static void printOtherPars(struct bed *clickedPar, struct bed *pars)
/* pirnt out other pairs of pars, keeping chroms lined up that were not
* selected */
{
webPrintLinkTableNewRow();
webPrintWideCenteredLabelCell("Other PARs", 3);
struct bed *par1;
for (par1 = pars; par1 != NULL; par1 = par1->next->next)
{
webPrintLinkTableNewRow();
if (sameString(par1->chrom, clickedPar->chrom))
printHomPairRow(par1, par1->next);
else
printHomPairRow(par1->next, par1);
}
}
static void rnaStructurePrint(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Print out rnaStructure table. */
{
static boolean firstTime = TRUE;
static char *names[2] =
{"5' UTR", "3' UTR"};
static char *tables[2] = {"foldUtr5", "foldUtr3"};
int side;
if (firstTime)
{
rnaTrashDirsInit(tables, ArraySize(tables));
firstTime = FALSE;
}
webPrintLinkTableStart();
webPrintLabelCell("Region");
webPrintLabelCell("Fold Energy");
webPrintLabelCell("Bases");
webPrintLabelCell("Energy/Base");
webPrintWideCenteredLabelCell("Display As", 3);
for (side = 0; side < ArraySize(names); ++side)
{
char *table = tables[side];
struct sqlResult *sr;
char query[256], **row;
safef(query, sizeof(query), "select * from %s where name = '%s'",
table, geneId);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
struct rnaFold fold;
int bases;
char psName[128];
/* Load fold and save it as postScript. */
rnaFoldStaticLoad(row, &fold);
safef(psName, sizeof(psName), "../trash/%s/%s_%s.ps", table, table, geneId);
if (!fileExists(psName))
{
FILE *f;
f = popen("../cgi-bin/RNAplot", "w");
if (f != NULL)
{
fprintf(f, ">%s\n", psName); /* This tells where to put file. */
fprintf(f, "%s\n%s\n", fold.seq, fold.fold);
pclose(f);
}
}
/* Print row of table, starting with energy terms . */
hPrintf("</TR><TR>");
bases = strlen(fold.seq);
webPrintLinkCell(names[side]);
webPrintLinkCellStart();
hPrintf("%1.2f", fold.energy);
webPrintLinkCellEnd();
webPrintLinkCellStart();
hPrintf("%d", bases);
webPrintLinkCellEnd();
webPrintLinkCellStart();
hPrintf("%1.3f", fold.energy/bases);
webPrintLinkCellEnd();
/* Print link to png image. */
webPrintLinkCellStart();
hPrintf("<A HREF=\"%s?%s&%s=%s&%s=%s&%s=%s\" class=\"toc\" TARGET=_blank>",
geneCgi, cartSidUrlString(cart),
hggMrnaFoldRegion, table,
hggMrnaFoldPs, psName,
hggDoRnaFoldDisplay, "picture");
hPrintf(" Picture ");
hPrintf("</A>");
webPrintLinkCellEnd();
/* Print link to PostScript. */
webPrintLinkCellStart();
hPrintf("<A HREF=\"%s\" class=\"toc\">", psName);
hPrintf(" PostScript ");
hPrintf("</A>");
webPrintLinkCellEnd();
/* Print link to text. */
webPrintLinkCellStart();
hPrintf("<A HREF=\"%s?%s&%s=%s&%s=%s\" class=\"toc\" TARGET=_blank>",
geneCgi, cartSidUrlString(cart),
hggMrnaFoldRegion, table,
hggDoRnaFoldDisplay, "text");
hPrintf(" Text ");
hPrintf("</A>");
webPrintLinkCellEnd();
}
sqlFreeResult(&sr);
}
webPrintLinkTableEnd();
hPrintf("<BR>The RNAfold program from the ");
hPrintf("<A HREF=\"http://www.tbi.univie.ac.at/~ivo/RNA/\" TARGET=_blank>");
hPrintf("Vienna RNA Package</A> is used to perform the ");
hPrintf("secondary structure predictions and folding calculations. ");
hPrintf("The estimated folding energy is in kcal/mol. The more ");
hPrintf("negative the energy, the more secondary structure the RNA ");
hPrintf("is likely to have.");
}
