cfe9afe019db302a08e0cc40ae19e7541540f2d7
angie
  Wed Jan 7 12:12:11 2015 -0800
Added annoStreamer{Get,Set}Name so that we're not stuck with awfully long filenames etc.
diff --git src/lib/annoStreamer.c src/lib/annoStreamer.c
index f44c733..b037c64 100644
--- src/lib/annoStreamer.c
+++ src/lib/annoStreamer.c
@@ -1,154 +1,167 @@
 /* annoStreamer -- returns items sorted by genomic position to successive nextRow calls */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "annoStreamer.h"
 #include "errAbort.h"
 
 // ----------------------- annoStreamer base methods --------------------------
 
 struct asObject *annoStreamerGetAutoSqlObject(struct annoStreamer *self)
 /* Return parsed autoSql definition of this streamer's data type. */
 {
 return self->asObj;
 }
 
 void annoStreamerSetAutoSqlObject(struct annoStreamer *self, struct asObject *asObj)
 /* Use new asObj and update internal state derived from asObj. */
 {
 self->asObj = asObj;
 self->numCols = slCount(asObj->columnList);
 }
 
+char *annoStreamerGetName(struct annoStreamer *self)
+/* Returns cloned name of streamer; free when done. */
+{
+return cloneString(self->name);
+}
+
+void annoStreamerSetName(struct annoStreamer *self, char *name)
+/* Sets streamer name to clone of name. */
+{
+freez(&(self->name));
+self->name = cloneString(name);
+}
+
 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. */
 {
 freez(&(self->chrom));
 if (chrom == NULL)
     {
     self->positionIsGenome = TRUE;
     self->regionStart = self->regionEnd = 0;
     }
 else
     {
     self->positionIsGenome = FALSE;
     self->chrom = cloneString(chrom);
     self->regionStart = rStart;
     if (rEnd == 0)
 	rEnd = annoAssemblySeqSize(self->assembly, chrom);
     self->regionEnd = rEnd;
     }
 }
 
 static char *annoStreamerGetHeader(struct annoStreamer *self)
 /* Default method: return NULL. */
 {
 return NULL;
 }
 
 void annoStreamerSetFilters(struct annoStreamer *self, struct annoFilter *newFilters)
 /* Replace any existing filters with newFilters.  It is up to calling code to
  * free old filters and allocate newFilters. */
 {
 self->filters = newFilters;
 }
 
 void annoStreamerAddFilters(struct annoStreamer *self, struct annoFilter *newFilters)
 /* Add newFilter(s).  It is up to calling code to allocate newFilters. */
 {
 self->filters = slCat(newFilters, self->filters);
 }
 
 void annoStreamerInit(struct annoStreamer *self, struct annoAssembly *assembly,
 		      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. */
 {
 self->assembly = assembly;
 self->getAutoSqlObject = annoStreamerGetAutoSqlObject;
 self->setAutoSqlObject = annoStreamerSetAutoSqlObject;
 self->setRegion = annoStreamerSetRegion;
 self->getHeader = annoStreamerGetHeader;
 self->setFilters = annoStreamerSetFilters;
 self->addFilters = annoStreamerAddFilters;
 self->positionIsGenome = TRUE;
 self->setAutoSqlObject(self, asObj);
 if (name == NULL)
     errAbort("annoStreamerInit: need non-NULL name");
 self->name = cloneString(name);
 }
 
 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. */
 {
 if (pSelf == NULL)
     return;
 struct annoStreamer *self = *pSelf;
 freez(&(self->name));
 freez(&(self->chrom));
 freez(pSelf);
 }
 
 INLINE boolean findColumn(struct asColumn *columns, char *name, int *retIx, char **retName)
 /* Scan columns for name.
  * If found, set retIx to column index, set retName to clone of name, and return TRUE.
  * If not found, set retIx to -1, set retName to NULL, and return FALSE; */
 {
 int ix = asColumnFindIx(columns, name);
 if (retIx != NULL)
     *retIx = ix;
 if (retName != NULL)
     {
     if (ix >= 0)
 	*retName = cloneString(name);
     else
 	*retName = NULL;
     }
 return (ix >= 0);
 }
 
 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. */
 {
 struct asColumn *columns = self->asObj->columnList;
 if (findColumn(columns, "chrom", retChromIx, retChromField))
     {
     if (findColumn(columns, "chromStart", retStartIx, retStartField))
 	return findColumn(columns, "chromEnd", retEndIx, retEndField);
     else return (findColumn(columns, "txStart", retStartIx, retStartField) &&
 		 findColumn(columns, "txEnd", retEndIx, retEndField));
     }
 else if (findColumn(columns, "tName", retChromIx, retChromField))
     return (findColumn(columns, "tStart", retStartIx, retStartField) &&
 	    findColumn(columns, "tEnd", retEndIx, retEndField));
 else if (findColumn(columns, "genoName", retChromIx, retChromField))
     return (findColumn(columns, "genoStart", retStartIx, retStartField) &&
 	    findColumn(columns, "genoEnd", retEndIx, retEndField));
 return FALSE;
 }
 
 struct annoStreamRows *annoStreamRowsNew(struct annoStreamer *streamerList)
 /* Returns an array of aSR, one for each streamer in streamerList.
  * Typically array is reused by overwriting elements' rowList pointers.
  * Free array when done. */
 {
 int streamerCount = slCount(streamerList);
 struct annoStreamRows *data = NULL;
 AllocArray(data, streamerCount);
 struct annoStreamer *streamer = streamerList;
 int i = 0;
 for (;  i < streamerCount;  i++, streamer = streamer->next)
     data[i].streamer = streamer;
 return data;
 }