src/hg/hgTracks/bigBedTrack.c 1.1

Index: src/hg/hgTracks/bigBedTrack.c
===================================================================
RCS file: src/hg/hgTracks/bigBedTrack.c
diff -N src/hg/hgTracks/bigBedTrack.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/hgTracks/bigBedTrack.c	1 Dec 2009 05:49:35 -0000	1.1
@@ -0,0 +1,123 @@
+/* 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);
+}
+
+
+
+void bigBedDrawDense(struct track *tg, int seqStart, int seqEnd,
+        struct hvGfx *hvg, int xOff, int yOff, int width,
+        MgFont *font, Color color)
+{
+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);
+}