Multiple alignment and RNA secondary structure annotation
");
for (lineStart = 0; lineStart < maf->textSize; lineStart = lineEnd)
{
int size;
lineEnd = lineStart + lineSize;
if (lineEnd >= maf->textSize)
lineEnd = maf->textSize;
size = lineEnd - lineStart;
fprintf(f, "%-*s %.*s\n", srcChars, positionTag, lineSize, adjPosString + lineStart);
for (mc = maf->components, i = 0; mc != NULL; mc = mc->next, i++)
{
fprintf(f, "%-*s ", srcChars, mc->src);
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, "");
/* 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, "Color legend
"); fprintf(f, "| GRAY: | Not part of annotated pair, no substitution. |
| LT. PURPLE: | Not part of annotated pair, substitution. |
| BLACK: | Compatible with annotated pair, no substitutions. |
| BLUE: | Compatible with annotated pair, single substitution. |
| GREEN: | Compatible with annotated pair, double substitution. |
| RED: | Not compatible with annotated pair, single substitution. |
| ORANGE: | Not compatible with annotated pair, double substitution. |
| MAGENTA: | Not compatible with annotated pair, involves gap. |
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 htmlPrintSecStrDrawing(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, "
RNA secondary structure drawing
![\"ERROR:](\"http://genome.ucsc.edu/evoFold/%s/%s/%s.png\")
", fprintf(f,"
![\"ERROR:](\"../evoFold/%s/%s/%s.png\")
", database, item->chrom, item->name); fprintf(f,""); } freeMem(seq); +printf("
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("chromStart, item->chromEnd, cgiEncode(item->name)); +printf("\" TARGET=_blank>%s
", "click here to go to moma.ki.au.dk/genome-mirror."); } 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; char option[128]; char *speciesOrder = NULL; /* print header */ genericHeader(tdb, itemName); /* printRfamUrl(itemName); */ genericBedClick(conn, tdb, itemName, start, 6); htmlHorizontalLine(); /* get the rnaSecStr and maf from db */ sprintf(extraWhere, "chromStart = %d and name = '%s'", start, itemName); sr = hExtendedChromQuery(conn, table, seqName, extraWhere, FALSE, NULL, &rowOffset); row = sqlNextRow(sr); item = rnaSecStrLoad(row + rowOffset); 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 */ +/* Draw structure for evoFold */ +if (sameWord(tdb->table, "evofold")) + { htmlHorizontalLine(); htmlPrintSecStrDrawing(stdout, item); + } /* track specific html */ printTrackHtml(tdb); /* clean up */ mafAliFree(&maf); rnaSecStrFree(&item); sqlFreeResult(&sr); hFreeConn(&conn); }