ae8dc8ab5e2c121398f31531c701ea064fb19aeb
braney
  Thu Apr 4 07:05:40 2019 -0700
add the ability to search the MANE track

diff --git src/hg/hgTracks/lolly.c src/hg/hgTracks/lolly.c
new file mode 100644
index 0000000..ed6ffb6
--- /dev/null
+++ src/hg/hgTracks/lolly.c
@@ -0,0 +1,160 @@
+/* lolly -- load and draw lollipops */
+
+/* Copyright (C) 2019 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
+#include "common.h"
+#include "obscure.h"
+#include "hgTracks.h"
+#include "bedCart.h"
+#include "bigWarn.h"
+#include "lolly.h"
+#include "limits.h"
+
+static int trackHeight;
+
+struct lollipop
+{
+struct lollipop *next;
+double val;
+unsigned start;
+unsigned radius;
+unsigned height;
+Color color;
+};
+
+static void lollipopDrawItems(struct track *tg, int seqStart, int seqEnd,
+        struct hvGfx *hvg, int xOff, int yOff, int width, 
+        MgFont *font, Color color, enum trackVisibility vis)
+/* Draw a list of lollipop structures. */
+{
+double scale = scaleForWindow(width, seqStart, seqEnd);
+struct lollipop *popList = tg->items, *pop;
+
+if (popList == NULL)
+    return;
+
+for (pop = popList; pop; pop = pop->next)
+    {
+    int sx = ((pop->start - seqStart) + .5) * scale; // x coord of center (lower region)
+    hvGfxLine(hvg, sx, yOff + trackHeight, sx , yOff+(trackHeight - pop->height), pop->color);
+    hvGfxCircle(hvg, sx, yOff + trackHeight - pop->radius - pop->height, pop->radius, pop->color, TRUE);
+    }
+}
+
+void lollipopLeftLabels(struct track *tg, int seqStart, int seqEnd,
+	struct hvGfx *hvg, int xOff, int yOff, int width, int height,
+	boolean withCenterLabels, MgFont *font, Color color,
+	enum trackVisibility vis)
+{
+}
+
+
+static int lollipopHeight(struct track *tg, enum trackVisibility vis)
+/* calculate height of all the lollipops being displayed */
+{
+if ( tg->visibility == tvDense)
+    return  tl.fontHeight;
+trackHeight = 5 * tl.fontHeight;
+return 5 * tl.fontHeight;
+}
+
+static void lollipopMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end,
+                                                                int x, int y, int width, int height)
+{
+}
+                                                               
+
+double calcVarianceFromSums(double sum, double sumSquares, bits64 n)
+/* Calculate variance. */
+{   
+double var = sumSquares - sum*sum/n;
+if (n > 1)
+    var /= n-1;
+return var;
+}   
+    
+double calcStdFromSums(double sum, double sumSquares, bits64 n)
+/* Calculate standard deviation. */
+{   
+return sqrt(calcVarianceFromSums(sum, sumSquares, n));
+}
+
+int cmpHeight(const void *va, const void *vb)
+{
+const struct lollipop *a = *((struct lollipop **)va);
+const struct lollipop *b = *((struct lollipop **)vb);
+return a->height - b->height;
+}
+
+void lollipopLoadItems(struct track *tg)
+{
+struct lm *lm = lmInit(0);
+struct bbiFile *bbi =  fetchBbiForTrack(tg);
+struct bigBedInterval *bb, *bbList =  bigBedIntervalQuery(bbi, chromName, winStart, winEnd, 0, lm);
+char *bedRow[bbi->fieldCount];
+char startBuf[16], endBuf[16];
+struct lollipop *popList = NULL, *pop;
+unsigned lollipopField = atoi(trackDbSetting(tg->tdb, "lollipopField"));
+double sumData = 0.0, sumSquares = 0.0;
+//double minVal = DBL_MAX, maxVal = -DBL_MAX;
+unsigned count = 0;
+                    
+for (bb = bbList; bb != NULL; bb = bb->next)
+    {
+    AllocVar(pop);
+    slAddHead(&popList, pop);
+    bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
+    double val = atof(bedRow[lollipopField]);
+    pop->val = val;
+    pop->start = atoi(bedRow[1]);
+    count++;
+    sumData += val;
+    sumSquares += val * val;
+    }
+
+double average = sumData/count;
+double stdDev = calcStdFromSums(sumData, sumSquares, count);
+
+for(pop = popList; pop; pop = pop->next)
+    {
+    if (pop->val > average + stdDev / 5)
+        {
+        pop->color = MG_RED;
+        pop->radius = 8;
+        pop->height = 3 * tl.fontHeight;
+        }
+    else if (pop->val < average - stdDev / 5)
+        {
+        pop->color = MG_GREEN;
+        pop->radius = 3;
+        pop->height = 1 * tl.fontHeight;
+        }
+    else
+        {
+        pop->color = MG_GRAY;
+        pop->radius = 5;
+        pop->height = 2 * tl.fontHeight;
+        }
+        
+    }
+slSort(&popList, cmpHeight);
+tg->items = popList;
+}
+
+void lollipopMethods(struct track *track, struct trackDb *tdb, 
+                                int wordCount, char *words[])
+/* Interact track type methods */
+{
+char *ourWords[2];
+ourWords[0] = "bigBed";
+ourWords[1] = "4";
+bigBedMethods(track, tdb,2,ourWords);
+if (tdb->visibility == tvDense)
+    return;
+track->loadItems = lollipopLoadItems;
+track->drawItems = lollipopDrawItems;
+track->totalHeight = lollipopHeight; 
+track->drawLeftLabels = lollipopLeftLabels;
+track->mapItem = lollipopMapItem;
+}