a47364d48ccd5b8ee8cdf7b47b7ba9edcfd66f1f braney Wed Apr 16 10:58:32 2014 -0700 fix a crashing bug in hgCustom if the description field is empty on anassembly hub diff --git src/hg/inc/wiggle.h src/hg/inc/wiggle.h index c76868f..c0f69de 100644 --- src/hg/inc/wiggle.h +++ src/hg/inc/wiggle.h @@ -1,524 +1,524 @@ /* wiggle.h was originally generated by the autoSql program, which also * generated wiggle.c and wiggle.sql. This header links the database and * the RAM representation of objects. */ #ifndef WIGGLE_H #define WIGGLE_H #include "cart.h" #include "histogram.h" #include "portable.h" #define WIGGLE_NUM_COLS 13 struct wiggle /* Wiggle track values to display as y-values (first 4 fields are bed4) */ { struct wiggle *next; /* Next in singly linked list. */ char *chrom; /* Human chromosome or FPC contig */ unsigned chromStart; /* Start position in chromosome */ unsigned chromEnd; /* End position in chromosome */ char *name; /* Name of item */ unsigned span; /* each value spans this many bases */ unsigned count; /* number of values in this block */ unsigned offset; /* offset in File to fetch data */ char *file; /* path name to data file, one byte per value */ double lowerLimit; /* lowest data value in this block */ double dataRange; /* lowerLimit + dataRange = upperLimit */ unsigned validCount; /* number of valid data values in this block */ double sumData; /* sum of the data points, for average and stddev calc */ double sumSquares; /* sum of data points squared, for stddev calc */ }; void wiggleStaticLoad(char **row, struct wiggle *ret); /* Load a row from wiggle table into ret. The contents of ret will * be replaced at the next call to this function. */ struct wiggle *wiggleLoad(char **row); /* Load a wiggle from row fetched with select * from wiggle * from database. Dispose of this with wiggleFree(). */ struct wiggle *wiggleLoadAll(char *fileName); /* Load all wiggle from whitespace-separated file. * Dispose of this with wiggleFreeList(). */ struct wiggle *wiggleLoadAllByChar(char *fileName, char chopper); /* Load all wiggle from chopper separated file. * Dispose of this with wiggleFreeList(). */ #define wiggleLoadAllByTab(a) wiggleLoadAllByChar(a, '\t'); /* Load all wiggle from tab separated file. * Dispose of this with wiggleFreeList(). */ struct wiggle *wiggleCommaIn(char **pS, struct wiggle *ret); /* Create a wiggle out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new wiggle */ void wiggleFree(struct wiggle **pEl); /* Free a single dynamically allocated wiggle such as created * with wiggleLoad(). */ void wiggleFreeList(struct wiggle **pList); /* Free a list of dynamically allocated wiggle's */ void wiggleOutput(struct wiggle *el, FILE *f, char sep, char lastSep); /* Print out wiggle. Separate fields with sep. Follow last field with lastSep. */ #define wiggleTabOut(el,f) wiggleOutput(el,f,'\t','\n'); /* Print out wiggle as a line in a tab-separated file. */ #define wiggleCommaOut(el,f) wiggleOutput(el,f,',',','); /* Print out wiggle as a comma separated list including final comma. */ /* -------------- End autoSql Generated Code -------------------------- */ /* BASE_0 and BASE_1 - use where any coordinate conversions are to * be done, this will allow them to easily be found in case of * confusion. */ #define BASE_0(x) (x-1) #define BASE_1(x) (x+1) #define DEFAULT_MIN_Yv 0.0 #define DEFAULT_MAX_Yv 127.0 #define DEFAULT_MIN_BED_GRAPH 0.0 #define DEFAULT_MAX_BED_GRAPH 1000.0 #define DEFAULT_HEIGHT_PER "128" #define MIN_HEIGHT_PER 11 #define WIG_NO_DATA 128 #define MAX_WIG_VALUE 127 #define MAX_OPT_STRLEN 128 struct wiggleDatum /* a single instance of a wiggle data value */ { unsigned chromStart; /* Start position in chromosome, 0 relative */ double value; }; struct asciiDatum /* a single instance of a wiggle data value (trying float here to save space */ { unsigned chromStart; /* Start position in chromosome, 0 relative */ float value; }; struct wiggleData /* linked list of wiggle data values */ { struct wiggleData *next; /* Next in singly linked list. */ char *chrom; /* chromosome or contig */ unsigned chromStart; /* Start position, first value */ unsigned chromEnd; /* End position, last value */ unsigned span; /* each value spans this many bases */ unsigned count; /* number of values in this block */ double lowerLimit; /* lowest data value in this block */ double dataRange; /* lowerLimit + dataRange = upperLimit */ double sumData; /* sum of the data points, for average and stddev calc */ double sumSquares; /* sum of data points squared, for stddev calc */ struct wiggleDatum *data; /* many individual data items here */ }; struct wiggleStats /* linked list of wiggle statistics */ { struct wiggleStats *next; /* Next in singly linked list. */ char *chrom; /* chromosome or contig */ unsigned chromStart; /* Start position, first value */ unsigned chromEnd; /* End position, last value */ unsigned span; /* each value spans this many bases */ unsigned count; /* number of values in this block */ double lowerLimit; /* lowest data value in this block */ double dataRange; /* lowerLimit + dataRange = upperLimit */ double mean; /* mean of data points */ double variance; /* variance of data points */ double stddev; /* standard deviation of data points */ }; struct wigAsciiData /* linked list of wiggle data in ascii form */ { struct wigAsciiData *next; /* next in singly linked list */ char *chrom; /* chrom name for this set of data */ unsigned span; /* span for this set of data */ unsigned count; /* number of values in this block */ double dataRange; /* for resolution calculation */ struct asciiDatum *data; /* individual data items here */ }; struct wiggleArray /* one big in-memory linear array of data */ { struct wiggleArray *next; /* might be more than one chrom */ char *chrom; /* chrom name for this set of data */ unsigned winStart; /* winEnd - winStart */ unsigned winEnd; /* will be the length of data */ float *data; /* all data winStart to winEnd */ }; #include "hdb.h" #define HTI_IS_WIGGLE (hti->spanField[0] !=0) /* anonymous declaration of track to take care of the use of this struct * in the wigSetCart definition below. Prevents compiler warnings on * lib/wiggleCart.c and doesn't disturb the usage in hg/hgTracks/...c */ struct track; /* in hgTracks/wigTrack.c */ void wigSetCart(struct track *track, char *dataID, void *dataValue); /* set one of the variables in the wigCart */ /* in lib/wiggleCart.c */ void wigFetchMinMaxYWithCart(struct cart *cart, struct trackDb *tdb, char *name, double *min, double *max, double *tDbMin, double *tDbMax, int wordCount, char **words); #define wigFetchMinMaxY(tdb,min,max,tDbMin,tDbMax,wordCount,words) \ wigFetchMinMaxYWithCart(cart,(tdb),(tdb)->track,(min),(max),(tDbMin),(tDbMax),\ (wordCount),(words)) /* return min,max Y ranges from trackDb or cart */ void wigFetchMinMaxLimitsWithCart(struct cart *cart, struct trackDb *tdb, char *name, double *min, double *max,double *tDbMin, double *tDbMax); #define wigFetchMinMaxLimits(tdb,min,max,tDbMin,tDbMax) \ wigFetchMinMaxLimitsWithCart(cart,(tdb),(tdb)->track,(min),(max),(tDbMin),(tDbMax)) /* for bedGraph types, return min,max Y ranges from trackDb or cart */ void wigFetchMinMaxPixelsWithCart(struct cart *cart, struct trackDb *tdb, char *name, int *Min, int *Max, int *Default); #define wigFetchMinMaxPixels(tdb,Min,Max,Default) \ wigFetchMinMaxPixelsWithCart(cart,(tdb),(tdb)->track,(Min),(Max),(Default)) /* return pixels heights allowable from trackDb or cart */ enum wiggleGridOptEnum wigFetchTransformFuncWithCart(struct cart *cart, struct trackDb *tdb, char *name,char **optString); #define wigFetchTransformFunc(tdb,optString) \ wigFetchTransformFuncWithCart(cart,(tdb),(tdb)->track,(optString)) /* return transformFunc setting */ enum wiggleGridOptEnum wigFetchAlwaysZeroWithCart(struct cart *cart, struct trackDb *tdb, char *name,char **optString); #define wigFetchAlwaysZero(tdb,optString) \ wigFetchAlwaysZeroWithCart(cart,(tdb),(tdb)->track,(optString)) /* return alwaysZero setting */ enum wiggleGridOptEnum wigFetchHorizontalGridWithCart(struct cart *cart, struct trackDb *tdb, char *name,char **optString); #define wigFetchHorizontalGrid(tdb,optString) \ wigFetchHorizontalGridWithCart(cart,(tdb),(tdb)->track,(optString)) /* return horizontalGrid setting */ enum wiggleScaleOptEnum wigFetchAutoScaleWithCart(struct cart *cart, struct trackDb *tdb, char *name, char **optString); #define wigFetchAutoScale(tdb,optString) \ wigFetchAutoScaleWithCart(cart,(tdb),(tdb)->track,(optString)) /* return autoScale setting */ enum wiggleGraphOptEnum wigFetchGraphTypeWithCart(struct cart *cart, struct trackDb *tdb, char *name, char **optString); #define wigFetchGraphType(tdb,optString) \ wigFetchGraphTypeWithCart(cart,(tdb),(tdb)->track,(optString)) /* return graph type, line(points) or bar graph */ +enum wiggleAggregateFunctionEnum wigFetchAggregateFunctionWithCart(struct cart *cart, struct trackDb *tdb, + char *name, char **optString); + enum wiggleWindowingEnum wigFetchWindowingFunctionWithCart(struct cart *cart, struct trackDb *tdb, char *name, char **optString); #define wigFetchWindowingFunction(tdb,optString) \ wigFetchWindowingFunctionWithCart(cart,(tdb),(tdb)->track,(optString)) /* return windowing function, Maximum, Mean, Minimum */ enum wiggleSmoothingEnum wigFetchSmoothingWindowWithCart(struct cart *cart, struct trackDb *tdb, char *name, char **optString); #define wigFetchSmoothingWindow(tdb,optString) \ wigFetchSmoothingWindowWithCart(cart,(tdb),(tdb)->track,(optString)) /* return smoothing window size N: [0:16] */ enum wiggleYLineMarkEnum wigFetchYLineMarkWithCart(struct cart *cart, struct trackDb *tdb, char *name, char **optString); #define wigFetchYLineMark(tdb,optString) \ wigFetchYLineMarkWithCart(cart,(tdb),(tdb)->track,(optString)) /* return On/Off status of y= line marker */ void wigFetchYLineMarkValueWithCart(struct cart *cart,struct trackDb *tdb, char *name, double *tDbYMark ); #define wigFetchYLineMarkValue(tdb,tDbYMark) \ wigFetchYLineMarkValueWithCart(cart,(tdb),(tdb)->track,(tDbYMark)) /* return value for the y line marker to be drawn */ -char *wigFetchAggregateValWithCart(struct cart *cart, struct trackDb *tdb); -/* Return aggregate value for track. */ - boolean wigIsOverlayTypeAggregate(char *aggregate); /* Return TRUE if aggregater type is one of the overlay ones. */ int *wiggleSpanList(struct sqlConnection *conn, struct trackDb *tdb); /****** spanList - fetch list of spans from trackDb *********************/ /* cart and trackDb strings */ #define VIEWLIMITS "viewLimits" #define DEFAULTVIEWLIMITS "defaultViewLimits" #define VIEWLIMITSMAX "viewLimitsMax" #define MIN_Y "minY" #define MAX_Y "maxY" #define MIN_LIMIT "minLimit" #define MAX_LIMIT "maxLimit" #define MAXHEIGHTPIXELS "maxHeightPixels" #define HEIGHTPER "heightPer" #define HORIZGRID "horizGrid" #define GRIDDEFAULT "gridDefault" #define TRANSFORMFUNC "transformFunc" #define ALWAYSZERO "alwaysZero" #define AUTOSCALE "autoScale" #define AUTOSCALEDEFAULT "autoScaleDefault" #define LINEBAR "lineBar" #define AGGREGATE "aggregate" #define GRAPHTYPE "graphType" #define GRAPHTYPEDEFAULT "graphTypeDefault" #define WINDOWINGFUNCTION "windowingFunction" #define SMOOTHINGWINDOW "smoothingWindow" #define YLINEONOFF "yLineOnOff" #define YLINEMARK "yLineMark" #define SPANLIST "spanList" #define MAX_SPAN_COUNT 128 #define MAX_SMOOTHING 16 /* compute the data value give the bin */ /* #define BIN_TO_VALUE(bin,lowerLimit,range) ((range > 0.0) ? \ lowerLimit+((double)bin/(double)MAX_WIG_VALUE*range) : lowerLimit) */ #define BIN_TO_VALUE(bin,lowerLimit,range) \ lowerLimit+(range*((double)bin/(double)MAX_WIG_VALUE)) /* This needs to be adjusted for data with positive and * negative values, a special bin for 0 needs to be set aside and * the positive and negative values kept separately */ #if defined(DEBUG) /* dbg */ extern void wigProfileEnter(); extern long wigProfileLeave(); #define DBGMSGSZ 1023 extern char dbgMsg[DBGMSGSZ+1]; extern void wigDebugPrint(char * name); #endif /* in lib/wigAsciiToBinary.c */ struct wigEncodeOptions /* passing options to the wigAsciiToBinary function */ { int lift; /* lift all incoming coordinates by this amount */ boolean noOverlap; /* enforce no overlapping data verification */ boolean flagOverlapSpanData; /* verify span data doesn't overlap */ long long wibSizeLimit; /* governor on ct trash files */ }; /* during wigAsciiToBinary, these starting limits are for the complete set * of data, they must change from these initial defaults during * processing */ #define wigEncodeStartingUpperLimit -1.0e+300 #define wigEncodeStartingLowerLimit 1.0e+300 void wigAsciiToBinary(char *wigAscii, char *wigFile, char *wibFile, double *upperLimit, double *lowerLimit, struct wigEncodeOptions *options ); /* given the three file names, read the wigAscii file and produce * the wigFile and wibFile outputs, return the upper and lower * limits for all the data */ /* the object wiggleDataStream is implemented in lib/wigDataStream.c */ enum wigCompare /* type of comparison to be calculated */ { wigNoOp_e, wigInRange_e, wigLessThan_e, wigLessEqual_e, wigEqual_e, wigNotEqual_e, wigGreaterEqual_e, wigGreaterThan_e, }; enum wigCompare wigCompareFromString(char *string); /* Given a string return corresponding cmp code. */ boolean wigCompareValFilter(double val, enum wigCompare cmp, double ll, double ul); /* Return TRUE if val passes comparison filter. */ enum wigDataFetchType /* bit masks to specify type of data to fetch via getData() */ { wigFetchNoOp = 1, wigFetchAscii = 2, wigFetchBed = 4, wigFetchStats = 8, wigFetchDataArray = 16, wigFetchRawStats = 32, }; struct wiggleDataStream /* object definition to access wiggle data, in DB or from file */ { /******************** public methods *****************/ void (*freeAscii)(struct wiggleDataStream *wds); /* free the ascii list results */ void (*freeBed)(struct wiggleDataStream *wds); /* free the bed list results */ void (*freeStats)(struct wiggleDataStream *wds); /* free the stats list results */ void (*freeArray)(struct wiggleDataStream *wds); /* free the data array results */ void (*freeConstraints)(struct wiggleDataStream *wds); /* unset all the constraints */ void (*setMaxOutput)(struct wiggleDataStream *wds, unsigned long long maxOut); /* set the maximum # of values to return */ void (*setPositionConstraint)(struct wiggleDataStream *wds, int winStart, int winEnd); /* work only within specified position */ void (*setChromConstraint)(struct wiggleDataStream *wds, char *chr); /* work only on specified chrom */ void (*setSpanConstraint)(struct wiggleDataStream *wds, unsigned span); /* work only on specified span */ void (*setDataConstraint)(struct wiggleDataStream *wds, char *dataConstraint, double lowerLimit, double upperLimit); /* setting data compare limits */ int (*bedOut)(struct wiggleDataStream *wds, char *fileName, boolean sort); /* output the bed list results */ void (*statsOut)(struct wiggleDataStream *wds, char *db, char *fileName, boolean sort, boolean htmlOut, boolean withHeader, boolean leaveTableOpen); /* output the stats list results */ int (*asciiOut)(struct wiggleDataStream *wds,char *db, char *fileName, boolean sort, boolean rawDataOut); /* output the ascii list results */ void (*sortResults)(struct wiggleDataStream *wds); /* sort if you want to, the Outs do this too */ float *(*asciiToDataArray)(struct wiggleDataStream *wds, unsigned long long count, size_t *returned); /* convert the AsciiData list to a float array */ unsigned long long (*getDataViaBed)(struct wiggleDataStream *wds, char *db, char *table, int operations, struct bed **bedList); /* fetch data constrained by bedList, * return is number of data values found */ unsigned long long (*getData)(struct wiggleDataStream *wds, char *db, char *table, int operations); /* fetch data from db.table or file table, * return is number of data values found */ /***** PRIVATE attributes, for internal use only, look, don't touch */ char *db; /* database name */ char *tblName; /* the table or file name */ struct lineFile *lf; /* file handle in case of file */ /* data return structures */ struct wigAsciiData *ascii; /* list of wiggle data values */ struct bed *bed; /* data in bed format */ struct wiggleStats *stats; /* list of wiggle stats */ struct wiggleArray *array; /* one big in-memory array of data */ unsigned long long maxOutput; /* maximum items fetched */ boolean isFile; /* TRUE == it is a file, FALSE == DB */ boolean bedConstrained; /* signal to output routines */ boolean useDataConstraint; /* to simplify checking if it is on */ enum wigCompare wigCmpSwitch; /* for compare function switch */ char *dataConstraint; /* one of < = >= <= == != 'in range' */ double limit_0; /* for constraint comparison */ double limit_1; /* for constraint comparison */ unsigned char ucLowerLimit; /* for comparison direct to bytes */ unsigned char ucUpperLimit; /* for comparison direct to bytes */ char *sqlConstraint; /* extra SQL constraints */ unsigned int currentSpan; /* for use during reading */ char *currentChrom; /* for use during reading */ char *wibFile; /* for use during reading */ struct udcFile *wibFH; /* wibFile handle */ struct sqlConnection *conn; /* SQL connection when talking to db */ struct sqlResult *sr; /* SQL result when talking to db */ char *chrName; /* for chrom==chrName on file reads */ unsigned spanLimit; /* for span==spanLimit on file reads */ int winStart; /* for fetches between winStart, winEnd */ int winEnd; /* for fetches between winStart, winEnd */ int offset; /* offset to add to positions on output */ unsigned long long rowsRead; /* reading stats, SQL rows read */ unsigned long long validPoints; /* reading stats, number of data bytes */ unsigned long long noDataPoints; /* reading stats, NO_DATA bytes */ unsigned long long bytesRead; /* reading stats, total wib bytes */ unsigned long long bytesSkipped; /* reading stats, bytes not examined */ unsigned long long valuesMatched; /* reading stats, number of data bytes */ unsigned long long totalBedElements; /* on all bed lists */ }; /* in lib/wigDataStream.c */ /* Two methods to create and destroy object */ struct wiggleDataStream *wiggleDataStreamNew(); void wiggleDataStreamFree(struct wiggleDataStream **wds); /* A couple of routines not strictly part of the object methods, but they do work with the object and pick stuff out of it. */ void wigPrintDataConstraint(struct wiggleDataStream *wds, FILE * fh); /* output string to file handle fh indicating current data constraint */ void statsPreamble(struct wiggleDataStream *wds, char *chrom, int winStart, int winEnd, unsigned span, unsigned long long valuesMatched, char *table2); /* common beginning to wiggle stats displays */ void wigStatsHeader(struct wiggleDataStream *wds, FILE * fh, boolean htmlOut); /* begin wiggle stats table */ void wigStatsTableHeading(FILE * fh, boolean htmlOut); /* Print the single html (or text) table row for statistics column headings */ /* verbose level guidelines */ #define VERBOSE_ALWAYS_ON 1 #define VERBOSE_CHR_LEVEL 2 #define VERBOSE_SQL_ROW_LEVEL 3 #define VERBOSE_PER_VALUE_LEVEL 4 #define VERBOSE_HIGHEST 5 /* in lib/wiggleUtils.c */ void printHistoGram(struct histoResult *histoResults, boolean html); /* This function wigFetchData is being phased out, use the * wiggleDataStream to do this business. There is one use of * this in hgText - itself to be phased out someday. */ struct wiggleData *wigFetchData(char *db, char *table, char *chromName, int winStart, int winEnd, boolean summaryOnly, boolean freeData, int tableId, boolean (*wiggleCompare)(int tableId, double value, boolean summaryOnly, struct wiggle *wiggle), char *constraints, struct bed **bedList, unsigned maxBedElements, struct wiggleStats **wsList); /* return linked list of wiggle data between winStart, winEnd * summaryOnly TRUE will not look at all the data, just the * summaries in the table rows */ #define WIG_SUMMARY_ONLY TRUE #define WIG_DATA_NOT_RETURNED TRUE #define WIG_RETURN_DATA FALSE #define WIG_ALL_DATA FALSE void wigFreeData(struct wiggleData **wigData); /* free everything in the wiggleData structure */ #define wiggleDataFreeList(a) wigFreeData(a) int minSpan(struct sqlConnection *conn, char *table, char *chrom, int winStart, int winEnd, struct cart *cart, struct trackDb *tdb); /* determine minimum span in this area */ int spanInUse(struct sqlConnection *conn, char *table, char *chrom, int winStart, int winEnd, struct cart *cart); /* determine span used in drawing in hgTracks */ #define wiggleAsText \ "table wiggle\n" \ "\"Wiggle track values to display as y-values (first 6 fields are bed6)\"\n" \ " (\n" \ " string chrom; \"Reference sequence chromosome or scaffold\"\n" \ " uint chromStart; \"Start position in chromosome\"\n" \ " uint chromEnd; \"End position in chromosome\"\n" \ " string name; \"Name of item\"\n" \ " uint span; \"each value spans this many bases\"\n" \ " uint count; \"number of values in this block\"\n" \ " uint offset; \"offset in File to fetch data\"\n" \ " string file; \"path name to data file, one byte per value\"\n" \ " double lowerLimit; \"lowest data value in this block\"\n" \ " double dataRange; \"lowerLimit + dataRange = upperLimit\"\n" \ " uint validCount; \"number of valid data values in this block\"\n" \ " double sumData; \"sum of the data points, for average and stddev calc\"\n" \ " double sumSquares; \"sum of data points squared, for stddev calc\"\n" \ " )\n" #endif /* WIGGLE_H */