/* hgTables - shared data between hgTables modules. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef HGTABLES_H #define HGTABLES_H #include "jksql.h" #include "localmem.h" #include "dystring.h" #include "hdb.h" #include "hCommon.h" #include "customTrack.h" #include "grp.h" #include "joiner.h" #include "hPrint.h" #include "hui.h" struct region /* A part (or all) of a chromosome. */ { struct region *next; char *chrom; /* Chromosome. */ int start; /* Zero-based. */ int end; /* Non-inclusive. */ boolean fullChrom; /* If TRUE it's full chromosome. */ char *name; /* possibly the encode region name */ }; /* Global variables - generally set during initialization and then read-only. */ extern struct cart *cart; /* This holds cgi and other variables between clicks. */ extern struct hash *oldVars; /* The cart before new cgi stuff added. */ extern char *genome; /* Name of genome - mouse, human, etc. */ extern char *database; /* Current database, often but not always dbDatabase. */ extern char *freezeName; /* Date of assembly. */ extern struct trackDb *fullTrackList; /* List of all tracks in database. */ extern struct hash *fullTableToTdbHash; /* All tracks and subtracks keyed by ->table field. */ extern struct trackDb *curTrack; /* Currently selected track. */ extern struct grp *fullGroupList; /* List of all groups. */ extern struct grp *curGroup; /* Currently selected group. */ extern struct customTrack *theCtList; /* List of custom tracks. */ extern char *curTable; /* Current selected table. */ extern struct joiner *allJoiner; /* Info on how to join tables. */ #define GALAXY_URL_BASE "https://usegalaxy.org" #define GALAXY_URL_APP GALAXY_URL_BASE "/tool_runner" /* --------------- HTML Helpers ----------------- */ void hPrintSpaces(int count); /* Print a number of non-breaking spaces. */ void writeHtmlCell(char *text); /* Write out a cell in an HTML table, making text not too big, * and stripping html tags and breaking spaces.... */ void htmlOpen(char *format, ...) /* Start up a page that will be in html format. */ #if defined(__GNUC__) __attribute__((format(printf, 1, 2))) #endif ; void htmlClose(); /* Close down html format page. */ void textOpen(); /* Start up page in text format. (No need to close this). */ void explainWhyNoResults(FILE *f); /* Put up a little explanation to user of why they got nothing. */ char *curTableLabel(); /* Return label for current table - track short label if it's a track, * otherwise track name. */ char *getScriptName(); /* returns script name from environment or hardcoded for command line */ void printTrackHtml(struct trackDb *tdb); /* If trackDb has html for table, print it out in a new section. */ /* ---------- Other UI stuff. ----------------------*/ boolean varOn(char *var); /* Return TRUE if variable exists and is set. */ void printMainHelp(); /* Put up main page help info. */ void printDownloadLink(char *typeLabel, char *fileName); /* print a link to the file, so the user can download it right here */ boolean printTypeHelpDesc(char *fileType); /* print a little link to our help docs given a file type. Return true if file type is a big* file format. */ struct grp *showGroupField(char *groupVar, char *event, char *groupScript, struct sqlConnection *conn, boolean allTablesOk); /* Show group control. Returns selected group. */ struct trackDb *showTrackField(struct grp *selGroup, char *trackVar, char *event, char *trackScript, boolean disableNoGenome); /* Show track control. Returns selected track. */ char *showTableField(struct trackDb *track, char *varName, boolean useJoiner); /* Show table control and label. */ struct slName *getDbListForGenome(); /* Get list of selectable databases. */ char *findSelDb(); /* Find user selected database (as opposed to genome database). */ struct slName *tablesForDb(char *db); /* Find tables associated with database. */ /* --------- Utility functions --------------------- */ void nbSpaces(int count); /* Print some non-breaking spaces. */ boolean anyCompression(); /* Check if any compressed file output has been requested */ void initGroupsTracksTables(); /* Get list of groups that actually have something in them. */ struct region *getRegions(); /* Consult cart to get list of regions to work on. */ boolean isRegionWholeGenome(); /* Return TRUE if the current region is the whole genome. */ struct region *getRegionsFullGenome(); /* Get a region list that covers all of each chromosome. */ char *getRegionName(); /* Get a name for selected region. Don't free this. */ boolean fullGenomeRegion(); /* Return TRUE if region is full genome. */ boolean isNoGenomeDisabled(char *db, char *table); /* Return TRUE if table (or a track with which it is associated) has 'tableBrowser noGenome' * and region is genome. */ void checkNoGenomeDisabled(char *db, char *table); /* Before producing output, make sure that the URL hasn't been hacked to make a * genome-wide query on a noGenome table. */ struct sqlResult *regionQuery(struct sqlConnection *conn, char *table, char *fields, struct region *region, boolean isPositional, char *extraWhere); /* Construct and execute query for table on region. */ void dbOverrideFromTable(char buf[256], char **pDb, char **pTable); /* If *pTable includes database, overrider *pDb with it, using * buf to hold string. */ struct grp *findSelectedGroup(struct grp *groupList, char *cgiVar); /* Find user-selected group if possible. If not then * go to various levels of defaults. */ struct trackDb *findSelectedTrack(struct trackDb *trackList, struct grp *group, char *varName); /* Find selected track - from CGI variable if possible, else * via various defaults. */ struct trackDb *findTrack(char *name, struct trackDb *trackList); /* Find track, or return NULL if can't find it. */ struct trackDb *mustFindTrack(char *name, struct trackDb *trackList); /* Find track or squawk and die. */ struct asObject *asForTableNoTdb(struct sqlConnection *conn, char *table); /* Get autoSQL description if any associated with table. Don't try tdb */ struct asObject *asForTable(struct sqlConnection *conn, char *table); /* Get autoSQL description if any associated with table. */ char *connectingTableForTrack(char *rawTable); /* Return table name to use with all.joiner for track. * You can freeMem this when done. */ char *chromTable(struct sqlConnection *conn, char *table); /* Get chr1_table if it exists, otherwise table. * You can freeMem this when done. */ char *getDbTable(char *db, char *table); /* If table already contains its real database as a dot-prefix, then * return a clone of table; otherwise alloc and return db.table . */ void doTabOutTable(char *database, char *table, FILE *f, struct sqlConnection *conn, char *fields, char outSep); /* Do tab-separated output on table. */ struct slName *fullTableFields(char *db, char *table); /* Return list of fields in db.table.field format. */ struct bed *getFilteredBeds(struct sqlConnection *conn, char *table, struct region *region, struct lm *lm, int *retFieldCount); /* Get list of beds on single region that pass filtering. */ void bedSqlFieldsExceptForChrom(struct hTableInfo *hti, int *retFieldCount, char **retFields); /* Given tableInfo figure out what fields are needed to * add to a database query to have information to create * a bed. The chromosome is not one of these fields - we * assume that is already known since we're processing one * chromosome at a time. Return a comma separated (no last * comma) list of fields that can be freeMem'd, and the count * of fields (this *including* the chromosome). */ struct bed *bedFromRow( char *chrom, /* Chromosome bed is on. */ char **row, /* Row with other data for bed. */ int fieldCount, /* Number of fields in final bed. */ boolean isPsl, /* True if in PSL format. */ boolean isGenePred, /* True if in GenePred format. */ boolean isBedWithBlocks, /* True if BED with block list. */ boolean *pslKnowIfProtein,/* Have we figured out if psl is protein? */ boolean *pslIsProtein, /* True if we know psl is protien. */ struct lm *lm); /* Local memory pool */ /* Create bed from a database row when we already understand * the format pretty well. The bed is allocated inside of * the local memory pool lm. Generally use this in conjunction * with the results of a SQL query constructed with the aid * of the bedSqlFieldsExceptForChrom function. */ struct bed *getAllIntersectedBeds(struct sqlConnection *conn, char *table, struct lm *lm); /* Get list of beds in selected regions that pass intersection * (and filtering). Do lmCleanup (not bedFreeList) when done. */ struct bed *cookedBedList(struct sqlConnection *conn, char *table, struct region *region, struct lm *lm, int *retFieldCount); /* Get data for track in region after all processing steps (filtering * intersecting etc.) in BED format. */ struct bed *cookedBedsOnRegions(struct sqlConnection *conn, char *table, struct region *regionList, struct lm *lm, int *retFieldCount); /* Get cooked beds on all regions. */ struct hTableInfo *getHtiOnDb(char *db, char *table); /* Return primary table info. */ struct hTableInfo *getHti(char *db, char *table, struct sqlConnection *conn); /* Return primary table info. Conn should be open to db. */ struct hTableInfo *maybeGetHti(char *db, char *table, struct sqlConnection *conn); /* Return primary table info, but don't abort if table not there. Conn should be open to db. */ struct hTableInfo *maybeGetHtiOnDb(char *db, char *table); /* Return primary table info, but don't abort if table not there. */ boolean htiIsPositional(struct hTableInfo *hti); /* Return TRUE if hti looks like it's from a positional table. */ boolean isPositional(char *db, char *table); /* Return TRUE if it looks to be a positional table. */ boolean isSqlStringType(char *type); /* Return TRUE if type is a stringish SQL type. */ boolean isSqlEnumType(char *type); /* Return TRUE if type is an enum. */ boolean isSqlSetType(char *type); /* Return TRUE if type is a set. */ boolean isSqlNumType(char *type); /* Return TRUE if it is a numerical SQL type. */ boolean isSqlIntType(char *type); /* Return TRUE if it is an integer SQL type. */ void sqlFieldTypeFree(struct sqlFieldType **pFt); /* Free resources used by sqlFieldType */ void sqlFieldTypeFreeList(struct sqlFieldType **pList); /* Free a list of dynamically allocated sqlFieldType's */ struct sqlFieldType *sqlListFieldsAndTypes(struct sqlConnection *conn, char *table); /* Get list of fields including their names and types. The type currently is just * a MySQL type string. */ /* ------------- Functions related to joining and filtering ------------*/ void sepOutSelectedFields( char *primaryDb, /* The primary database. */ char *primaryTable, /* The primary table. */ FILE *f, /* file for output, null for stdout */ struct slName *fieldList, /* List of db.table.field */ char outSep); /* The separator for the output */ /* Do tab-separated output on selected fields, which may * or may not include multiple tables. */ boolean anyFilter(); /* Return TRUE if any filter set. */ struct joinerDtf *filteringTables(); /* Get list of tables we're filtering on as joinerDtf list (with * the field entry NULL). */ char *filterClause(char *db, char *table, char *chrom, char *extraClause); /* Get filter clause (something to put after 'where') * for table */ char *filterFieldVarName(char *db, char *table, char *field, char *type); /* Return variable name for filter page. */ /* Some types of filter vars. */ #define filterDdVar "dd" #define filterCmpVar "cmp" #define filterPatternVar "pat" #define filterRawLogicVar "rawLogic" #define filterRawQueryVar "rawQuery" #define filterDataValueVar "dataValue" #define filterMaxOutputVar "maxOutput" /* --------- Functions related to intersecting. --------------- */ boolean canIntersect(char *db, char *table); /* Return true if table supports intersection, i.e. it exists and is positional. */ boolean anyIntersection(); /* Return TRUE if there's an intersection to do. */ char *intersectOp(); /* Get intersect op from CGI var and make sure it's ok. */ boolean intersectionIsBpWise(); /* Return TRUE if the intersection/union operation is base pair-wise. */ Bits *bitsForIntersectingTable(struct sqlConnection *conn, struct region *region, int chromSize, boolean isBpWise); /* Get a bitmap that corresponds to the table we are intersecting with. * Consult CGI vars to figure out what table it is. */ boolean intersectOverlapFilter(char *op, double moreThresh, double lessThresh, double overlap); /* Return TRUE if have enough (or not too much) overlap according to thresholds and op. */ /* --------- Functions related to correlation. --------------- */ boolean anyCorrelation(); /* Return TRUE if there's a correlation to do. */ /* variables managed by correlate page. */ #define hgtaCorrelateMaxLimitCount "hgta_corrMaxLimitCount" #define hgtaCorrelateWinSize "hgta_corrWinSize" boolean correlateTrackTableOK(struct trackDb *tdb, char *table); /* is this table OK to correlate with ? */ /* --------- Functions related to composite tracks/subtracks. ------------- */ boolean anySubtrackMerge(char *db, char *table); /* Return TRUE if a subtrack merge has been specified on db.table. */ boolean subtrackMergeIsBpWise(); /* Return TRUE if the subtrack merge operation is base pair-wise. */ boolean isSubtrackMerged(char *tableName); /* Return true if tableName has been selected for subtrack merge. */ char *describeSubtrackMerge(char *linePrefix); /* Return a multi-line string that describes the specified subtrack merge, * with each line beginning with linePrefix. */ void doSubtrackMergePage(struct sqlConnection *conn); /* Respond to subtrack merge create/edit button */ void doClearSubtrackMerge(struct sqlConnection *conn); /* Respond to click on clear intersection. */ void doSubtrackMergeSubmit(struct sqlConnection *conn); /* Respond to submit on intersect page. */ #define NO_RESULTS "\n# No results returned from query.\n\n" /* --------- CGI/Cart Variables --------------------- */ /* Command type variables - control which page is up. Get stripped from * cart. */ #define hgtaDo "hgta_do" /* All commands start with this and are removed * from cart. */ #define hgtaDoMainPage "hgta_doMainPage" #define hgtaDoTopSubmit "hgta_doTopSubmit" #define hgtaDoSummaryStats "hgta_doSummaryStats" #define hgtaDoSchema "hgta_doSchema" #define hgtaDoPasteIdentifiers "hgta_doPasteIdentifiers" #define hgtaDoClearPasteIdentifierText "hgta_doClearPasteIdentifierText" #define hgtaDoPastedIdentifiers "hgta_doPastedIdentiers" #define hgtaDoUploadIdentifiers "hgta_doUploadIdentifiers" #define hgtaDoClearIdentifiers "hgta_doClearIdentifiers" #define hgtaDoFilterPage "hgta_doFilterPage" #define hgtaDoFilterSubmit "hgta_doFilterSubmit" #define hgtaDoFilterMore "hgta_doFilterMore" #define hgtaDoClearFilter "hgta_doClearFilter" #define hgtaDoIntersectPage "hgta_doIntersectPage" #define hgtaDoClearIntersect "hgta_doClearIntersect" #define hgtaDoIntersectMore "hgta_doIntersectMore" #define hgtaDoIntersectSubmit "hgta_doIntersectSubmit" #define hgtaDoCorrelatePage "hgta_doCorrelatePage" #define hgtaDoClearCorrelate "hgta_doClearCorrelate" #define hgtaDoClearContinueCorrelate "hgta_doClearContinueCorrelate" #define hgtaDoCorrelateSubmit "hgta_doCorrelateSubmit" #define hgtaDoCorrelateMore "hgta_doCorrelateMore" #define hgtaDoCorrelateSubmit "hgta_doCorrelateSubmit" #define hgtaDoSubtrackMergePage "hgta_doSubtrackMergePage" #define hgtaDoClearSubtrackMerge "hgta_doClearSubtrackMerge" #define hgtaDoSubtrackMergeSubmit "hgta_doSubtrackMergeSubmit" #define hgtaDoTest "hgta_doTest" #define hgtaDoSchemaTable "hgta_doSchemaTable" #define hgtaDoSchemaDb "hgta_doSchemaDb" #define hgtaDoValueHistogram "hgta_doValueHistogram" #define hgtaDoValueRange "hgta_doValueRange" #define hgtaDoPrintSelectedFields "hgta_doPrintSelectedFields" #define hgtaDoGalaxySelectedFields "hgta_doGalaxySelectedFields" #define hgtaDoSelectFieldsMore "hgta_doSelectFieldsMore" #define hgtaDoClearAllFieldPrefix "hgta_doClearAllField." #define hgtaDoSetAllFieldPrefix "hgta_doSetAllField." #define hgtaDoGenePredSequence "hgta_doGenePredSequence" #define hgtaDoGenomicDna "hgta_doGenomicDna" #define hgtaDoGetBed "hgta_doGetBed" #define hgtaDoGetCustomTrackGb "hgta_doGetCustomTrackGb" #define hgtaDoGetCustomTrackTb "hgta_doGetCustomTrackTb" #define hgtaDoGetCustomTrackFile "hgta_doGetCustomTrackFile" #define hgtaDoRemoveCustomTrack "hgta_doRemoveCustomTrack" #define hgtaDoGalaxyQuery "hgta_doGalaxyQuery" #define hgtaDoGreatOutput "hgta_doGreatOutput" #define hgtaDoGreatQuery "hgta_doGreatQuery" #define hgtaDoGsLogin "hgta_doGsLogin" #define hgtaGsUser "hgta_gsUser" #define hgtaGsPassword "hgta_gsPassword" #define hgtaDoLookupPosition "hgta_doLookupPosition" #define hgtaDoMetaData "hgta_doMetaData" #define hgtaDoSetUserRegions "hgta_doSetUserRegions" #define hgtaDoClearSetUserRegionsText "hgta_doClearSetUserRegionsText" #define hgtaUserRegionsFile "hgta_userRegionsFile" #define hgtaUserRegionsDb "hgta_userRegionsDb" #define hgtaEnteredUserRegions "hgta_enteredUserRegions" #define hgtaEnteredUserRegionFile "hgta_enteredUserRegionFile" #define hgtaDoSubmitUserRegions "hgta_doSubmitUserRegions" #define hgtaDoClearUserRegions "hgta_doClearUserRegions" #define hgtaRegionTypeUserRegions "userRegions" #define hgtaRegionTypeEncode "encode" #define hgtaRegionTypeGenome "genome" #define hgtaRegionTypeRange "range" #define hgtaDoPalOut "hgta_palOut" #define hgtaDoPal "hgta_doPal" /* Other CGI variables. */ #define hgtaGroup "hgta_group" #define hgtaTrack "hgta_track" #define hgtaSelDb "hgta_selDb" #define hgtaRegionType "hgta_regionType" #define hgtaCompressType "hgta_compressType" #define hgtaOutSep "hgta_outSep" #define hgtaRange "position" #define hgtaOffsetStart "hgta_offsetStart" #define hgtaOffsetEnd "hgta_offsetEnd" #define hgtaOffsetRelativeTo "hgta_offsetRelativeTo" #define hgtaOutputType "hgta_outputType" #define hgtaOutputPad "hgta_outputPad" #define hgtaOutFileName "hgta_outFileName" #define hgtaDatabase "hgta_database" /* In most cases use "db" */ #define hgtaTable "hgta_table" #define hgtaHistoTable "hgta_histoTable" #define hgtaPastedIdentifiers "hgta_pastedIdentifiers" #define hgtaIdentifierFile "hgta_identifierFile" #define hgtaIdentifierTable "hgta_identifierTable" #define hgtaIdentifierDb "hgta_identifierDb" #define hgtaFilterTable "hgta_filterTable" #define hgtaFieldSelectTable "hgta_fieldSelectTable" #define hgtaGeneSeqType "hgta_geneSeqType" #define hgtaPrintCustomTrackHeaders "hgta_printCustomTrackHeaders" #define hgtaCtName "hgta_ctName" #define hgtaCtDesc "hgta_ctDesc" #define hgtaCtVis "hgta_ctVis" #define hgtaCtUrl "hgta_ctUrl" #define hgtaCtWigOutType "hgta_ctWigOutType" #define hgtaMetaStatus "hgta_metaStatus" #define hgtaMetaVersion "hgta_metaVersion" #define hgtaMetaDatabases "hgta_metaDatabases" #define hgtaMetaTables "hgta_metaTables" #define hgtaMafTable "hgta_mafTable" /* These intersection page vars come in pairs so we can cancel. */ #define hgtaIntersectGroup "hgta_intersectGroup" #define hgtaNextIntersectGroup "hgta_nextIntersectGroup" #define hgtaIntersectTrack "hgta_intersectTrack" #define hgtaNextIntersectTrack "hgta_nextIntersectTrack" #define hgtaIntersectTable "hgta_intersectTable" #define hgtaNextIntersectTable "hgta_nextIntersectTable" #define hgtaIntersectOp "hgta_intersectOp" #define hgtaNextIntersectOp "hgta_nextIntersectOp" #define hgtaMoreThreshold "hgta_moreThreshold" #define hgtaNextMoreThreshold "hgta_nextMoreThreshold" #define hgtaLessThreshold "hgta_lessThreshold" #define hgtaNextLessThreshold "hgta_nextLessThreshold" #define hgtaInvertTable "hgta_invertTable" #define hgtaNextInvertTable "hgta_nextInvertTable" #define hgtaInvertTable2 "hgta_invertTable2" #define hgtaNextInvertTable2 "hgta_nextInvertTable2" /* These correlate page vars come in pairs so we can cancel. */ #define hgtaCorrelateGroup "hgta_correlateGroup" #define hgtaNextCorrelateGroup "hgta_nextCorrelateGroup" #define hgtaCorrelateTrack "hgta_correlateTrack" #define hgtaNextCorrelateTrack "hgta_nextCorrelateTrack" #define hgtaCorrelateOp "hgta_correlateOp" #define hgtaNextCorrelateOp "hgta_nextCorrelateOp" #define hgtaCorrelateTable "hgta_correlateTable" #define hgtaNextCorrelateTable "hgta_nextCorrelateTable" #define hgtaCorrelateTable "hgta_correlateTable" #define hgtaNextCorrelateTable "hgta_nextCorrelateTable" #define hgtaCorrelateWindowSize "hgta_CorrelateWindowSize" #define hgtaNextCorrelateWindowSize "hgta_nextCorrelateWindowSize" /* Subtrack merge vars (also in pairs so we can cancel). */ #define hgtaSubtrackMergePrefix "hgta_subtrackMerge" #define hgtaNextSubtrackMergePrefix "hgta_nextSubtrackMerge" #define hgtaSubtrackMergePrimary hgtaSubtrackMergePrefix "Primary" #define hgtaNextSubtrackMergePrimary hgtaNextSubtrackMergePrefix "Primary" #define hgtaSubtrackMergeOp hgtaSubtrackMergePrefix "Op" #define hgtaNextSubtrackMergeOp hgtaNextSubtrackMergePrefix "Op" #define hgtaSubtrackMergeMoreThreshold hgtaSubtrackMergePrefix "MoreThreshold" #define hgtaNextSubtrackMergeMoreThreshold hgtaNextSubtrackMergePrefix "MoreThreshold" #define hgtaSubtrackMergeLessThreshold hgtaSubtrackMergePrefix "LessThreshold" #define hgtaNextSubtrackMergeLessThreshold hgtaNextSubtrackMergePrefix "LessThreshold" #define hgtaSubtrackMergeWigOp hgtaSubtrackMergePrefix "WigOp" #define hgtaNextSubtrackMergeWigOp hgtaNextSubtrackMergePrefix "WigOp" #define hgtaSubtrackMergeRequireAll hgtaSubtrackMergePrefix "RequireAll" #define hgtaNextSubtrackMergeRequireAll hgtaNextSubtrackMergePrefix "RequireAll" #define hgtaSubtrackMergeUseMinScore hgtaSubtrackMergePrefix "UseMinScore" #define hgtaNextSubtrackMergeUseMinScore hgtaNextSubtrackMergePrefix "UseMinScore" #define hgtaSubtrackMergeMinScore hgtaSubtrackMergePrefix "MinScore" #define hgtaNextSubtrackMergeMinScore hgtaNextSubtrackMergePrefix "MinScore" /* Prefix for variables managed by field selector. */ #define hgtaFieldSelectPrefix "hgta_fs." /* Prefix for variables managed by filter page. */ #define hgtaFilterPrefix "hgta_fil." /* Prefix for variables containing filters themselves. */ #define hgtaFilterVarPrefix hgtaFilterPrefix "v." /* Prefix for temp name files created for custom tracks */ #define hgtaCtTempNamePrefix "hgtct" /* Output types. */ #define outPrimaryTable "primaryTable" #define outSequence "sequence" #define outSelectedFields "selectedFields" #define outSchema "schema" #define outSummaryStats "stats" #define outBed "bed" #define outGff "gff" #define outCustomTrack "customTrack" #define outHyperlinks "hyperlinks" #define outWigData "wigData" #define outWigBed "wigBed" #define outChromGraphData "chromGraphData" #define outMicroarrayNames "microarrayNames" #define outMicroarrayGroupings "microarrayGroupings" #define outGalaxy "galaxyQuery" #define outMaf "maf" #define outPalOptions "fasta" #define outTab "tab" #define outCsv "csv" /* For disabling tables in 'tableBrowser noGenome' settings, when region is genome */ #define NO_GENOME_CLASS " class=\"hgtaNoGenome\" title=\"Position range queries only\"" /* --------- Identifier list handling stuff. ------------ */ char *identifierFileName(); /* File name identifiers are in, or NULL if no such file. */ struct hash *identifierHash(char *db, char *table); /* Return hash full of identifiers from the given table (or NULL). */ char *getIdField(char *db, struct trackDb *track, char *table, struct hTableInfo *hti); /* Get ID field for table, or NULL if none. FreeMem result when done */ char *identifierWhereClause(char *idField, struct hash *idHash); /* If the number of pasted IDs is reasonably low, return a where-clause component for the IDs. */ /* --------- Summary and stats stuff -------------- */ long long basesInRegion(struct region *regionList, int limit); /* Count up all bases in regions to limit number of regions, 0 == no limit */ long long gapsInRegion(struct sqlConnection *conn, struct region *regionList, int limit); /* Return count of gaps in all regions to limit number of regions, * limit=0 == no limit, do them all */ void percentStatRow(char *label, long long p, long long q); /* Print label, p, and p/q */ void numberStatRow(char *label, long long x); /* Print label, x in table. */ void floatStatRow(char *label, double x); /* Print label, x in table. */ void stringStatRow(char *label, char *val); /* Print label, string value. */ void wigFilterStatRow(struct sqlConnection *conn); /* Put row in statistics table that says what wig filter is on. */ /* ----------- Filter stuff in filterFields.c. -------- */ void cgiToCharFilter(char *dd, char *pat, enum charFilterType *retCft, char **retVals, boolean *retInv); /* Given a "does/doesn't" and a (list of) literal chars from CGI, fill in * retCft, retVals and retInv to make a filter. */ void cgiToStringFilter(char *dd, char *pat, enum stringFilterType *retSft, char ***retVals, boolean *retInv); /* Given a "does/doesn't" and a (list of) regexps from CGI, fill in * retCft, retVals and retInv to make a filter. */ void cgiToDoubleFilter(char *cmp, char *pat, enum numericFilterType *retNft, double **retVals); /* Given a comparison operator and a (pair of) integers from CGI, fill in * retNft and retVals to make a filter. */ void cgiToLongFilter(char *cmp, char *pat, enum numericFilterType *retNft, long long **retVals); /* Given a comparison operator and a (pair of) integers from CGI, fill in * retNft and retVals to make a filter. */ void cgiToIntFilter(char *cmp, char *pat, enum numericFilterType *retNft, int **retVals); /* Given a comparison operator and a (pair of) integers from CGI, fill in * retNft and retVals to make a filter. */ /* ----------- ChromGraph stuff in chromGraph.c. --------- */ boolean isChromGraph(struct trackDb *track); /* Return TRUE if it's a chromGraph track */ void doOutChromGraphDataCt(struct trackDb *track, char *table); /* Print out data points in region for chromGraph custom track. */ void doSummaryStatsChromGraph(struct sqlConnection *conn); /* Put up page showing summary stats for chromGraph track. */ /* ----------- hgPal stuff in pal.c ------------------------------*/ boolean isPalCompatible(struct sqlConnection *conn, struct trackDb *track, char *table); /* Return TRUE if table is genePred and there is a maf. */ void doOutPalOptions( struct sqlConnection *conn); /* Output protein alignment page */ /* ----------- Maf stuff in maf.c ------------------------------*/ boolean isMafTable(char *database, struct trackDb *track, char *table); /* Return TRUE if table is maf. */ void doOutMaf(struct trackDb *track, char *table, struct sqlConnection *conn); /* Output regions as MAF. */ void doHalMaf(struct trackDb *track, char *table, struct sqlConnection *conn); /* Output HAL regions as MAF. */ /* ----------- Wiggle business in wiggle.c -------------------- */ #define MAX_REGION_DISPLAY 1000 enum wigOutputType /* type of output requested from static int wigOutRegion() */ { wigOutData, wigOutBed, wigDataNoPrint, }; boolean isWiggle(char *db, char *table); /* Return TRUE if db.table is a wiggle. */ boolean isBedGraph(char *table); /* Return TRUE if table is specified as a bedGraph in the current database's * trackDb. */ struct bed *getWiggleAsBed( char *db, char *table, /* Database and table. */ struct region *region, /* Region to get data for. */ char *filter, /* Filter to add to SQL where clause if any. */ struct hash *idHash, /* Restrict to id's in this hash if non-NULL. */ struct lm *lm, /* Where to allocate memory. */ struct sqlConnection *conn); /* SQL connection to work with */ /* Return a bed list of all items in the given range in table. * Cleanup result via lmCleanup(&lm) rather than bedFreeList. */ struct bed *getBedGraphAsBed(struct sqlConnection *conn, char *table, struct region *region); /* Extract a bedList in region from the given bedGraph table -- * subtrack merge, filtering and intersection are handled here. */ void wiggleMinMax(struct trackDb *tdb, double *min, double *max); /* obtain wiggle data limits from trackDb or cart or settings */ struct wigAsciiData *getWiggleAsData(struct sqlConnection *conn, char *table, struct region *region); /* return the wigAsciiData list */ struct wigAsciiData *getWiggleData(struct sqlConnection *conn, char *table, struct region *region, int maxOut, int spanConstraint); /* like getWiggleAsData above, but with specific spanConstraint and * a different data limit count, return the wigAsciiData list */ boolean checkWigDataFilter(char *db, char *table, char **constraint, double *ll, double *ul); /* check if filter exists, return its values, call with db="ct" for * custom tracks */ void doOutWigBed(struct trackDb *track, char *table, struct sqlConnection *conn); /* Return wiggle data in bed format. */ void doOutWigData(struct trackDb *track, char *table, struct sqlConnection *conn); /* Return wiggle data in variableStep format. */ void doSummaryStatsWiggle(struct sqlConnection *conn); /* Put up page showing summary stats for wiggle track. */ void wigShowFilter(struct sqlConnection *conn); /* print out wiggle data value filter */ /* ----------- BigWig business in bigWig.c -------------------- */ boolean isBigWig(char *database, char *table, struct trackDb *parent, struct customTrack *(*ctLookupName)(char *table)); /* Local test to see if something is bigWig. Handles hub tracks unlike hIsBigWig. */ boolean isBigWigTable(char *table); /* Return TRUE if table is bedGraph in current database's trackDb. */ char *bigFileNameFromCtOrHub(char *table, struct sqlConnection *conn); /* If table is a custom track or hub track, return the bigDataUrl setting; * otherwise return NULL. Do a freeMem on returned string when done. */ char *bigDataIndexFromCtOrHub(char *table, struct sqlConnection *conn); /* If table is a custom track or hub track, return the bigDataIndex setting; * otherwise return NULL. Do a freeMem on returned string when done. */ char *bigWigFileName(char *table, struct sqlConnection *conn); /* Return file name associated with bigWig. This handles differences whether it's * a custom or built-in track. Do a freeMem on returned string when done. */ #define bigBedFileName(table, conn) bigWigFileName(table, conn) struct hTableInfo *bigWigToHti(char *table); /* Get fields of bigWig into hti structure. */ int mathWigOutRegion(struct trackDb *track, char *table, struct sqlConnection *conn, struct region *region, int maxOut, enum wigOutputType wigOutType); /* Write out mathWig for region, doing intersecting and filtering as need be. */ int bigWigOutRegion(char *table, struct sqlConnection *conn, struct region *region, int maxOut, enum wigOutputType wigOutType); /* Write out bigWig for region, doing intersecting and filtering as need be. */ void doSummaryStatsBigWig(struct sqlConnection *conn); /* Put up page showing summary stats for bigWig track. */ struct bed *bigWigIntervalsToBed(struct sqlConnection *conn, char *table, struct region *region, struct lm *lm); /* Return a list of unfiltered, unintersected intervals in region as bed (for * secondary table in intersection). */ void showSchemaBigWigNoTable(char *db, char *table, struct trackDb *tdb); /* Show schema on bigWig. */ /* ----------- BigBed business in bigBed.c -------------------- */ boolean isBigBed(char *database, char *table, struct trackDb *parent, struct customTrack *(*ctLookupName)(char *table)); /* Local test to see if something is big bed. Handles hub tracks unlike hIsBigBed. */ char *bigBedFileName(char *table, struct sqlConnection *conn); /* Return file name associated with bigBed. This handles differences whether it's * a custom or built-in track or hub. Do a freeMem on returned string when done. */ struct hTableInfo *bigBedToHti(char *table, struct sqlConnection *conn); /* Get fields of bigBed into hti structure. */ struct slName *bigBedGetFields(char *table, struct sqlConnection *conn); /* Get fields of bigBed as simple name list. */ struct sqlFieldType *bigBedListFieldsAndTypes(struct trackDb *tdb, struct sqlConnection *conn); /* Get fields of bigBed as list of sqlFieldType. */ struct bed *bigBedGetFilteredBedsOnRegions(struct sqlConnection *conn, char *db, char *table, struct region *regionList, struct lm *lm, int *retFieldCount); /* Get list of beds from bigBed, in all regions, that pass filtering. */ void bigBedTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f, char outSep); /* Print out selected fields from Big Bed. If fields is NULL, then print out all fields. */ struct slName *randomBigBedIds(char *table, struct sqlConnection *conn, int count); /* Return some arbitrary IDs from a bigBed file. */ void showSchemaBigBed(char *table, struct trackDb *tdb); /* Show schema on bigBed. */ /* More stuff in bigBed.c that makes use of autoSql files. */ struct sqlFieldType *sqlFieldTypesFromAs(struct asObject *as); /* Convert asObject to list of sqlFieldTypes */ /* HAL stuff from hal.c */ boolean isHalTable(char *table); /* Return TRUE if table corresponds to a HAL file. */ struct slName *halGetFields(char *table); /* Get fields of hal as simple name list. */ void halTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f); /* BAM stuff from bam.c */ boolean isLongTabixTable(char *table); /* Return TRUE if table corresponds to a longTabix file. */ struct slName *getLongTabixFields(); /* Get fields of bam as simple name list. */ void longTabixTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f, char outSep); /* Print out selected fields from long tabix. If fields is NULL, then print out all fields. */ struct hTableInfo *longTabixToHti(char *table); /* Get standard fields of BAM into hti structure. */ struct bed *longTabixGetFilteredBedsOnRegions(struct sqlConnection *conn, char *db, char *table, struct region *regionList, struct lm *lm, int *retFieldCount); /* Get list of beds from long tabix, in all regions, that pass filtering. */ struct sqlFieldType *longTabixListFieldsAndTypes(); /* Get fields of BAM as list of sqlFieldType. */ void showSchemaLongTabix(char *table, struct trackDb *tdb); /* Show schema on long tabix. */ boolean isBamTable(char *table); /* Return TRUE if table corresponds to a BAM file. */ struct slName *bamGetFields(); /* Get fields of bam as simple name list. */ struct sqlFieldType *bamListFieldsAndTypes(); /* Get fields of BAM as list of sqlFieldType. */ struct hTableInfo *bamToHti(char *table); /* Get standard fields of BAM into hti structure. */ void showSchemaBam(char *table, struct trackDb *tdb); /* Show schema on bam. */ void bamTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f, char outSep); /* Print out selected fields from BAM. If fields is NULL, then print out all fields. */ struct bed *bamGetFilteredBedsOnRegions(struct sqlConnection *conn, char *db, char *table, struct region *regionList, struct lm *lm, int *retFieldCount); /* Get list of beds from BAM, in all regions, that pass filtering. */ struct slName *randomBamIds(char *table, struct sqlConnection *conn, int count); /* Return some semi-random qName based IDs from a BAM file. */ /* Hi-C stuff from hic.c */ struct hTableInfo *hicToHti(char *table); /* Get standard fields of hic into hti structure. */ boolean isHicTable(char *table); /* Return TRUE if table corresponds to a hic file. */ struct slName *hicGetFields(); /* Get fields of hic as simple name list. We represent hic with an interact structure, so * this is really just an interact as object. */ struct sqlFieldType *hicListFieldsAndTypes(); /* Get fields of hic as list of sqlFieldType (again, this is really just the list of interact fields. */ void showSchemaHic(char *table, struct trackDb *tdb); /* Show schema on hic. */ void hicTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f, char outSep); /* Print out selected fields from hic. If fields is NULL, then print out all fields. */ struct bed *hicGetFilteredBedsOnRegions(struct sqlConnection *conn, char *db, char *table, struct region *regionList, struct lm *lm, int *retFieldCount); /* Get list of beds from HIC, in all regions, that pass filtering. */ void hicMainPageConfig(struct cart *cart, struct trackDb *tdb); /* Display Hi-C-specific track configuration options (resolution, normalization) on * the main page. */ /* VCF (Variant Call Format) stuff from vcf.c */ extern char *vcfDataLineAutoSqlString; boolean isVcfTable(char *table, boolean *retIsTabix); /* Return TRUE if table corresponds to a VCF file. * If retIsTabix is non-NULL, set *retIsTabix to TRUE if this is vcfTabix (not just vcf). */ struct slName *vcfGetFields(); /* Get fields of VCF as simple name list. */ struct sqlFieldType *vcfListFieldsAndTypes(); /* Get fields of VCF as list of sqlFieldType. */ struct hTableInfo *vcfToHti(char *table, boolean isTabix); /* Get standard fields of VCF into hti structure. */ void showSchemaVcf(char *table, struct trackDb *tdb, boolean isTabix); /* Show schema on VCF. */ void vcfTabOut(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f, boolean isTabix); /* Print out selected fields from VCF. If fields is NULL, then print out all fields. */ struct bed *vcfGetFilteredBedsOnRegions(struct sqlConnection *conn, char *db, char *table, struct region *regionList, struct lm *lm, int *retFieldCount, boolean isTabix); /* Get list of beds from VCF, in all regions, that pass filtering. */ struct slName *randomVcfIds(char *table, struct sqlConnection *conn, int count, boolean isTabix); /* Return some semi-random IDs from a VCF file. */ /* ----------- Custom track stuff. -------------- */ struct customTrack *getCustomTracks(); /* Get custom track list. */ struct customTrack *ctLookupName(char *name); /* Lookup name in custom track list */ void removeNamedCustom(struct customTrack **pList, char *name); /* Remove named custom track from list if it's on there. */ void flushCustomTracks(); /* Flush custom track list. */ struct slName *getBedFields(int fieldCount); /* Get list of fields for bed of given size. */ struct bedFilter *bedFilterForCustomTrack(char *ctName); /* If the user specified constraints, then translate them to a bedFilter. */ struct bed *customTrackGetFilteredBeds(char *db, char *name, struct region *regionList, struct lm *lm, int *retFieldCount); /* Get list of beds from custom track of given name that are * in current regions and that pass filters. You can bedFree * this when done. */ struct customTrack *newCt(char *ctName, char *ctDesc, int visNum, char *ctUrl, int fields); /* Make a new custom track record for the query results. */ struct hTableInfo *ctToHti(struct customTrack *ct); /* Create an hTableInfo from a customTrack. */ void doTabOutDb( char *db, char *dbVarName, char *table, char *tableVarName, FILE *f, struct sqlConnection *conn, char *fields, char outSep); /* Do tab-separated output on fields of a single table. */ void doTabOutCustomTracks(char *db, char *table, struct sqlConnection *conn, char *fields, FILE *f, char outSep); /* Print out selected fields from custom track. If fields * is NULL, then print out all fields. */ /* ----------- Bed/joining stuff -------------- */ struct bed *getRegionAsBed( char *db, char *table, /* Database and table. */ struct region *region, /* Region to get data for. */ char *filter, /* Filter to add to SQL where clause if any. */ struct hash *idHash, /* Restrict to id's in this hash if non-NULL. */ struct lm *lm, /* Where to allocate memory. */ int *retFieldCount); /* Number of fields. */ /* Return a bed list of all items in the given range in table. * Cleanup result via lmCleanup(&lm) rather than bedFreeList. */ struct bed *getRegionAsMergedBed( char *db, char *table, /* Database and table. */ struct region *region, /* Region to get data for. */ char *filter, /* Filter to add to SQL where clause if any. */ struct hash *idHash, /* Restrict to id's in this hash if non-NULL. */ struct lm *lm, /* Where to allocate memory. */ int *retFieldCount); /* Number of fields. */ /* Return a bed list of all items in the given range in subtrack-merged table. * Cleanup result via lmCleanup(&lm) rather than bedFreeList. */ struct bed *dbGetFilteredBedsOnRegions(struct sqlConnection *conn, char *db, char *dbVarName, char *table, char *tableVarName, struct region *regionList, struct lm *lm, int *retFieldCount); /* Get list of beds from database in region that pass filtering. */ /* ----------- Page displayers -------------- */ void doMainPage(struct sqlConnection *conn); /* Put up the first page user sees. */ void mainPageAfterOpen(struct sqlConnection *conn); /* Put up main page assuming htmlOpen()/htmlClose() * will happen in calling routine. */ void doTest(); /* Put up a page to see what happens. */ void doTableSchema(char *db, char *table, struct sqlConnection *conn); /* Show schema around table. */ void doSchema(struct sqlConnection *conn); /* Show schema around current track. */ void doValueHistogram(char *field); /* Put up value histogram. */ void doValueRange(char *field); /* Put up value histogram. */ void doPasteIdentifiers(struct sqlConnection *conn); /* Respond to paste identifiers button. */ void doClearPasteIdentifierText(struct sqlConnection *conn); /* Respond to clear within paste identifier page. */ void doPastedIdentifiers(struct sqlConnection *conn); /* Process submit in past identifiers page. */ void doUploadIdentifiers(struct sqlConnection *conn); /* Respond to upload identifiers button. */ void doClearIdentifiers(struct sqlConnection *conn); /* Respond to clear identifiers button. */ void doPrintSelectedFields(); /* Actually produce selected field output as text stream. */ void doSelectFieldsMore(); /* Continue with select fields dialog. */ void doClearAllField(char *dbTable); /* Clear all checks by fields in db.table. */ void doSetAllField(char *dbTable); /* Set all checks by fields in db.table. */ void doOutPrimaryTable(char *table, struct sqlConnection *conn); /* Dump out primary table. */ void doOutSelectedFields(char *table, struct sqlConnection *conn); /* Put up select fields (for tab-separated output) page. */ void doOutSequence(struct sqlConnection *conn); /* Output sequence page. */ void doOutBed(char *table, struct sqlConnection *conn); /* Put up form to select BED output format. */ void doOutHyperlinks(char *table, struct sqlConnection *conn); /* Output as genome browser hyperlinks. */ void doOutGff(char *table, struct sqlConnection *conn, boolean outputGtf); /* Save as GFF/GTF. */ void doOutCustomTrack(char *table, struct sqlConnection *conn); /* Put up form to select Custom Track output format. */ void doOutGalaxyQuery (struct trackDb *track, char *table, unsigned int hguid); /* print options page for background query */ void doSummaryStats(struct sqlConnection *conn); /* Put up page showing summary stats for track. */ void doFilterPage(struct sqlConnection *conn); /* Respond to filter create/edit button */ void doFilterMore(struct sqlConnection *conn); /* Continue with Filter Page. */ void doFilterSubmit(struct sqlConnection *conn); /* Respond to submit on filters page. */ void doClearFilter(struct sqlConnection *conn); /* Respond to click on clear filter. */ void doIntersectPage(struct sqlConnection *conn); /* Respond to intersect create/edit button */ void doClearIntersect(struct sqlConnection *conn); /* Respond to click on clear intersection. */ void doIntersectMore(struct sqlConnection *conn); /* Continue working in intersect page. */ void doIntersectSubmit(struct sqlConnection *conn); /* Finish working in intersect page. */ void doCorrelatePage(struct sqlConnection *conn); /* Respond to correlate create/edit button */ void doClearContinueCorrelate(struct sqlConnection *conn); /* Respond to click on clear selections from correlation calculate page. */ void doClearCorrelate(struct sqlConnection *conn); /* Respond to click on clear correlate. */ void doCorrelateMore(struct sqlConnection *conn); /* Continue working in correlate page. */ void doCorrelateSubmit(struct sqlConnection *conn); /* Finish working in correlate page. */ void doGenePredSequence(struct sqlConnection *conn); /* Output genePred sequence. */ void doGenePredPal(struct sqlConnection *conn); /* Output genePred protein alignment. */ void doGenomicDna(struct sqlConnection *conn); /* Get genomic sequence (UI has already told us how). */ void doGetBed(struct sqlConnection *conn); /* Get BED output (UI has already told us how). */ void doGetCustomTrackTb(struct sqlConnection *conn); /* Get Custom Track output (UI has already told us how) in Table Browser. */ void doGetCustomTrackGb(struct sqlConnection *conn); /* Get Custom Track output (UI has already told us how) in Genome Browser. */ void doGetCustomTrackFile(struct sqlConnection *conn); /* Get Custom Track file output (UI has already told us how). */ void doRemoveCustomTrack(struct sqlConnection *conn); /* Remove custom track file. */ void doSummaryStatsBed(struct sqlConnection *conn); /* Put up page showing summary stats for track that is in database * or that is bed-format custom. */ void doSubmitUserRegions(struct sqlConnection *conn); /* Process submit in set regions page. */ void doSetUserRegions(struct sqlConnection *conn); /* Respond to set regions button. */ void doClearUserRegions(struct sqlConnection *conn); /* Respond to clear user regions button. */ char *userRegionsFileName(); /* File name defined regions are in, or NULL if no such file. */ struct region *getUserRegions(char *fileName); /* Get user defined regions from fileName. */ void doClearSetUserRegionsText(struct sqlConnection *conn); /* Respond to clear within user regions enter page. */ /* --------------- Galaxy functions --------------- */ boolean doGalaxy (); /* Has the send query results to Galaxy checkbox been selected? */ void printGalaxySubmitButtons (); /* print submit button to send query results to Galaxy */ void startGalaxyForm (); /* start form to send parameters to Galaxy, also send required params */ void sendParamsToGalaxy(char *doParam, char *paramVal); /* intermediate page for formats printed directly from top form */ void verifyGalaxyFormat(const char *output); /* print warning about not using hyperlinks output formtat with Galaxy */ /* --------------- GREAT functions --------------- */ boolean doGreat(); /* Has the send query results to GREAT checkbox been selected? */ void verifyGreatFormat(const char *output); /* check that specified outupt format is acceptable for GREAT; errAbort if not */ void verifyGreatAssemblies(); /* check that specified assembly is acceptable for GREAT; errAbort if not */ void printGreatSubmitButtons(); /* print submit button to send query results to GREAT */ void startGreatForm(); /* start form to send parameters to GREAT, also send required params */ void doGetGreatOutput(void (*dispatch)()); /* Generate output that GREAT will read via doGetGreatResults. */ void doGreatTopLevel(); /* intermediate page for sending to GREAT directly from top form */ /* --------------- GenomeSpace functions --------------- */ boolean isGenomeSpaceEnabled(); /* genomeSpace is enabled by the presence of GS config settings. */ boolean doGenomeSpace(); /* Has the send query results to GenomeSpace checkbox been selected? */ boolean checkGsReady(); /* check that GS requirements are met */ void doGsLogin(struct sqlConnection *conn); /* Process user password post. */ void gsSendToDM(); /* upload the generated file to DM */ void getBackgroundStatus(char *url); /* fetch status as the latest complete html block available */ void startBackgroundWork(char *exec, char **pWorkUrl); /* deal with forking off child for background work * and setting up the trash file for communicating * from the child to the browser */ /* --------------- wikiTrack functions --------------- */ struct hTableInfo *wikiHti(); /* Create an hTableInfo for the wikiTrack. */ void doSummaryStatsWikiTrack(struct sqlConnection *conn); /* Put up page showing summary stats for wikiTrack. */ struct bed *wikiTrackGetFilteredBeds(char *name, struct region *regionList, struct lm *lm, int *retFieldCount); /* Get list of beds from the wikiTrack * in current regions and that pass * filters. You can bedFree this when done. */ /* --------------- microarray track functions ------------- */ boolean isMicroarray(struct trackDb *parent, char *table); /* Return TRUE if table is specified as a microarray in the current database's * trackDb. */ void doOutMicroarrayNames(struct trackDb *tdb); /* Show the microarray names from .ra file */ #define uglyw warn /* Warn for debugging purposes. */ int bigFileMaxOutput(); /* return maxOut value (cart variable defined on curTable) */ #endif /* HGTABLES_H */