62645bb6b4e4b6792b8d52777b93ed3b65b42c7a
kuhn
  Wed Sep 7 10:34:32 2011 -0700
added NOTE about needing the latest Java to run VARNA in some OS/browser combos
diff --git src/hg/hgc/rnaFoldClick.c src/hg/hgc/rnaFoldClick.c
index bbe2a52..0c12f38 100644
--- src/hg/hgc/rnaFoldClick.c
+++ src/hg/hgc/rnaFoldClick.c
@@ -362,31 +362,33 @@
     fprintf(f, "<center><h2> RNA secondary structure drawing </h2></center>");
     fprintf(f,"<B>");
 
     // Could consider to serve up all EvoFold .png files from our public server in the future
     // fprintf(f,"<IMG SRC=\"http://genome.ucsc.edu/evoFold/%s/%s/%s.png\" border = '2' ALT=\"ERROR: VARA plotting failed.\"</B><BR>",
     fprintf(f,"<IMG SRC=\"../evoFold/%s/%s/%s.png\" border = '2' ALT=\"ERROR: symlink to file not found.\"</B><BR>",
             database, item->chrom, item->name);
     fprintf(f,"</B>");
     }
 
 freeMem(seq);
 printf("<p>The UCSC Genome Browser mirror site at the Molecular Diagnostic Laboratory (MDL) at Aarhus University Hospital Skejby in Denmark offers a VARNA Java applet to view the above RNA structure with more options, ");
 printf("<A HREF=\"");
 printf("http://genome-mirror.moma.ki.au.dk/cgi-bin/hgc?db=%s&c=%s&l=%d&r=%d&o=%d&t=%d&g=evofold&i=%s",
 database, item->chrom, item->chromStart, item->chromEnd, item->chromStart, item->chromEnd, cgiEncode(item->name)); // c, l and r are needed because mirror may have no cart for us.  Not actually used, however.
-printf("\" TARGET=_blank>%s</A></p>", "click here to go to genome-mirror.moma.ki.au.dk.");
+printf("\" TARGET=_blank>%s</A>.", "click here to go to genome-mirror.moma.ki.au.dk");
+fprintf(f,"  <B><FONT COLOR = RED>NOTE:</FONT> some operating system/browser combinations require ");
+fprintf(f," the latest version of Java for this to work properly.</FONT></B></P>");
 }
 
 void htmlPrintSecStrEvofoldV2Drawing(FILE *f, struct rnaSecStr *item)
 {
 char fileName[512];
 struct dnaSeq *seq;
 seq = hChromSeq(database, item->chrom, item->chromStart, item->chromEnd);
 touppers(seq->dna);
 if (item->strand[0] == '-')
     reverseComplement(seq->dna, seq->size);
 memSwapChar(seq->dna, seq->size, 'T', 'U');
 
 safef(fileName, sizeof(fileName), "/gbdb/%s/evoFoldV2/%s/%s.png",
        database, item->chrom, item->name);
 if (fileExists(fileName))
@@ -394,31 +396,33 @@
     fprintf(f, "<center><h2> RNA secondary structure drawing </h2></center>");
     fprintf(f,"<B>");
 
     // Could consider to serve up all EvoFold .png files from our public server in the future
     // fprintf(f,"<IMG SRC=\"http://genome.ucsc.edu/evoFold/%s/%s/%s.png\" border = '2' ALT=\"ERROR: VARA plotting failed.\"</B><BR>",
     fprintf(f,"<IMG SRC=\"../evoFoldV2/%s/%s/%s.png\" border = '2' ALT=\"ERROR:  symlink to file not found.\"</B><BR>",
             database, item->chrom, item->name);
     fprintf(f,"</B>");
     }
 
 freeMem(seq);
 printf("<p>The UCSC Genome Browser mirror site at the Molecular Diagnostic Laboratory (MDL) at Aarhus University Hospital Skejby in Denmark offers a VARNA Java applet to view the above RNA structure with more options, ");
 printf("<A HREF=\"");
 printf("http://genome-mirror.moma.ki.au.dk/cgi-bin/hgc?db=%s&c=%s&l=%d&r=%d&o=%d&t=%d&g=evofoldV2&i=%s",
 database, item->chrom, item->chromStart, item->chromEnd, item->chromStart, item->chromEnd, cgiEncode(item->name));  // c, l and r are needed because mirror may have no cart for us.  Not actually used, however.
-printf("\" TARGET=_blank>%s</A></p>", "click here to go to genome-mirror.moma.ki.au.dk.");
+printf("\" TARGET=_blank>%s</A>.", "click here to go to genome-mirror.moma.ki.au.dk");
+fprintf(f," <B><FONT COLOR = RED>NOTE:</FONT> some operating system/browser combinations require ");
+fprintf(f," the latest version of Java for this to work properly.</FONT></B></P>");
 }
 
 void doRnaSecStr(struct trackDb *tdb, char *itemName)
 /* Handle click on rnaSecStr type elements. */
 {
 char *table = tdb->table;
 struct sqlConnection *conn = hAllocConn(database);
 struct sqlResult *sr;
 struct rnaSecStr *item;
 char extraWhere[256];
 char **row;
 int  rowOffset = 0;
 char *mafTrack = trackDbRequiredSetting(tdb, "mafTrack");
 int start = cartInt(cart, "o");
 struct mafAli *maf;