ee9a6c5c63eba2d963a5d7581185b1004fffe964
angie
  Mon Apr 15 14:06:10 2013 -0700
Added indentifying name to annoStreamer for output header info and better error messages. refs #6152
diff --git src/inc/annoStreamer.h src/inc/annoStreamer.h
index ab8fa6e..4536688 100644
--- src/inc/annoStreamer.h
+++ src/inc/annoStreamer.h
@@ -1,95 +1,96 @@
 /* annoStreamer -- returns items sorted by genomic position to successive nextRow calls */
 
 #ifndef ANNOSTREAMER_H
 #define ANNOSTREAMER_H
 
 #include "annoAssembly.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.
 
 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; if chrom is NULL, region is whole genome.
      * This must called on all annoGrator components in query, not a subset. */
 
     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 annoRow *(*nextRow)(struct annoStreamer *self, struct lm *lm);
     /* Get the next item from this source.  Use localmem lm to store returned annoRow. */
 
     void (*close)(struct annoStreamer **pSelf);
     /* Close connection to source and free self. */
 
     // Public members -- callers are on the honor system to access these read-only.
     struct annoAssembly *assembly;	// Genome assembly that provides coords for annotations
     struct asObject *asObj;		// Annotation data definition
+    char *name;				// Short identifier, e.g. name of file or database table
     struct annoFilter *filters;		// Filters to constrain output
     char *chrom;			// Non-NULL if querying a particular region
     uint regionStart;			// If chrom is non-NULL, region start coord
     uint regionEnd;			// If chrom is non-NULL, region end coord
     boolean positionIsGenome;		// True if doing a whole-genome query
     enum annoRowType rowType;		// Type of annotations (words or wiggle data)
     int numCols;			// For word-based annotations, number of words/columns
     };
 
 // ---------------------- 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. */
 
 void annoStreamerInit(struct annoStreamer *self, struct annoAssembly *assembly,
-		      struct asObject *asObj);
+		      struct asObject *asObj, char *name);
 /* 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 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. */
 
 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