44027478d0f745cc34c843717bee4a6a397b6022
max
  Mon Aug 10 09:05:32 2026 -0700
hgc: route transMap, retrogene and literature alignments to the modern view too, refs #37893

These three click pages live in their own files (transMapClick.c, retroClick.c,
pubs.c) and called htmlFramesetStart directly, so they were missed when the other
alignment handlers moved to the modern single-page view. They all render through
showSomeAlignment, so exporting alnModernStart (was static) and swapping their
htmlFramesetStart call for it is enough: with modernAlignPage set they now show
the modern page (neutral, non-BLAT chrome), and the classic frameset otherwise.

diff --git src/hg/hgc/pubs.c src/hg/hgc/pubs.c
index ff135532923..1c008a4b35a 100644
--- src/hg/hgc/pubs.c
+++ src/hg/hgc/pubs.c
@@ -1103,31 +1103,31 @@
     seq->dna = cloneString(row[0]);
     seq->size = strlen(seq->dna);
     }
 sqlFreeResult(&sr);
 
 return seq;
 }
 
 void pubsAli(struct sqlConnection *conn, char *pslTable, char *seqTable, char *item)
 /* this is just a ripoff from htcCdnaAli, similar to markd's transMapAli */
 {
 bioSeq *oSeq = NULL;
 
 char title[1024];
 safef(title, sizeof title, "Literature Sequence vs Genomic");
-htmlFramesetStart(title);
+alnModernStart(title);
 
 struct psl *psl = getAlignments(conn, pslTable, item);
 if (psl == NULL)
     errAbort("Couldn't find alignment at %s:%s", pslTable, item);
 
 oSeq = getSeq(conn, seqTable, item);
 
 if (oSeq == NULL)  
     errAbort("%s is in pslTable but not in sequence table. Internal error.", item);
 
 enum gfType qt;
 if (psl->qSize!=oSeq->size) 
     {
     qt = gftProt;
     // trying to correct pslMap's changes to qSize/qStarts and blockSizes