a75cfac22803c312074299aa0dcf286ca336ce89
braney
  Wed Aug 27 13:28:08 2025 -0700
ongoing work on quickLift hgc page plus a fix for genepreds that don't
successfully quickLift

diff --git src/hg/hgTracks/quickLift.c src/hg/hgTracks/quickLift.c
index 1a3a2ef12cd..13be31161bc 100644
--- src/hg/hgTracks/quickLift.c
+++ src/hg/hgTracks/quickLift.c
@@ -31,131 +31,149 @@
 return color;
 }
 
 static void initializeHighlightColors()
 {
 if (highlightColors == NULL)
     {
     highlightColors = needMem(sizeof(Color) * 5);
  
     //lengthLimit = atoi(cfgOptionDefault("quickLift.lengthLimit", "10000"));
 
     highlightColors[QUICKTYPE_INSERT] = getColor("quickLift.insColor","255,0,0,255");
     highlightColors[QUICKTYPE_DEL] = getColor("quickLift.delColor","0,255,0,255");
     highlightColors[QUICKTYPE_DOUBLE] = getColor("quickLift.doubleColor","0,0,255,255");
     highlightColors[QUICKTYPE_MISMATCH] = getColor("quickLift.mismatchColor","255,0,0,255");
-    highlightColors[QUICKTYPE_NOTHING] = getColor("quickLift.nothingColor","1,1,1,1");
     }
 }
 
 
 static void drawTri(struct hvGfx *hvg, int x1, int x2, int y, Color color)
 /* Draw traingle. */
 {
 struct gfxPoly *poly = gfxPolyNew();
 int half = (x2 - x1) / 2;
 
 gfxPolyAddPoint(poly, x1, y);
 gfxPolyAddPoint(poly, x1+half, y+2*half);
 gfxPolyAddPoint(poly, x2, y);
 hvGfxDrawPoly(hvg, poly, color, TRUE);
 gfxPolyFree(&poly);
 }
 
 void maybeDrawQuickLiftLines( struct track *tg, int seqStart, int seqEnd,
                       struct hvGfx *hvg, int xOff, int yOff, int width,
                       MgFont *font, Color color, enum trackVisibility vis)
 /* Draw the indel regions in quickLifted tracks as a highlight. */
 {
 char *quickLiftFile = cloneString(trackDbSetting(tg->tdb, "quickLiftUrl"));
 if (quickLiftFile == NULL)
     return;
 
 initializeHighlightColors();
 boolean drawTriangle = FALSE;
-if (startsWith("quickLiftChain", trackHubSkipHubName(tg->track)))
+// this should be checking the type not the name
+if (sameString("bigQuickLiftChain", tg->tdb->type)) //startsWith("quickLiftChain", trackHubSkipHubName(tg->track)))
     drawTriangle = TRUE;
 char *liftDb = trackDbSetting(tg->tdb, "quickLiftDb");
 struct quickLiftRegions *regions = quickLiftGetRegions(database, liftDb, quickLiftFile, chromName, seqStart, seqEnd);
 struct quickLiftRegions *hr = regions;
 
 int fontHeight = mgFontLineHeight(tl.font);
 int height = tg->height;
 if (!drawTriangle && isCenterLabelIncluded(tg))
     {
     height += fontHeight;
     yOff -= fontHeight;
     }
 
-//mapBoxHc(hvg, seqStart, seqEnd, xOff, yOff, width,  tg->height, tg->track,  "fart", "hallo");
+if (drawTriangle && (hr == NULL))  // if there are no differences make a map for the whole track
+    mapBoxHc(hvg, seqStart, seqEnd, xOff, yOff, width,  tg->height, tg->track,  hr->id, "identical");
+
+int pos = xOff;
+char * lastId = 0;
 for(; hr; hr = hr->next)
     {
     unsigned int hexColor = highlightColors[hr->type];
     double scale = scaleForWindow(width, seqStart, seqEnd);
     int x1 = xOff + scale * (hr->chromStart - seqStart);
     int w =  scale * (hr->chromEnd - hr->chromStart);
     if (w == 0) 
         w = 1;
     hvGfxSetClip(hvg, xOff, yOff, width, height);  // we're drawing in the center label at the moment
     int startX, endX;
     char mouseOver[4096];
 
-    if (hr->type == QUICKTYPE_NOTHING)
-        {
-        safef(mouseOver, sizeof mouseOver, "identical");
-        mapBoxHc(hvg, hr->chromStart, hr->chromEnd, x1, yOff, w, height, tg->track, hr->id, mouseOver);
-        }
-    else
-        {
     if (drawTriangle)
         {
         startX = x1 + w/2 - fontHeight/2;
         endX = x1 + w/2 + fontHeight/2 ;
         drawTri(hvg, startX, endX , yOff, hexColor);
+        if (drawTriangle && (x1 > pos))
+            mapBoxHc(hvg, seqStart, seqEnd, pos, yOff, startX - pos,  tg->height, tg->track,  hr->id, "identical");
+        pos = endX;
         }
     else
         {
         startX = x1;
         endX = x1 + w;
         hvGfxBox(hvg, startX, yOff, w, height, hexColor);
         continue;
         }
 
     if (hr->type == QUICKTYPE_MISMATCH)
         safef(mouseOver, sizeof mouseOver, "mismatch %c->%c", *hr->otherBases, *hr->bases);
     else if (hr->chromStart == hr->chromEnd)
         safef(mouseOver, sizeof mouseOver, "deletion %ldbp (%.*s)", hr->oChromEnd - hr->oChromStart, hr->otherBaseCount, hr->otherBases);
     else if (hr->oChromStart == hr->oChromEnd)
         safef(mouseOver, sizeof mouseOver, "insertion %ldbp (%.*s)", hr->chromEnd - hr->chromStart, hr->baseCount, hr->bases);
     else
         safef(mouseOver, sizeof mouseOver, "double %ldbp", hr->oChromEnd - hr->oChromStart);
 
     mapBoxHc(hvg, seqStart, seqEnd, startX, yOff, endX - startX, height, tg->track, hr->id, mouseOver);
+    lastId = hr->id;
     }
-    }
+if (drawTriangle && (pos != xOff))
+    mapBoxHc(hvg, seqStart, seqEnd, pos, yOff, width - pos,  tg->height, tg->track, lastId, "identical");
+
 }
 
 void quickLiftDraw(struct track *tg, int seqStart, int seqEnd,
         struct hvGfx *hvg, int xOff, int yOff, int width,
         MgFont *font, Color color, enum trackVisibility vis)
 {
 //mapBoxHc(hvg, seqStart, seqEnd, xOff, yOff, width,  tg->height, tg->track,  "fart", "hallo");
 maybeDrawQuickLiftLines( tg, seqStart, seqEnd, hvg, xOff, yOff, width, font, color, vis);
 }
 
+static int quickLiftTotalHeight(struct track *tg, enum trackVisibility vis)
+/* Return configured height of track. */
+{
+return tg->lineHeight;
+}
+
+static void quickLiftDoLeftLabels(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)
+/* For now, draw no left labels. */
+{
+return;
+}
+
 void quickLiftChainMethods(struct track *tg, struct trackDb *tdb,
 	int wordCount, char *words[])
 /* Fill in custom parts of quickLift chains */
 {
 struct cartOptions *chainCart;
 
 AllocVar(chainCart);
 tg->extraUiData = (void *) chainCart;
 
 tg->isBigBed = TRUE;
 
 void bigChainLoadItems(struct track *tg);
 tg->loadItems = bigChainLoadItems;
 tg->drawItems = quickLiftDraw;
-int linkedFeaturesFixedTotalHeightNoOverflow(struct track *tg, enum trackVisibility vis);
-tg->totalHeight = linkedFeaturesFixedTotalHeightNoOverflow;
+tg->totalHeight = quickLiftTotalHeight;
+tg->drawLeftLabels = quickLiftDoLeftLabels;
+tg->mapsSelf = TRUE;
 }