981ef07d25e4560559dae28d3e316913569944d7 tdreszer Fri Jul 6 17:51:06 2012 -0700 Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way. diff --git src/hg/inc/trackDb.h src/hg/inc/trackDb.h index 9cf4b4d..afe0207 100644 --- src/hg/inc/trackDb.h +++ src/hg/inc/trackDb.h @@ -1,625 +1,634 @@ /* 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. */ #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; struct trackDb /* This describes an annotation track. */ { 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 */ #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 *settingsHash; /* Hash for settings. Not saved in database. * Don't use directly, rely on trackDbSetting to access. */ /* additional info, determined from settings */ - 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 supertracks */ // NOTE: can only be on 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 tracks: true if this is a supertrack with pseudo-vis 'show' */ + 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 - And example is the metadata looked looked up once in the metaTbl and used again and again. */ + 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. }; #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 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)) +//#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 +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 +// --- 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 through some code paths +// --- 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. */ void trackDbOverridePriority(struct hash *tdHash, char *priorityRa); /* Override priority settings using a ra file. */ struct trackDb *trackDbFromRa(char *raFile, char *releaseTag); /* Load track info from ra file into list. If releaseTag is non-NULL * then only load tracks that mesh with release. */ struct trackDb *trackDbFromOpenRa(struct lineFile *lf, char *releaseTag); /* 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. */ 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(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. */ 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. */ char *trackDbGetSupertrackName(struct trackDb *tdb); /* Find name of supertrack if this track is a member */ float trackDbFloatSettingOrDefault(struct trackDb *tdb, char *name, float defaultVal); /* Return setting, convert to a float, or defaultVal if none exists */ void trackDbSuperMemberSettings(struct trackDb *tdb); /* Set fields in trackDb to indicate this is a member of a * supertrack. */ void trackDbSuperMarkup(struct trackDb *tdbList); /* Get info from supertrack setting. There are 2 forms: * Parent: 'supertrack on [show]' * Child: 'supertrack <parent> [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, 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; 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 }; 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. 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. { return startsWithWord("bigBed", 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); } 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); } boolean trackDbSettingBlocksConfiguration(struct trackDb *tdb, boolean onlyAjax); // Configuration dialogs may be explicitly blocked in tracDb settings #endif /* TRACKDB_H */