30632e578f8f276e1d2a6e021dc9cb8eb5e882f4 kate Mon May 1 15:54:05 2017 -0700 Add name2 to schema, to support alternate names. refs #18736 diff --git src/hg/inc/barChartBed.h src/hg/inc/barChartBed.h index ac7274a..a29b6c9 100644 --- src/hg/inc/barChartBed.h +++ src/hg/inc/barChartBed.h @@ -1,111 +1,109 @@ /* barChartBed.h was originally generated by the autoSql program, which also * generated barChartBed.c and barChartBed.sql. This header links the database and * the RAM representation of objects. */ #ifndef BARCHARTBED_H #define BARCHARTBED_H #include "jksql.h" -#define BARCHARTBED_NUM_COLS 10 +#define BARCHARTBED_NUM_COLS 11 extern char *barChartBedCommaSepFieldNames; struct barChartBed -/* BED6+4 with additional fields for category count and median values, and sample matrix fields */ +/* BED6+5 with additional fields for category count and median values, and sample matrix fields */ { struct barChartBed *next; /* Next in singly linked list. */ char *chrom; /* Reference sequence chromosome or scaffold */ unsigned chromStart; /* Start position in chromosome */ unsigned chromEnd; /* End position in chromosome */ char *name; /* Name or ID of item, ideally both human readable and unique */ - unsigned score; /* Score from 0-1000; typically derived from total of median value from all categories */ + unsigned score; /* Score from 0-1000, typically derived from total of median value from all categories */ char strand[2]; /* + or - for strand. Use . if not applicable */ + char *name2; /* Alternative name for item */ unsigned expCount; /* Number of categories */ float *expScores; /* Comma separated list of category values */ - long long _dataOffset; /* Offset of sample data in data matrix file, for boxplot on details page. */ - int _dataLen; /* Length of sample data row in data matrix file. */ + long long _dataOffset; /* Offset of sample data in data matrix file, for boxplot on details page */ + int _dataLen; /* Length of sample data row in data matrix file */ }; struct barChartBed *barChartBedLoadByQuery(struct sqlConnection *conn, char *query); /* Load all barChartBed from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with barChartBedFreeList(). */ void barChartBedSaveToDb(struct sqlConnection *conn, struct barChartBed *el, char *tableName, int updateSize); /* Save barChartBed as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct barChartBed *barChartBedLoad(char **row); /* Load a barChartBed from row fetched with select * from barChartBed * from database. Dispose of this with barChartBedFree(). */ struct barChartBed *barChartBedLoadAll(char *fileName); /* Load all barChartBed from whitespace-separated file. * Dispose of this with barChartBedFreeList(). */ struct barChartBed *barChartBedLoadAllByChar(char *fileName, char chopper); /* Load all barChartBed from chopper separated file. * Dispose of this with barChartBedFreeList(). */ #define barChartBedLoadAllByTab(a) barChartBedLoadAllByChar(a, '\t'); /* Load all barChartBed from tab separated file. * Dispose of this with barChartBedFreeList(). */ struct barChartBed *barChartBedCommaIn(char **pS, struct barChartBed *ret); /* Create a barChartBed out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new barChartBed */ void barChartBedFree(struct barChartBed **pEl); /* Free a single dynamically allocated barChartBed such as created * with barChartBedLoad(). */ void barChartBedFreeList(struct barChartBed **pList); /* Free a list of dynamically allocated barChartBed's */ void barChartBedOutput(struct barChartBed *el, FILE *f, char sep, char lastSep); /* Print out barChartBed. Separate fields with sep. Follow last field with lastSep. */ #define barChartBedTabOut(el,f) barChartBedOutput(el,f,'\t','\n'); /* Print out barChartBed as a line in a tab-separated file. */ #define barChartBedCommaOut(el,f) barChartBedOutput(el,f,',',','); /* Print out barChartBed as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ - #include "basicBed.h" #define BARCHART_OFFSET_COLUMN "_dataOffset" #define BARCHART_LEN_COLUMN "_dataLen" void barChartBedCreateTable(struct sqlConnection *conn, char *table); /* Create barChart format table of given name. */ struct bed *barChartSimpleBedLoad(char **row); /* Load a bed from row containing barChart bed fields. * This is reuses autoSql barChartBedLoad, but with a full-size bed. Dispose of this with bedFree() */ struct barChartBed *barChartBedLoadOptionalOffsets(char **row, boolean hasOffsets); /* TODO: remove this -- offsets field will be required (though may be 0) */ /* Load a barChartBed from row fetched with select * from barChartBed * from database or file. Also supports schema lacking file offet and length for details. . Dispose of this with barChartBedFree(). */ - float barChartTotalValue(struct barChartBed *bed); /* Return total of all category values */ float barChartMaxValue(struct barChartBed *bed, int *categIdRet); /* Return value and id of category with highest value for this item */ - #endif /* BARCHARTBED_H */