61f9643c131fb8ff8d1fbf75d8562c98668d61c7
chmalee
  Mon Feb 26 13:14:46 2024 -0800
Make codon numbers in mouseovers show up at the cds color level and not just the cds number level, fix incorrect mouseovers on introns that was broken by previous change, refs #32815

diff --git src/hg/hgTracks/cds.c src/hg/hgTracks/cds.c
index dab510d..e4e9b7e 100644
--- src/hg/hgTracks/cds.c
+++ src/hg/hgTracks/cds.c
@@ -1306,31 +1306,31 @@
     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 codonIndex = !codonNumbering || !zoomedToCodonNumberLevel ? 0 : 1;
+    int codonIndex = 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,"");
 
@@ -1496,31 +1496,30 @@
 		sf->end = currentEnd;
                 if (strlen(partialCodonSeq) == 3) 
                     sf->grayIx = codonToGrayIx(partialCodonSeq, altColor,
                             &foundStart, !posStrand, colorStopStart);
                 else
                     sf->grayIx = GRAYIX_CDS_ERROR;
                 strcpy(partialCodonSeq,"" );
 
                 /*update frame based on bases appended*/
                 frame -= currentSize;
 		}
             else
                 errAbort("%s: Too much dna (%d - %d = %d)<br>\n", lf->name, 
 			 currentEnd, currentStart, currentSize);
 
-            if (codonIndex)
             sf->codonIndex = codonIndex++;
             slAddHead(&sfList, sf);
             if(posStrand)
                 currentStart = currentEnd;
             else
                 currentEnd = currentStart;
 	    } // end loop on codons within exon
 
 	/* coding + UTR exon */
 	if (posStrand && (exonEnd < ends[i]) &&
 	    exonEnd < winEnd && ends[i] > winStart)
 	    {
             AllocVar(sf);
             sf->start = exonEnd;
             sf->end = ends[i];
@@ -1737,31 +1736,31 @@
     }
 }
 
 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 *qSeq, int qOffset, 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 && ( e - s >= 3))  // don't put exon numbers on split codons because there isn't space.
+if (zoomedToCodonNumberLevel && 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,