void jsReloadOnBackButton(struct cart *cart)
/* Add some javascript to detect that the back button (or reload) has been pressed,
* and to resubmit in that case to redraw the page with the latest cart contents. */
// __detectback trick from
// http://siphon9.net/loune/2009/07/detecting-the-back-or-refresh-button-click/
// Yes, I know this along with every other inline <script> here belongs in a .js module
{
jsInlineF(
"document.write(\"<form style='display: none'><input name='__detectback' id='__detectback' "
"value=''></form>\");\n"
"function checkPageBackOrRefresh() {\n"
" if (document.getElementById('__detectback').value) {\n"
" return true;\n"
" } else {\n"
" document.getElementById('__detectback').value = 'been here';\n"
" return false;\n"
" }\n"
"}\n"
"window.onload = function() { "
" if (checkPageBackOrRefresh()) { \n"
" if (window.location.search == '?%s') { \n"
// We already have the hgsid-only URL that we want, reload it.
// (necessary for IE because IE doesn't reload on replace,
// unless window.location and/or window.search changes)
" window.location.reload(true);\n"
" } else { \n"
" window.location.replace('%s?%s');\n"
" } \n"
" } "
"};\n"
, cartSidUrlString(cart), cgiScriptName(), cartSidUrlString(cart));
}
void printCcdsUrl(struct sqlConnection *conn, char *ccdsId)
/* Print out CCDS hgc URL for a gene */
{
printf("../cgi-bin/hgc?%s&g=ccdsGene&i=%s&c=%s&o=%d&l=%d&r=%d&db=%s",
cartSidUrlString(cart), ccdsId, seqName,
winStart, winStart, winEnd, database);
}
void printSections(struct section *sectionList, struct sqlConnection *conn,
char *geneId)
/* Print each section in turn. */
{
struct section *section;
for (section = sectionList; section != NULL; section = section->next)
{
boolean isOpen = sectionIsOpen(section);
char *otherState = (isOpen ? "1" : "0");
char *indicator = (isOpen ? "-" : "+");
char *indicatorImg = (isOpen ? "../images/remove.gif" : "../images/add.gif");
struct dyString *header = dyStringNew(0);
//keep the following line for future debugging need
//printf("<br>printing %s section\n", section->name);fflush(stdout);
dyStringPrintf(header, "<A NAME=\"%s\"></A>", section->name);
char *closeVarName = sectionCloseVar(section->name);
dyStringPrintf(header, "<A HREF=\"%s?%s&%s=%s#%s\" class=\"bigBlue\"><IMG src=\"%s\" alt=\"%s\" class=\"bigBlue\"></A> ",
geneCgi, cartSidUrlString(cart), closeVarName, otherState, section->name, indicatorImg, indicator);
dyStringAppend(header, section->longLabel);
webNewSection("%s",header->string);
if (isOpen)
{
long startTime = clock1000();
section->print(section, conn, geneId);
section->printTime = clock1000() - startTime;
}
else
{
printf("Press \"+\" in the title bar above to open this section.");
}
dyStringFree(&header);
}
}
static void linkToDetailsCellPrint(struct column *col, struct genePos *gp,
struct sqlConnection *conn)
/* Print a link to known genes details page. */
{
char *s = col->cellVal(col, gp, conn);
fillInKnownPos(gp, conn);
hPrintf("<TD>");
hPrintf("<A HREF=\"../cgi-bin/hgGene?%s&%s=%s&%s=%s&%s=%s&%s=%d&%s=%d\">",
cartSidUrlString(cart),
"db", database,
"hgg_gene", gp->name,
"hgg_chrom", gp->chrom,
"hgg_start", gp->start,
"hgg_end", gp->end);
if (s == NULL)
{
hPrintf("n/a");
}
else
{
hPrintEncodedNonBreak(s);
freeMem(s);
}
hPrintf("</A></TD>");
}
void cellSimplePrint(struct column *col, struct subjInfo *si,
struct sqlConnection *conn)
/* This just prints one field from table. */
{
char *s = col->cellVal(col, si, conn);
boolean isSubjID = sameString(col->name,"subjId");
hPrintf("<TD>");
if (s == NULL)
{
hPrintf("N/A");
}
else
{
if (isSubjID)
hPrintf("<A HREF=\"gsidSubj?%s&hgs_subj=%s&submit=Go%c21\">",cartSidUrlString(cart),s, '%');
if (sameString(s,""))
{
freeMem(s);
s = cloneString(" ");
}
if (! (sameString(col->name,"dnaSeqs") || sameString(col->name,"aaSeqs")) )
hPrintNonBreak(s);
else
/* special processing for DNA and protein sequences */
hPrintf("%s", s);
if (isSubjID)
hPrintf("</A>");
freeMem(s);
}
hPrintf("</TD>\n");
}
static void printOurRefseqUrl(FILE *f, char *accession)
/* Print URL for Entrez browser on a nucleotide. */
{
fprintf(f, "../cgi-bin/hgc?%s&g=refGene&i=%s&c=%s&o=%d&l=%d&r=%d&db=%s",
cartSidUrlString(cart), accession, curGeneChrom, curGeneStart, curGeneStart,
curGeneEnd, database);
}
void doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
cart = theCart;
char *db = cartUsualString(cart, "db", hDefaultDb());
cartWebStart(cart, db, "Public Sessions");
/* Not in a form; can't use cartSaveSession() to set up an hgsid input */
printf ("<script>var common = {hgsid:\"%s\"};</script>\n", cartSessionId(cart));
jsIncludeDataTablesLibs();
printf("<p>Sessions allow users to save snapshots of the Genome Browser "
"and its current configuration, including displayed tracks, position, "
"and custom track data. The Public Sessions tool allows users to easily "
"share those sessions that they deem interesting with the rest of the "
"world's researchers. You can add your own sessions to this list by "
"checking the appropriate box on the "
"<a href=\"../cgi-bin/hgSession?%s\">Session Management</a> page.</p>\n"
"<p>See the "
"<a href=\"../goldenPath/help/hgSessionHelp.html\">Sessions User's Guide</a> "
"for more information.\n</p>", cartSidUrlString(cart));
showGalleryTab();
cartWebEnd();
}
static void printCcdsUrlForSrcDb(struct sqlConnection *conn, struct ccdsInfo *ccdsInfo)
/* Print out CCDS hgc URL for a refseq, ensembl, or vega gene, if it
* exists. */
{
printf("../cgi-bin/hgc?%s&g=ccdsGene&i=%s&c=%s&o=%d&l=%d&r=%d&db=%s",
cartSidUrlString(cart), ccdsInfo->ccds, seqName,
winStart, winStart, winEnd, database);
}
void printMgcDetailsUrl(char *acc, int start)
/* print out an URL to link to MGC details pages from another details page in
* the browser.*/
{
// pass zero coordiates for window to indicate this isn't a browser click
printf("../cgi-bin/hgc?%s&g=mgcGenes&o=%d&i=%s&l=0&r=0&db=%s",
cartSidUrlString(cart), start, acc, database);
}
static void addLinkExtras(struct link *link, struct dyString *dy)
/* Add extra identifiers if specified in the .ra. */
{
if (link->useHgsid)
dyStringPrintf(dy, "&%s", cartSidUrlString(cart));
if (link->useDb)
dyStringPrintf(dy, "&db=%s", database);
}
static void transRegCodeAnchor(struct transRegCode *trc)
/* Print anchor to transRegCode details page. */
{
printf("<A HREF=\"../cgi-bin/hgc?%s", cartSidUrlString(cart));
printf("&g=transRegCode");
printf("&i=%s", trc->name);
printf("&o=%d", trc->chromStart);
printf("&c=%s", trc->chrom);
printf("\">");
}
void colSortLink(struct column *col)
/* print link that will activate sorting on the column */
{
char *plusMinus = "%2B"; /* "+" cgi encoded */
if (sameString(orderOn+1,col->name)&&orderOn[0]=='+')
plusMinus = "-";
hPrintf("<A href=\"gisaidTable?org=%s&db=%s&%s&%s=%s%s\" >",
genome, database, cartSidUrlString(cart), orderVarName, plusMinus, col->name);
}
struct serverTable *findServer(char *db, boolean isTrans)
/* Return server for given database. Db can either be
* database name or description. */
{
if (trackHubDatabase(db))
{
struct serverTable *hubSt = trackHubServerTable(db, isTrans);
if (hubSt != NULL)
return hubSt;
errAbort("Cannot get blat server parameters for track hub with database %s\n", db);
}
static struct serverTable st;
struct sqlConnection *conn = hConnectCentral();
char query[256];
struct sqlResult *sr;
char **row;
char dbActualName[32];
/* If necessary convert database description to name. */
sqlSafef(query, sizeof(query), "select name from dbDb where name = '%s'", db);
if (!sqlExists(conn, query))
{
sqlSafef(query, sizeof(query), "select name from dbDb where description = '%s'", db);
if (sqlQuickQuery(conn, query, dbActualName, sizeof(dbActualName)) != NULL)
db = dbActualName;
}
/* Do a little join to get data to fit into the serverTable. */
sqlSafef(query, sizeof(query), "select dbDb.name,dbDb.description,blatServers.isTrans"
",blatServers.host,blatServers.port,dbDb.nibPath "
"from dbDb,blatServers where blatServers.isTrans = %d and "
"dbDb.name = '%s' and dbDb.name = blatServers.db",
isTrans, db);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) == NULL)
{
errAbort("Can't find a server for %s database %s. Click "
"<A HREF=\"/cgi-bin/hgBlat?%s&command=start&db=%s\">here</A> "
"to reset to default database.",
(isTrans ? "translated" : "DNA"), db,
cartSidUrlString(cart), hDefaultDb());
}
st.db = cloneString(row[0]);
st.genome = cloneString(row[1]);
st.isTrans = atoi(row[2]);
st.host = cloneString(row[3]);
st.port = cloneString(row[4]);
st.nibDir = hReplaceGbdbSeqDir(row[5], st.db);
sqlFreeResult(&sr);
hDisconnectCentral(&conn);
return &st;
}
static void printGenomicAnchor(char *table, char *itemName,
char *chrom, int start, int end)
/* Print genomic sequence anchor. */
{
hPrintf("<A HREF=\"%s?%s", hgcName(),
cartSidUrlString(cart));
hPrintf("&g=htcGeneInGenome&i=%s", itemName);
hPrintf("&c=%s&l=%d&r=%d", chrom, start, end);
hPrintf("&o=%s&table=%s", table, table);
hPrintf("\" class=\"toc\">");
}
static void prUcscGenesLinks(struct sqlConnection *conn, struct cloneInfo *ci)
/* generate links to UCSC or known genes */
{
struct geneSimilarities *ucscGenes
= geneSimilaritiesBuildAt(conn, TRUE, ci->acc, seqName, ci->start,
ci->gpTbl, "knownGene");
if (ucscGenes->genes != NULL)
{
/* just use cloest one */
struct genePred *gene = ucscGenes->genes->gene;
webPrintLinkTableNewRow();
webPrintLinkCellStart();
printf("<A href=\"../cgi-bin/hgGene?%s&db=%s&hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=knownGene\">UCSC Gene %s</A>",
cartSidUrlString(cart), database, gene->name, seqName, gene->txStart, gene->txEnd, gene->name);
webPrintLinkCellEnd();
}
geneSimilaritiesFree(&ucscGenes);
}
void doTargetQuery(struct targetPcrServer *server, struct gfPcrInput *gpi,
int maxSize, int minPerfect, int minGood)
/* Send a query to a non-genomic target PCR server and print the results. */
{
struct gfPcrOutput *gpoList;
char seqDir[PATH_LEN];
splitPath(server->targetDb->seqFile, seqDir, NULL, NULL);
if (endsWith("/", seqDir))
seqDir[strlen(seqDir) - 1] = '\0';
gpoList = gfPcrViaNet(server->host, server->port, seqDir, gpi,
maxSize, minPerfect, minGood);
if (gpoList != NULL)
{
struct gfPcrOutput *gpo;
char urlFormat[2048];
printf("The sequences and coordinates shown below are from %s, "
"not from the genome assembly. The links lead to the "
"Genome Browser at the position of the entire target "
"sequence.<BR>\n",
server->targetDb->description);
printf("<TT><PRE>");
for (gpo = gpoList; gpo != NULL; gpo = gpo->next)
{
/* Not used as a format here; we modify the name used for position: */
safef(urlFormat, sizeof(urlFormat), "%s?%s&db=%s&position=%s"
"&hgPcrResult=pack",
hgTracksName(), cartSidUrlString(cart), server->targetDb->db,
pcrResultItemAccession(gpo->seqName));
if (gpo->strand == '-')
printf("<EM>Warning: this amplification is on the reverse-"
"complement of %s</EM>.\n", gpo->seqName);
gfPcrOutputWriteOne(gpo, "fa", urlFormat, stdout);
printf("\n");
}
printf("</PRE></TT>");
writePcrResultTrack(gpoList, server->targetDb->db, server->targetDb->name);
}
else
{
printf("No matches to %s %s in %s", gpi->fPrimer, gpi->rPrimer,
server->targetDb->description);
}
}
void clickOnImage(struct sqlConnection *conn)
/* Handle click on image - calculate position in forward to genome browser. */
{
int x = cartInt(cart, hggClickX);
int y = cartInt(cart, hggClickY);
struct genoLay *gl = ggLayout(conn, linesOfGraphs(), graphsPerLine());
struct genoLayChrom *chrom = genoLayChromAt(gl, x, y);
if (chrom != NULL)
{
int base = gl->basesPerPixel*(x - chrom->x);
int start = base-500000, end=base+500000;
if (start<0) start=0;
printf("Location: ../cgi-bin/hgTracks?db=%s&%s&position=%s:%d-%d&hgGenomeClick=image\r\n\r\n",
database, cartSidUrlString(cart), chrom->fullName, start+1, end);
}
else
{
hggDoUsualHttp();
}
}
void otherOrgPepLink(struct otherOrg *otherOrg, char *command, char *label,
char *id, struct sqlConnection *conn)
/* Print link that will invoke self to work on other organism peptide. */
{
boolean gotIt = FALSE;
webPrintLinkCellStart();
if (id != NULL)
{
if (otherOrg->db != NULL && otherOrg->pepTable != NULL)
{
char dbTable[128];
safef(dbTable, sizeof(dbTable), "%s.%s", otherOrg->db, otherOrg->pepTable);
if (sqlTableExists(conn, dbTable))
{
struct sqlResult *sr;
char **row;
char query[256];
safef(query, sizeof(query), "select seq from %s where name = '%s'",
dbTable, id);
sr = sqlGetResult(conn, query);
if ((row = sqlNextRow(sr)) != NULL)
{
gotIt = TRUE;
hPrintf("<A HREF=\"%s?%s&%s=%s&%s=%s&%s=%s\" class=\"toc\">",
geneCgi, cartSidUrlString(cart),
command, "on",
hggOtherPepTable, dbTable,
hggOtherId, id);
hPrintf("%s", label);
hPrintf("</A>");
}
sqlFreeResult(&sr);
}
}
}
if (!gotIt)
hPrintf(" ");
webPrintLinkCellEnd();
}
static void printCcdsHgGeneUrl(struct sqlConnection *conn, char *ccdsId, char* kgId)
/* output a URL to hgGene for a ccds */
{
char where[128];
struct genePredReader *gpr;
struct genePred *ccdsGene = NULL, *kgGene = NULL;
/* get ccds genePred to get location */
sqlSafefFrag(where, sizeof(where), "chrom = '%s' and name = '%s'", seqName, ccdsId);
gpr = genePredReaderQuery(conn, "ccdsGene", where);
ccdsGene = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
if (ccdsGene == NULL)
errAbort("%s not found in ccdsGene table for chrom %s", ccdsId, seqName);
else if (ccdsGene->next != NULL)
errAbort("multiple %s rows found in ccdsGene table for chrom %s", ccdsId, seqName);
/* get KG genePred, as need exact location for link */
sqlSafefFrag(where, sizeof(where), "name = '%s' and strand = '%s'", kgId,
ccdsGene->strand);
gpr = genePredReaderRangeQuery(conn, "knownGene", seqName,
ccdsGene->txStart, ccdsGene->txEnd, where);
kgGene = genePredReaderAll(gpr);
genePredReaderFree(&gpr);
if (kgGene == NULL)
errAbort("%s not found in knownGene table for chrom %s", kgId, seqName);
else if (kgGene->next != NULL)
errAbort("multiple %s rows found in knownGene table for chrom %s", kgId, seqName);
printf("../cgi-bin/hgGene?%s&%s=%s&%s=%s&%s=%s&%s=%d&%s=%d",
cartSidUrlString(cart),
"db", database,
"hgg_gene", kgId,
"hgg_chrom", seqName,
"hgg_start", kgGene->txStart,
"hgg_end", kgGene->txEnd);
genePredFree(&ccdsGene);
genePredFree(&kgGene);
}
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>");
}
void doQuery(struct pcrServer *server, struct gfPcrInput *gpi,
int maxSize, int minPerfect, int minGood)
/* Send a query to a genomic assembly PCR server and print the results. */
{
struct gfPcrOutput *gpoList =
gfPcrViaNet(server->host, server->port, server->seqDir, gpi,
maxSize, minPerfect, minGood);
if (gpoList != NULL)
{
char urlFormat[2048];
safef(urlFormat, sizeof(urlFormat), "%s?%s&db=%s&position=%%s:%%d-%%d"
"&hgPcrResult=pack",
hgTracksName(), cartSidUrlString(cart), server->db);
printf("<TT><PRE>");
gfPcrOutputWriteAll(gpoList, "fa", urlFormat, "stdout");
printf("</PRE></TT>");
writePcrResultTrack(gpoList, server->db, NULL);
}
else
{
printf("No matches to %s %s in %s %s", gpi->fPrimer, gpi->rPrimer,
server->genome, server->description);
}
}
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();
}
static void printCcds(char *kgId, struct sqlConnection *conn)
/* Print out CCDS ids most closely matching the kg. */
{
struct ccdsGeneMap *ccdsKgs = NULL;
if (sqlTablesExist(conn, "ccdsKgMap"))
ccdsKgs = ccdsGeneMapSelectByGene(conn, "ccdsKgMap", kgId, 0.0);
if (ccdsKgs != NULL)
{
struct ccdsGeneMap *ccdsKg;
hPrintf("<B>CCDS:</B> ");
/* since kg is not by location (even though we have a
* curGeneStart/curGeneEnd), we need to use the location in the
* ccdsGeneMap */
for (ccdsKg = ccdsKgs; ccdsKg != NULL; ccdsKg = ccdsKg->next)
{
if (ccdsKg != ccdsKgs)
hPrintf(", ");
hPrintf("<A href=\"../cgi-bin/hgc?%s&g=ccdsGene&i=%s&c=%s&o=%d&l=%d&r=%d&db=%s\">%s</A>",
cartSidUrlString(cart), ccdsKg->ccdsId, ccdsKg->chrom, ccdsKg->chromStart, ccdsKg->chromStart,
ccdsKg->chromEnd, database, ccdsKg->ccdsId);
}
hPrintf("<BR>\n");
}
}
void describeFields(char *db, char *table,
struct asObject *asObj, struct sqlConnection *conn)
/* Print out an HTML table showing table fields and types, and optionally
* offering histograms for the text/enum fields. */
{
struct sqlResult *sr;
char **row;
#define TOO_BIG_FOR_HISTO 500000
boolean tooBig = (sqlTableSize(conn, table) > TOO_BIG_FOR_HISTO);
char query[256];
struct slName *exampleList, *example;
boolean showItemRgb = FALSE;
showItemRgb=bedItemRgb(findTdbForTable(db, curTrack, table, ctLookupName));
// should we expect itemRgb instead of "reserved"
sqlSafef(query, sizeof(query), "select * from %s limit 1", table);
exampleList = storeRow(conn, query);
sqlSafef(query, sizeof(query), "describe %s", table);
sr = sqlGetResult(conn, query);
hTableStart();
hPrintf("<TR><TH>field</TH>");
if (exampleList != NULL)
hPrintf("<TH>example</TH>");
hPrintf("<TH>SQL type</TH> ");
if (!tooBig)
hPrintf("<TH>info</TH> ");
if (asObj != NULL)
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
example = exampleList;
while ((row = sqlNextRow(sr)) != NULL)
{
if (showItemRgb && (sameWord(row[0],"reserved")))
hPrintf("<TR><TD><TT>itemRgb</TT></TD> ");
else
hPrintf("<TR><TD><TT>%s</TT></TD> ", row[0]);
if (exampleList != NULL)
{
hPrintf("<TD>");
if (example != NULL)
hPrintf("%s", cleanExample(example->name));
else
hPrintf("n/a");
hPrintf("</TD>");
}
// enums/sets with many items can make for painfully wide rows in the table --
// add spaces between quoted list values:
if (stringIn("','", row[1]))
{
struct dyString *spaced = dyStringSub(row[1], "','", "', '");
hPrintf("<TD><TT>%s</TT></TD>", spaced->string);
}
else
hPrintf("<TD><TT>%s</TT></TD>", row[1]);
if (!tooBig)
{
hPrintf(" <TD>");
if ((isSqlStringType(row[1]) && !sameString(row[1], "longblob")) ||
isSqlEnumType(row[1]) || isSqlSetType(row[1]))
{
hPrintf("<A HREF=\"%s", getScriptName());
hPrintf("?%s", cartSidUrlString(cart));
hPrintf("&%s=%s", hgtaDatabase, db);
hPrintf("&%s=%s", hgtaHistoTable, table);
hPrintf("&%s=%s", hgtaDoValueHistogram, row[0]);
hPrintf("\">");
hPrintf("values");
hPrintf("</A>");
}
else if (isSqlNumType(row[1]))
{
hPrintf("<A HREF=\"%s", getScriptName());
hPrintf("?%s", cartSidUrlString(cart));
hPrintf("&%s=%s", hgtaDatabase, db);
hPrintf("&%s=%s", hgtaHistoTable, table);
hPrintf("&%s=%s", hgtaDoValueRange, row[0]);
hPrintf("\">");
hPrintf("range");
hPrintf("</A>");
}
else
{
hPrintf(" ");
}
hPrintf("</TD>");
}
if (asObj != NULL)
{
struct asColumn *asCol = asColumnFind(asObj, row[0]);
hPrintf(" <TD>");
if (asCol != NULL)
hPrintf("%s", asCol->comment);
else
{
if (sameString("bin", row[0]))
hPrintf("Indexing field to speed chromosome range queries.");
else
hPrintf(" ");
}
hPrintf("</TD>");
}
puts("</TR>");
if (example != NULL)
example = example->next;
}
hTableEnd();
sqlFreeResult(&sr);
}
boolean doGetBedOrCt(struct sqlConnection *conn, boolean doCt,
boolean doCtFile, boolean redirectToGb)
/* Actually output bed or custom track. Return TRUE unless no results. */
{
char *db = cloneString(database);
char *table = curTable;
struct hTableInfo *hti = getHti(db, table, conn);
struct featureBits *fbList = NULL, *fbPtr;
struct customTrack *ctNew = NULL;
boolean doCtHdr = (cartUsualBoolean(cart, hgtaPrintCustomTrackHeaders, FALSE)
|| doCt || doCtFile);
char *ctWigOutType = cartCgiUsualString(cart, hgtaCtWigOutType, outWigData);
char *fbQual = fbOptionsToQualifier();
char fbTQ[128];
int fields = hTableInfoBedFieldCount(hti);
boolean gotResults = FALSE;
struct region *region, *regionList = getRegions();
boolean isBedGr = isBedGraph(curTable);
boolean isBgWg = isBigWigTable(curTable);
boolean needSubtrackMerge = anySubtrackMerge(database, curTable);
boolean doDataPoints = FALSE;
boolean isWig = isWiggle(database, table);
struct wigAsciiData *wigDataList = NULL;
struct dataVector *dataVectorList = NULL;
boolean doRgb = bedItemRgb(hTrackDbForTrack(db, curTable));
if (!cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE) && !doCt)
{
textOpen();
}
if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE))
fputs("#", stdout);
if ((isWig || isBedGr || isBgWg) && sameString(outWigData, ctWigOutType))
doDataPoints = TRUE;
for (region = regionList; region != NULL; region = region->next)
{
struct bed *bedList = NULL, *bed;
struct lm *lm = lmInit(64*1024);
struct dataVector *dv = NULL;
if (isWig && doDataPoints)
{
if (needSubtrackMerge)
{
dv = wiggleDataVector(curTrack, curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else
{
int count = 0;
struct wigAsciiData *wigData = NULL;
struct wigAsciiData *asciiData;
struct wigAsciiData *next;
wigData = getWiggleAsData(conn, curTable, region);
for (asciiData = wigData; asciiData; asciiData = next)
{
next = asciiData->next;
if (asciiData->count)
{
slAddHead(&wigDataList, asciiData);
++count;
}
}
slReverse(&wigDataList);
}
}
else if (isBedGr && doDataPoints)
{
dv = bedGraphDataVector(curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else if (isBgWg && doDataPoints)
{
dv = bigWigDataVector(curTable, conn, region);
if (dv != NULL)
slAddHead(&dataVectorList, dv);
}
else if (isWig || isBgWg)
{
dv = wiggleDataVector(curTrack, curTable, conn, region);
bedList = dataVectorToBedList(dv);
dataVectorFree(&dv);
}
else if (isBedGr)
{
bedList = getBedGraphAsBed(conn, curTable, region);
}
else
{
bedList = cookedBedList(conn, curTable, region, lm, &fields);
}
/* this is a one-time only initial creation of the custom track
* structure to receive the results. gotResults turns it off after
* the first time.
*/
if (doCtHdr && !gotResults &&
((bedList != NULL) || (wigDataList != NULL) ||
(dataVectorList != NULL)))
{
ctNew = beginCustomTrack(table, fields,
doCt, (isWig || isBedGr || isBgWg), doDataPoints);
}
if (doDataPoints && (wigDataList || dataVectorList))
gotResults = TRUE;
else
{
if ((fbQual == NULL) || (fbQual[0] == 0))
{
for (bed = bedList; bed != NULL; bed = bed->next)
{
if (bed->name != NULL)
{
subChar(bed->name, ' ', '_');
}
if (doCt)
{
struct bed *dupe = cloneBed(bed); /* Out of local memory. */
slAddHead(&ctNew->bedList, dupe);
}
else
{
if (doRgb)
bedTabOutNitemRgb(bed, fields, stdout);
else
bedTabOutN(bed, fields, stdout);
}
gotResults = TRUE;
}
}
else
{
safef(fbTQ, sizeof(fbTQ), "%s:%s", hti->rootName, fbQual);
fbList = fbFromBed(db, fbTQ, hti, bedList, 0, 0, FALSE, FALSE);
if (fields >= 6)
fields = 6;
else if (fields >= 4)
fields = 4;
else
fields = 3;
if (doCt && ctNew)
{
ctNew->fieldCount = fields;
safef(ctNew->tdb->type, strlen(ctNew->tdb->type)+1,
"bed %d", fields);
}
for (fbPtr=fbList; fbPtr != NULL; fbPtr=fbPtr->next)
{
if (fbPtr->name != NULL)
{
char *ptr = strchr(fbPtr->name, ' ');
if (ptr != NULL)
*ptr = 0;
}
if (doCt)
{
struct bed *fbBed = fbToBedOne(fbPtr);
slAddHead(&ctNew->bedList, fbBed );
}
else
{
if (fields >= 6)
hPrintf("%s\t%d\t%d\t%s\t%d\t%c\n",
fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name,
0, fbPtr->strand);
else if (fields >= 4)
hPrintf("%s\t%d\t%d\t%s\n",
fbPtr->chrom, fbPtr->start, fbPtr->end, fbPtr->name);
else
hPrintf("%s\t%d\t%d\n",
fbPtr->chrom, fbPtr->start, fbPtr->end);
}
gotResults = TRUE;
}
featureBitsFreeList(&fbList);
}
}
bedList = NULL;
lmCleanup(&lm);
}
if (!gotResults)
{
hPrintf(NO_RESULTS);
}
else if (doCt)
{
int wigDataSize = 0;
/* Load existing custom tracks and add this new one: */
struct customTrack *ctList = getCustomTracks();
removeNamedCustom(&ctList, ctNew->tdb->table);
if (doDataPoints)
{
if (needSubtrackMerge || isBedGr || isBgWg)
{
slReverse(&dataVectorList);
wigDataSize = dataVectorWriteWigAscii(dataVectorList, ctNew->wigAscii, 0, NULL);
// TODO: see if can make prettier wig output here that
// doesn't necessarily have one value per base
}
else
{
struct wiggleDataStream *wds = NULL;
/* create an otherwise empty wds so we can print out the list */
wds = wiggleDataStreamNew();
wds->ascii = wigDataList;
wigDataSize = wds->asciiOut(wds, db, ctNew->wigAscii, TRUE, FALSE);
#if defined(DEBUG) /* dbg */
/* allow file readability for debug */
chmod(ctNew->wigAscii, 0666);
#endif
wiggleDataStreamFree(&wds);
}
}
else
slReverse(&ctNew->bedList);
slAddHead(&ctList, ctNew);
/* Save the custom tracks out to file (overwrite the old file): */
customTracksSaveCart(db, cart, ctList);
/* Put up redirect-to-browser page. */
if (redirectToGb)
{
char browserUrl[256];
char headerText[512];
int redirDelay = 3;
safef(browserUrl, sizeof(browserUrl),
"%s?%s&db=%s", hgTracksName(), cartSidUrlString(cart), database);
safef(headerText, sizeof(headerText),
"<META HTTP-EQUIV=\"REFRESH\" CONTENT=\"%d;URL=%s\">",
redirDelay, browserUrl);
webStartHeader(cart, database, headerText,
"Table Browser: %s %s: %s", hOrganism(database),
freezeName, "get custom track");
if (doDataPoints)
{
hPrintf("There are %d data points in custom track. ", wigDataSize);
}
else
{
hPrintf("There are %d items in custom track. ",
slCount(ctNew->bedList));
}
hPrintf("You will be automatically redirected to the genome browser in\n"
"%d seconds, or you can \n"
"<A HREF=\"%s\">click here to continue</A>.\n",
redirDelay, browserUrl);
}
}
else if (doDataPoints)
{
if (needSubtrackMerge || isBedGr || isBgWg)
{
slReverse(&dataVectorList);
dataVectorWriteWigAscii(dataVectorList, "stdout", 0, NULL);
}
else
{
/* create an otherwise empty wds so we can print out the list */
struct wiggleDataStream *wds = NULL;
wds = wiggleDataStreamNew();
wds->ascii = wigDataList;
wds->asciiOut(wds, db, "stdout", TRUE, FALSE);
wiggleDataStreamFree(&wds);
}
}
return gotResults;
}
void doImage(struct sqlConnection *conn)
/* Put up image page. */
{
int imageId = cartUsualInt(cart, hgpId, 0);
char *sidUrl = cartSidUrlString(cart);
char buf[1024];
char url[1024];
char *p = NULL;
char dir[256];
char name[128];
char extension[64];
int w = 0, h = 0;
htmlSetBgColor(0xE0E0E0);
htmStart(stdout, "do image");
puts(
"<script type=\"text/JavaScript\">"
"document.getElementsByTagName('html')[0].style.height=\"100%\";"
"document.getElementsByTagName('body')[0].style.height=\"100%\";"
"</script>"
);
if (!visiGeneImageSize(conn, imageId, &w, &h))
imageId = 0;
if (imageId != 0)
{
printf("<B>");
smallCaption(conn, imageId);
printf(".</B> Click image to zoom in, drag or arrow keys to move. "
"Caption is below.<BR>\n");
p=visiGeneFullSizePath(conn, imageId);
splitPath(p, dir, name, extension);
#ifdef DEBUG
safef(buf,sizeof(buf),"../bigImageTest.html?url=%s%s/%s&w=%d&h=%d",
dir,name,name,w,h);
#else
safef(buf,sizeof(buf),"../bigImage.html?url=%s%s/%s&w=%d&h=%d",
dir,name,name,w,h);
#endif
printf("<IFRAME name=\"bigImg\" width=\"100%%\" height=\"90%%\" SRC=\"%s\"></IFRAME><BR>\n", buf);
fullCaption(conn, imageId);
safef(buf,sizeof(buf),"%s%s%s", dir, name, extension);
safef(url,sizeof(url),"%s?%s=go&%s&%s=%d",
hgVisiGeneCgiName(), hgpDoDownload, sidUrl, hgpId, imageId);
printf("<B>Full-size image:</B> %d x %d <A HREF='%s'> download </A> ", w, h, url);
/* Currently this is dangerous for users with less than 1 GB RAM to use
on large images, because their machines can thrash themselves into a coma.
X-windows (i.e. used by FireFox) will allocate 5 bytes per pixel.
If the image size in pixels times 5 exceeds real ram size, then
Linux thrashes incessantly. But you can hit ctrl-alt-F1 to
get a text only screen, then kill the bad processes (FF) and then
you can restore desktop with ctrl-alt-F7. Hiram says that's a
feature credited to SCO-Unix. On my 1GB machines at work/home,
I never encountered any problem what-so-ever, even with the
largest visiGene AllenBrain - about 19000x9000 pix.
printf(" <A HREF='%s'> view </A>\n", buf);
*/
printf("\n");
}
htmlEnd();
}
void doFrame(struct sqlConnection *conn, boolean forceImageToList)
/* Make a html frame page. Fill frame with thumbnail, control bar,
* and image panes. */
{
int imageId = cartUsualInt(cart, hgpId, 0);
char *sidUrl = cartSidUrlString(cart);
char *listSpec = cartUsualString(cart, hgpListSpec, "");
struct tempName matchTempName;
char *matchFile = NULL;
struct visiMatch *matchList = visiSearch(conn, listSpec);
#ifdef SOON
if (!cartUsualBoolean(cart, hgpIncludeMutants, FALSE))
matchList = removeMutants(conn, matchList);
#endif /* SOON */
matchList = onePerImageFile(conn, matchList);
weighMatches(conn, matchList);
slSort(&matchList, visiMatchCmpWeight);
if (forceImageToList)
{
if (matchList != NULL)
imageId = matchList->imageId;
else
imageId = 0;
}
trashDirFile(&matchTempName, "vg", "visiMatch", ".tab");
matchFile = matchTempName.forCgi;
saveMatchFile(matchFile, matchList);
cartSetString(cart, hgpMatchFile, matchFile);
cartSetInt(cart, hgpId, imageId);
//puts("\n");
puts("<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01 Frameset//EN\" \"http://www.w3.org/TR/html4/frameset.dtd\">");
printf("<HTML>\n");
printf("<HEAD>\n");
printf("<TITLE>\n");
printf("%s ", hgVisiGeneShortName());
printf("%s",titleMessage);
printf("</TITLE>\n");
printf("</HEAD>\n");
printf(" <frameset rows=\"27,*\">\n");
printf(" <frame name=\"controls\" src=\"%s?%s=go&%s&%s=%d\" noresize marginwidth=\"0\" marginheight=\"0\" frameborder=\"0\">\n",
hgVisiGeneCgiName(), hgpDoControls, sidUrl, hgpId, imageId);
printf(" <frameset cols=\"230,*\"> \n");
printf(" <frame src=\"%s?%s=go&%s&%s=%d\" noresize frameborder=\"0\" name=\"list\">\n",
hgVisiGeneCgiName(), hgpDoThumbnails, sidUrl, hgpId, imageId);
printf(" <frame src=\"%s?%s=go&%s&%s=%d\" name=\"image\" noresize frameborder=\"0\">\n",
hgVisiGeneCgiName(), hgpDoImage, sidUrl, hgpId, imageId);
printf(" </frameset>\n");
printf(" <noframes>\n");
printf(" <body>\n");
printf(" <p>This web page uses frames, but your browser doesn't support them.</p>\n");
printf(" </body>\n");
printf(" </noframes>\n");
printf("</frameset>\n");
printf("</HTML>\n");
}
void configurePage()
/* Put up configuration page. */
{
cartWebStart(cart, database, "Configure Genome Graphs");
hPrintf("<FORM ACTION=\"../cgi-bin/hgGenome\" METHOD=GET>\n");
cartSaveSession(cart);
hPrintf("<TABLE>\n");
hPrintf("<TR>\n");
hPrintf("<TD>\n");
hPrintf("image width: ");
cgiMakeIntVar(hggImageWidth, cartUsualInt(cart, hggImageWidth, hgDefaultPixWidth), 4);
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf("graph height: ");
cgiMakeIntVar(hggGraphHeight, graphHeight(), 3);
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf(" graphs per line: ");
makeNumMenu(hggGraphsPerLine, minGraphsPerLine, maxGraphsPerLine,
graphsPerLine());
hPrintf("</TD>\n");
hPrintf("<TD>\n");
hPrintf(" lines of graphs: ");
makeNumMenu(hggLinesOfGraphs, minLinesOfGraphs, maxLinesOfGraphs,
linesOfGraphs());
hPrintf("</TD>\n");
hPrintf("</TR>\n");
hPrintf("</TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("chromosome layout: ");
cgiMakeDropList(hggChromLayout, chromLayouts, ArraySize(chromLayouts),
chromLayout());
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("numerical labels: ");
cartMakeCheckBox(cart, hggLabels, TRUE);
hPrintf(" <I>Label axis on left for first graph and on right for last graph</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("highlight missing: ");
cartMakeCheckBox(cart, hggYellowMissing, FALSE);
hPrintf(" <I>Highlight background in yellow/gray if there is missing data in first graph</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
hPrintf("region padding: ");
cgiMakeIntVar(hggRegionPad, regionPad(), 6);
hPrintf(" <I>Number of bases to add to either side of regions over threshold</I>");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("<TABLE><TR><TD>\n");
cgiMakeButton("submit", "submit");
hPrintf("</TD></TR></TABLE>\n");
hPrintf("</TD>\n");
hPrintf("</FORM>\n");
webNewSection("Configure Graphs");
hPrintf("Click on the hyperlink by the graph name to configure it.");
hTableStart();
hPrintf("<TR><TH>name</TH>");
hPrintf("<TH>description</TH></TR>");
struct slRef *ref;
for (ref = ggList; ref != NULL; ref = ref->next)
{
struct genoGraph *gg = ref->val;
/* Only show custom graphs, stand-alone DB graphs, and composite */
/* graphs. Don't show subGraphs part of a composite. */
if (gg->isSubGraph == FALSE)
{
char *tmp = cgiEncode(gg->name);
hPrintf("<TR><TD><A HREF=\"../cgi-bin/hgGenome?%s&%s=on&g=%s\">",
cartSidUrlString(cart), hggConfigureOne, tmp);
freeMem(tmp);
hPrintf("%s</A></TD>", gg->shortLabel);
hPrintf("<TD>%s</TD></TR>\n", gg->longLabel);
}
}
hTableEnd();
cartWebEnd();
}
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.");
}
static void trackConfig(struct track *trackList, struct group *groupList,
char *groupTarget, int changeVis)
/* Put up track configurations. If groupTarget is
* NULL then set visibility for tracks in all groups. Otherwise,
* just set it for the given group. If vis is -2, then visibility is
* unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc. */
{
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
char pname[512];
char gname[512];
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
struct group *group;
boolean showedRuler = FALSE;
setRulerMode();
changeTrackVis(groupList, groupTarget, changeVis);
/* Set up ruler mode according to changeVis. */
#ifdef BOB_DOESNT_LIKE
if (changeVis != -2)
{
if (groupTarget == NULL ||
(groupList != NULL && sameString(groupTarget, groupList->name)))
{
if (changeVis == -1)
rulerMode = tvFull;
else
rulerMode = changeVis;
}
}
#endif /* BOB_DOESNT_LIKE */
jsInit();
cgiMakeHiddenVar(configGroupTarget, "none");
boolean isFirstNotCtGroup = TRUE;
for (group = groupList; group != NULL; group = group->next)
{
struct trackRef *tr;
if (group->trackList == NULL)
continue;
/* check if group section should be displayed */
char *otherState;
char *indicator;
char *indicatorImg;
boolean isOpen = !isCollapsedGroup(group);
collapseGroupGoodies(isOpen, FALSE, &indicatorImg,
&indicator, &otherState);
hTableStart();
hPrintf("<TR NOWRAP>");
hPrintf("<TH NOWRAP align=\"left\" colspan=3 BGCOLOR=#536ED3>");
hPrintf("\n<A NAME='%sGroup'></A>",group->name);
hPrintf("<input type=hidden name='%s' id='%s' value=%d>",
collapseGroupVar(group->name),collapseGroupVar(group->name), (isOpen?0:1));
hPrintf("<A HREF='%s?%s&%s=%s#%sGroup' class='bigBlue'><IMG height=22 width=22 onclick=\"return toggleTrackGroupVisibility(this,'%s');\" id='%s_button' src='%s' alt='%s' class='bigBlue' title='%s this group'></A> ",
hgTracksName(), cartSidUrlString(cart),collapseGroupVar(group->name),
otherState, group->name, group->name, group->name, indicatorImg, indicator,isOpen?"Collapse":"Expand");
hPrintf("<B> %s</B> ", wrapWhiteFont(group->label));
hPrintf(" ");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
"onClick=\"document.mainForm.%s.value='%s'; %s\" title='Hide all tracks in this groups'>",
configHideAll, "hide all", configGroupTarget, group->name,
jsSetVerticalPosition("mainForm"));
hPrintf(" ");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
"onClick=\"document.mainForm.%s.value='%s'; %s\" title='Show all tracks in this groups'>",
configShowAll, "show all", configGroupTarget, group->name,
jsSetVerticalPosition("mainForm"));
hPrintf(" ");
hPrintf("<INPUT TYPE=SUBMIT NAME=\"%s\" VALUE=\"%s\" "
"onClick=\"document.mainForm.%s.value='%s'; %s\" title='Show default tracks in this group'>",
configDefaultAll, "default", configGroupTarget, group->name,
jsSetVerticalPosition("mainForm"));
hPrintf(" ");
/* do not want all the submit buttons named the same. It is
* confusing to the javascript submit() function.
*/
char submitName[256];
safef(submitName, sizeof(submitName), "%sSubmit", group->name);
cgiMakeButtonWithMsg(submitName, "submit","Submit your selections and view them in the browser");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf(" ");
hPrintf(" ");
hPrintf(" ");
hPrintf("%s", wrapWhiteFont("Group Order: "));
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TH>\n");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf("<TH>\n");
safef(pname, sizeof(pname), "%s.priority",group->name);
hDoubleVar(pname, (double)group->priority, 4);
hPrintf("</TH>\n");
if (isOpen)
hPrintf("<TH align=CENTER BGCOLOR=#536ED3><B> %s</B></TH> ", wrapWhiteFont("Group"));
hPrintf("\n");
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TR>\n");
/* First non-CT group gets ruler. */
if (!showedRuler && isFirstNotCtGroup &&
differentString(group->name, "user"))
{
showedRuler = TRUE;
hPrintf("<TR %sid='%s-0'>",(isOpen ? "" : "style='display: none'"), group->name);
hPrintf("<TD>");
hPrintf("<A HREF=\"%s?%s=%u&c=%s&g=%s&hgTracksConfigPage=configure\">", hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart),
chromName, RULER_TRACK_NAME);
hPrintf("%s</A>", RULER_TRACK_LABEL);
hPrintf("</TD>");
hPrintf("<TD>");
hTvDropDownClass("ruler", rulerMode, FALSE, rulerMode ? "normalText" : "hiddenText");
hPrintf("</TD>");
hPrintf("<TD>");
hPrintf("Chromosome position in bases. (Clicks here zoom in 3x)");
hPrintf("</TD>");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf("<TD>");
hPrintf("</TD>");
hPrintf("<TD>");
hPrintf("</TD>");
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TR>\n");
}
if (differentString(group->name, "user"))
isFirstNotCtGroup = FALSE;
/* Scan track list to determine which supertracks have visible member
* tracks, and to insert a track in the list for the supertrack.
* Sort tracks and supertracks together by priority */
groupTrackListAddSuper(cart, group);
if (!withPriorityOverride)
{
/* sort hierarchically by priority, considering supertracks */
struct trackRef *refList = NULL, *ref;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
if (tdbIsSuperTrackChild(track->tdb))
/* ignore supertrack member tracks till supertrack is found */
continue;
AllocVar(ref);
ref->track = track;
slAddTail(&refList, ref);
if (tdbIsSuper(track->tdb))
{
struct trackRef *tr2;
for (tr2 = group->trackList; tr2 != NULL; tr2 = tr2->next)
{
char *parent = tr2->track->tdb->parentName;
if (parent && sameString(parent, track->track))
{
AllocVar(ref);
ref->track = tr2->track;
slAddTail(&refList, ref);
}
}
}
}
group->trackList = refList;
}
/* Loop through this group and display */
int rowCount=1;
for (tr = group->trackList; tr != NULL; tr = tr->next)
{
struct track *track = tr->track;
struct trackDb *tdb = track->tdb;
hPrintf("<TR %sid='%s-%d'>",(isOpen ? "" : "style='display: none'"),group->name, rowCount++);
hPrintf("<TD NOWRAP>");
if (tdbIsSuperTrackChild(tdb))
/* indent members of a supertrack */
hPrintf(" ");
// Print an icon before the title when one is defined
hPrintPennantIcon(track->tdb);
if (track->hasUi)
hPrintf("<A %s%s%s HREF=\"%s?%s=%u&g=%s&hgTracksConfigPage=configure\">",
tdb->parent ? "TITLE=\"Part of super track: " : "",
tdb->parent ? tdb->parent->shortLabel : "",
tdb->parent ? "...\"" : "", hgTrackUiName(),
cartSessionVarName(), cartSessionId(cart), track->track);
hPrintf(" %s", track->shortLabel);
if (tdbIsSuper(track->tdb))
hPrintf("...");
if (track->hasUi)
hPrintf("</A>");
hPrintf("</TD>");
hPrintf("<TD NOWRAP>");
if (tdbIsSuperTrackChild(tdb))
/* indent members of a supertrack */
hPrintf(" ");
/* If track is not on this chrom print an informational
message for the user. */
if (hTrackOnChrom(track->tdb, chromName))
{
if (tdbIsSuper(track->tdb))
{
/* supertrack dropdown is hide/show */
superTrackDropDown(cart, track->tdb, 1);
}
else
{
/* check for option of limiting visibility to one mode */
hTvDropDownClassVisOnly(track->track, track->visibility,
track->canPack, (track->visibility == tvHide) ?
"hiddenText" : "normalText",
trackDbSetting(track->tdb, "onlyVisibility"));
}
}
else
hPrintf("[No data-%s]", chromName);
hPrintf("</TD>");
hPrintf("<TD NOWRAP>");
hPrintf("%s", track->longLabel);
hPrintf("</TD>");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
if (withPriorityOverride)
{
hPrintf("<TD>");
safef(pname, sizeof(pname), "%s.priority",track->track);
hDoubleVar(pname, (double)track->priority, 4);
hPrintf("</TD>");
hPrintf("<TD>\n");
/* suppress group pull-down for supertrack members */
if (tdbIsSuperTrackChild(track->tdb))
hPrintf(" ");
else
{
safef(gname, sizeof(gname), "%s.group",track->track);
printGroupListHtml(gname, groupList, track->groupName);
}
hPrintf("</TD>");
}
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("</TR>\n");
}
hTableEnd();
hPrintf("<BR>");
}
}
