3b51318fe05fce338719b56a70d44f1436ff5311
kate
  Tue Dec 5 12:37:26 2017 -0800
Fix problems with computing centers and position starts (esp. noticeable for SNPs). Also some cleanup. refs #17512

diff --git src/hg/hgTracks/longRangeTrack.c src/hg/hgTracks/longRangeTrack.c
index 383c7d0..99ff5ee 100644
--- src/hg/hgTracks/longRangeTrack.c
+++ src/hg/hgTracks/longRangeTrack.c
@@ -10,138 +10,142 @@
 if ( tg->visibility == tvDense)
     return  tl.fontHeight;
 int min, max, deflt, current; 
 cartTdbFetchMinMaxPixels(cart, tg->tdb, LONG_MINHEIGHT, LONG_MAXHEIGHT, atoi(LONG_DEFHEIGHT),
                                 &min, &max, &deflt, &current);
 return tg->height = current;
 }
 
 static Color longRangeItemColor(struct track *tg, void *item, struct hvGfx *hvg)
 /* Return color to draw a long range item */
 {
 struct longRange *lr = item;
 if (lr->hasColor)
     {
     struct rgbColor itemRgb;
+    // There must be a better way...
     itemRgb.r = (lr->rgb & 0xff0000) >> 16;
     itemRgb.g = (lr->rgb & 0xff00) >> 8;
     itemRgb.b = lr->rgb & 0xff;
     return hvGfxFindColorIx(hvg, itemRgb.r, itemRgb.g, itemRgb.b);
     }
 return tg->ixColor;
 }
 
 static void longRangeDraw(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 longTabix structures. */
 {
 double scale = scaleForWindow(width, seqStart, seqEnd);
 struct bed *beds = tg->items;
 unsigned int maxWidth;
 struct longRange *longRange;
 char buffer[1024];
 char itemBuf[2048];
-char statusBuf[2048];
-
 safef(buffer, sizeof buffer, "%s.%s", tg->tdb->track, LONG_MINSCORE);
 double minScore = sqlDouble(cartUsualString(cart, buffer, LONG_DEFMINSCORE));
 struct longRange *longRangeList = parseLongTabix(beds, &maxWidth, minScore);
 
 for(longRange=longRangeList; longRange; longRange=longRange->next)
     {
     safef(itemBuf, sizeof itemBuf, "%d", longRange->id);
-    safef(statusBuf, sizeof statusBuf, "%g %s:%d %s:%d", longRange->score, longRange->sChrom, longRange->s, longRange->eChrom, longRange->e);
+    struct dyString *ds = dyStringNew(0);
+    if (!longRange->hasColor)
+        dyStringPrintf(ds, "%g ", longRange->score);
+    dyStringPrintf(ds, "%s:%d %s:%d", longRange->sChrom, longRange->s, longRange->eChrom, longRange->e);
+    char *statusBuf = dyStringCannibalize(&ds);
+
     color = longRangeItemColor(tg, longRange, hvg);
-    boolean sOnScreen = (longRange->s >= seqStart) && (longRange->s < seqEnd);
-    unsigned sx = 0, ex = 0;
-    if (sOnScreen)
-        sx = (longRange->s - seqStart) * scale + xOff;
+    int sx = ((longRange->s - seqStart) + .5) * scale + xOff; // x coord of center (lower region)
+    int sFootWidth = scale * (double)longRange->sw / 2;       // width in pixels of half foot (lower)
+    int ex = ((longRange->e - seqStart) + .5) * scale + xOff;
+    int eFootWidth = scale * (double)longRange->ew / 2;
 
     if (differentString(longRange->sChrom, longRange->eChrom))
         {
-        if (!sOnScreen)
-            continue;
+        // different chromosomes
+        // FIXME: Most of this code should be shared with same chrom display
 
         // draw the foot
-        int footWidth = scale * (longRange->sw / 2);
+        int footWidth = sFootWidth;
         hvGfxLine(hvg, sx - footWidth, yOff, sx + footWidth, yOff, color);
 
         int height = tg->height/2;
         if (tg->visibility == tvDense)
             height = tg->height;
         unsigned yPos = yOff + height;
         hvGfxLine(hvg, sx, yOff, sx, yPos, color);
         if (tg->visibility == tvFull)
             {
             mapBoxHgcOrHgGene(hvg, longRange->s, longRange->s, sx - 2, yOff, 4, tg->height/2,
                                    tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
 
             safef(buffer, sizeof buffer, "%s:%d",  longRange->eChrom, longRange->e);
             hvGfxTextCentered(hvg, sx, yPos + 2, 4, 4, MG_BLUE, font, buffer);
             int width = vgGetFontStringWidth(hvg->vg, font, buffer);
             int height = vgGetFontPixelHeight(hvg->vg, font);
             mapBoxHgcOrHgGene(hvg, longRange->s, longRange->s, sx - width/2, yPos, width, height,
                                    tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
             }
+        continue;
         }
-    else 
-        {
+
+    // same chromosome
+    boolean sOnScreen = (longRange->s >= seqStart) && (longRange->s < seqEnd);
     boolean eOnScreen = (longRange->e >= seqStart) && (longRange->e < seqEnd);
     if (!(sOnScreen || eOnScreen))
         continue;
 
-        if (eOnScreen)
-            ex = (longRange->e - seqStart) * scale + xOff;
-
     double longRangeWidth = longRange->e - longRange->s;
     int peak = (tg->height - 15) * ((double)longRangeWidth / maxWidth) + yOff + 10;
     if (tg->visibility == tvDense)
         peak = yOff + tg->height;
 
     if (sOnScreen)
         {
-            int footWidth = scale * (longRange->sw / 2);
-            hvGfxLine(hvg, sx - footWidth, yOff, sx + footWidth, yOff, color);
+        // draw foot of 'lower' region
+        hvGfxLine(hvg, sx - sFootWidth, yOff, sx + sFootWidth, yOff, color);
+
+        // draw vertical
         hvGfxLine(hvg, sx, yOff, sx, peak, color);
         }
     if (eOnScreen)
         {
-            int footWidth = scale * (longRange->ew / 2);
-            hvGfxLine(hvg, ex - footWidth, yOff, ex + footWidth, yOff, color);
-            hvGfxLine(hvg, ex, yOff, ex, peak, color);
+        // draw foot of 'upper' region
+        hvGfxLine(hvg, ex - eFootWidth, yOff, ex + eFootWidth, yOff, color);
+
+        // draw vertical
+        hvGfxLine(hvg, ex, yOff, ex, peak, color); //OLD
         }
 
     if (tg->visibility == tvFull)
         {
-            unsigned sPeak = sOnScreen ? sx : xOff;
+        // draw link between regions (dense mode just shows feet ??)
         unsigned ePeak = eOnScreen ? ex : xOff + width;
-
+        unsigned sPeak = sOnScreen ? sx : xOff;
         hvGfxLine(hvg, sPeak, peak, ePeak, peak, color);
-            safef(statusBuf, sizeof statusBuf, "%g %s:%d %s:%d", longRange->score, longRange->sChrom, longRange->s, longRange->eChrom, longRange->e);
 
         if (sOnScreen)
             mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, sx - 2, yOff, 4, peak - yOff,
                                    tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
         if (eOnScreen)
             mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, ex - 2, yOff, 4, peak - yOff,
                                    tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
 
         mapBoxHgcOrHgGene(hvg, longRange->s, longRange->e, sPeak, peak-2, ePeak - sPeak, 4,
                                tg->track, itemBuf, statusBuf, NULL, TRUE, NULL);
-
-            }
         }
     }
 }
 
 void longRangeDrawLeftLabels(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)
 {
 }
 
 void longRangeMethods(struct track *tg, struct trackDb *tdb)
 {
 tg->drawLeftLabels = longRangeDrawLeftLabels;
 tg->drawItems = longRangeDraw;