src/hg/hgTables/wiggle.c 1.68

Index: src/hg/hgTables/wiggle.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTables/wiggle.c,v
retrieving revision 1.67
retrieving revision 1.68
diff -b -B -U 4 -r1.67 -r1.68
--- src/hg/hgTables/wiggle.c	10 Mar 2009 01:25:24 -0000	1.67
+++ src/hg/hgTables/wiggle.c	12 Mar 2009 16:45:16 -0000	1.68
@@ -4,8 +4,9 @@
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "dystring.h"
+#include "localmem.h"
 #include "portable.h"
 #include "obscure.h"
 #include "jksql.h"
 #include "cheapcgi.h"
@@ -19,22 +20,14 @@
 #include "customTrack.h"
 #include "wiggle.h"
 #include "hmmstats.h"
 #include "correlate.h"
-#include "bbiFile.h"
-#include "bigWig.h"
 #include "hgTables.h"
 
 static char const rcsid[] = "$Id$";
 
 extern char *maxOutMenu[];
 
-enum wigOutputType 
-/*	type of output requested from static int wigOutRegion()	*/
-    {
-    wigOutData, wigOutBed, wigDataNoPrint,
-    };
-
 
 /*	a common set of stuff is accumulating in the various
  *	routines that call getData.  For the moment make it a macro,
  *	perhaps later it can turn into a routine of its own.
@@ -79,8 +72,13 @@
 char varPrefix[128];
 struct hashEl *varList, *var;
 char *pat = NULL;
 char *cmp = NULL;
+if (constraint != NULL)
+    *constraint = NULL;	// Make sure return variable gets set to something at least. 
+
+if (isCustomTrack(table))
+    db = "ct";
 
 safef(varPrefix, sizeof(varPrefix), "%s%s.%s.", hgtaFilterVarPrefix, db, table);
 
 varList = cartFindPrefix(cart, varPrefix);
@@ -241,8 +240,16 @@
 static struct bed *bedTable2(struct sqlConnection *conn,
 	struct region *region, char *table2)
 /*	get a bed list, possibly complement, for table2	*/
 {
+/* This use of bedTable rather than a bitmap is not really working. The
+ * rest of the table browser does intersection at the exon level, while
+ * the wig code, which this is part of, does it at the gene level.  I
+ * noticed it while working on the corresponding routines for bigWig,
+ * which I'm building to work with bitmaps at the exon level.  I'm not
+ * sure it's worth fixing this code since nobody has complained, and we're
+ * probably going to be doing mostly bigWig rather than wig in the future. 
+ *    -JK */
 boolean invTable2 = cartCgiUsualBoolean(cart, hgtaInvertTable2, FALSE);
 char *op = cartString(cart, hgtaIntersectOp);
 struct bed *bedList = NULL;
 struct lm *lm1 = lmInit(64*1024);
@@ -460,28 +467,8 @@
 dataVectorFree(&dv);
 return resultCount;
 }
 
-static int bigWigOutRegion(char *table, struct sqlConnection *conn,
-			     struct region *region, int maxOut,
-			     enum wigOutputType wigOutType)
-/* Read in bigWig as dataVector (filtering is handled there), 
- * intersect if necessary, and print it out. */
-{
-int resultCount = 0;
-char *wigFileName = bigWigFileName(table, conn);
-if (wigFileName)
-    {
-    struct bbiFile *bwf = bigWigFileOpen(wigFileName);
-    if (bwf)
-	resultCount = bigWigIntervalDump(bwf, region->chrom, region->start, region->end, 
-		maxOut, stdout);
-    bbiFileClose(&bwf);
-    }
-freeMem(wigFileName);
-return resultCount;
-}
-
 
 static struct trackDb *trackDbWithWiggleSettings(char *table)
 /* Get trackDb for a table in the database -- or if it has a parent/composite 
  * track, then return that because it contains the wiggle settings. */
@@ -727,28 +714,8 @@
 
 
 /***********   PUBLIC ROUTINES  *********************************/
 
-char *bigWigFileName(char *table, struct sqlConnection *conn)
-/* Return file name associated with bigWig.  This handles differences whether it's
- * a custom or built-in track.  Do a freeMem on returned string when done. */
-{
-char *fileName = NULL;
-if (isCustomTrack(table))
-    {
-    struct customTrack *ct = lookupCt(table);
-    if (ct != NULL)
-        fileName = cloneString(trackDbSetting(ct->tdb, "dataUrl"));
-    }
-else
-    {
-    char query[256];
-    safef(query, sizeof(query), "select fileName from %s", table);
-    fileName = sqlQuickString(conn, query);
-    }
-return fileName;
-}
-
 struct dataVector *bedGraphDataVector(char *table,
 	struct sqlConnection *conn, struct region *region)
 /* Read in bedGraph as dataVector and return it.  Filtering, subtrack merge 
  * and intersection are handled. */
@@ -778,30 +745,8 @@
     }
 return dv;
 }
 
-#ifdef SOON
-struct dataVector *bigWigDataVector(char *table,
-	struct sqlConnection *conn, struct region *region)
-/* Read in bigWig as dataVector and return it.  Filtering, subtrack merge 
- * and intersection are handled. */
-{
-struct dataVector *dv = NULL;
-
-if (anySubtrackMerge(database, table))
-    dv = mergedWigDataVector(table, conn, region);
-else
-    {
-    char *fileName = bigWigFileName(table, conn);
-    struct dataVector *allocDataVector(char *chrom, int size)
-    struct trackTable *tt1 = trackTableNew(tdb, table, conn);
-    dv = dataVectorFetchOneRegion(tt1, region, conn);
-    intersectDataVector(table, dv, region, conn);
-    }
-return dv;
-}
-#endif /* SOON */
-
 
 struct dataVector *wiggleDataVector(struct trackDb *tdb, char *table,
 	struct sqlConnection *conn, struct region *region)
 /* Read in wiggle as dataVector and return it.  Filtering, subtrack merge 
@@ -871,14 +816,8 @@
     }
 return(typeWiggle);
 }
 
-boolean isBigWig(char *table)
-/* Return TRUE if table corresponds to a bigWig file. */
-{
-return trackIsType(table, "bigWig");
-}
-
 boolean isBedGraph(char *table)
 /* Return TRUE if table is specified as a bedGraph in the current database's 
  * trackDb. */
 {
@@ -1308,71 +1247,21 @@
 stringStatRow("region", regionName);
 numberStatRow("bases in region", regionSize);
 numberStatRow("bases in gaps", gapTotal);
 floatStatRow("load and calc time", 0.001*wigFetchTime);
-stringStatRow("filter", (anyFilter() ? "on" : "off"));
-stringStatRow("intersection", (anyIntersection() ? "on" : "off"));
+wigFilterStatRow(conn);
+stringStatRow("intersection", cartUsualString(cart, hgtaIntersectTable, "off"));
 hTableEnd();
 htmlClose();
 }	/*	void doSummaryStatsWiggle(struct sqlConnection *conn)	*/
 
-void doSummaryStatsBigWig(struct sqlConnection *conn)
-/* Put up page showing summary stats for bigWig track. */
-{
-struct trackDb *track = curTrack;
-char *table = curTable;
-char *shortLabel = (track == NULL ? table : track->shortLabel);
-char *fileName = bigWigFileName(table, conn);
-struct bbiFile *bwf = bigWigFileOpen(fileName);
-
-htmlOpen("%s (%s) Big Wig Summary Statistics", shortLabel, table);
-
-struct region *region, *regionList = getRegions();
-double sumData = 0, sumSquares = 0, minVal = 0, maxVal = 0;
-bits64 validCount = 0;
-for (region = regionList; region != NULL; region = region->next)
-    {
-    struct bbiSummaryElement sum;
-    if (bbiSummaryArrayExtended(bwf, region->chrom, region->start, region->end, bigWigIntervalQuery, 
-    	1, &sum))
-        {
-	if (validCount == 0)
-	    {
-	    minVal = sum.minVal;
-	    maxVal = sum.maxVal;
-	    }
-	sumData += sum.sumData;
-	sumSquares += sum.sumSquares;
-	validCount += sum.validCount;
-	}
-    }
-
-
-hTableStart();
-floatStatRow("mean", sumData/validCount);
-floatStatRow("min", minVal);
-floatStatRow("max", maxVal);
-floatStatRow("standard deviation", calcStdFromSums(sumData, sumSquares, validCount));
-numberStatRow("bases with data", validCount);
-bits64 regionSize = basesInRegion(regionList, 0);
-bits64 gapTotal = gapsInRegion(conn, regionList, 0);
-numberStatRow("bases with sequence", regionSize - gapTotal);
-numberStatRow("bases in region", regionSize);
-hTableEnd();
-
-bbiFileClose(&bwf);
-htmlClose();
-}
-
 void wigShowFilter(struct sqlConnection *conn)
 /* print out wiggle data value filter */
 {
 double ll, ul;
 char *constraint;
 
-if ( (isCustomTrack(curTable) &&
-	checkWigDataFilter("ct", curTable, &constraint, &ll, &ul))
-	|| checkWigDataFilter(database, curTable, &constraint, &ll, &ul))
+if (checkWigDataFilter(database, curTable, &constraint, &ll, &ul))
     {
     if (constraint && sameWord(constraint, "in range"))
 	{
 	hPrintf("  data value %s [%g : %g)\n", constraint, ll, ul);