/* customFactory - a polymorphic object for handling * creating various types of custom tracks. */ /* Copyright (C) 2009 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef CUSTOMFACTORY_H #define CUSTOMFACTORY_H #ifndef CUSTOMPP_H #include "customPp.h" #endif #ifndef CUSTOMTRACK_H #include "customTrack.h" #endif struct customFactory /* customFactory - a polymorphic object for handling * creating various types of custom tracks. */ { struct customFactory *next; char *name; /* Name - psl, bed, wig, chromGraph, etc. */ boolean (*recognizer)(struct customFactory *fac, struct customPp *cpp, char *type, struct customTrack *track); /* Called by custom tracks framework. Track line if any will * be read in already and parsed into type and track. * Type may be NULL, filled in from type= part of track line. * settings is all the this=that in the track line. * This routine is allowed to fill in some of track structure if * it returns TRUE. */ struct customTrack * (*loader)(struct customFactory *fac, struct hash *chromHash, /* Hash to store chrom names, filled in here */ struct customPp *cpp, /* Source of input */ struct customTrack *track, /* Skeleton of track, filled in here */ boolean dbRequested); /* If true load into temp database */ /* Load up a custom track. The track line is already parsed (and * available in the settings hash). This routine reads from cpp * until the next track line or until end of file. If dbRequested is * TRUE it will attempt to load track into a MySQL database. * Returns track (or in some cases tracks) that it loads. */ }; /*** Some externally defined factories. ***/ extern struct customFactory chromGraphFactory; /*** Some helper functions factories can call. ***/ char *customFactoryNextTilTrack(struct customPp *cpp); /* Return next line. Return NULL at end of input or at line starting with * "track." */ char *customFactoryNextRealTilTrack(struct customPp *cpp); /* Return next "real" line (not blank, not comment). * Return NULL at end of input or at line starting with * "track." */ char *customTrackTempDb(); /* Get custom database. If first time set up some * environment variables that the loaders will need. */ void customFactorySetupDbTrack(struct customTrack *track); /* Fill in fields most database-resident custom tracks need. */ /*** Interface to custom factory system. ***/ struct customFactory *customFactoryFind(char *genomeDb, struct customPp *cpp, char *type, struct customTrack *track); /* Figure out factory that can handle this track. The track is * loaded from the track line if any, and type is the type element * if any from that track. */ void customFactoryAdd(struct customFactory *fac); /* Add factory to global custom track factory list. */ struct customTrack *customFactoryParse(char *genomeDb, char *text, boolean isFile, struct slName **retBrowserLines); /* Parse text into a custom set of tracks. Text parameter is a * file name if 'isFile' is set. Die if the track is not for genomeDb. */ struct customTrack *customFactoryParseAnyDb(char *genomeDb, char *text, boolean isFile, struct slName **retBrowserLines, boolean doParallelLoad); /* Parse text into a custom set of tracks. Text parameter is a * file name if 'isFile' is set. Track does not have to be for hGetDb(). * If doParallelLoad is true, load the big tracks */ void customFactoryTestExistence(char *genomeDb, char *fileName, boolean *retGotLive, boolean *retGotExpired, struct customTrack **retTrackList); /* Test existence of custom track fileName. If it exists, parse it just * enough to tell whether it refers to database tables and if so, whether * they are alive or have expired. If they are live, touch them to keep * them active. */ /* HACK ALERT - The table browser needs to be able to encode its wiggle * data. This function is temporarily global until a proper method * is used to work this business into the table browser custom * tracks. Currently this is also called from customSaveTracks() * in customTrack.c in violation of this object's hidden methods. */ void wigLoaderEncoding(struct customTrack *track, char *wigAscii, boolean dbRequested); /* encode wigAscii file into .wig and .wib files */ char *customDocParse(char *text); /* Return description text, expanding URLs as for custom track data */ char *ctInitialPosition(struct customTrack *ct); /* return initial position plucked from browser lines, or * first item in track, or NULL if no items or browser line */ char *ctDataUrl(struct customTrack *ct); /* return URL where data can be reloaded, if any */ char *ctHtmlUrl(struct customTrack *ct); /* return URL where doc can be reloaded, if any */ char *ctInputType(struct customTrack *ct); /* return type of input */ int ctItemCount(struct customTrack *ct); /* return number of 'items' in track, or -1 if unknown */ char *ctFirstItemPos(struct customTrack *ct); /* return position of first item in track, or NULL if wiggle or * other "non-item" track */ char *ctGenome(struct customTrack *ct); /* return database setting */ char *ctOrigTrackLine(struct customTrack *ct); /* return initial setting by user for track line */ void customTrackUpdateFromConfig(struct customTrack *ct, char *genomeDb, char *config, struct slName **retBrowserLines); /* update custom track from config containing track line and browser lines * Return browser lines */ char *customTrackUserConfig(struct customTrack *ct); /* return user-defined track line and browser lines */ void customFactoryEnableExtraChecking(boolean enable); /* Enable/disable extra checking of custom tracks in customFactoryParse. * E.g. extra checking is great the first time we read in a custom track, * but we don't need it for every hgTracks call. */ boolean isValidBigDataUrl(char *url, boolean doAbort); /* return True if the URL is a valid bigDataUrl. * It can be a local filename if this is allowed by udc.localDir */ boolean customFactoryParallelLoad(char *bdu, char *type); /* Is this a data type that should be loaded in parallel ? */ #endif /* CUSTOMFACTORY_H */