static void transformToCanonical(struct searchResult *list,
struct sqlConnection *conn)
/* Transform search results to canonical versions. */
{
struct dyString *dy = newDyString(1024);
char *cannon = genomeSetting("canonicalTable");
char *isoform = genomeSetting("isoformTable");
struct sqlResult *sr;
char **row;
struct searchResult *el;
for (el = list; el != NULL; el = el->next)
{
dyStringClear(dy);
sqlDyStringPrintf(dy,
"select %s.transcript,%s.chrom,%s.chromStart,%s.chromEnd,%s.protein ",
cannon, cannon, cannon, cannon, cannon);
sqlDyStringPrintf(dy,
"from %s,%s ",
isoform, cannon);
sqlDyStringPrintf(dy,
"where %s.transcript = '%s' ",
isoform, el->gp.name);
sqlDyStringPrintf(dy,
"and %s.clusterId = %s.clusterId",
isoform, cannon);
sr = sqlGetResult(conn, dy->string);
if ((row = sqlNextRow(sr)) != NULL)
genePosFillFrom5(&el->gp, row);
sqlFreeResult(&sr);
}
dyStringFree(&dy);
}
struct genePos *knownPosAll(struct sqlConnection *conn)
/* Get all positions in knownGene table. */
{
char query[1024];
// just for side-effect of adding NOSQLINJ prefix
if (showOnlyCanonical())
sqlSafef(query, sizeof query, "%-s", genomeSetting("allGeneQuery"));
else
sqlSafef(query, sizeof query, "%-s", genomeSetting("allTranscriptQuery"));
return genePosFromQuery(conn, query, FALSE);
}
struct genePos *knownPosOne(struct sqlConnection *conn, char *name)
/* Get all positions of named gene. */
{
char query[1024];
sqlSafef(query, sizeof(query), genomeSetting("oneGeneQuery"), name);
return genePosFromQuery(conn, query, FALSE);
}
static struct genePos *findKnownAccessions(struct sqlConnection *conn,
char *search)
/* Return list of known accessions. */
{
search = transcriptToCanonical(conn, search);
return findGenePredPos(conn, genomeSetting("geneTable"), search);
}
static struct genePred *getCurGenePred(struct sqlConnection *conn)
/* Return current gene in genePred. */
{
char *track = genomeSetting("knownGene");
char table[HDB_MAX_TABLE_STRING];
boolean hasBin;
char query[256];
struct sqlResult *sr;
char **row;
struct genePred *gp = NULL;
if (!hFindSplitTable(sqlGetDatabase(conn), curGeneChrom, track, table, sizeof table, &hasBin))
errAbort("track %s not found", track);
bool hasAttrId = sqlColumnExists(conn, table, "alignId");
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s' "
"and chrom = '%s' and txStart=%d and txEnd=%d"
, table, curGeneId, curGeneChrom, curGeneStart, curGeneEnd);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
gp = genePredLoad(row + hasBin);
#define ALIGNIDFIELD 11 // Gencode Id
if (hasAttrId)
curAlignId = cloneString(row[ALIGNIDFIELD]);
else
curAlignId = gp->name;
}
sqlFreeResult(&sr);
if (gp == NULL)
errAbort("getCurGenePred: Can't find %s", query);
return gp;
}
static void showMrnaFromGenePred(struct sqlConnection *conn,
char *geneId, char *geneName)
/* Get mRNA sequence for gene from gene prediction. */
{
char *table = genomeSetting("knownGene");
struct sqlResult *sr;
char **row;
char query[256];
boolean hasBin = hIsBinned(sqlGetDatabase(conn), table);
hPrintf("<TT><PRE>");
safef(query, sizeof(query),
"select * from %s where name='%s'"
" and chrom='%s' and txStart=%d and txEnd=%d",
table, geneId, curGeneChrom, curGeneStart, curGeneEnd);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
struct genePred *gene = genePredLoad(row+hasBin);
struct bed *bed = bedFromGenePred(gene);
struct dnaSeq *seq = hSeqForBed(sqlGetDatabase(conn), bed);
hPrintf(">%s (%s predicted mRNA)\n", geneId, geneName);
writeSeqWithBreaks(stdout, seq->dna, seq->size, 50);
dnaSeqFree(&seq);
bedFree(&bed);
genePredFree(&gene);
}
else
errAbort("Couldn't find %s at %s:%d-%d", geneId,
curGeneChrom, curGeneStart, curGeneEnd);
sqlFreeResult(&sr);
hPrintf("</TT></PRE>");
}
static void showSeq(struct sqlConnection *conn, char *geneId,
char *geneName, char *tableId)
/* Show some sequence. */
{
char *table = genomeSetting(tableId);
showSeqFromTable(conn, geneId, geneName, table);
}
void setupColumnKnownPos(struct column *col, char *parameters)
/* Set up column that links to genome browser based on known gene
* position. */
{
genePredPosMethods(col, genomeSetting("geneTable"));
col->cellVal = knownPosCellVal;
}
static char *transcriptToCanonical(struct sqlConnection *conn, char *transcript)
/* Translate transcript to canonical ID if possible, otherwise just return
* a copy of transcript. */
{
struct dyString *dy = newDyString(1024);
char *cannon = genomeSetting("canonicalTable");
char *isoform = genomeSetting("isoformTable");
char buf[128];
char *result = NULL;
sqlDyStringPrintf(dy, "select %s.transcript from %s,%s where %s.transcript = '%s'",
cannon, isoform, cannon, isoform, transcript);
sqlDyStringPrintf(dy, " and %s.clusterId = %s.clusterId", isoform, cannon);
result = sqlQuickQuery(conn, dy->string, buf, sizeof(buf));
if (result != NULL)
return(cloneString(result));
else
return(cloneString(transcript));
}
void doKgMethod()
/* display knownGene.html content (UCSC Known Genes
* Method, Credits, and Data Use Restrictions) */
{
cartWebStart(cart, database, "Methods, Credits, and Use Restrictions");
struct trackDb *tdb = hTrackDbForTrack(database, genomeSetting("knownGene"));
hPrintf("%s", tdb->html);
cartWebEnd();
}
char *genoQuery(char *id, char *settingName, struct sqlConnection *conn)
/* Look up sql query in genome.ra given by settingName,
* plug id into it, and return. */
{
char query[256];
char *sql = genomeSetting(settingName);
sqlSafef(query, sizeof(query), sql, id);
return sqlQuickString(conn, query);
}
struct genePos *knownPosFirst(struct sqlConnection *conn)
/* Get first gene in known gene table. */
{
char query[1024];
// just for side-effect of adding NOSQLINJ prefix
sqlSafef(query, sizeof query, "%-s", genomeSetting("allGeneQuery"));
struct genePos *gp = genePosFromQuery(conn, query, TRUE);
return gp;
}
void webMain(struct sqlConnection *conn)
/* Set up fancy web page with hotlinks bar and
* sections. */
{
struct section *sectionList = NULL;
printDescription(curGeneId, conn);
sectionList = loadSectionList(conn);
printIndex(sectionList);
struct trackDb *tdb = hTrackDbForTrack(database, genomeSetting("knownGene"));
printUpdateTime(database, tdb, NULL);
printSections(sectionList, conn, curGeneId);
}
static char *findGeneId(struct sqlConnection *conn, char *name)
/* Given some sort of gene name, see if it is in our primary gene table, and if not
* look it up in alias table if we have one. */
{
/* Just check if it's in the main gene table, and if so return input name. */
char *mainTable = genomeSetting("knownGene");
char query[256];
sqlSafef(query, sizeof(query), "select count(*) from %s where name = '%s'", mainTable, name);
if (sqlQuickNum(conn, query) > 0)
return name;
else
{
/* check OMIM gene symbol table first */
if (sqlTableExists(conn, "omimGeneSymbol"))
{
sqlSafef(query, sizeof(query), "select geneSymbol from omimGeneSymbol where geneSymbol= '%s'", name);
char *symbol = sqlQuickString(conn, query);
if (symbol != NULL)
{
sqlSafef(query, sizeof(query), "select kgId from kgXref where geneSymbol = '%s'", symbol);
char *kgId = sqlQuickString(conn, query);
if (kgId != NULL)
{
/* The canonical gene is preferred */
sqlSafef(query, sizeof(query),
"select c.transcript from knownCanonical c,knownIsoforms i where i.transcript = '%s' and i.clusterId=c.clusterId", kgId);
char *canonicalKgId = sqlQuickString(conn, query);
if (canonicalKgId != NULL)
{
return canonicalKgId;
}
else
return(kgId);
}
}
}
}
char *alias = genomeOptionalSetting("kgAlias");
if (alias != NULL && sqlTableExists(conn, alias))
{
sqlSafef(query, sizeof(query), "select kgID from %s where alias = '%s'", alias, name);
char *id = sqlQuickString(conn, query);
if (id == NULL)
hUserAbort("Couldn't find %s in %s.%s or %s.%s", name, database, mainTable, database, alias);
return id;
}
else
hUserAbort("Couldn't find %s in %s.%s", name, database, mainTable);
return NULL;
}
void printGenomicSeqLink(struct sqlConnection *conn, char *geneId,
char *chrom, int start, int end)
/* Figure out known genes table, position of gene, link it. */
{
char *table = genomeSetting("knownGene");
webPrintWideCellStart(3, HG_COL_TABLE);
printGenomicAnchor(table, geneId, chrom, start, end);
hPrintf("Genomic Sequence (%s:", chrom);
printLongWithCommas(stdout, start+1);
hPrintf("-");
printLongWithCommas(stdout, end);
hPrintf(")</A>");
webPrintLinkCellEnd();
}
void doOtherProteinAli(struct sqlConnection *conn,
char *localId, char *localName)
/* Put up page that shows alignment between this protein sequence
* and other species. */
{
char *otherTable = cartString(cart, hggOtherPepTable);
char *otherId = cartString(cart, hggOtherId);
char *localTable = genomeSetting("knownGenePep");
bioSeq *localSeq = getSeq(conn, localTable, localId);
bioSeq *otherSeq = getSeq(conn, otherTable, otherId);
if (localSeq != NULL && otherSeq != NULL)
{
struct axtScoreScheme *ss = axtScoreSchemeProteinDefault();
if (axtAffineSmallEnough(localSeq->size, otherSeq->size))
{
struct axt *axt = axtAffine(localSeq, otherSeq, ss);
hPrintf("<TT><PRE>");
if (axt != NULL)
{
printf("ID (including gaps) %3.1f%%, coverage (of both) %3.1f%%, score %d\n",
axtIdWithGaps(axt)*100,
axtCoverage(axt, localSeq->size, otherSeq->size)*100,
axt->score);
printf("Alignment between %s (top %s %daa) and\n",
localName, localSeq->name, localSeq->size);
printf("%s homolog (bottom %s %daa)\n",
otherTable, otherSeq->name, otherSeq->size);
printf("\n");
axtPrintTraditional(axt, 60, ss, stdout);
axtFree(&axt);
}
else
{
printf("%s and %s don't align\n", localSeq->name, otherSeq->name);
}
hPrintf("</PRE></TT>");
}
else
{
printf("Sorry, %s (%d amino acids) and %s (%d amino acids) are too big to align",
localSeq->name, localSeq->size, otherSeq->name, otherSeq->size);
}
}
else
{
warn("Couldn't get sequences, database out of sync?");
}
}
char *getSwissProtAcc(struct sqlConnection *conn, struct sqlConnection *spConn,
char *geneId)
/* Look up SwissProt id. Return NULL if not found. FreeMem this when done.
* spConn is existing SwissProt database conn. May be NULL. */
{
char *proteinSql = genomeSetting("proteinSql");
char query[256];
char *someAcc, *primaryAcc = NULL;
if (isRgdGene(conn))
{
return(getRgdGeneUniProtAcc(curGeneId, conn));
}
sqlSafef(query, sizeof(query), proteinSql, geneId);
someAcc = sqlQuickString(conn, query);
if (someAcc == NULL || someAcc[0] == 0)
return NULL;
primaryAcc = spFindAcc(spConn, someAcc);
freeMem(someAcc);
return primaryAcc;
}
void sequenceTablePrint(struct section *section, struct sqlConnection *conn,
char *geneId)
/* Print the sequence table. */
{
char *table = genomeSetting("knownGene");
struct dyString *query = newDyString(0);
char **row;
struct sqlResult *sr;
char *chrom;
int start,end;
/* Print the current position. */
webPrintLinkTableStart();
printGenomicSeqLink(conn, geneId, curGeneChrom, curGeneStart, curGeneEnd);
printMrnaSeqLink(conn,geneId);
printProteinSeqLink(conn,geneId);
webPrintLinkTableEnd();
/* Print out any additional positions. */
dyStringPrintf(query, "select chrom,txStart,txEnd from %s", table);
dyStringPrintf(query, " where name = '%s'", curGeneId);
dyStringPrintf(query, " and (chrom != '%s'", curGeneChrom);
dyStringPrintf(query, " or txStart != %d", curGeneStart);
dyStringPrintf(query, " or txEnd != %d)", curGeneEnd);
sr = sqlGetResult(conn, query->string);
while ((row = sqlNextRow(sr)) != NULL)
{
struct sqlConnection *conn2 = hAllocConn(database);
chrom = row[0];
start = atoi(row[1]);
end = atoi(row[2]);
webPrintLinkTableStart();
printGenomicSeqLink(conn2, geneId, chrom, start, end);
webPrintLinkTableEnd();
hFreeConn(&conn2);
}
sqlFreeResult(&sr);
freeDyString(&query);
}
static void getGenePosition(struct sqlConnection *conn)
/* Get gene position from database. */
{
char *table = genomeSetting("knownGene");
char query[256];
struct sqlResult *sr;
char **row;
sqlSafef(query, sizeof(query),
"select chrom,txStart,txEnd from %s where name = '%s'"
, table, curGeneId);
sr = sqlGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
{
curGeneChrom = cloneString(row[0]);
curGeneStart = atoi(row[1]);
curGeneEnd = atoi(row[2]);
}
else
hUserAbort("Couldn't find %s in %s.%s", curGeneId, database, table);
sqlFreeResult(&sr);
}
void printProteinSeqLink(struct sqlConnection *conn, char *geneId)
/* Print out link to fetch protein. */
{
char *table = genomeSetting("knownGenePep");
char query[256];
char title[128];
safef(query, sizeof(query),
"select length(seq) from %s where name='%s'" , table, geneId);
int protSize = sqlQuickNum(conn, query);
if (protSize > 0)
{
safef(title, sizeof(title), "Protein (%d aa)", protSize);
printSeqLink(conn, geneId, "knownGenePep", hggDoGetProteinSeq,
title, 1);
}
else
{
webPrintLinkCellStart();
hPrintf("No protein");
webPrintLinkCellEnd();
}
}
char *descriptionString(char *id, struct sqlConnection *conn)
/* return description as it would be printed in html, can free after use */
{
char *descrBySql = NULL;
char *summaryTables = genomeOptionalSetting("summaryTables");
struct dyString *description = dyStringNew(0);
descrBySql = genoQuery(id, "descriptionSql", conn);
dyStringPrintf(description, "<B>Description:</B> ");
if (descrBySql != NULL)
dyStringPrintf(description, "%s<BR>\n", descrBySql);
else
dyStringPrintf(description, "%s<BR>\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 = abbreviateSummary(summary);
dyStringPrintf(description, "<B>%s",
genomeSetting("summarySource"));
if (genomeOptionalSetting("summaryIdSql"))
{
char *summaryId = genoQuery(id, "summaryIdSql", conn);
if (summaryId != NULL)
dyStringPrintf(description, " (%s)", summaryId);
}
dyStringPrintf(description, ":</B> %s", summary);
freez(&summary);
dyStringPrintf(description, "<BR>\n");
}
}
}
return dyStringCannibalize(&description);
}
struct genePred *getCurGenePred(struct sqlConnection *conn)
/* Return current gene in genePred. */
{
char *track = genomeSetting("knownGene");
char table[64];
boolean hasBin;
char query[256];
struct sqlResult *sr;
char **row;
struct genePred *gp = NULL;
hFindSplitTable(sqlGetDatabase(conn), curGeneChrom, track, table, &hasBin);
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s' "
"and chrom = '%s' and txStart=%d and txEnd=%d"
, table, curGeneId, curGeneChrom, curGeneStart, curGeneEnd);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
gp = genePredLoad(row + hasBin);
sqlFreeResult(&sr);
if (gp == NULL)
errAbort("getCurGenePred: Can't find %s", query);
return gp;
}
static void genePredPosPrint(struct column *col, struct genePos *gp,
struct sqlConnection *conn)
/* Print genome position with hyperlink to browser. */
{
char *pos = col->cellVal(col, gp, conn);
char *chrom;
int start, end;
hPrintf("<TD>");
if (pos == NULL)
hPrintf("n/a");
else
{
char numBuf[32];
hgParseChromRange(database, pos, &chrom, &start, &end);
sprintLongWithCommas(numBuf, (start+end+1)/2);
hPrintf("<A HREF=\"%s?db=%s&position=%s&%s&%s=full\">",
hgTracksName(), database, pos, cartSidUrlString(cart), genomeSetting("geneTable"));
hPrintf("%s %s</A>", chrom, numBuf);
freeMem(pos);
}
hPrintf("</TD>");
}
static void printSeqLink(struct sqlConnection *conn, char *geneId,
char *tableId, char *command, char *label, int colCount)
/* Print out link to mRNA or protein. */
{
char *table = genomeSetting(tableId);
boolean gotHyperlink = FALSE;
webPrintWideCellStart(colCount, HG_COL_TABLE);
if (sqlTableExists(conn, table))
{
char query[512];
safef(query, sizeof(query), "select count(*) from %s where name = '%s'",
table, geneId);
if (sqlExists(conn, query))
{
hPrintf("<A HREF=\"../cgi-bin/hgGene?%s&%s=1&hgg_gene=%s\" class=\"toc\">",
cartSidUrlString(cart), command, geneId);
hPrintf("%s</A>", label);
gotHyperlink = TRUE;
}
}
if (!gotHyperlink)
hPrintf("%s", label);
webPrintLinkCellEnd();
}
void cartMain(struct cart *theCart)
/* We got the persistent/CGI variable cart. Now
* set up the globals and make a web page. */
{
hgBotDelay();
cart = theCart;
getDbAndGenome(cart, &database, &genome, oldVars);
initGenbankTableNames(database);
getGenomeSettings();
if (cartVarExists(cart, hggDoKgMethod))
doKgMethod();
else if (cartVarExists(cart, hggDoTxInfoDescription))
doTxInfoDescription();
else
{
struct sqlConnection *conn = NULL;
char *geneName = cartUsualString(cart, hggGene, NULL);
if (isEmpty(geneName))
{
// Silly googlebots.
hUserAbort("Error: the hgg_gene parameter is missing from the cart and the CGI params.");
}
/* if kgProtMap2 table exists, this means we are doing KG III */
if (hTableExists(database, "kgProtMap2")) kgVersion = KG_III;
conn = hAllocConn(database);
curGeneId = findGeneId(conn, geneName);
getGenePosition(conn);
curGenePred = getCurGenePred(conn);
curGeneName = getGeneName(curGeneId, conn);
spConn = hAllocConn(UNIPROT_DB_NAME);
swissProtAcc = getSwissProtAcc(conn, spConn, curGeneId);
if (isRgdGene(conn)) swissProtAcc=getRgdGeneUniProtAcc(curGeneId, conn);
/* Check command variables, and do the ones that
* don't want to put up the hot link bar etc. */
if (cartVarExists(cart, hggDoGetMrnaSeq))
doGetMrnaSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoWikiTrack))
doWikiTrack(conn);
else if (cartVarExists(cart, hggDoGetProteinSeq))
doGetProteinSeq(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoRnaFoldDisplay))
doRnaFoldDisplay(conn, curGeneId, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinSeq))
doOtherProteinSeq(conn, curGeneName);
else if (cartVarExists(cart, hggDoOtherProteinAli))
doOtherProteinAli(conn, curGeneId, curGeneName);
else
{
/* Default case - start fancy web page. */
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
struct trackDb *tdb = hTrackDbForTrack(database, genomeSetting("knownGene"));
isGencode = trackDbSettingOn(tdb, "isGencode");
isGencode2 = trackDbSettingOn(tdb, "isGencode2");
cartWebStart(cart, database, "%s Gene %s (%s) Description and Page Index",
genome, curGeneName, isGencode2 ? curGeneId : curAlignId);
webMain(conn, tdb);
cartWebEnd();
}
hFreeConn(&spConn);
hFreeConn(&conn);
}
cartRemovePrefix(cart, hggDoPrefix);
}
static void domainsPrint(struct section *section,
struct sqlConnection *conn, char *geneId)
/* Print out protein domains. */
{
char *db = sqlGetDatabase(conn);
struct slName *el, *list;
list = spExtDbAcc1List(spConn, swissProtAcc, "Interpro");
if (list != NULL)
{
char query[256], **row, **row2;
struct sqlResult *sr, *sr2;
hPrintf("<B>InterPro Domains: </B> ");
hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/protein/%s\" TARGET=_blank>",
swissProtAcc);
hPrintf("Graphical view of domain structure</A><BR>");
sqlSafef(query, sizeof(query),
"select extAcc1,extAcc2 from extDbRef,extDb"
" where extDbRef.acc = '%s'"
" and extDb.val = 'Interpro' and extDb.id = extDbRef.extDb"
, swissProtAcc);
sr = sqlGetResult(spConn, query);
while ((row = sqlNextRow(sr)) != NULL)
{
//hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
//hPrintf("%s</A> - %s<BR>\n", row[0], row[1]);
char interPro[256];
char *pdb = hPdbFromGdb(db);
safef(interPro, 128, "%s.interProXref", pdb);
if (hTableExists(db, interPro))
{
sqlSafef(query, sizeof(query),
"select description from %s where accession = '%s' and interProId = '%s'",
interPro, swissProtAcc, row[0]);
sr2 = sqlGetResult(conn, query);
if ((row2 = sqlNextRow(sr2)) != NULL)
{
hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
hPrintf("%s</A> - %s <BR>\n", row[0], row2[0]);
}
sqlFreeResult(&sr2);
}
else
{
hPrintf("<A HREF=\"http://www.ebi.ac.uk/interpro/entry/%s\" TARGET=_blank>", row[0]);
hPrintf("%s</A> - %s<BR>\n", row[0], row[1]);
}
}
hPrintf("<BR>\n");
slFreeList(&list);
}
if (kgVersion == KG_III)
{
/* Do Pfam domains here. */
list = getPfamDomainList(conn, geneId);
if (list != NULL)
{
hPrintf("<B>Pfam Domains:</B><BR>");
for (el = list; el != NULL; el = el->next)
{
char query[256];
char *description;
sqlSafef(query, sizeof(query),
"select description from pfamDesc where pfamAC='%s'", el->name);
description = sqlQuickString(conn, query);
if (description == NULL)
description = cloneString("n/a");
hPrintf("<A HREF=\"http://pfam.xfam.org/family?acc=%s\" TARGET=_blank>",
el->name);
hPrintf("%s</A> - %s<BR>\n", el->name, description);
freez(&description);
}
slFreeList(&list);
hPrintf("<BR>\n");
}
/* Do SCOP domains here */
list = getDomainList(conn, geneId, "Scop");
if (list != NULL)
{
hPrintf("<B>SCOP Domains:</B><BR>");
for (el = list; el != NULL; el = el->next)
{
char query[256];
char *description;
sqlSafef(query, sizeof(query),
"select description from scopDesc where acc='%s'", el->name);
description = sqlQuickString(conn, query);
if (description == NULL)
description = cloneString("n/a");
hPrintf("<A HREF=\"http://scop.berkeley.edu/sunid=%s\" TARGET=_blank>",
el->name);
hPrintf("%s</A> - %s<BR>\n", el->name, description);
freez(&description);
}
slFreeList(&list);
hPrintf("<BR>\n");
}
}
else
{
list = spExtDbAcc1List(spConn, swissProtAcc, "Pfam");
if (list != NULL)
{
char *pfamDescSql = genomeSetting("pfamDescSql");
hPrintf("<B>Pfam Domains:</B><BR>");
for (el = list; el != NULL; el = el->next)
{
char query[256];
char *description;
sqlSafef(query, sizeof(query), pfamDescSql, el->name);
description = sqlQuickString(conn, query);
if (description == NULL)
description = cloneString("n/a");
hPrintf("<A HREF=\"http://pfam.xfam.org/family?acc=%s\" TARGET=_blank>",
el->name);
hPrintf("%s</A> - %s<BR>\n", el->name, description);
freez(&description);
}
slFreeList(&list);
hPrintf("<BR>\n");
}
}
list = spExtDbAcc1List(spConn, swissProtAcc, "PDB");
if (list != NULL)
{
struct sqlConnection *conn2 = sqlConnect(db);
char query[256], **row;
struct sqlResult *sr;
int column = 0, maxColumn=3, rowCount=0;
hPrintf("<B>Protein Data Bank (PDB) 3-D Structure</B><BR>");
sqlSafef(query, sizeof(query),
"select extAcc1,extAcc2 from extDbRef,extDb"
" where extDbRef.acc = '%s'"
" and extDb.val = 'PDB' and extDb.id = extDbRef.extDb"
, swissProtAcc);
sr = sqlGetResult(spConn, query);
hPrintf("<TABLE><TR>\n");
while ((row = sqlNextRow(sr)) != NULL)
{
if (++column > maxColumn)
{
hPrintf("</TR><TR>");
column = 1;
if (rowCount == 0)
{
hPrintf("<TD ALIGN=CENTER COLSPAN=4><I>To conserve bandwidth, only the images from the first %d structures are shown.</I>", maxColumn);
hPrintf("</TR><TR>");
}
++rowCount;
}
hPrintf("<TD>");
hPrintf("<A HREF=\"http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=%s\" TARGET=_blank>", row[0]);
if (rowCount < 1)
hPrintf("<IMG SRC=\"http://www.rcsb.org/pdb/images/%s_asym_r_250.jpg\"><BR>", row[0]);
hPrintf("%s</A> - %s ", row[0], row[1]);
// include links LS-SNP and to launch viewer in PDB chimera
struct tempName chimerax;
lsSnpPdbChimeraSnpAnn(conn, row[0], NULL, &chimerax);
hPrintf(" <A HREF=\"%s\">Chimera</A>", chimerax.forHtml);
if (lsSnpPdbHasPdb(conn2, row[0]))
hPrintf(" <A HREF=\"%s\" TARGET=_blank>LS-SNP</A>", lsSnpPdbGetUrlPdbSnp(row[0], NULL));
hPrintf("</TD>\n");
}
hPrintf("</TR></TABLE>\n");
hPrintf("<A href=\"../goldenPath/help/chimera.html\" TARGET=_blank>Chimera help</A>\n");
hPrintf("<BR><BR>\n");
slFreeList(&list);
sqlDisconnect(&conn2);
}
/* Do modBase link. */
{
hPrintf("<B>ModBase Predicted Comparative 3D Structure on ");
modBaseAnchor(swissProtAcc);
hPrintf("%s", swissProtAcc);
hPrintf("</A></B><BR>\n");
hPrintf("<TABLE><TR>");
hPrintf("<TD>");
modBaseAnchor(swissProtAcc);
hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s\"></A></TD>", swissProtAcc);
hPrintf("<TD>");
modBaseAnchor(swissProtAcc);
hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=x°ree=90\"></A></TD>", swissProtAcc);
hPrintf("<TD>");
modBaseAnchor(swissProtAcc);
hPrintf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=y°ree=90\"></A></TD>", swissProtAcc);
hPrintf("</TR><TR>\n");
hPrintf("<TD ALIGN=CENTER>Front</TD>");
hPrintf("<TD ALIGN=CENTER>Top</TD>");
hPrintf("<TD ALIGN=CENTER>Side</TD>");
hPrintf("</TR></TABLE>\n");
hPrintf("<I>The pictures above may be empty if there is no "
"ModBase structure for the protein. The ModBase structure "
"frequently covers just a fragment of the protein. You may "
"be asked to log onto ModBase the first time you click on the "
"pictures. It is simplest after logging in to just click on "
"the picture again to get to the specific info on that model.</I>");
}
}
char *linkGetUrl(struct link *link, struct sqlConnection *conn,
char *geneId)
/* Return URL string if possible or NULL if not. FreeMem this when done. */
{
char query[512];
struct sqlResult *sr;
char **row;
char *url = NULL;
/* Some special case code here for things that need to
* do more than check a table. */
if (sameString(link->name, "family"))
{
if (!hgNearOk(database))
return NULL;
}
if (sameString(link->name, "protBrowser"))
{
if (!hgPbOk(database))
return NULL;
/* special processing for PB, since we need the protein ID, instead everything key off from gene ID */
/* use UniProt accession instead of displayID, because display ID sometimes changes */
if (swissProtAcc == NULL || swissProtAcc[0] == 0)
return NULL;
if (isRgdGene(conn))
{
safef(query, sizeof(query), "../cgi-bin/pbGlobal?proteinID=%s", swissProtAcc);
}
else
{
safef(query, sizeof(query), "../cgi-bin/pbTracks?db=%s&proteinID=%s", database, swissProtAcc);
}
return(cloneString(query));
}
if (sameString(link->name, "tbSchema"))
{
char *geneTable = genomeSetting("knownGene");
struct trackDb *tdb = hTrackDbForTrack(sqlGetDatabase(conn), geneTable);
struct dyString *dy = NULL;
if (tdb == NULL)
return NULL;
dy = newDyString(256);
dyStringPrintf(dy, link->url, tdb->grp, geneTable, geneTable);
trackDbFree(&tdb);
addLinkExtras(link, dy);
return dyStringCannibalize(&dy);
}
geneId = cloneAndCut(geneId, link->preCutAt);
safef(query, sizeof(query), link->idSql, geneId);
sr = sqlGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL && row[0][0] != 0) /* If not null or empty */
{
struct dyString *dy = newDyString(0);
char *name = cloneAndCut(row[0], link->postCutAt);
dyStringPrintf(dy, link->url, name, row[1], row[2], row[3]);
addLinkExtras(link, dy);
url = dyStringCannibalize(&dy);
freez(&name);
}
sqlFreeResult(&sr);
freeMem(geneId);
return url;
}
