e9cd3eef710ba3141d58ef119006b7d2327e5b7f
markd
  Wed Dec 9 13:52:01 2020 -0800
fixed accidently backout of master changes in the last merge

diff --git src/hg/hgTracks/cds.c src/hg/hgTracks/cds.c
index 965a08f..d6e4c67 100644
--- src/hg/hgTracks/cds.c
+++ src/hg/hgTracks/cds.c
@@ -1147,33 +1147,31 @@
     partialCodonSeq[0] = '\0';
 
     if (lf->orientation > 0) //positive strand
     {
         i0 = 0; iN = blockCount; iInc = 1;
         posStrand = TRUE;
     }
     else
     {
         i0 = blockCount-1; iN=-1; iInc = -1;
         posStrand = FALSE;
     }
 
     bool altColor = FALSE;
     unsigned cds5Prime = posStrand ? cdsStart : cdsEnd;
-    int width = winEnd - winStart;
-    // width cutoff really should be based on (a) how many codons this gene has, (2) the current font and (3) image width.
-    int codonIndex = !codonNumbering || width > 60 ? 0 : 1;
+    int codonIndex = !codonNumbering || !zoomedToCodonNumberLevel ? 0 : 1;
     for (i=i0; (iInc*i)<(iInc*iN); i=i+iInc)
 	{
         int exonStart = starts[i];
         int exonEnd = ends[i];
         if (useExonFrames)
 	    {
             if(exonFrames[i] > 0)
                 frame = 3 - exonFrames[i];
             else
                 frame = 0;
 	    }
 
         if(frame == 0)
             strcpy(partialCodonSeq,"");
 
@@ -1567,31 +1565,31 @@
     }
 }
 
 void baseColorDrawItem(struct track *tg,  struct linkedFeatures *lf, 
 		       int grayIx, struct hvGfx *hvg, int xOff, 
                        int y, double scale, MgFont *font, int s, int e, 
                        int heightPer, boolean zoomedToCodonLevel, 
                        struct dnaSeq *mrnaSeq, struct simpleFeature *sf, struct psl *psl, 
 		       enum baseColorDrawOpt drawOpt,
                        int maxPixels, int winStart, 
                        Color originalColor)
 /* Draw codon/base-colored item. */
 {
 char codon[64] = " ";
 Color color = colorAndCodonFromGrayIx(hvg, codon, grayIx, originalColor);
-if (sf->codonIndex)
+if (sf->codonIndex && ( e - s >= 3))  // don't put exon numbers on split codons because there isn't space.
     safef(codon, sizeof(codon), "%c %d", codon[0], sf->codonIndex);
 /* When we are zoomed out far enough so that multiple bases/codons share the 
  * same pixel, we have to draw differences in a separate pass (baseColorOverdrawDiff)
  * so don't waste time drawing the differences here: */
 boolean zoomedOutToPostProcessing =
     ((drawOpt == baseColorDrawDiffBases && !zoomedToBaseLevel) ||
      (drawOpt == baseColorDrawDiffCodons && !zoomedToCdsColorLevel));
 
 if (drawOpt == baseColorDrawGenomicCodons && (e-s <= 3))
     {
     if (lf->highlightColor)
 	{
 	drawScaledBox(hvg, s, e, scale, xOff, y, heightPer, 
 			    lf->highlightColor);
 	drawScaledBoxWithText(hvg, s, e, scale, xOff, y+1, heightPer-2,