edu for the login, * as we have only one single server for user accounts. * Returns a string in the format * http(s)://<host>/cgi-bin/ e.g. http://genome.ucsc.edu/cgi-bin/ * - the <host> is coming from the wiki.host variable in hg.conf. * - https is used unless login.useHttps=off in hg.conf * * If login.relativeLink=on is set, return only the empty string. * (see hLocalCgiBinUrl) * Result has to be free'd. */ 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. */ boolean hIsBrowserbox(); /* Return TRUE if this is the browserbox virtual machine */ boolean hIsGbic(); /* Return TRUE if this mirror has been installed by the installation script */ boolean hIsPreviewHost(void); /* Return TRUE if this is running on preview web-server. The preview * server is a mirror of the development server provided for public * early access. */ char *hBrowserName(); /* Return browser name based on host name */ boolean hTrackOnChrom(struct trackDb *tdb, char *chrom); /* Return TRUE if track exists on this chromosome. */ boolean trackDataAccessible(char *database, struct trackDb *tdb); /* Return TRUE if underlying data are accessible - meaning the track has either * a bigDataUrl with remote URL (http:// etc), a bigDataUrl with an existing local file, * or a database table with the same name. * Note: this returns FALSE for composite tracks; use this on subtracks or simple tracks. */ struct trackDb *trackDbPolishAfterLinkup(struct trackDb *tdbList, char *db); /* Do various massaging that can only be done after parent/child * relationships are established. */ struct trackDb *hTrackDb(char *db); /* Load tracks associated with current db. * Supertracks are loaded as a trackDb, but are not in the returned list, * but are accessible via the parent pointers of the member tracks. Also, * the supertrack trackDb subtrack fields are not set here (would be * incompatible with the returned list) * Returns list sorted by priority * NOTE: this result is cached, do not free it ! */ struct trackDb *hTrackDbWithCartVersion(char *db, int *retCartVersion); /* Do hTrackDb AND return cartVersion. */ struct trackDb *tdbForTrack(char *db, char *track,struct trackDb **tdbList); /* Load trackDb object for a track. If track is composite, its subtracks * will also be loaded and inheritance will be handled; if track is a * subtrack then inheritance will be handled. (Unless a subtrack has * "noInherit on"...) This will die if the current database does not have * a trackDb, but will return NULL if track is not found. * MAY pass in prepopulated trackDb list, or may receive the trackDb list as an inout. */ #define hTrackDbForTrack(db,track) tdbForTrack(db,track,NULL) struct trackDb *hTrackDbForTrackAndAncestors(char *db, char *track); /* Load trackDb object for a track. If need be grab its ancestors too. * This does not load children. hTrackDbForTrack will handle children, and * is actually faster if being called on lots of tracks. This function * though is faster on one or two tracks. */ // WARNING: this works for hub and db tracks but not custom tracks. struct trackDb *hCompositeTrackDbForSubtrack(char *db, struct trackDb *sTdb); /* Given a trackDb that may be for a subtrack of a composite track, * return the trackDb for the composite track if we can find it, else NULL. * Note: if the composite trackDb is found and returned, then its subtracks * member will contain a newly allocated tdb like sTdb (but not ==). */ struct hTableInfo *hFindTableInfoWithConn(struct sqlConnection *conn, char *chrom, char *rootName); /* Find table information, with conn as part of input parameters. Return NULL if no table. */ struct hTableInfo *hFindTableInfo(char *db, char *chrom, char *rootName); /* Find table information in specified db. Return NULL if no table. */ int hTableInfoBedFieldCount(struct hTableInfo *hti); /* Return number of BED fields needed to save hti. */ boolean hFindChromStartEndFields(char *db, char *table, char retChrom[HDB_MAX_FIELD_STRING], char retStart[HDB_MAX_FIELD_STRING], char retEnd[HDB_MAX_FIELD_STRING]); /* Given a table return the fields for selecting chromosome, start, and end. */ boolean hIsBinned(char *db, char *table); /* Return TRUE if a table is binned. */ int hFieldIndex(char *db, char *table, char *field) /* Return index of field in table or -1 if it doesn't exist. */; boolean hHasField(char *db, char *table, char *field); /* Return TRUE if table has field */ boolean hFieldHasIndex(char *db, char *table, char *field); /* Return TRUE if a SQL index exists for table.field. */ boolean hFindFieldsAndBin(char *db, char *table, char retChrom[HDB_MAX_FIELD_STRING], char retStart[HDB_MAX_FIELD_STRING], char retEnd[HDB_MAX_FIELD_STRING], boolean *retBinned); /* Given a table return the fields for selecting chromosome, start, end, * and whether it's binned . */ boolean hFindSplitTable(char *db, char *chrom, char *rootName, char *retTableBuf, int tableBufSize, boolean *hasBin); /* Find name of table in a given database that may or may not * be split across chromosomes. Return FALSE if table doesn't exist. * * Do not ignore the return value. * This function does NOT tell you whether or not the table is split. * It tells you if the table exists. */ struct slName *hSplitTableNames(char *db, char *rootName); /* Return a list of all split tables for rootName, or of just rootName if not * split, or NULL if no such tables exist. */ int hBinLevels(void); /* Return number of levels to bins. */ int hBinFirstShift(void); /* Return amount to shift a number to get to finest bin. */ int hBinNextShift(void); /* Return amount to shift a numbe to get to next coarser bin. */ int hFindBin(int start, int end); /* Given start,end in chromosome coordinates assign it * a bin. There's a bin for each 128k segment, for each * 1M segment, for each 8M segment, for each 64M segment, * and for each chromosome (which is assumed to be less than * 512M.) A range goes into the smallest bin it will fit in. */ void hAddBinToQueryGeneral(char *binField, int start, int end, struct dyString *query); /* Add clause that will restrict to relevant bins to query. allow bin field name to be specified */ void hAddBinToQuery(int start, int end, struct dyString *query); /* Add clause that will restrict to relevant bins to query. */ struct sqlResult *hRangeQuery(struct sqlConnection *conn, char *rootTable, char *chrom, int start, int end, char *extraWhere, int *retRowOffset); /* Construct and make a query to tables that may be split and/or * binned. */ struct sqlResult *hOrderedRangeQuery(struct sqlConnection *conn, char *rootTable, char *chrom, int start, int end, char *extraWhere, int *retRowOffset); /* Construct and make a query to tables that may be split and/or * binned. Forces return values to be sorted by chromosome start. */ struct sqlResult *hExtendedRangeQuery( struct sqlConnection *conn, /* Open SQL connection. */ char *rootTable, /* Table (not including any chrN_) */ char *chrom, int start, int end, /* Range. */ char *extraWhere, /* Extra things to add to where clause. */ boolean order, /* If true order by start position (can be slow). */ char *fields, /* If non-NULL comma separated field list. */ int *retRowOffset); /* Returns offset past bin field. */ /* Range query with lots of options. */ struct sqlResult *hChromQuery(struct sqlConnection *conn, char *rootTable, char *chrom, char *extraWhere, int *retRowOffset); /* Construct and make a query across whole chromosome to tables * that may be split and/or * binned. */ struct sqlResult *hExtendedChromQuery( struct sqlConnection *conn, /* Open SQL connection. */ char *rootTable, /* Table (not including any chrN_) */ char *chrom, /* Chromosome. */ char *extraWhere, /* Extra things to add to where clause. */ boolean order, /* If true order by start position (can be slow). */ char *fields, /* If non-NULL comma separated field list. */ int *retRowOffset); /* Returns offset past bin field. */ /* Chromosome query fields for tables that may be split and/or binned, * with lots of options. */ int hOffsetPastBin(char *db, char *chrom, char *table); /* Return offset into a row of table that skips past bin * field if any. */ boolean hgParseChromRange(char *db, char *spec, char **retChromName, int *retWinStart, int *retWinEnd); /* Parse something of form chrom:start-end into pieces. * if db != NULL then check with chromInfo for names */ boolean hgIsChromRange(char *db, char *spec); /* Returns TRUE if spec is chrom:N-M for some human * chromosome chrom and some N and M. */ struct trackDb *hMaybeTrackInfo(struct sqlConnection *conn, char *trackName); /* Load trackDb object for a track. If track is composite, its subtracks * will also be loaded and inheritance will be handled; if track is a * subtrack then inheritance will be handled. (Unless a subtrack has * "noInherit on"...) Don't die if conn has no trackDb table. Return NULL * if trackName is not found. */ struct trackDb *hTrackInfo(struct sqlConnection *conn, char *trackName); /* Look up track in database, errAbort if it's not there. */ boolean hTrackCanPack(char *db, char *trackName); /* Return TRUE if this track can be packed. */ bool hTrackIsSubtrack(char *db, char *trackName); /* Return TRUE if this track is a subtrack. */ char *hGetTrackForTable(char *db, char *table); /* Given a table name, get first track associated with it. */ char *hGetTableForTrack(char *db, char *track); /* Given a track name, get table associated with it. */ char *hTrackOpenVis(char *db, char *trackName); /* Return "pack" if track is packable, otherwise "full". */ struct dbDb *hGetIndexedDatabases(void); /* Get list of all active databases. * Dispose of this with dbDbFreeList. */ struct dbDb *hGetIndexedDatabasesForClade(char *db); /* Get list of active databases in db's clade. * Dispose of this with dbDbFreeList. */ struct slPair *hGetCladeOptions(); /* Return a list of slPairs, each containing clade menu value (hgcentral.clade.name, e.g. 'mammal') * and clade menu label (hgcentral.clade.label, e.g. 'Mammal'), * useful for constructing a clade menu. */ struct slPair *hGetGenomeOptionsForClade(char *clade); /* Return a list of slPairs, each containing genome menu value and menu label, * useful for constructing a genome menu for the given clade. */ struct slPair *hGetDbOptionsForGenome(char *genome); /* Return a list of slPairs, each containing db menu value and menu label, * useful for constructing an assembly menu for the given genome. */ struct slName *hLiftOverFromDbs(void); /* Return a list of names of the DBs in the * fromDb column of the liftOverChain.*/ struct slName *hLiftOverToDbs(char *fromDb); /* Return a list of names of the DBs in the * toDb column of the liftOverChain. * If fromDb!=NULL, return only those with that * fromDb. */ struct slName *hLiftOverFromOrgs(void); /* Return a list of names of organisms that * have databases in the fromDb column of * liftOverChain.*/ struct slName *hLiftOverToOrgs(char *fromDb); /* Return a list of names of the organisms with * databases in the toDb column of the liftOverChain. * If fromDb!=NULL, return only those with that * 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 *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. */ 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 *hOrgShortName(char *org); /* Get the short name for an organism. Returns NULL if org is NULL. * WARNING: static return */ char *hOrgShortForDb(char *db); /* look up the short organism scientific name given an organism db. * WARNING: static return */ 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 *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); /* Purpose: Return the default database matching the organism. param organism - The organism for which we are trying to get the default database. return - The default database name for this organism */ char *hDefaultGenomeForClade(char *clade); /* Return highest relative priority genome for clade. */ char *sqlGetField(char *db, char *tblName, char *fldName, char *condition); /* Return a single field from the database, table name, field name, and a condition string */ struct hash *hChromSizeHash(char *db); /* Get hash of chromosome sizes for database. Just hashFree it when done. */ struct hash *hChromSizeHashFromFile(char *fileName); /* Get hash of chromosome sizes from 2- or 3-column chrom.sizes file. hashFree when done. */ struct slName *hChromList(char *db); /* Get the list of chrom names from the database's chromInfo table. */ struct mafAli *mafLoadInRegion(struct sqlConnection *conn, char *table, char *chrom, int start, int end); /* Return list of alignments in region. */ struct mafAli *axtLoadAsMafInRegion(struct sqlConnection *conn, char *table, char *chrom, int start, int end, char *tPrefix, char *qPrefix, int tSize, struct hash *qSizeHash); /* Return list of alignments in region from axt external file as a maf. */ char *hgDirForOrg(char *org); /* Make directory name from organism name - getting * rid of dots and spaces. */ struct hash *hgReadRa(char *genome, char *database, char *rootDir, char *rootName, struct hash **retHashOfHash); /* Read in ra in root, root/org, and root/org/database. * Returns a list of hashes, one for each ra record. Optionally * if retHashOfHash is non-null it returns there a * a hash of hashes keyed by the name field in each * ra sub-hash. */ char *addCommasToPos(char *db, char *position); /* add commas to the numbers in a position * returns pointer to static */ boolean parsePosition(char *position, char **retChrom, uint *retStart, uint *retEnd); /* If position is word:number-number (possibly with commas & whitespace), * set retChrom, retStart (subtracting 1) and retEnd, and return TRUE. * Otherwise return FALSE and leave rets unchanged. */ struct grp* hLoadGrps(char *db); /* load the grp tables using the list configured in hg.conf, returning a list * sorted by priority. */ void setMinIndexLengthForTrashCleaner(); /* set the minimum index size so trash cleaner will not die * on custom tracks on hubs that are not currently loading. * However, they might be re-established in the future, * and we want to allow it to proceed without failure * in order to touch the trash database table access times, * preserving them from the trash cleaner. * Only the trash cleaner should call this: * src/hg/utils/refreshNamedCustomTracks/refreshNamedCustomTracks.c */ int hGetMinIndexLength(char *db); /* get the minimum index size for the given database that won't smoosh * together chromNames such that any group of smooshed entries has a * cumulative size greater than the the largest chromosome. Allow one * exception cuz we're nice */ int chrStrippedCmp(char *chrA, char *chrB); /* compare chrom names after stripping chr, Scaffold_ or ps_ prefix */ int chrNameCmp(char *str1, char *str2); /* Compare chromosome names by number, then suffix. str1 and str2 must * match the regex "chr([0-9]+|[A-Za-z0-9]+)(_[A-Za-z0-9_]+)?". */ int chrSlNameCmp(const void *el1, const void *el2); /* Compare chromosome names by number, then suffix. el1 and el2 must be * slName **s (as passed in by slSort) whose names match the regex * "chr([0-9]+|[A-Za-z0-9]+)(_[A-Za-z0-9_]+)?". */ int chrNameCmpWithAltRandom(char *str1, char *str2); /* Compare chromosome or linkage group names str1 and str2 * to achieve this order: * chr1 .. chr22 * chrX * chrY * chrM * chr1_{alt,fix,hap*,random} .. chr22_{alt,fix,hap*,random} * chrUns */ int chrSlNameCmpWithAltRandom(const void *el1, const void *el2); /* Compare chromosome or linkage group names str1 and str2 * to achieve this order: * chr1 .. chr22 * chrX * chrY * chrM * chr1_{alt,fix,hap*,random} .. chr22_{alt,fix,hap*,random} * chrUn* */ int bedCmpExtendedChr(const void *va, const void *vb); /* Compare to sort based on chrom,chromStart. Use extended * chrom name comparison, that strip prefixes and does numeric compare */ int compareDbs(char *dbA, char *dbB); /* Compare two org# e.g. mm6 vs. mm16 or mm6 vs. hg17 * Return > 0 if dbA > dbB, < 0 if less than, and 0 if equal */ int getTableSize(char *db, char *table); /* Get count of rows in a table in the primary database */ struct slName *getDomainList(struct sqlConnection *conn, char *ucscGeneId, char *domainDb); struct slName *getPfamDomainList(struct sqlConnection *conn, char *ucscGeneId); boolean isUnknownChrom(char *dataBase, char *chromName); /* Return true if chrom is one of our "unknown" chromomsomes (e.g. chrUn). */ char *hGenbankModDate(char *acc, struct sqlConnection *conn); /* Get string for genbank last modification date, or NULL if not found.. * Free resulting string. */ struct trackDb *findTdbForTable(char *db,struct trackDb *parent,char *table, struct customTrack *(*ctLookupName)(char *table)); /* Find or creates the tdb for this table. Might return NULL! (e.g. all tables) * If this is a custom track, pass in function ctLookupName(table) which looks up a * custom track by name, otherwise pass NULL */ char *findTypeForTable(char *db,struct trackDb *parent,char *table, struct customTrack *(*ctLookupName)(char *table)); /* Finds the TrackType for this Table */ boolean trackIsType(char *database, char *table, struct trackDb *parent, char *type, struct customTrack *(*ctLookupName)(char *table)); /* Return TRUE track is a specific type. Type should be something like "bed" or * "bigBed" or "bigWig" * if table has no parent trackDb pass NULL for parent * If this is a custom track, pass in function ctLookupName(table) which looks up a * custom track by name, otherwise pass NULL */ boolean hIsBigWig(char *database, char *table, struct trackDb *parent, struct customTrack *(*ctLookupName)(char *table)); /* Return TRUE if table corresponds to a bigWig file. * if table has no parent trackDb pass NULL for parent * If this is a custom track, pass in function ctLookupName(table) which looks up a * custom track by name, otherwise pass NULL */ boolean hIsBigBed(char *database, char *table, struct trackDb *parent, struct customTrack *(*ctLookupName)(char *table)); /* Return TRUE if table corresponds to a bigBed file. * if table has no parent trackDb pass NULL for parent * If this is a custom track, pass in function ctLookupName(table) which looks up a * custom track by name, otherwise pass NULL */ char *bbiNameFromSettingOrTable(struct trackDb *tdb, struct sqlConnection *conn, char *table); /* Return file name from bigDataUrl or little table. */ char *bbiNameFromSettingOrTableChrom(struct trackDb *tdb, struct sqlConnection *conn, char *table, char *seqName); /* Return file name from bigDataUrl or little table that might have a seqName column. * If table does have a seqName column, return NULL if there is no file for seqName. */ #define dbdDbTableConfVariable "dbDbTableName" #define defaultDbdDbTableName "dbDb" #define defaultDbTableConfVariable "defaultDbTableName" #define defaultDefaultDbTableName "defaultDb" #define genomeCladeTableConfVariable "genomeCladeTableName" #define defaultGenomeCladeTableName "genomeClade" #define cladeTableConfVariable "cladeTableName" #define defaultCladeTableName "clade" char *dbDbTable(); /* Return the name of the dbDb table. */ char *cladeTable(); /* Return the name of the clade table. */ char *defaultDbTable(); /* Return the name of the defaultDb table. */ char *genomeCladeTable(); /* Return the name of the genomeClade table. */ struct trackDb *hFindLatestSnpTrack(char *db, char *suffix, struct trackDb **pFullTrackList); /* Return the 'snpNNN<suffix>' track with the highest build number, if any. * suffix may be NULL to get the 'All SNPs' table (as opposed to Common, Flagged, Mult). */ char *hFindLatestSnpTableConn(struct sqlConnection *conn, char *suffix); /* Return the name of the 'snp1__<suffix>' table with the highest build number, if any. * suffix may be NULL to get the 'All SNPs' table (as opposed to Common, Flagged, Mult). */ char *hFindLatestGencodeTableConn(struct sqlConnection *conn, char *suffix); /* Return the 'wgEncodeGencode<suffix>V<version>' table with the highest version number, if any. * If suffix is NULL, it defaults to Basic. */ boolean hDbHasNcbiRefSeq(char *db); /* Return TRUE if db has NCBI's RefSeq alignments and annotations. */ char *hRefSeqAccForChrom(char *db, char *chrom); /* Return the RefSeq NC_000... accession for chrom if we can find it, else just chrom. * db must never change. */ char *abbreviateRefSeqSummary(char *summary); /* strip off the uninformative parts from the RefSeq Summary text: the repetitive note * about the publication subset and the Evidence-Data-Notes */ boolean isMito(char *chrom); /* Return True if chrom is chrM or chrMT */ char *hdbDefaultKnownDb(char *db); /* Get the default knownGene database from the defaultKnown table. */ char *hdbGetMasterGeneTrack(char *knownDb); /* Get the native gene track for a knownGene database. */ boolean trackDataAccessibleHash(char *database, struct trackDb *tdb, struct hash *gbdbHash); /* Return TRUE if underlying data are accessible - meaning the track has either * a bigDataUrl with remote URL (http:// etc), a bigDataUrl with an existing local file, * or a database table with the same name. * Note: this returns FALSE for composite tracks; use this on subtracks or simple tracks. * * if gbdbHash is not NULL, use it when looking for the file */ unsigned hdbGetTrackCartVersion(); /* Get the cart version that our current trackDb wants to use. */ #endif /* HDB_H */