src/hg/hgTracks/bigBedTrack.c 1.5

Index: src/hg/hgTracks/bigBedTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/bigBedTrack.c,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/hgTracks/bigBedTrack.c	6 Feb 2010 20:45:12 -0000	1.4
+++ src/hg/hgTracks/bigBedTrack.c	10 Feb 2010 01:51:16 -0000	1.5
@@ -1,141 +1,141 @@
 /* bigBed - stuff to handle loading and display of bigBed type tracks in browser. 
  * Mostly just links to bed code, but handles a few things itself, like the dense
  * drawing code. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hgTracks.h"
 #include "hmmstats.h"
 #include "localmem.h"
 #include "wigCommon.h"
 #include "bbiFile.h"
 #include "obscure.h"
 #include "bigWig.h"
 #include "bigBed.h"
 
 char *bbiNameFromTable(struct sqlConnection *conn, char *table)
 /* Return file name from little table. */
 {
 char query[256];
 safef(query, sizeof(query), "select fileName from %s", table);
 char *fileName = sqlQuickString(conn, query);
 if (fileName == NULL)
     errAbort("Missing fileName in %s table", table);
 return fileName;
 }
 
+struct bbiFile *fetchBbiForTrack(struct track *track)
+/* Fetch bbiFile from track, opening it if it is not already open. */
+{
+struct bbiFile *bbi = track->bbiFile;
+if (bbi == NULL)
+    {
+    struct sqlConnection *conn = hAllocConn(database);
+    char *fileName = bbiNameFromTable(conn, track->mapName);
+    hFreeConn(&conn);
+    bbi = track->bbiFile = bigBedFileOpen(fileName);
+    }
+return bbi;
+}
+
 struct bigBedInterval *bigBedSelectRange(struct sqlConnection *conn, struct track *track,
 	char *chrom, int start, int end, struct lm *lm)
 /* Return list of intervals in range. */
 {
-struct bbiFile *bbi = track->bbiFile;
+struct bbiFile *bbi = fetchBbiForTrack(track);
 int maxItems = maximumTrackItems(track) + 1;
 struct bigBedInterval *result = bigBedIntervalQuery(bbi, chrom, start, end, maxItems, lm);
 if (slCount(result) >= maxItems)
     {
     track->limitedVis = tvDense;
     track->limitedVisSet = TRUE;
     result = NULL;
     }
 return result;
 }
 
 void bigBedAddLinkedFeaturesFrom(struct sqlConnection *conn, struct track *track,
 	char *chrom, int start, int end, int scoreMin, int scoreMax, boolean useItemRgb,
 	int fieldCount, struct linkedFeatures **pLfList)
 /* Read in items in chrom:start-end from bigBed file named in track->bbiFileName, convert
  * them to linkedFeatures, and add to head of list. */
 {
 struct lm *lm = lmInit(0);
 struct trackDb *tdb = track->tdb;
 struct bigBedInterval *bb, *bbList = bigBedSelectRange(conn, track, chrom, start, end, lm);
 char *bedRow[32];
 char startBuf[16], endBuf[16];
 
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
     struct bed *bed = bedLoadN(bedRow, fieldCount);
     struct linkedFeatures *lf = bedMungToLinkedFeatures(&bed, tdb, fieldCount,
     	scoreMin, scoreMax, useItemRgb);
     slAddHead(pLfList, lf);
     }
 lmCleanup(&lm);
 }
 
 
 boolean canDrawBigBedDense(struct track *tg)
 /* Return TRUE if conditions are such that can do the fast bigBed dense data fetch and
  * draw. */
 {
 return tg->isBigBed;
-#ifdef OLD
-/* Unfortunately bigBed datasets are so big, that running filters on them is not so practical
- * in the dense mode. */
-if (!tg->isBigBed)
-    return FALSE;
-int scoreFilter = cartOrTdbInt(cart, tg->tdb, "scoreFilter", 0);
-return scoreFilter == 0 && trackDbSetting(tg->tdb, "colorByStrand") == NULL;
-#endif /* OLD */
 }
 
 
 void bigBedDrawDense(struct track *tg, int seqStart, int seqEnd,
         struct hvGfx *hvg, int xOff, int yOff, int width,
         MgFont *font, Color color)
 /* Use big-bed summary data to quickly draw bigBed. */
 {
 struct bbiSummaryElement summary[width];
-if (bigBedSummaryArrayExtended(tg->bbiFile, chromName, seqStart, seqEnd, width, summary))
+struct bbiFile *bbi = fetchBbiForTrack(tg);
+if (bigBedSummaryArrayExtended(bbi, chromName, seqStart, seqEnd, width, summary))
     {
     char *denseCoverage = trackDbSettingClosestToHome(tg->tdb, "denseCoverage");
     if (denseCoverage != NULL)
         {
 	double startVal = 0, endVal = atof(denseCoverage);
 	if (endVal <= 0)
 	    {
-	    struct bbiSummaryElement sumAll = bbiTotalSummary(tg->bbiFile);
+	    struct bbiSummaryElement sumAll = bbiTotalSummary(bbi);
 	    double mean = sumAll.sumData/sumAll.validCount;
 	    double std = calcStdFromSums(sumAll.sumData, sumAll.sumSquares, sumAll.validCount);
 	    rangeFromMinMaxMeanStd(0, sumAll.maxVal, mean, std, &startVal, &endVal);
 	    }
 	int x;
 	for (x=0; x<width; ++x)
 	    {
 	    if (summary[x].validCount > 0)
 		{
 		Color color = shadesOfGray[grayInRange(summary[x].maxVal, startVal, endVal)];
 		hvGfxBox(hvg, x+xOff, yOff, 1, tg->heightPer, color);
 		}
 	    }
 	}
     else
 	{
 	int x;
 	for (x=0; x<width; ++x)
 	    {
 	    if (summary[x].validCount > 0)
 		{
 		hvGfxBox(hvg, x+xOff, yOff, 1, tg->heightPer, color);
 		}
 	    }
 	}
     }
 }
 
 void bigBedMethods(struct track *track, struct trackDb *tdb, 
                                 int wordCount, char *words[])
 /* Set up bigBed methods. */
 {
 complexBedMethods(track, tdb, TRUE, wordCount, words);
-if (track->bbiFile == NULL)
-    {
-    struct sqlConnection *conn = hAllocConn(database);
-    char *fileName = bbiNameFromTable(conn, track->mapName);
-    hFreeConn(&conn);
-    track->bbiFile = bigBedFileOpen(fileName);
-    }
 }