src/hg/hgTracks/bigBedTrack.c 1.2

Index: src/hg/hgTracks/bigBedTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/bigBedTrack.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/hgTracks/bigBedTrack.c	1 Dec 2009 05:49:35 -0000	1.1
+++ src/hg/hgTracks/bigBedTrack.c	14 Jan 2010 22:36:30 -0000	1.2
@@ -1,123 +1,134 @@
 /* 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 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;
 int maxItems = maximumTrackItems(track) + 1;
 if (bbi == NULL)
     {
     char *fileName = bbiNameFromTable(conn, track->mapName);
     bbi = track->bbiFile = bigBedFileOpen(fileName);
     }
 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. */
+{
+if (!tg->isBigBed)
+    return FALSE;
+int scoreFilter = cartOrTdbInt(cart, tg->tdb, "scoreFilter", 0);
+return scoreFilter == 0;
+}
+
 
 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))
     {
     char *denseCoverage = trackDbSettingClosestToHome(tg->tdb, "denseCoverage");
     if (denseCoverage != NULL)
         {
 	double startVal = 0, endVal = atof(denseCoverage);
 	if (endVal <= 0)
 	    {
 	    struct bbiSummaryElement sumAll = bbiTotalSummary(tg->bbiFile);
 	    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);
 }