c8c7f5c3d5b590e37dfd321d99b7dd3f1baaa3c1
braney
  Tue Apr 9 13:12:00 2019 -0700
some tweaks to GDC cancer track, bigBed filters, and lollipop manual
ranges

diff --git src/hg/hgTracks/lolly.c src/hg/hgTracks/lolly.c
index 3b4c7f7..f0a5c7d 100644
--- src/hg/hgTracks/lolly.c
+++ src/hg/hgTracks/lolly.c
@@ -1,283 +1,285 @@
 /* lolly -- load and draw lollys */
 
 /* 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"
 #include "float.h"
 #include "bigBedFilter.h"
 
 
 static int lollyPalette[] =
 {
 0x1f77b4, 0xff7f0e, 0x2ca02c, 0xd62728, 0x9467bd, 0x8c564b, 0xe377c2, 0x7f7f7f, 0xbcbd22, 0x17becf
 };
 
 struct lolly
 {
 struct lolly *next;
 char *name;
 double val;
 unsigned start;
 unsigned end;
 unsigned radius;
 unsigned height;
 Color color;
 };
 
 static void lollyDrawItems(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 lolly structures. */
 {
 double scale = scaleForWindow(width, seqStart, seqEnd);
 struct lolly *popList = tg->items, *pop;
 int trackHeight = tg->lollyCart->height;
 
 if (popList == NULL)
     return;
 
 if ( tg->visibility == tvDense)
     {
     for (pop = popList; pop; pop = pop->next)
         {
         int sx = ((pop->start - seqStart) + .5) * scale + xOff; // x coord of center (lower region)
         hvGfxLine(hvg, sx, yOff, sx , yOff+ tl.fontHeight, pop->color);
         }
     return;
     }
 
 for (pop = popList; pop; pop = pop->next)
     {
     int sx = ((pop->start - seqStart) + .5) * scale + xOff; // x coord of center (lower region)
     hvGfxLine(hvg, sx, yOff + trackHeight, sx , yOff+(trackHeight - pop->height), MG_GRAY);
     }
 for (pop = popList; pop; pop = pop->next)
     {
     int sx = ((pop->start - seqStart) + .5) * scale + xOff; // x coord of center (lower region)
     hvGfxCircle(hvg, sx, yOff + trackHeight - pop->radius - pop->height, pop->radius, pop->color, TRUE);
     mapBoxHgcOrHgGene(hvg, pop->start, pop->end, sx - pop->radius, yOff + trackHeight - pop->radius - pop->height - pop->radius, 2 * pop->radius,2 * pop->radius,
                        tg->track, pop->name, pop->name, NULL, TRUE, NULL);
     }
 }
 
 void lollyLeftLabels(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)
 {
 int fontHeight = tl.fontHeight+1;
 int centerLabel = (height/2)-(fontHeight/2);
 if ( tg->visibility == tvDense)
     {
     hvGfxText(hvg, xOff, yOff+fontHeight, color, font, tg->shortLabel);
     return;
     }
 
 hvGfxText(hvg, xOff, yOff+centerLabel, color, font, tg->shortLabel);
 
 if (isnan(tg->lollyCart->upperLimit))
     {
     hvGfxTextRight(hvg, xOff, yOff + 2 * 5 , width - 1, fontHeight, color,
         font, "NO DATA");
     return;
     }
 
 char upper[1024];
 safef(upper, sizeof(upper), "%g -",   tg->lollyCart->upperLimit);
 hvGfxTextRight(hvg, xOff, yOff + 2 * 5 , width - 1, fontHeight, color,
     font, upper);
 char lower[1024];
 if (tg->lollyCart->lowerLimit < tg->lollyCart->upperLimit)
     {
     safef(lower, sizeof(lower), "%g _", tg->lollyCart->lowerLimit);
     hvGfxTextRight(hvg, xOff, yOff+height-fontHeight - 2 * 5, width - 1, fontHeight,
         color, font, lower);
     }
 }
 
 
 static int lollyHeight(struct track *tg, enum trackVisibility vis)
 /* calculate height of all the lollys being displayed */
 {
 if ( tg->visibility == tvDense)
     return  tl.fontHeight;
 
 return tg->lollyCart->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 lolly *a = *((struct lolly **)va);
 const struct lolly *b = *((struct lolly **)vb);
 return a->height - b->height;
 }
 
 void lollyLoadItems(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 lolly *popList = NULL, *pop;
 unsigned lollyField = 5;
 struct lollyCartOptions *lollyCart = tg->lollyCart;
 char *setting = trackDbSetting(tg->tdb, "lollyField");
 if (setting != NULL)
     lollyField = atoi(setting);
 double minVal = DBL_MAX, maxVal = -DBL_MAX;
 double sumData = 0.0, sumSquares = 0.0;
 unsigned count = 0;
 
 int trackHeight = tg->lollyCart->height;
 struct bigBedFilter *filters = bigBedBuildFilters(cart, bbi, tg->tdb);
                     
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
 
     if (!bigBedFilterInterval(bedRow, filters))
         continue;
 
     double val = atof(bedRow[lollyField - 1]);
     if (!((lollyCart->autoScale == wiggleScaleAuto) ||  ((val >= lollyCart->minY) && (val <= lollyCart->maxY) )))
         continue;
 
     AllocVar(pop);
     slAddHead(&popList, pop);
     pop->val = val;
     pop->start = atoi(bedRow[1]);
     pop->end = atoi(bedRow[2]);
     pop->name = cloneString(bedRow[3]);
     count++;
     sumData += val;
     sumSquares += val * val;
     if (val > maxVal)
         maxVal = val;
     if (val < minVal)
         minVal = val;
     }
 
 if (count == 0)
-    tg->lollyCart->upperLimit = tg->lollyCart->lowerLimit = NAN;
-else
+    lollyCart->upperLimit = lollyCart->lowerLimit = NAN;
+else if (lollyCart->autoScale == wiggleScaleAuto)
     {
-    tg->lollyCart->upperLimit = maxVal;
-    tg->lollyCart->lowerLimit = minVal;
+    lollyCart->upperLimit = maxVal;
+    lollyCart->lowerLimit = minVal;
     }
 
-double range = maxVal - minVal;
+double range = lollyCart->upperLimit - lollyCart->lowerLimit;
 int usableHeight = trackHeight - 2 * 5 * 2; 
 for(pop = popList; pop; pop = pop->next)
     {
     pop->radius = 5;
     pop->color = MG_RED;
     if (range == 0.0)
         {
         pop->height = usableHeight ;
         pop->color = lollyPalette[0] | 0xff000000;
         }
     else
         {
-        pop->height = usableHeight * (pop->val  - minVal) / range + 5 * 2;
-        int colorIndex = 8 * (pop->val  - minVal) / range;
+        pop->height = usableHeight * (pop->val  - lollyCart->lowerLimit) / range + 5 * 2;
+        int colorIndex = 8 * (pop->val  - lollyCart->lowerLimit) / range;
         pop->color = lollyPalette[colorIndex] | 0xff000000;
         }
     }
 
 /*
 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;
 }
 
 static struct lollyCartOptions *lollyCartOptionsNew(struct cart *cart, struct trackDb *tdb, 
                                 int wordCount, char *words[])
 {
 struct lollyCartOptions *lollyCart;
 AllocVar(lollyCart);
 
 int maxHeightPixels;
 int minHeightPixels;
 int defaultHeight;  /*  pixels per item */
 int settingsDefault;
 
 cartTdbFetchMinMaxPixels(cart, tdb, MIN_HEIGHT_PER, atoi(DEFAULT_HEIGHT_PER), atoi(DEFAULT_HEIGHT_PER),
                                 &minHeightPixels, &maxHeightPixels, &settingsDefault, &defaultHeight);
 lollyCart->height = defaultHeight;
 
 lollyCart->autoScale = wigFetchAutoScaleWithCart(cart,tdb, tdb->track, NULL);
 
 double tDbMinY;     /*  data range limits from trackDb type line */
 double tDbMaxY;     /*  data range limits from trackDb type line */
 char *trackWords[8];     /*  to parse the trackDb type line  */
 int trackWordCount = 0;  /*  to parse the trackDb type line  */
 wigFetchMinMaxYWithCart(cart, tdb, tdb->track, &lollyCart->minY, &lollyCart->maxY, &tDbMinY, &tDbMaxY, trackWordCount, trackWords);
+lollyCart->upperLimit = lollyCart->maxY;
+lollyCart->lowerLimit = lollyCart->minY;
 
 return lollyCart;
 }
 
 void lollyMethods(struct track *track, struct trackDb *tdb, 
                                 int wordCount, char *words[])
 /* bigLolly track type methods */
 {
 struct lollyCartOptions *lollyCart = lollyCartOptionsNew(cart, tdb, wordCount, words);
 char *ourWords[2];
 ourWords[0] = "bigBed";
 ourWords[1] = "4";
 bigBedMethods(track, tdb,2,ourWords);
 if (tdb->visibility == tvDense)
     return;
 track->loadItems = lollyLoadItems;
 track->drawItems = lollyDrawItems;
 track->totalHeight = lollyHeight; 
 track->drawLeftLabels = lollyLeftLabels;
 track->lollyCart = lollyCart;
 }