Index: src/hg/hgc/wiggleClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/wiggleClick.c,v
retrieving revision 1.32
retrieving revision 1.33
diff -b -B -U 1000000 -r1.32 -r1.33
--- src/hg/hgc/wiggleClick.c	12 Aug 2009 21:20:26 -0000	1.32
+++ src/hg/hgc/wiggleClick.c	4 Jan 2010 19:12:27 -0000	1.33
@@ -1,257 +1,258 @@
 /* Handle details pages for wiggle tracks. */
 
 #include "common.h"
 #include "wiggle.h"
 #include "cart.h"
 #include "hgc.h"
 #include "hCommon.h"
 #include "hgColors.h"
 #include "obscure.h"
 #include "hmmstats.h"
 #include "customTrack.h"
 #include "bigWig.h"
 
 static char const rcsid[] = "$Id$";
 
 void genericWiggleClick(struct sqlConnection *conn, struct trackDb *tdb, 
 	char *item, int start)
 /* Display details for Wiggle data tracks.
  *	conn may be NULL for custom tracks when from file */
 {
 char *chrom = cartString(cart, "c");
 char table[64];
 boolean hasBin;
 unsigned span = 0;
 struct wiggleDataStream *wds = wiggleDataStreamNew();
 unsigned long long valuesMatched = 0;
 struct histoResult *histoGramResult;
 float *valuesArray = NULL;
 size_t valueCount = 0;
 struct customTrack *ct = NULL;
 boolean isCustom = FALSE;
 int operations = wigFetchStats;	/*	default operation */
 
 if (startsWith("ct_", tdb->tableName))
     {
     ct = lookupCt(tdb->tableName);
     if (!ct)
         {
         warn("<P>wiggleClick: can not find custom wiggle track '%s'</P>", tdb->tableName);
         return;
         }
     if (! ct->wiggle)
         {
         warn("<P>wiggleClick: called to do stats on a custom track that isn't wiggle data ?</P>");
         return;
         }
     if (ct->dbTrack)
 	{
 	safef(table,ArraySize(table), "%s", ct->dbTableName);
 	span = minSpan(conn, table, chrom, winStart, winEnd, cart, tdb);
 	}
     else
 	{
 	safef(table,ArraySize(table), "%s", ct->wigFile);
 	span = 0;	/*	cause all spans to be examined	*/
 	}
     isCustom = TRUE;
     }
 else
     {
     hFindSplitTable(database, seqName, tdb->tableName, table, &hasBin);
     /*span = spanInUse(conn, table, chrom, winStart, winEnd, cart);*/
     span = minSpan(conn, table, chrom, winStart, winEnd, cart, tdb);
     }
 
 /*	if for some reason we don't have a chrom and win positions, this
  *	should be run in a loop that does one chrom at a time.  In the
  *	case of hgc, there seems to be a chrom and a position.
  */
 wds->setSpanConstraint(wds, span);
 wds->setChromConstraint(wds, chrom);
 wds->setPositionConstraint(wds, winStart, winEnd);
 
 /*	If our window is less than some number of points, we can do
  *	the histogram too.
  */
 #define MAX_WINDOW_ALLOW_STATS	100000001
 #define MAX_WINDOW_ALLOW_STRING	"100,000,000"
 if ((winEnd - winStart) < MAX_WINDOW_ALLOW_STATS)
 	operations |= wigFetchAscii;
 
 /*	We want to also fetch the actual data values so we can run a
  *	histogram function on them.  You can't fetch the data in the
  *	form of the data array since the span information is then lost.
  *	We have to do the ascii data list format, and prepare that to
  *	send to the histogram function.
  */
 
 if (isCustom)
     {
     if (ct->dbTrack)
 	valuesMatched = wds->getData(wds, CUSTOM_TRASH, table, operations);
     else
 	valuesMatched = wds->getData(wds, (char *)NULL, table, operations);
     }
 else
     valuesMatched = wds->getData(wds, database, table, operations);
 
 statsPreamble(wds, chrom, winStart, winEnd, span, valuesMatched, NULL);
 
 /*	output statistics table
  *		(+sort, +html output, +with header, +close table)
  */
 wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, FALSE);
 
 if ((winEnd - winStart) < MAX_WINDOW_ALLOW_STATS)
     {
     char *words[16];
     int wordCount = 0;
     char *dupe = cloneString(tdb->type);
     double minY, maxY, tDbMinY, tDbMaxY;
     float hMin, hMax, hRange;
 
     wordCount = chopLine(dupe, words);
 
     wigFetchMinMaxY(tdb, &minY, &maxY, &tDbMinY, &tDbMaxY, wordCount, words);
     hMin = min(minY,tDbMinY);
     hMax = max(maxY,tDbMaxY);
     hRange = hMax - hMin;
 
     /*	convert the ascii data listings to one giant float array 	*/
     valuesArray = wds->asciiToDataArray(wds, valuesMatched, &valueCount);
 
     /* let's see if we really want to use the range from the track type
      *	line, or the actual range in this data.  If there is a good
      *	actual range in the data, use that instead
      */
-    if (hRange > 0.0) {
+    if (hRange > 0.0) 
+    	{
 	if (wds->stats->dataRange != 0)
 	    hRange = 0.0;
     }
 
     /*	If we have a valid range, use a specified 20 bin histogram
      *	NOTE: pass 21 as binCount to get a 20 bin histogram
      */
     if (hRange > 0.0)
 	histoGramResult = histoGram(valuesArray, valueCount, (hRange/20.0),
 	    (unsigned) 21, hMin, hMin, hMax, (struct histoResult *)NULL);
     else
 	histoGramResult = histoGram(valuesArray, valueCount,
 	    NAN, (unsigned) 0, NAN, (float) wds->stats->lowerLimit,
 		(float) (wds->stats->lowerLimit + wds->stats->dataRange),
 		    (struct histoResult *)NULL);
 
     /*	histoGram() may return NULL if it doesn't work, that's OK, the
      *	print out will indicate no results  (TRUE == html output)
      */
     printHistoGram(histoGramResult, TRUE);
 
     freeHistoGram(&histoGramResult);
     freeMem(valuesArray);
     }
 else
     {
     printf("<P>(viewing windows of fewer than %s bases will also"
 	" display a histogram)</P>\n", MAX_WINDOW_ALLOW_STRING);
     }
 
 wiggleDataStreamFree(&wds);
 }
 
 void bbiIntervalStatsReport(struct bbiInterval *bbList, char *table, 
 	char *chrom, bits32 start, bits32 end)
 /* Write out little statistical report in HTML */
 {
 /* Loop through list and calculate some stats. */
 bits64 iCount = 0;
 bits64 iTotalSize = 0;
 bits32 biggestSize = 0, smallestSize = BIGNUM;
 struct bbiInterval *bb;
 double sum = 0.0, sumSquares = 0.0;
 double minVal = bbList->val, maxVal = bbList->val;
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     iCount += 1;
     bits32 size = bb->end - bb->start;
     iTotalSize += size;
     if (biggestSize < size)
         biggestSize = size;
     if (smallestSize > size)
         smallestSize = size;
     double val = bb->val;
     sum += val;
     sumSquares += val * val;
     if (minVal > val)
         minVal = val;
     if (maxVal < val)
         maxVal = val;
     }
 
 char num1Buf[64], num2Buf[64]; /* big enough for 2^64 (and then some) */
 sprintLongWithCommas(num1Buf, iCount);
 sprintLongWithCommas(num2Buf, iTotalSize);
 bits32 winSize = end-start;
 printf("<B>Statistics on:</B> %s <B>items covering</B> %s bases (%4.2f%% coverage)<BR>\n",
 	num1Buf, num2Buf, 100.0*iTotalSize/winSize);
 printf("<B>Average item spans</B> %4.2f <B>bases.</B> ", (double)iTotalSize/iCount);
 if (biggestSize != smallestSize)
     {
     sprintLongWithCommas(num1Buf, biggestSize);
     sprintLongWithCommas(num2Buf, smallestSize);
     printf("<B>Minimum span</B> %s <B>maximum span</B> %s", num1Buf, num2Buf);
     }
 printf("<BR>\n");
 
 printf("<B>Average value</B> %g <B>min</B> %g <B>max</B> %g <B> standard deviation </B> %g<BR>\n",
 	sum/iCount, minVal, maxVal, calcStdFromSums(sum, sumSquares, iCount));
 }
 
 static void bigWigClick(struct trackDb *tdb, char *fileName)
 /* Display details for BigWig data tracks. */
 {
 char *chrom = cartString(cart, "c");
 
 /* Open BigWig file and get interval list. */
 struct bbiFile *bbi = bigWigFileOpen(fileName);
 struct lm *lm = lmInit(0);
 struct bbiInterval *bbList = bigWigIntervalQuery(bbi, chrom, winStart, winEnd, lm);
 
 char num1Buf[64], num2Buf[64]; /* big enough for 2^64 (and then some) */
 sprintLongWithCommas(num1Buf, BASE_1(winStart));
 sprintLongWithCommas(num2Buf, winEnd);
 printf("<B>Position: </B> %s:%s-%s<BR>\n", chrom, num1Buf, num2Buf );
 sprintLongWithCommas(num1Buf, winEnd-winStart);
 printf("<B>Total Bases in view: </B> %s <BR>\n", num1Buf);
 
 if (bbList != NULL)
     {
     bbiIntervalStatsReport(bbList, tdb->tableName, chrom, winStart, winEnd);
     }
 else
     {
     printf("<P>No data overlapping current position.</P>");
     }
 
 
 lmCleanup(&lm);
 bbiFileClose(&bbi);
 }
 
 void genericBigWigClick(struct sqlConnection *conn, struct trackDb *tdb, 
 	char *item, int start)
 /* Display details for BigWig built in tracks. */
 {
 char query[256];
 safef(query, sizeof(query), "select fileName from %s", tdb->tableName);
 char *fileName = sqlQuickString(conn, query);
 if (fileName == NULL)
     errAbort("Missing fileName in %s table", tdb->tableName);
 bigWigClick(tdb, fileName);
 }
 
 void bigWigCustomClick(struct trackDb *tdb)
 /* Display details for BigWig custom tracks. */
 {
 bigWigClick(tdb, trackDbSetting(tdb, "bigDataUrl"));
 }

