/* trackDb.h was originally generated by the autoSql program, which also * generated trackDb.c and trackDb.sql. This header links the database and * the RAM representation of objects. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef TRACKDB_H #define TRACKDB_H struct trackDb; // forward definition for use in cart.h #include "common.h" #ifndef JKSQL_H #include "jksql.h" #endif #ifndef LINEFILE_H #include "linefile.h" #endif #ifndef CART_H #include "cart.h" #endif #define TRACKDB_NUM_COLS 21 // Forward definitions struct tdbExtras; // A structure to keep track of our min and max values if we're a wig struct minMax { double min, max; }; /* DO NOT CHANGE THE TRACKDB STRUCTURE WITHOUT INCREMENTING THE VERSION NUMBER */ /* This number is tacked onto the end of cached trackDb entries to make sure we * don't use a cached structure that has different contents. */ #define TRACKDB_VERSION 7 struct trackDb /* This describes an annotation track. */ /* DO NOT CHANGE THE TRACKDB STRUCTURE WITHOUT INCREMENTING THE VERSION NUMBER */ { struct trackDb *next; /* Next in singly linked list. Next sibling in tree. */ char *track; /* Symbolic ID of Track - used in cart. Is tableName in database historically. */ char *table; /* Symbolic ID of Table - used in database. Same as track usually. */ char *shortLabel; /* Short label displayed on left */ char *type; /* Track type: bed, psl, genePred, etc. */ char *longLabel; /* Long label displayed in middle */ unsigned char visibility; /* 0=hide, 1=dense, 2=full, 3=pack, 4=squish */ float priority; /* 0-100 - where to position. 0 is top */ unsigned char colorR; /* Color red component 0-255 */ unsigned char colorG; /* Color green component 0-255 */ unsigned char colorB; /* Color blue component 0-255 */ unsigned char altColorR; /* Light color red component 0-255 */ unsigned char altColorG; /* Light color green component 0-255 */ unsigned char altColorB; /* Light color blue component 0-255 */ unsigned char useScore; /* 1 if use score, 0 if not */ /* DO NOT CHANGE THE TRACKDB STRUCTURE WITHOUT INCREMENTING THE VERSION NUMBER */ #ifndef __cplusplus unsigned char private; /* 1 if only want to show it on test site */ #else unsigned char priv; /* don't conflict with C++ keyword */ #endif int restrictCount; /* Number of chromosomes this is on (0=all though!) */ char **restrictList; /* List of chromosomes this is on */ char *url; /* URL to link to when they click on an item */ char *html; /* Some html to display when they click on an item */ char *grp; /* Which group track belongs to */ unsigned char canPack; /* 1 if can pack track display, 0 otherwise */ char *settings; /* Name/value pairs for track-specific stuff */ struct hash *viewHash; /* Hash for settings. Not saved in database.*/ struct hash *settingsHash; /* Hash for settings. Not saved in database. * Don't use directly, rely on trackDbSetting to access. */ /* additional info, determined from settings */ /* DO NOT CHANGE THE TRACKDB STRUCTURE WITHOUT INCREMENTING THE VERSION NUMBER */ char treeNodeType; // bit map containing defining supertrack, composite and children // of same (may be parent & child) struct trackDb *parent; // parent of composite or superTracks struct trackDb *subtracks; // children of composite not supers. NOTE: only in one sl at a time! struct slRef *children; // children of folders (superTracks) only. // Needed as slRef since these children are on the main trackList // and can't be in 2 sl's at once char *parentName; // set if this is a supertrack member boolean isShow; // for supertracks: true if supertrack with pseudo-vis 'show' struct hash *overrides; /* If not NULL, this is an override * entry. It contains the names, but not the * values of the fields and settings that were * specified in the entry. */ struct tdbExtras *tdbExtras;// This struct allows storing extra values which may be used // multiple times within a single cgi. An example is the metadata // looked up once in the metaDb and used again and again. struct hash *isNewFilterHash; // if a field is specified in the "new" way, the trackDb variable will be in this hash char *errMessage; // if there's an error in the trackDb specification, there will be a message in here char *originalTrack; /* Normally NULL, if populated holds the track name to use to fetch cart variables. */ /* DO NOT CHANGE THE TRACKDB STRUCTURE WITHOUT INCREMENTING THE VERSION NUMBER */ }; #define FOLDER_MASK 0x10 #define COMPOSITE_MASK 0x20 #define MULTI_TRACK_MASK 0x80 #define FOLDER_CHILD_MASK 0x01 #define COMPOSITE_CHILD_MASK 0x02 #define COMPOSITE_VIEW_MASK 0x04 #define MULTI_TRACK_CHILD_MASK 0x08 #define PARENT_MASK 0xF0 #define CHILD_MASK 0x0F #define TREETYPE_MASK 0xFF #define PARENT_NODE(nodeType) ((nodeType) & PARENT_MASK) #define CHILD_NODE(nodeType) ((nodeType) & CHILD_MASK) #define FOLDER_NODE(nodeType) ((nodeType) & FOLDER_MASK) #define COMPOSITE_NODE(nodeType) ((nodeType) & COMPOSITE_MASK) #define MULTI_TRACK_NODE(nodeType) ((nodeType) & MULTI_TRACK_MASK) #define CONTAINER_NODE(nodeType) ((nodeType) & (MULTI_TRACK_MASK | COMPOSITE_MASK)) #define FOLDER_CHILD_NODE(nodeType) ((nodeType) & FOLDER_CHILD_MASK) #define COMPOSITE_CHILD_NODE(nodeType) ((nodeType) & COMPOSITE_CHILD_MASK) #define COMPOSITE_VIEW_NODE(nodeType) ((nodeType) & COMPOSITE_VIEW_MASK) #define MULTI_TRACK_CHILD_NODE(nodeType) ((nodeType) & MULTI_TRACK_CHILD_MASK) #define CONTAINER_CHILD_NODE(nodeType) ((nodeType) & \ (MULTI_TRACK_CHILD_MASK | COMPOSITE_CHILD_MASK)) #define INDEPENDENT_NODE(nodeType) (((nodeType) & TREETYPE_MASK) == 0 ) #define SOLO_NODE(nodeType) (((nodeType) & TREETYPE_MASK) <= FOLDER_CHILD_MASK) //#define tdbIsParent(tdb) ((tdb)->subtracks) //#define tdbIsChild(tdb) ((tdb)->parent ) //#define tdbIsTreeLeaf(tdb) ( CHILD_NODE((tdb)->treeNodeType) && !tdbIsParent(tdb)) //#define tdbIsTreeRoot(tdb) (PARENT_NODE((tdb)->treeNodeType) && !tdbIsChild(tdb) ) //#define tdbIsTreeBranch(tdb) ( !INDEPENDENT_NODE((tdb)->treeNodeType) // && tdbIsParent(tdb) && tdbIsChild(tdb)) //#define tdbIsNotInTree(tdb) ( INDEPENDENT_NODE((tdb)->treeNodeType) // && !tdbIsParent(tdb) && !tdbIsChild(tdb)) // --- Folders are superTracks. Currently only one level deep INLINE void tdbMarkAsFolder(struct trackDb *tdb) // Marks a trackDb struct as a supertrack { tdb->treeNodeType |= FOLDER_MASK; } #define tdbMarkAsSuperTrack(tdb) tdbMarkAsFolder(tdb) INLINE void tdbMarkAsFolderChild(struct trackDb *tdb) // Marks a trackDb struct as a child of a folder { tdb->treeNodeType |= FOLDER_CHILD_MASK; } #define tdbMarkAsSuperTrackChild(tdb) tdbMarkAsFolderChild(tdb) INLINE boolean tdbIsFolder(struct trackDb *tdb) // Is this trackDb struct marked as a folder ? { return tdb && FOLDER_NODE(tdb->treeNodeType); // && tdb->children // NOTE: The children list is not always filled in, but should be } #define tdbIsSuper(tdb) tdbIsFolder(tdb) #define tdbIsSuperTrack(tdb) tdbIsFolder(tdb) INLINE boolean tdbIsFolderContent(struct trackDb *tdb) // Is this trackDb struct marked as a contained in a folder ? { return tdb && tdb->parent && FOLDER_CHILD_NODE(tdb->treeNodeType); } #define tdbIsSuperTrackChild(tdb) tdbIsFolderContent(tdb) INLINE struct trackDb *tdbGetImmediateFolder(struct trackDb *tdb) // Return closest ancestor who is a folder track. { struct trackDb *parent = tdb->parent; for ( ; parent != NULL && !tdbIsFolder(parent); parent = parent->parent) ; return parent; } #define tdbGetSuperTrack(tdb) tdbGetImmediateFolder(tdb) // --- Composites are 2 or 3 level containers of tracks organized into a single hgTrackUi cfg page INLINE void tdbMarkAsComposite( struct trackDb *tdb) // Marks a trackDb struct as a composite track { tdb->treeNodeType |= COMPOSITE_MASK; } INLINE void tdbMarkAsCompositeView( struct trackDb *tdb) // Marks a trackDb struct as a view of a composite track { tdb->treeNodeType |= COMPOSITE_VIEW_MASK; } INLINE void tdbMarkAsCompositeChild( struct trackDb *tdb) // Marks a trackDb struct as a child or subtrack of a composite track { tdb->treeNodeType |= COMPOSITE_CHILD_MASK; } #define tdbMarkAsCompositeSubtrack(tdb) tdbMarkAsCompositeChild(tdb) INLINE boolean tdbIsComposite( struct trackDb *tdb) // Is this trackDb struct marked as a composite with children ? { return tdb && tdb->subtracks && COMPOSITE_NODE( tdb->treeNodeType); } INLINE boolean tdbIsCompositeView(struct trackDb *tdb) // Is this trackDb struct marked as a view of a composite track ? { return tdb && tdb->parent && tdb->subtracks && COMPOSITE_VIEW_NODE( tdb->treeNodeType); } INLINE boolean tdbIsCompositeChild(struct trackDb *tdb) // Is this trackDb struct marked as a child of a composite track ? { return tdb && tdb->parent && COMPOSITE_CHILD_NODE(tdb->treeNodeType); } #define tdbIsCompositeSubtrack(tdb) tdbIsCompositeChild(tdb) INLINE struct trackDb *tdbGetComposite(struct trackDb *tdb) // Return closest ancestor who is a composite track. { struct trackDb *parent = tdb->parent; for ( ; parent != NULL && !tdbIsComposite(parent); parent = parent->parent) ; return parent; } // --- MultiTracks are container tracks with one level of subtracks // combined into a unified hgTracks image track INLINE void tdbMarkAsMultiTrack( struct trackDb *tdb) // Marks a trackDb struct as a multiTrack (like multiWig) { tdb->treeNodeType |= MULTI_TRACK_MASK; } INLINE void tdbMarkAsMultiTrackChild( struct trackDb *tdb) // Marks a trackDb struct as a child of a multiTrack (like multiWig) { tdb->treeNodeType |= MULTI_TRACK_CHILD_MASK; } #define tdbMarkAsMultiTrackSubtrack(tdb) tdbMarkAsMultiTrackChild(tdb) INLINE boolean tdbIsMultiTrack( struct trackDb *tdb) // Is this trackDb struct marked as a multiTrack (like multiWig) ? { return tdb && tdb->subtracks && MULTI_TRACK_NODE( tdb->treeNodeType); } INLINE boolean tdbIsMultiTrackChild(struct trackDb *tdb) // Is this trackDb struct marked as a child of a multiTrack (like multiWig) ? { return tdb && tdb->parent && MULTI_TRACK_CHILD_NODE(tdb->treeNodeType); } #define tdbIsMultiTrackSubtrack(tdb) tdbIsMultiTrackChild(tdb) INLINE struct trackDb *tdbGetMultiTrack(struct trackDb *tdb) // Return closest ancestor who is a multiTrack. { struct trackDb *parent = tdb->parent; for ( ; parent != NULL && !tdbIsMultiTrack(parent); parent = parent->parent) ; return parent; } // --- CONTAINERS are composites or multiTracks, which behave in similar ways thru some code paths INLINE boolean tdbIsContainer( struct trackDb *tdb) // Is this trackDb struct marked as a composite or multiTrack with children ? { return tdb && tdb->subtracks && CONTAINER_NODE(tdb->treeNodeType); } INLINE boolean tdbIsContainerChild(struct trackDb *tdb) // Is this trackDb struct marked as a child of a composite or multiTrack ? { return tdb && tdb->parent && CONTAINER_CHILD_NODE(tdb->treeNodeType); } #define tdbIsSubtrack(tdb) tdbIsContainerChild(tdb) INLINE struct trackDb *tdbGetContainer(struct trackDb *tdb) // Return closest ancestor who is a container track. { struct trackDb *parent = tdb->parent; for ( ; parent != NULL && !tdbIsContainer(parent); parent = parent->parent) ; return parent; } // Solo (or stand alone) tracks are non-containers which may only be contained by folders INLINE boolean tdbIsSoloTrack(struct trackDb *tdb) // Is this trackDb struct marked as a solo so it should have data { return tdb && SOLO_NODE(tdb->treeNodeType); } #define tdbIsStandAlone(tdb) tdbIsSoloTrack(tdb) #define tdbIsDataTrack(tdb) (tdbIsSoloTrack(tdb) || tdbIsSubtrack(tdb)) // TrackUi Top level means composite, multitrack or solo // These are not folders, views or subtracks. #define tdbIsTrackUiTopLevel(tdb) (tdbIsContainer(tdb) || tdbIsSoloTrack(tdb)) #define DOWNLOADS_ONLY_TYPE "downloadsOnly" INLINE boolean tdbIsDownloadsOnly(struct trackDb *tdb) // Is this a downloadsOnly tdb { return (tdb && sameWord(tdb->type,DOWNLOADS_ONLY_TYPE)); } struct trackDb *trackDbLoad(char **row); /* Load a trackDb from row fetched with select * from trackDb * from database. Dispose of this with trackDbFree(). */ struct trackDb *trackDbLoadAll(char *fileName); /* Load all trackDb from whitespace-separated file. * Dispose of this with trackDbFreeList(). */ struct trackDb *trackDbLoadWhere(struct sqlConnection *conn, char *table, char *where); /* Load all trackDb from table that satisfy where clause. The * where clause may be NULL in which case whole table is loaded * Dispose of this with trackDbFreeList(). */ struct trackDb *trackDbLoadAllByChar(char *fileName, char chopper); /* Load all trackDb from chopper separated file. * Dispose of this with trackDbFreeList(). */ #define trackDbLoadAllByTab(a) trackDbLoadAllByChar(a, '\t'); /* Load all trackDb from tab separated file. * Dispose of this with trackDbFreeList(). */ struct trackDb *trackDbCommaIn(char **pS, struct trackDb *ret); /* Create a trackDb out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new trackDb */ void trackDbFree(struct trackDb **pEl); /* Free a single dynamically allocated trackDb such as created * with trackDbLoad(). */ void trackDbFreeList(struct trackDb **pList); /* Free a list of dynamically allocated trackDb's */ void trackDbOutput(struct trackDb *el, FILE *f, char sep, char lastSep); /* Print out trackDb. Separate fields with sep. Follow last field with lastSep. */ #define trackDbTabOut(el,f) trackDbOutput(el,f,'\t','\n'); /* Print out trackDb as a line in a tab-separated file. */ #define trackDbCommaOut(el,f) trackDbOutput(el,f,',',','); /* Print out trackDb as a comma separated list including final comma. */ /* ----------- End of AutoSQL generated code --------------------- */ struct trackDb *trackDbNew(); /* Allocate a new trackDb with just very minimal stuff filled in. */ int trackDbCmp(const void *va, const void *vb); /* Sort track by priority. */ int trackDbCmpShortLabel(const void *va, const void *vb); /* Sort track by shortLabel. */ void trackDbOverridePriority(struct hash *tdHash, char *priorityRa); /* Override priority settings using a ra file. */ struct trackDb *trackDbFromRa(char *raFile, char *releaseTag, struct dyString *incFiles); /* Load track info from ra file into list. If releaseTag is non-NULL * then only load tracks that mesh with release. if incFiles is non-null, * add included file names to it.*/ struct trackDb *trackDbFromOpenRa(struct lineFile *lf, char *releaseTag, struct dyString *incFiles); /* Load track info from ra file already opened as lineFile into list. If releaseTag is * non-NULL then only load tracks that mesh with release. If incFiles is not-NULL, put * list of included files in there. */ void trackDbPolish(struct trackDb *bt); /* Fill in missing values with defaults. */ void trackDbFieldsFromSettings(struct trackDb *td); /* Update trackDb fields from settings hash */ char *trackDbLocalSetting(struct trackDb *tdb, char *name); /* Return setting from tdb, but *not* any of it's parents. */ struct hash *trackDbHashSettings(struct trackDb *tdb); /* Force trackDb to hash up it's settings. Usually this is just * done on demand. Returns settings hash. */ struct hash *trackDbSettingsFromString(struct trackDb *tdb, char *string); /* Return hash of key/value pairs from string. Differs * from raFromString in that it passes the key/val * pair through the backwards compatability routines. */ boolean trackDbNoInheritField(char *field); /* Suppress inheritance of specific fields */ char *trackDbSetting(struct trackDb *tdb, char *name); /* Return setting string or NULL if none exists. */ void trackDbAddSetting(struct trackDb *bt, char *name, char *val); /* Add a setting to a trackDb rec */ boolean trackDbSettingOn(struct trackDb *tdb, char *name); /* Return true if a tdb setting is "on" "true" or "enabled". */ char *trackDbRequiredSetting(struct trackDb *tdb, char *name); /* Return setting string or squawk and die. */ char *trackDbSettingOrDefault(struct trackDb *tdb, char *name, char *defaultVal); /* Return setting string, or defaultVal if none exists */ struct hashEl *trackDbSettingsLike(struct trackDb *tdb, char *wildStr); /* Return a list of settings whose names match wildStr (may contain wildcard * characters). Free the result with hashElFreeList. */ float trackDbFloatSettingOrDefault(struct trackDb *tdb, char *name, float defaultVal); /* Return setting, convert to a float, or defaultVal if none exists */ void trackDbSuperMarkup(struct trackDb *tdbList); /* Get info from supertrack setting. There are 2 forms: * Parent: 'supertrack on [show]' * Child: 'supertrack [vis] * Returns NULL if there is no such setting */ char *trackDbInclude(char *raFile, char *line, char **releaseTag); /* Get include filename from trackDb line. Return NULL if line doesn't contain include */ char *trackDbOrigAssembly(struct trackDb *tdb); /* return setting from trackDb, if any */ void trackDbPrintOrigAssembly(struct trackDb *tdb, char *database); /* Print lift information from trackDb, if any */ // Not all track types have separate configuration typedef enum _eCfgType { cfgNone =0, cfgBedScore =1, cfgWig =2, cfgWigMaf =3, cfgPeak =4, cfgGenePred =5, cfgChain =6, cfgNetAlign =7, cfgBedFilt =8, cfgBam =9, cfgPsl =10, cfgVcf =11, cfgSnake =12, cfgLong =13, cfgBarChart =14, cfgInteract =15, cfgLollipop =16, cfgHic =17, cfgBigDbSnp =19, cfgBigRmsk =20, cfgUndetermined // Not specifically denied, but not determinable in lib code } eCfgType; eCfgType cfgTypeFromTdb(struct trackDb *tdb, boolean warnIfNecessary); /* determine what kind of track specific configuration is needed, warn if not multi-view compatible */ int configurableByAjax(struct trackDb *tdb, eCfgType cfgTypeIfKnown); // Is this track configurable by right-click popup, or in hgTrackUi subCfg? // returns 0 = nothing to cfg; <0=blocked via ajax; >0=allowed and will be cfgType if determinable void trackDbOverride(struct trackDb *td, struct trackDb *overTd); /* apply an trackOverride trackDb entry to a trackDb entry */ #ifdef OLD char *trackDbCompositeSettingByView(struct trackDb *parentTdb, char* view, char *name); /* Get a trackDb setting at the view level for a multiview composite. returns a string that must be freed */ #endif /* OLD */ char *trackDbSettingByView(struct trackDb *tdb, char *name); /* For a subtrack of a multiview composite, get a setting stored in the parent settingByView. returns a string that must be freed */ #define trackDbSettingClosestToHome(tdb, name) trackDbSetting(tdb, name) #ifdef OLD char *trackDbSettingClosestToHome(struct trackDb *tdb, char *name); /* Look for a trackDb setting from lowest level on up through chain of ancestors. */ #endif /* OLD */ char *trackDbSettingClosestToHomeOrDefault(struct trackDb *tdb, char *name, char *defaultVal); /* Look for a trackDb setting (or default) from lowest level on up through chain of ancestors. */ boolean trackDbSettingClosestToHomeOn(struct trackDb *tdb, char *name); /* Return true if a tdb setting closest to home is "on" "true" or "enabled". */ struct trackDb *subTdbFind(struct trackDb *parent,char *table); /* Return subTrack tdb if it exists in parent. */ struct trackDb *tdbFindOrCreate(char *db,struct trackDb *parent,char *table); /* Find or creates the tdb for this table. May return NULL. */ boolean tdbIsView(struct trackDb *tdb,char **viewName); // Is this tdb a view? Will fill viewName if provided char *tdbGetViewName(struct trackDb *tdb); // returns NULL the view name for view or child track (do not free) void parseColor(char *text, unsigned char *r, unsigned char *g, unsigned char *b); /* Turn comma-separated string of three numbers into three * color components. */ int parentTdbAbandonTablelessChildren(char *db, struct trackDb *parentTdb); /* abandons tableless children from a container tdb, such as a composite returns count of children that have been abandoned */ struct trackDb *trackDbLinkUpGenerations(struct trackDb *tdbList); /* Convert a list to a forest - filling in parent and subtrack pointers. * The exact topology of the forest is a little complex due to the * fact there are two "inheritance" systems - the superTrack system * and the subTrack system. In the superTrack system (which is on it's * way out) the superTrack's themselves have the tag: * superTrack on * and the children of superTracks have the tag: * superTrack parentName * In the subTrack system the parents have the tag: * compositeTrack on * and the children have the tag: * subTrack parentName * In this routine the subtracks are removed from the list, and stuffed into * the subtracks lists of their parents. The highest level parents stay on * the list. There can be multiple levels of inheritance. * For the supertracks the _parents_ are removed from the list. The only * reference to them in the returned forest is that they are in the parent * field of their children. The parents of supertracks have no subtracks * after this call currently. */ void trackDbPrioritizeContainerItems(struct trackDb *tdbList); /* Set priorities in containers if they have no priorities already set priorities are based upon 'sortOrder' setting or else shortLabel */ void trackDbAddTableField(struct trackDb *tdbList); /* Add table field by looking it up in settings. */ struct slRef *trackDbListGetRefsToDescendants(struct trackDb *tdbForest); /* Return reference list to everything in forest. Do slFreeList when done. */ struct slRef *trackDbListGetRefsToDescendantLeaves(struct trackDb *tdbForest); /* Return reference list all leaves in forest. Do slFreeList when done. */ int trackDbRefCmp(const void *va, const void *vb); /* Do trackDbCmp on list of references as opposed to actual trackDbs. */ int trackDbCountDescendants(struct trackDb *tdb); /* Count the number of tracks in subtracks list and their subtracks too . */ int trackDbCountDescendantLeaves(struct trackDb *tdb); /* Count the number of leaves in children list and their children. */ struct trackDb *trackDbTopLevelSelfOrParent(struct trackDb *tdb); /* Look for a parent who is a composite or multiTrack track and return that. Failing that * just return self. */ boolean trackDbUpdateOldTag(char **pTag, char **pVal); /* Look for obscolete tags and update them to new format. Return TRUE if any update * is done. Will allocate fresh memory for new tag and val if updated. */ boolean trackDbCheckValidRelease(char *tag); /* check to make sure release tag is valid */ struct slName *trackDbLocalSettingsWildMatch(struct trackDb *tdb, char *expression); // Return local settings that match expression else NULL. In alpha order. struct slName *trackDbSettingsWildMatch(struct trackDb *tdb, char *expression); // Return settings in tdb tree that match expression else NULL. In alpha order, no duplicates. // Forward defs for tdbExtras struct mdbObj; struct _membersForAll; struct _membership; enum filterCompositeType // Filter composites are drop-down checkbox-lists for selecting subtracks (eg hg19::HAIB TFBS) { fctNone=0, // do not offer filter for this dimension fctOne=1, // filter composite by one or all fctOneOnly=2, // filter composite by only one fctMulti=3, // filter composite by multiselect: all, one or many }; typedef struct _members { int count; char * groupTag; char * groupTitle; char **tags; char **titles; boolean *selected; char * setting; int *subtrackCount; // count of subtracks int *currentlyVisible; // count of visible subtracks struct slRef **subtrackList; // set of subtracks belonging to each subgroup member enum filterCompositeType fcType; // fctNone,fctOne,fctMulti } members_t; struct tdbExtras #define TDB_EXTRAS_EMPTY_STATE 666 // Struct for misc. data collected/calculated during CGI track setup that are cached for later use. // These extras are primarily used in hgTracks & hgTrackUi but can be used and expanded as needed. // CGI developers are encouraged to add to this structure for their own needs. { int fourState; // hgTrackUi subtracks use 4 state checkboxes (checked/un by enabled/dis) boolean reshapedComposite; // hgTracks should not "reshape" composites more than once. struct mdbObj *mdb; // several CGIs need repeated access to a tracks metadata struct _membersForAll *membersForAll; // hgTrackUi composites collect all view/dimension info struct _membership *membership; // hgTrackUi subtracks have individual membership info // Developer: please add your useful data that is costly to calculate/retrieve more than once struct hash *membersHash; // keep track of our children's min and max if we're scaling over all of them struct minMax *minMax; }; void tdbExtrasFree(struct tdbExtras **pTdbExtras); // Frees the tdbExtras structure int tdbExtrasFourState(struct trackDb *tdb); // Returns subtrack four state if known, else TDB_EXTRAS_EMPTY_STATE void tdbExtrasFourStateSet(struct trackDb *tdb,int fourState); // Sets subtrack four state boolean tdbExtrasReshapedComposite(struct trackDb *tdb); // Returns TRUE if composite has been declared as reshaped, else FALSE. void tdbExtrasReshapedCompositeSet(struct trackDb *tdb); // Declares that the composite has been reshaped. struct mdbObj *tdbExtrasMdb(struct trackDb *tdb); // Returns mdb metadata if already known, else NULL void tdbExtrasMdbSet(struct trackDb *tdb,struct mdbObj *mdb); // Sets the mdb metadata structure for later retrieval. struct _membersForAll *tdbExtrasMembersForAll(struct trackDb *tdb); // Returns composite view/dimension members for all, else NULL. void tdbExtrasMembersForAllSet(struct trackDb *tdb, struct _membersForAll *membersForAll); // Sets the composite view/dimensions members for all for later retrieval. members_t *tdbExtrasMembers(struct trackDb *tdb, char *groupNameOrTag); // Returns subtrack members if already known, else NULL void tdbExtrasMembersSet(struct trackDb *tdb, char *groupNameOrTag, members_t *members); // Sets the subtrack members for later retrieval. struct _membership *tdbExtrasMembership(struct trackDb *tdb); // Returns subtrack membership if already known, else NULL void tdbExtrasMembershipSet(struct trackDb *tdb,struct _membership *membership); // Sets the subtrack membership for later retrieval. char *tdbBigFileName(struct sqlConnection *conn, struct trackDb *tdb); // Return file name associated with bigWig. Do a freeMem on returned string when done. boolean rTdbTreeCanPack(struct trackDb *tdb); // Trees can pack as all or none, since they can share vis. void tdbSetCartVisibility(struct trackDb *tdb, struct cart *cart, char *vis); // Set visibility in the cart. Handles all the complications necessary for subtracks. // More INLINES which depend on what the definition of "is" is INLINE boolean tdbIsBigBed(struct trackDb *tdb) // Local test to see if something is big bed. Handles hub tracks unlike hIsBigBed. { // TODO: replace with table lookup (same as bigBedFind ?) return (!startsWithWord("bigWig", tdb->type) && startsWith("big", tdb->type)); } INLINE boolean tdbIsBigWig(struct trackDb *tdb) // Local test to see if something is big bed. Handles hub tracks unlike hIsBigBed. { return startsWithWord("bigWig", tdb->type) || startsWithWord("mathWig", tdb->type); } INLINE boolean tdbIsLongTabix(struct trackDb *tdb) // Return TRUE if tdb corresponds to a long tabix file. { return startsWithWord("longTabix", tdb->type); } INLINE boolean tdbIsBam(struct trackDb *tdb) // Return TRUE if tdb corresponds to a BAM file. { return startsWithWord("bam", tdb->type); } INLINE boolean tdbIsVcf(struct trackDb *tdb) // Return TRUE if tdb corresponds to a VCF file. { return startsWithWord("vcfTabix", tdb->type) || startsWithWord("vcf", tdb->type); } INLINE boolean tdbIsHic(struct trackDb *tdb) // Return TRUE if tdb corresponds to a HIC file. { return startsWithWord("hic", tdb->type); } INLINE boolean tdbIsBedGraph(struct trackDb *tdb) // Return TRUE if tdb corresponds to a bedGraph track. { return startsWithWord("bedGraph", tdb->type); } boolean trackDbSettingBlocksConfiguration(struct trackDb *tdb, boolean onlyAjax); // Configuration dialogs may be explicitly blocked in tracDb settings struct slPair *trackDbMetaPairs(struct trackDb *tdb); /* Read in metadata given a trackDb entry. This routine understands the three ways * that metadata can be represented in a trackDb stanza: "metadata" lines per stanza, * or a tab-separated or tagStorm file with a foreign key specified by the "meta" tag. */ char *trackDbViewSetting(struct trackDb *tdb, char *name); /* Return view setting from tdb, but *not* any of it's parents. */ struct trackDb *lmCloneTdb(struct lm *lm, struct trackDb *tdb, struct trackDb *parent, struct hash *superHash); /* clone a single tdb structure. Will clone its children if it has any */ struct trackDb *lmCloneTdbList(struct lm *lm, struct trackDb *list, struct trackDb *parent, struct hash *superHash); /* clone a list of tdb structures. */ struct trackDb *lmCloneSuper(struct lm *lm, struct trackDb *tdb, struct hash *superHash); /* clone a super track tdb structure. */ void trackDbHubCloneTdbListToSharedMem(char *trackDbUrl, struct trackDb *list, unsigned long size, char *incFiles); /* For this hub, Allocate shared memory and clone trackDb list into it. incFiles has a list of include files that may be null. */ void trackDbCloneTdbListToSharedMem(char *db, char *tdbPathString, struct trackDb *list, unsigned long size); /* For this native db, allocate shared memory and clone trackDb list into it. */ struct trackDb *trackDbCache(char *db, char *tdbPathString, time_t time); /* Check to see if this db and trackDb table has a cached trackDb. */ struct trackDb *trackDbHubCache(char *trackDbUrl, time_t time); /* Check to see if this hub has a cached trackDb. */ boolean trackDbCacheOn(); /* Check to see if we're caching trackDb contents. */ boolean trackSettingIsFile(char *setting); /* Returns TRUE if setting found in trackDb stanza is a file setting that * would benefit from directory $D substitution among other things - looks for * settings that ends in "Url" and a few others. */ char *labelAsFiltered(char *label); /* add text to label to indicate filter is active */ char *labelAsFilteredNumber(char *label, unsigned number); /* add text to label to indicate filter is active */ int trackDbGetCartVersion(); /* Get the highest cart version that a set of trackDb entries has specified. */ #endif /* TRACKDB_H */