752e20a9a1dc08793c5b529bbeac4ce5836a6be4
braney
  Fri Sep 4 17:13:55 2026 -0700
hgc: stop five details-page handlers from aborting over a missing piece.

chromSeqFileExists() opened its connection with sqlConnect() and only then
asked whether the database existed, so it aborted before it could answer.
The otherDb of a chain or net track is often not a local database at all --
a GenArk hub assembly, or one long retired -- so use sqlMayConnect() and
return FALSE. This is 112 of the failures the TrackCheck robot reports, most
of them hg38 net tracks against HPRC assemblies. Also moved the disconnect
out of the if, where it leaked a connection whenever a database had no
chromInfo table, and dropped the now-redundant sqlDatabaseExists() call,
which was itself a second connection.

mgcCloneInfoLoad() aborted when a clone carried no MGC: id in
hgFixed.mrnaClone. Nothing on the page reads that field, and a clone can
legitimately have only an IMAGE: id, so the check went away rather than the
page. hDbOrganism() aborted for an assembly that has left dbDb but is still
named by a maf component, which hg16.evofold does via mm3; it now falls back
on the database name.

The pgSnp SIFT and Polyphen prediction tables are loaded separately from the
tracks that name them, so a machine can have the track and not the table, as
hgwbeta and the RR do for hg18. Check with hTableExists first and say the
predictions are unavailable instead of letting the query take the page down.
Same treatment for the RNA fold diagram: a non-zero ghostscript exit now
drops only the diagram and keeps the rest of the page, including the
PseudoViewer link.

Two of these report an unavailable piece through warn(), which still marks
the page for the robot. That is deliberate -- the missing hg18 tables and
the RNA fold diagram are real defects, and the log should keep naming them
until they are fixed. On the RNA fold diagram in particular: RNAplot
truncates the sequence id it is given to 42 characters, and the trash path
we build is already 41, so it has never written the file ghostscript is
asked to convert. That is worth its own fix.

refs #37424

diff --git src/hg/hgc/rnaFoldClick.c src/hg/hgc/rnaFoldClick.c
index e792152fd40..bcf9afa10a1 100644
--- src/hg/hgc/rnaFoldClick.c
+++ src/hg/hgc/rnaFoldClick.c
@@ -1,570 +1,584 @@
 /* Handle details pages for rna fold (evofold) tracks. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "jksql.h"
 #include "hgMaf.h"
 #include "maf.h"
 #include "cart.h"
 #include "hgc.h"
 #include "hCommon.h"
 #include "hgColors.h"
 #include "obscure.h"
 #include "customTrack.h"
 #include "htmshell.h"
 #include "rnautil.h"
 #include "rnaSecStr.h"
 #include "memalloc.h"
 #include "hgConfig.h"
 #include "pipeline.h"
 
 
 /* Taken from hgc.c (should probably be in hgc.h)*/
 #define RED 0xFF0000
 #define GREEN 0x00FF00
 #define BLUE 0x0000FF
 #define BLACK 0x000000
 #define CYAN 0x00FFFF
 #define GRAY 0xcccccc
 #define LTGRAY 0x999999
 #define ORANGE 0xDD6600
 #define MAGENTA 0xFF00FF
 
 #define LTPURPLE 0x9966CC
 #define SCORE_SHADES_COUNT 10
 
 void printRfamUrl(char *itemName)
 /* Print a link to the Rfam entry corresponding to the item. */
 {
 char *query = cloneString(itemName);
 char *end   = strchr(query, '.');
 if (!end)
     return;
 else
     *end = 0;
 printf("<p><A HREF=\"");
 printf("http://www.sanger.ac.uk/cgi-bin/Rfam/seqget.pl?name=%s", query);
 printf("\" TARGET=_blank>%s</A></p>", itemName);
 freeMem(query);
 }
 
 void doubleArray2binArray(double *scores, int size, double minScore, double maxScore, int *binArray, int binCount)
 /* Will assign a bin to each score in 'scores' and store it in 'binArray' */
 {
 int i;
 for (i = 0; i < size; i++)
     binArray[i] = assignBin(scores[i], minScore, maxScore, binCount);
 }
 
 void htmlColorPrintString(FILE *f, char *s, int *colorFormat, int *colors, int L)
 /* Prints s to f wrapping characters in html tags for coloring
  * according to colorFormat and colors. colorFormat must be of same
  * length as s. Each position of colorFormat defines which of the
  * colors to use. Use 0 for default color. If L is non-NULL it
  * defines a mximum length to print.*/
 {
 int i;
 
 if (!L || (L && strlen(s)<L) )
     L = strlen(s);
 
 fprintf(f, "<span style='color:#%06X;'>", colors[0]); /* default color */
 for (i = 0; i < L; i++)
     {
     if (colorFormat[i] == 0)
 	fprintf(f, "%c", s[i]);
     else
 	fprintf(f, "<span style='color:#%06X;'>%c</span>", colors[ colorFormat[i] ], s[i]);
     }
 fprintf(f, "</span>");
 }
 
 void mafAndFoldHeader(FILE *f)
 /* Print header for maf and fold the section*/
 {
 fprintf(f, "<center><h2> Multiple alignment and RNA secondary structure annotation </h2></center>");
 }
 
 void mkPosString(char *s, int size)
 /* Make a string-ruler with a decimal every tenth position */
 {
 int i, d;
 for (i = 0, d = 0; i < size; i++)
     if (i%10 == 0)
 	{
 	s[i] = '0' + d;
 	d++;
 	if (d == 10)
 	  d = 0;
 	}
     else
 	s[i] = ' ';
 s[size] = '\0';
 }
 
 char *mkScoreString(double *scores, int L, char *referenceText)
     /* allocate string of score symbols, adjust for gaps in reference sequene */
 {
 char *s = (char *) needMem(L+1);
 char *scoreString = NULL;
 int i, n;
 for (i=0;i<L;i++)
     {
     n    = floor(10 *scores[i]);
     if (n == 10)
 	n = 9;
     if (n < 0 || n > 9)
 	errAbort( "Score not between 0 and 1\n" );
     s[i] = '0' + n;
     }
 s[L] = 0;
 scoreString = gapAdjustFold(s, referenceText);
 freeMem(s);
 return scoreString;
 }
 
 int *mkScoreColorFormat(double *scores, int L, char *referenceText)
   /* allocate string of score colors (gray shades), adjust for gaps in reference sequene */
 {
 int *v = NULL;
 int *scoreColorFormat = NULL;
 v = (int *) needMem(L *sizeof(int) );
 doubleArray2binArray(scores, L, 0.0, 1.0, v, SCORE_SHADES_COUNT);
 scoreColorFormat = gapIntArrayAdjust(v, referenceText);
 freeMem(v);
 return scoreColorFormat;
 }
 
 void defineMafSubstColors(int **p2mafColors)
 /* Defines the colors used for maf coloring. Must corrspsond to the
  * markCompensatoryMutations function.*/
 {
 int *mafColors;
 AllocArray(*p2mafColors, 8);
 mafColors = *p2mafColors;
 mafColors[0]    = LTGRAY;   /* not pairing */
 mafColors[1]    = LTPURPLE; /* not pairing, substitution */
 mafColors[2]    = BLACK;    /* compatible with pairing */
 mafColors[3]    = BLUE;     /* compatible with pairing, single substitution  */
 mafColors[4]    = GREEN;    /* compensatory change */
 mafColors[5]    = RED;      /* not compatible with fold, single subs */
 mafColors[6]    = ORANGE;   /* not compatible with fold, double subs */
 mafColors[7]    = MAGENTA;  /* not compatible with fold, involves indel */
 }
 
 char *hDbOrganism(char *databaseIn)
 /* Function to get organism from the genome db */
 {
 struct sqlConnection *connCentral = hConnectCentral();
 char buf[256];
 char query[256];
 char *res = NULL;
 char *database;
 char *chp;
 
 database = cloneString(databaseIn);
 
 // process special case like "hg19.chr21"
 chp = strstr(database, ".");
 if (chp != NULL)
     {
     *chp = '\0';
     }
 
 sqlSafef(query, sizeof(query), "select organism from dbDb where name = '%s'", database);
 if(sqlQuickQuery(connCentral, query, buf, sizeof(buf)) == NULL)
-    // this can happen in mirrors (see #8490).
-    errAbort("organism '%s' not found in dbDb", database);
+    // This can happen in mirrors (see #8490), and also for an assembly that has
+    // been retired from dbDb but is still named by a maf component (see #37424).
+    // Fall back on the database name, which is all we know about it.
+    res = cloneString(database);
 else
     res = cloneString(buf);
 hDisconnectCentral(&connCentral);
 freez(&database);
 return res;
 }
 
 
 void htmlPrintMafAndFold(FILE *f, struct mafAli *maf, char *fold, double *scores, int lineSize)
 /* HTML pretty print maf and fold to f. If scores is non-null then
  * scores are indicated below alignemnt.*/
 {
 struct mafComp *mc;
 int  i, N, lineStart, lineEnd;
 int  *pairList = NULL;
 int  *mafColors = NULL;
 int  **mafColorFormats = NULL;
 int  *scoreColorFormat = NULL;
 int  scoreColors[]  = {0x999999,0x888888,0x777777,0x666666,0x555555,0x444444,0x333333,0x222222,0x111111,0x000000};
 char *scoreString = 0;
 char *pairSymbols;
 char *posString, *adjPosString;
 char *adjFold;
 char foldTag[]       = "SS anno";
 char scoresTag[]     = "score  ";
 char positionTag[]   = "offset";
 char pairSymbolsTag[]= "pair symbol";
 char *referenceText  = maf->components->text; /* first sequence in the alignment */
 int  srcChars        = max( strlen(foldTag), strlen(pairSymbolsTag));
 int  refLength       = strlen(referenceText);
 int  foldLength      = strlen(fold);
 
 
 /* Adjust fold to gap structure in referenceText */
 adjFold = gapAdjustFold(fold, referenceText);
 
 /* make arrays for color formatting */
 N = slCount(maf->components);
 AllocArray(mafColorFormats, N);
 for (i = 0; i < N; i++)
     AllocArray(mafColorFormats[i], refLength);
 fold2pairingList(adjFold, refLength, &pairList);
 
 for (mc = maf->components, i = 0; mc != NULL; mc = mc->next, i++)
     markCompensatoryMutations(mc->text, referenceText, pairList, mafColorFormats[i]);
 defineMafSubstColors(&mafColors);
 
 /* Make pos string */
 posString = needMem(foldLength + 1);
 mkPosString(posString, foldLength);
 adjPosString = gapAdjustFold(posString, referenceText);
 
 /* Make a symbol string indicating pairing partner */
 pairSymbols = (char *) needMem(refLength + 1);
 mkPairPartnerSymbols(pairList, pairSymbols, refLength);
 
 /* Make the score string and its colorFormat */
 if (scores)
      {
      scoreString      = mkScoreString(scores, foldLength, referenceText);
      scoreColorFormat = mkScoreColorFormat(scores, foldLength, referenceText);
      }
 
 /* Find max. length of source (species) field. */
 for (mc = maf->components; mc != NULL; mc = mc->next)
     {
     int len = strlen(mc->src)+strlen(hDbOrganism(mc->src)) + 1;
     if (srcChars < len)
         srcChars = len;
     }
 
 /* Pretty print maf and fold */
 fprintf(f, "<PRE><TT>");
 for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd)
     {
     // int size;  unused variable
     char buf[256];
     lineEnd = lineStart + lineSize;
     if (lineEnd >= maf->textSize)
         lineEnd = maf->textSize;
     // size = lineEnd - lineStart;  unused variable
     fprintf(f, "%-*s %.*s\n", srcChars, positionTag, lineSize, adjPosString + lineStart);
     for (mc = maf->components, i = 0; mc != NULL; mc = mc->next, i++)
         {
 	safef(buf, sizeof(buf), "%s/%s", mc->src, hDbOrganism(mc->src));
 	fprintf(f, "%-*s ", srcChars, buf);
 	htmlColorPrintString(f, mc->text + lineStart, mafColorFormats[i] + lineStart, mafColors, lineSize);
 	fprintf(f, "\n");
 	}
     fprintf(f, "%-*s %.*s\n", srcChars, foldTag, lineSize, adjFold + lineStart);
     fprintf(f, "%-*s %.*s\n", srcChars, pairSymbolsTag, lineSize, pairSymbols + lineStart);
     if (scores)
 	{
 	fprintf(f, "%-*s ", srcChars, scoresTag);
 	htmlColorPrintString(f, scoreString + lineStart, scoreColorFormat + lineStart, scoreColors, lineSize);
 	fprintf(f, "\n");
 	}
     fprintf(f, "\n");
     }
 fprintf(f, "</PRE></TT>");
 
 /* clean up*/
 freeMem(posString);
 freeMem(adjPosString);
 freeMem(adjFold);
 freeMem(pairSymbols);
 if (scores)
     {
     freeMem(scoreString);
     freeMem(scoreColorFormat);
     }
 for (i = 0; i < N; i++)
     freeMem(mafColorFormats[i]);
 freeMem(mafColorFormats);
 }
 
 void mafAndFoldLegend(FILE *f)
 /* Print legend for the maf and fold section */
 {
 char *s          = "0123456789";
 int colorFormat[] = {0,1,2,3,4,5,6,7,8,9};
 int colors[]      = {0x999999,0x888888,0x777777,0x666666,0x555555,0x444444,0x333333,0x222222,0x111111,0x000000};
 fprintf(f, "<h3> Color legend </h3>");
 fprintf(f, "<TABLE BORDER=0>");
 fprintf(f, "<TR> <TD style='color:#%06X;'> GRAY:       </TD> "
            "<TD> Not part of annotated pair, no substitution. <BR>             </TD> </TR>",
            LTGRAY);
 fprintf(f, "<TR> <TD style='color:#%06X;'> LT. PURPLE: </TD> "
            "<TD> Not part of annotated pair, substitution. <BR>                </TD> </TR>",
            LTPURPLE);
 fprintf(f, "<TR> <TD style='color:#%06X;'> BLACK:      </TD> "
            "<TD> Compatible with annotated pair, no substitutions.<BR>         </TD> </TR>",
            BLACK);
 fprintf(f, "<TR> <TD style='color:#%06X;'> BLUE:       </TD> "
            "<TD> Compatible with annotated pair, single substitution.<BR>      </TD> </TR>",
            BLUE);
 fprintf(f, "<TR> <TD style='color:#%06X;'> GREEN:      </TD> "
            "<TD> Compatible with annotated pair, double substitution.<BR>      </TD> </TR>",
            GREEN);
 fprintf(f, "<TR> <TD style='color:#%06X;'> RED:        </TD> "
            "<TD> Not compatible with annotated pair, single substitution. <BR> </TD> </TR>",
            RED);
 fprintf(f, "<TR> <TD style='color:#%06X;'> ORANGE:     </TD> "
            "<TD> Not compatible with annotated pair, double substitution. <BR> </TD> </TR>",
            ORANGE);
 fprintf(f, "<TR> <TD style='color:#%06X;'> MAGENTA:    </TD> "
            "<TD> Not compatible with annotated pair, involves gap. <BR>        </TD> </TR>",
            MAGENTA);
 fprintf(f, "</TABLE>");
 /* Score legend */
 fprintf(f, "<BR>SCORE:   min ");
 htmlColorPrintString(f, s, colorFormat, colors, 0);
 fprintf(f, " max");
 }
 
 struct mafAli *mafFromRnaSecStrItem(char *mafTrack, struct rnaSecStr *item)
 {
 struct mafAli *maf;
 maf = hgMafFrag(database, mafTrack, item->chrom, item->chromStart, item->chromEnd, item->strand[0], NULL, NULL);
 return maf;
 }
 
 void mafSortBySpeciesOrder(struct mafAli *maf, char *speciesOrder)
 /* Sort maf components by species. Excised from mafClick.c. */
 {
 int speciesCt;
 char *species[256];
 struct mafComp **newOrder, *mcThis;
 int i;
 int mcCount;
 
 mcCount = 0;
 speciesCt = chopLine(cloneString(speciesOrder), species);
 newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *));
 newOrder[mcCount++] = maf->components;
 
 for (i = 0; i < speciesCt; i++)
   {
     if ((mcThis = mafMayFindCompSpecies(maf, species[i], '.')) == NULL)
 	continue;
     newOrder[mcCount++] = mcThis;
   }
 
 maf->components = NULL;
 for (i = 0; i < mcCount; i++)
   {
     newOrder[i]->next = 0;
     slAddHead(&maf->components, newOrder[i]);
   }
 
 slReverse(&maf->components);
 }
 
 void htmlPrintSecStr(FILE *f, char *table, struct rnaSecStr *item, int start)
 /* Print out the details for an rnaStruct* table. */
 {
 // grab the sequence
 struct dnaSeq *seq = hChromSeq(database, item->chrom, item->chromStart, item->chromEnd);
 touppers(seq->dna);
 if (item->strand[0] == '-')
     reverseComplement(seq->dna, seq->size);
 toRna(seq->dna);
 
 // make sure the dna is not longer than the paren string
 seq->dna[strlen(item->secStr)] = 0;
 
 char *rnaPlotPath = cfgOptionDefault("rnaPlotPath", "../cgi-bin/RNAplot");
 mkdirTrashDirectory(table);
 
 char psName[512];
 safef(psName, sizeof(psName), "../trash/%s/%s_%s.ps", table, table, item->name);
 char *plotCmd[] = {rnaPlotPath, NULL};
 struct pipeline *plStruct = pipelineOpen1(plotCmd, pipelineWrite | pipelineNoAbort, "/dev/null", NULL, 0);
 FILE *of = pipelineFile(plStruct);
 if (of != NULL)
     {
     fprintf(of, ">%s\n", psName);        /* This tells where to put file. */
     fprintf(of, "%s\n%s\n", seq->dna, item->secStr);
     }
 pipelineClose(&plStruct);
 
 char pngName[256];
 char *rootName = cloneString(psName);
  
 chopSuffix(rootName);
 safef(pngName, sizeof(pngName), "%s.png", rootName);
 
 char outputBuf[1024];
 safef(outputBuf, sizeof outputBuf, "-sOutputFile=%s", pngName);
 char *pipeCmd[] = {"gs", "-sDEVICE=png16m", outputBuf, "-dBATCH","-dNOPAUSE","-q", psName, NULL};
 struct pipeline *pl = pipelineOpen1(pipeCmd, pipelineWrite | pipelineNoAbort, "/dev/null", NULL, 0);
 int sysRet = pipelineWait(pl);
-if (sysRet != 0)
-    errAbort("System call returned %d for:\n  %s", sysRet, pipelineDesc(pl));
 
 printf("<a target=blank href='http://pseudoviewer.inha.ac.kr/WSPV_quickSender.asp?seq=%s&str=%s&start=%d'>Display on PseudoViewer</a><BR>", seq->dna, item->secStr, start);
 htmlHorizontalLine();
+if (sysRet != 0)
+    {
+    /* Always fires today: RNAplot truncates the sequence id we hand it to 42
+     * characters and appends "_ss.ps", and psName's directory prefix is already 41
+     * characters, so RNAplot writes rnaStructRangan_<one letter>_ss.ps and gs is
+     * pointed at a file that was never created.  Drop just the diagram; the rest of
+     * the page is still worth showing.  refs #37424 */
+    printf("RNAFold diagram could not be made.<BR>");
+    warn("Could not make the RNA fold diagram: system call returned %d for:\n  %s",
+        sysRet, pipelineDesc(pl));
+    }
+else
+    {
     printf("RNAFold diagram:<BR>");
     printf("<IMG SRC='%s' border = '2'>", pngName);
     }
+}
 
 void htmlPrintSecStrEvofoldDrawing(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/evoFold/%s/%s.png",
        database, item->chrom, item->name);
 if (fileExists(fileName))
     {
     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>.", "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))
     {
     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>.", "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 = trackDbSetting(tdb, "mafTrack");
 int start = cartInt(cart, "o");
 struct mafAli *maf = NULL;
 char option[128];
 char *speciesOrder = NULL;
 boolean hasConf = sqlColumnExists(conn, table, "conf");
 
 /* print header */
 genericHeader(tdb, itemName);
 /* printRfamUrl(itemName); */
 genericBedClick(conn, tdb, itemName, start, 6);
 
 /* get the rnaSecStr and maf from db */
 sqlSafef(extraWhere, sizeof extraWhere, "chromStart = %d and name = '%s'", start, itemName);
 sr   = hExtendedChromQuery(conn, table, seqName, extraWhere,  FALSE, NULL, &rowOffset);
 row  = sqlNextRow(sr);
 if (hasConf)
     item = rnaSecStrLoadConf(row + rowOffset);
 else
     item = rnaSecStrLoad(row + rowOffset);
 if (mafTrack)
     {
     htmlHorizontalLine();
     maf  = mafFromRnaSecStrItem(mafTrack, item);
 
     /* order maf by species */
     safef(option, sizeof(option), "%s.speciesOrder", tdb->track);
     speciesOrder = cartUsualString(cart, option, NULL);
     if (speciesOrder == NULL)
       speciesOrder = trackDbSetting(tdb, "speciesOrder");
     if (speciesOrder)
       mafSortBySpeciesOrder(maf, speciesOrder);
 
     mafAndFoldHeader(stdout);
     htmlPrintMafAndFold(stdout, maf, item->secStr, item->conf, 100);
 
     mafAndFoldLegend(stdout);
     }
 
 /* Draw structure for rnaStruct* table */
 if (startsWith("rnaStruct", tdb->table))
     {
     htmlHorizontalLine();
     htmlPrintSecStr(stdout, tdb->table, item, start);
     }
 if (sameWord(tdb->table, "evofold"))
     {
     htmlHorizontalLine();
     htmlPrintSecStrEvofoldDrawing(stdout, item);
     }
 
 /* Draw structure for evoFoldV2 */
 if (sameWord(tdb->table, "evofoldV2"))
     {
     htmlHorizontalLine();
     htmlPrintSecStrEvofoldV2Drawing(stdout, item);
     }
 
 /* track specific html */
 printTrackHtml(tdb);
 
 /* clean up */
 mafAliFree(&maf);
 rnaSecStrFree(&item);
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }