\n", descrBySql); else dyStringPrintf(description, "%s
\n", "No description available"); freez(&descrBySql); if (summaryTables != NULL) { if (sqlTablesExist(conn, summaryTables)) { char *summary = genoQuery(id, "summarySql", conn); if (summary != NULL && summary[0] != 0) { summary = abbreviateRefSeqSummary(summary); dyStringPrintf(description, "%s", genomeSetting("summarySource")); if (genomeOptionalSetting("summaryIdSql")) { char *summaryId = genoQuery(id, "summaryIdSql", conn); if (summaryId != NULL) dyStringPrintf(description, " (%s)", summaryId); } dyStringPrintf(description, ": %s", summary); freez(&summary); dyStringPrintf(description, "
\n"); } } } return dyStringCannibalize(&description); } static char *getGencodeGeneId(struct sqlConnection *conn, char *id, char *buffer, int bufSize) { char query[256]; sqlSafef(query, sizeof(query), "select protein from knownCanonical c, knownIsoforms i where i.clusterId=c.clusterId and i.transcript='%s'" ,id); return sqlQuickQuery(conn, query, buffer, bufSize ); } static void printDescription(char *id, struct sqlConnection *conn, struct trackDb *tdb) /* Print out description of gene given ID. */ { char *description = descriptionString(id, conn); int i, exonCnt = 0, cdsExonCnt = 0; int cdsStart, cdsEnd; hPrintf("%s", description); freez(&description); /* print genome position and size */ char buffer[1024]; char *commaPos; if (isGencode || isGencode2 || isGencode3) { hPrintf("Gencode Transcript: %s
\n", isGencode2 || isGencode3 ? curGeneId : curAlignId);; char buffer[1024]; hPrintf("Gencode Gene: %s
\n", getGencodeGeneId(conn, curGeneId, buffer, sizeof buffer)); } exonCnt = curGenePred->exonCount; safef(buffer, sizeof buffer, "%s:%d-%d", curGeneChrom, curGeneStart+1, curGeneEnd); commaPos = addCommasToPos(database, buffer); hPrintf("Transcript (Including UTRs)
\n"); hPrintf(" Position: %s %s ",trackHubSkipHubName(database), commaPos); sprintLongWithCommas(buffer, (long long)curGeneEnd - curGeneStart); hPrintf("Size: %s ", buffer); hPrintf("Total Exon Count: %d ", exonCnt); hPrintf("Strand: %s
\n",curGenePred->strand); cdsStart = curGenePred->cdsStart; cdsEnd = curGenePred->cdsEnd; /* count CDS exons */ if (cdsStart < cdsEnd) { for (i=0; i
\n"); safef(buffer, sizeof buffer, "%s:%d-%d", curGeneChrom, cdsStart+1, cdsEnd); commaPos = addCommasToPos(database, buffer); hPrintf(" Position: %s %s ",trackHubSkipHubName(database), commaPos); sprintLongWithCommas(buffer, (long long)cdsEnd - cdsStart); hPrintf("Size: %s ", buffer); hPrintf("Coding Exon Count: %d \n", cdsExonCnt); } fflush(stdout); } char *sectionSetting(struct section *section, char *name) /* Return section setting value if it exists. */ { return hashFindVal(section->settings, name); } char *sectionRequiredSetting(struct section *section, char *name) /* Return section setting. Squawk and die if it doesn't exist. */ { char *res = sectionSetting(section, name); if (res == NULL) errAbort("Can't find required %s field in %s in settings.ra", name, section->name); return res; } boolean sectionAlwaysExists(struct section *section, struct sqlConnection *conn, char *geneId) /* Return TRUE - for sections that always exist. */ { return TRUE; } void sectionPrintStub(struct section *section, struct sqlConnection *conn, char *geneId) /* Print out coming soon message for section. */ { hPrintf("coming soon!"); } struct section *sectionNew(struct hash *sectionRa, char *name) /* Create a section loading all but methods part from the * sectionRa. */ { struct section *section = NULL; struct hash *settings = hashFindVal(sectionRa, name); if (settings != NULL) { AllocVar(section); section->settings = settings; section->name = sectionSetting(section, "name"); section->shortLabel = sectionRequiredSetting(section, "shortLabel"); section->longLabel = sectionRequiredSetting(section, "longLabel"); section->priority = atof(sectionRequiredSetting(section, "priority")); section->exists = sectionAlwaysExists; section->print = sectionPrintStub; } return section; } int sectionCmpPriority(const void *va, const void *vb) /* Compare to sort sections based on priority. */ { const struct section *a = *((struct section **)va); const struct section *b = *((struct section **)vb); float dif = a->priority - b->priority; if (dif < 0) return -1; else if (dif > 0) return 1; else return 0; } static void addGoodSection(struct section *section, struct sqlConnection *conn, struct section **pList) /* Add section to list if it is non-null and exists returns ok. */ { //uglyf("
adding %s section \n", section->name);fflush(stdout); if (section == NULL || hashLookup(section->settings, "hide") != NULL) return; long startTime = clock1000(); if (section->exists(section, conn, curGeneId)) { section->checkTime = clock1000() - startTime; slAddHead(pList, section); } } struct section *loadSectionList(struct sqlConnection *conn) /* Load up section list - first load up sections.ra, and then * call each section loader. */ { struct hash *sectionRa = NULL; struct section *sectionList = NULL; readRa("section.ra", §ionRa); // Could be an ajax request for a single section! char *ajaxSection = cartOptionalString(cart, hggAjaxSection); if (ajaxSection != NULL) { // Currently only one section supports ajax update. if (sameString(ajaxSection,HGG_GENE_ALLELES)) { addGoodSection(allelesSection(conn, sectionRa), conn, §ionList); return sectionList; } } addGoodSection(linksSection(conn, sectionRa), conn, §ionList); addGoodSection(otherOrgsSection(conn, sectionRa), conn, §ionList); addGoodSection(malaCardsSection(conn, sectionRa), conn, §ionList); addGoodSection(ctdSection(conn, sectionRa), conn, §ionList); /*if (isRgdGene(conn)) { addGoodSection(ctdRgdGene2Section(conn, sectionRa), conn, §ionList); } else { addGoodSection(ctdSection(conn, sectionRa), conn, §ionList); } */ addGoodSection(rgdGeneRawSection(conn, sectionRa), conn, §ionList); addGoodSection(gtexSection(conn, sectionRa), conn, §ionList); /* temporarily disable microarray section for Zebrafish, until a bug is fixed */ if (strstr(database, "danRer") == NULL) { addGoodSection(microarraySection(conn, sectionRa), conn, §ionList); } addGoodSection(rnaStructureSection(conn, sectionRa), conn, §ionList); addGoodSection(domainsSection(conn, sectionRa), conn, §ionList); addGoodSection(altSpliceSection(conn, sectionRa), conn, §ionList); // addGoodSection(multipleAlignmentsSection(conn, sectionRa), conn, §ionList); addGoodSection(primersSection(conn, sectionRa), conn, §ionList); addGoodSection(swissProtCommentsSection(conn, sectionRa), conn, §ionList); addGoodSection(flyBaseRolesSection(conn, sectionRa), conn, §ionList); addGoodSection(flyBasePhenotypesSection(conn, sectionRa), conn, §ionList); addGoodSection(flyBaseSynonymsSection(conn, sectionRa), conn, §ionList); addGoodSection(bdgpExprInSituSection(conn, sectionRa), conn, §ionList); addGoodSection(goSection(conn, sectionRa), conn, §ionList); addGoodSection(gencodeSection(conn, sectionRa), conn, §ionList); addGoodSection(infoSection(conn, sectionRa), conn, §ionList); addGoodSection(methodSection(conn, sectionRa), conn, §ionList); addGoodSection(localizationSection(conn, sectionRa), conn, §ionList); addGoodSection(transRegCodeMotifSection(conn, sectionRa), conn, §ionList); addGoodSection(pathwaysSection(conn, sectionRa), conn, §ionList); addGoodSection(mrnaDescriptionsSection(conn, sectionRa), conn, §ionList); //addGoodSection(pseudoGeneSection(conn, sectionRa), conn, §ionList); addGoodSection(synonymSection(conn, sectionRa), conn, §ionList); addGoodSection(geneReviewsSection(conn, sectionRa), conn, §ionList); addGoodSection(allelesSection(conn, sectionRa), conn, §ionList); // addGoodSection(xyzSection(conn, sectionRa), conn, §ionList); slSort(§ionList, sectionCmpPriority); return sectionList; } void printIndex(struct section *sectionList) /* Print index to section. */ { int maxPerRow = 6, itemPos = 0; int rowIx = 0; struct section *section; hPrintf("
\n"); hPrintf("
\n"); webPrintLinkTableStart(); webPrintLabelCell("Page Index"); itemPos += 1; for (section=sectionList; section != NULL; section = section->next) { if (++itemPos > maxPerRow) { hPrintf("
printing %s section\n", section->name);fflush(stdout); dyStringPrintf(header, "", section->name); dyStringPrintf(header, "
section, check time, print time, total
\n");
for (section = sectionList; section != NULL; section = section->next)
{
boolean isOpen = sectionIsOpen(section);
int sectionTime = section->checkTime + section->printTime;
printf("%s, %d, %d, %d %s
\n", section->shortLabel, section->checkTime, section->printTime,
sectionTime, isOpen ? "" : "closed");
total += sectionTime;
}
printf("total = %d\n", total);
printf("