1d59c79ebf8d7596cf0beed61419bb267d5efb5c angie Wed Dec 19 15:37:45 2012 -0800 Adding annoStreamTab and simple test case.refs #6152 Performance will not be good for a series of queries to small regions on the same chromosome, because even if the regions don't overlap, we will have to reopen the file every time and start over just in case there are some items that start to the left of the region but overlap it. To fix that, we could add a queue for use when the region is smaller than a chromosome. Items that end to the right of the region would be kept in a queue in case they're needed in the next region query. When a new sub-chrom region query begins, if there are items in the queue that overlap the new region, they are used first and then we start reading from the file where we left off at the end of the last region. diff --git src/inc/annoStreamer.h src/inc/annoStreamer.h index e2cf8f1..a2bc66d 100644 --- src/inc/annoStreamer.h +++ src/inc/annoStreamer.h @@ -1,107 +1,115 @@ /* annoStreamer -- returns items sorted by genomic position to successive nextRow calls */ #ifndef ANNOSTREAMER_H #define ANNOSTREAMER_H #include "annoColumn.h" #include "annoFilter.h" #include "annoRow.h" // The real work of fetching and filtering data is left to subclass // implementations. The purpose of this module is to provide an // interface for communication with other components of the // annoGratorQuery framework, and simple methods shared by all // subclasses. // stub in order to avoid problems with circular .h references: struct annoGratorQuery; struct annoStreamer /* Generic interface to configure a data source's filters and output data, and then * retrieve data, which must be sorted by genomic position. Subclasses of this * will do all the actual work. */ { struct annoStreamer *next; // Public methods struct asObject *(*getAutoSqlObject)(struct annoStreamer *self); void (*setAutoSqlObject)(struct annoStreamer *self, struct asObject *asObj); /* Get and set autoSql representation (do not modify or free!) */ void (*setRegion)(struct annoStreamer *self, char *chrom, uint rStart, uint rEnd); /* Set genomic region for query (should be called only by annoGratorQuerySetRegion) */ char *(*getHeader)(struct annoStreamer *self); /* Get the file header as a string (possibly NULL, possibly multi-line). */ struct annoFilter *(*getFilters)(struct annoStreamer *self); void (*setFilters)(struct annoStreamer *self, struct annoFilter *newFilters); /* Get and set filters */ struct annoColumn *(*getColumns)(struct annoStreamer *self); void (*setColumns)(struct annoStreamer *self, struct annoColumn *newColumns); /* Get and set output fields */ struct annoRow *(*nextRow)(struct annoStreamer *self, struct lm *lm); /* Get next item's output fields from this source */ void (*close)(struct annoStreamer **pSelf); /* Close connection to source and free self. */ void (*setQuery)(struct annoStreamer *self, struct annoGratorQuery *query); /* For use by annoGratorQuery only: hook up query object after creation */ // Public members -- callers are on the honor system to access these read-only. struct annoGratorQuery *query; // The query object that owns this streamer. enum annoRowType rowType; int numCols; struct annoFilter *filters; struct annoColumn *columns; // Private members -- callers are on the honor system to access these using only methods above. boolean positionIsGenome; char *chrom; uint regionStart; uint regionEnd; struct asObject *asObj; }; // ---------------------- annoStreamer default methods ----------------------- struct asObject *annoStreamerGetAutoSqlObject(struct annoStreamer *self); /* Return parsed autoSql definition of this streamer's data type. */ void annoStreamerSetAutoSqlObject(struct annoStreamer *self, struct asObject *asObj); /* Use new asObj and update internal state derived from asObj. */ void annoStreamerSetRegion(struct annoStreamer *self, char *chrom, uint rStart, uint rEnd); /* Set genomic region for query; if chrom is NULL, position is genome. * Many subclasses should make their own setRegion method that calls this and * configures their data connection to change to the new position. */ struct annoFilter *annoStreamerGetFilters(struct annoStreamer *self); /* Return supported filters with current settings. Callers can modify and free when done. */ void annoStreamerSetFilters(struct annoStreamer *self, struct annoFilter *newFilters); /* Free old filters and use clone of newFilters. */ struct annoColumn *annoStreamerGetColumns(struct annoStreamer *self); /* Return supported columns with current settings. Callers can modify and free when done. */ void annoStreamerSetColumns(struct annoStreamer *self, struct annoColumn *columns); /* Free old columns and use clone of newColumns. */ void annoStreamerInit(struct annoStreamer *self, struct asObject *asObj); /* Initialize a newly allocated annoStreamer with default annoStreamer methods and * default filters and columns based on asObj. * In general, subclasses' constructors will call this first; override nextRow, close, * and probably setRegion and setQuery; and then initialize their private data. */ void annoStreamerFree(struct annoStreamer **pSelf); /* Free self. This should be called at the end of subclass close methods, after * subclass-specific connections are closed and resources are freed. */ void annoStreamerSetQuery(struct annoStreamer *self, struct annoGratorQuery *query); /* Set query (to be called only by annoGratorQuery which is created after streamers). */ +boolean annoStreamerFindBed3Columns(struct annoStreamer *self, + int *retChromIx, int *retStartIx, int *retEndIx, + char **retChromField, char **retStartField, char **retEndField); +/* Scan autoSql for recognized column names corresponding to BED3 columns. + * Set ret*Ix to list index of each column if found, or -1 if not found. + * Set ret*Field to column name if found, or NULL if not found. + * If all three are found, return TRUE; otherwise return FALSE. */ + #endif//ndef ANNOSTREAMER_H