void doPeakClusters(struct trackDb *tdb, char *item)
/* Display detailed info about a cluster of DNase peaks from other tracks. */
{
int start = cartInt(cart, "o");
char *table = tdb->table;
int rowOffset = hOffsetPastBin(database, seqName, table);
char query[256];
struct sqlResult *sr;
char **row;
struct bed *cluster = NULL;
struct sqlConnection *conn = hAllocConn(database);
cartWebStart(cart, database, "%s item details", tdb->shortLabel);
sqlSafef(query, sizeof(query),
"select * from %s where name = '%s' and chrom = '%s' and chromStart = %d",
table, item, seqName, start);
sr = sqlGetResult(conn, query);
row = sqlNextRow(sr);
if (row != NULL)
cluster = bedLoadN(row+rowOffset, 5);
sqlFreeResult(&sr);
if (cluster != NULL)
{
/* Get list of subgroups to display */
char *inputTableFieldDisplay = trackDbSetting(tdb, "inputTableFieldDisplay");
if (inputTableFieldDisplay != NULL)
{
struct slName *fieldList = stringToSlNames(inputTableFieldDisplay);
char *inputTrackTable = trackDbRequiredSetting(tdb, "inputTrackTable");
/* Print out some information about the cluster overall. */
printf("<B>Items in Cluster:</B> %s of %d<BR>\n", cluster->name,
sqlRowCount(conn, sqlCheckIdentifier(inputTrackTable)));
printf("<B>Cluster Score (out of 1000):</B> %d<BR>\n", cluster->score);
printPos(cluster->chrom, cluster->chromStart, cluster->chromEnd, NULL, TRUE, NULL);
/* In a new section put up list of hits. */
webNewSection("List of Items in Cluster");
webPrintLinkTableStart();
printClusterTableHeader(fieldList, FALSE, FALSE, TRUE);
printPeakClusterInfo(tdb, cart, conn, inputTrackTable, fieldList, cluster);
}
else
errAbort("Missing required trackDb setting %s for track %s",
"inputTableFieldDisplay", tdb->track);
webPrintLinkTableEnd();
}
printf("<A HREF=\"%s&g=htcListItemsAssayed&table=%s\" TARGET_blank>", hgcPathAndSettings(),
tdb->track);
printf("List all items assayed");
printf("</A><BR>\n");
webNewSection("Track Description");
printTrackHtml(tdb);
hFreeConn(&conn);
}
static void prAligns(struct sqlConnection *conn, struct cloneInfo *ci)
/* print table of alignments */
{
struct psl* pslList = getAlignments(conn, ci->pslTbl, ci->acc);
assert(pslList != NULL);
slSort(&pslList, pslCmpMatch);
// header, print note about order only if we have multiple alignments and didn't
// come from another details page
webNewSection("Alignments");
if ((pslList->next != NULL) && (winStart < winEnd))
printf("<span style='font-size:smaller;'><em>The alignment you clicked on is shown first.</em></span>\n");
webPrintLinkTableStart();
webPrintLabelCell("genomic (browser)");
webPrintLabelCell("span");
webPrintLabelCell(" ");
webPrintLabelCell("mRNA (alignment details)");
webPrintLabelCell("identity");
webPrintLabelCell("aligned");
// print with clicked alignment first
struct psl* psl;
int pass;
for (pass = 1; pass <= 2; pass++)
{
for (psl = pslList; psl != NULL; psl = psl->next)
if ((pass == 1) == (psl->tStart == ci->start))
{
webPrintLinkTableNewRow();
prAlign(conn, ci->pslTbl, psl);
}
}
webPrintLinkTableEnd();
}
static void prMethodsLink(struct sqlConnection *conn, char *track)
/* generate link to methods page */
{
webNewSection("Description and Methods");
printf("Click <A HREF=\"%s&g=htcTrackHtml&table=%s&c=%s&l=%d&r=%d\">here</A> for details",
hgcPathAndSettings(), track, seqName, winStart, winEnd);
}
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 prOrfeomeInfoLinks(struct sqlConnection *conn, char *acc, struct cloneInfo *ci)
/* print clone info and links */
{
webNewSection("ORFeome Clone Information and Links");
printf("<table border=0><tr valign=top><td>\n");
prCloneInfo(ci);
printf("<td>\n");
prOrfeomeCloneLinks(conn, acc, ci);
printf("</tr></table>\n");
}
void webDownloads()
{
webNewSection("Command Line Tool");
cgiParagraph(
"To lift genome annotations locally on Linux systems, download the "
"<A HREF=\"http://hgdownload.cse.ucsc.edu/admin/exe/\">"
"<I>liftOver</I></A> executable and the appropriate "
"<A HREF=\"http://hgdownload.cse.ucsc.edu/downloads.html#liftover\">"
"chain file</A>."
" Run <I>liftOver</I> with no arguments to see the usage message.\n");
}
static void showLinkedFilters(struct dbTable *dtList)
/* Put up a section with filters for each linked table. */
{
struct dbTable *dt;
for (dt = dtList; dt != NULL; dt = dt->next)
{
/* Put it up in a new section. */
webNewSection("%s.%s based filters", dt->db, dt->table);
filterControlsForTable(dt->db, dt->table);
}
}
static void prMgcInfoLinks(struct sqlConnection *conn, char *acc, struct mgcDb *mgcDb,
struct cloneInfo *ci)
/* print clone info and links */
{
webNewSection("%s Clone Information and Links", mgcDb->name);
printf("<table border=0><tr valign=top><td>\n");
prCloneInfo(ci);
printf("<td>\n");
prMgcCloneLinks(conn, mgcDb, ci);
printf("</tr></table>\n");
}
void printSections(struct section *sectionList, struct sqlConnection *conn,
char *subjId)
/* Print each section in turn. */
{
struct section *section;
for (section = sectionList; section != NULL; section = section->next)
{
webNewSection("<A NAME=\"%s\"></A>%s\n", section->name, section->longLabel);
section->print(section, conn, subjId);
}
}
static void showLinkedFields(struct dbTable *dtList)
/* Put up a section with fields for each linked table. */
{
struct dbTable *dt;
for (dt = dtList; dt != NULL; dt = dt->next)
{
/* Put it up in a new section. */
webNewSection("%s.%s fields", dt->db, dt->table);
showTableFields(dt->db, dt->table, FALSE);
}
}
void printTroubleShooting(struct coordConvRep *ccr)
{
/** print out the information used to try and convert */
webNewSection("Alignment Details:");
printf("<p>The following sequences from the original draft were aligned to determine the coordinates on the new draft:<br>\n");
webOutFasta(ccr->upSeq, ccr->to->version);
webOutFasta(ccr->midSeq, ccr->to->version);
webOutFasta(ccr->downSeq, ccr->to->version);
printf("<br><br>");
printf("<i><font size=-1>Comments, Questions, Bug Reports: <a href=\"mailto:[email protected]\">[email protected]</a></font></i>\n");
}
void doFlyreg(struct trackDb *tdb, char *item)
/* flyreg.org: Drosophila DNase I Footprint db. */
{
struct dyString *query = newDyString(256);
struct sqlConnection *conn = hAllocConn(database);
struct sqlResult *sr = NULL;
char **row;
int start = cartInt(cart, "o");
int end = cartInt(cart, "t");
char fullTable[HDB_MAX_TABLE_STRING];
boolean hasBin = FALSE;
char *motifTable = "flyregMotif";
struct dnaMotif *motif = NULL;
boolean isVersion2 = sameString(tdb->table, "flyreg2");
genericHeader(tdb, item);
if (!hFindSplitTable(database, seqName, tdb->table, fullTable, sizeof fullTable, &hasBin))
errAbort("track %s not found", tdb->table);
sqlDyStringPrintf(query, "select * from %s where chrom = '%s' and ",
fullTable, seqName);
hAddBinToQuery(start, end, query);
sqlDyStringPrintf(query, "chromStart = %d and name = '%s'", start, item);
sr = sqlGetResult(conn, query->string);
if ((row = sqlNextRow(sr)) != NULL)
{
struct flyreg2 fr;
if (isVersion2)
flyreg2StaticLoad(row+hasBin, &fr);
else
flyregStaticLoad(row+hasBin, (struct flyreg *)(&fr));
printf("<B>Factor:</B> %s<BR>\n", fr.name);
printf("<B>Target:</B> %s<BR>\n", fr.target);
if (isVersion2)
printf("<B>Footprint ID:</B> %06d<BR>\n", fr.fpid);
printf("<B>PubMed ID:</B> <A HREF=\"");
printEntrezPubMedUidUrl(stdout, fr.pmid);
printf("\" TARGET=_BLANK>%d</A><BR>\n", fr.pmid);
bedPrintPos((struct bed *)(&fr), 3, tdb);
if (hTableExists(database, motifTable))
{
motif = loadDnaMotif(item, motifTable);
if (motif != NULL)
motifHitSection(NULL, motif);
}
}
else
errAbort("query returned no results: \"%s\"", query->string);
dyStringFree(&query);
sqlFreeResult(&sr);
hFreeConn(&conn);
if (motif != NULL)
webNewSection("%s",tdb->longLabel);
printTrackHtml(tdb);
}
void webDataFormats()
{
webNewSection("Data Formats");
puts("<LI>");
puts(
"<A HREF=\"../goldenPath/help/customTrack.html#BED\" TARGET=_blank>"
"Browser Extensible Data (BED)</A>\n");
puts("</LI>");
puts("<LI>");
puts("Genomic Coordinate Position<BR>");
puts(" chrN<B>:</B>start<B>-</B>end");
puts("</LI>");
}
void motifMultipleHitsSection(struct dnaSeq **seqs, int count, struct dnaMotif *motif, char *title)
/* Print out section about motif, possibly with mutliple occurrences. */
{
// Detect inconsistent motif/pwm tables and suppress confusing display
if (motif != NULL)
{
if (seqs != NULL && motif->columnCount != seqs[0]->size)
{
warn("Motif seq length doesn't match PWM\n");
return;
}
}
webNewSection(title);
motifLogoAndMatrix(seqs, count, motif);
}
static void prRefSeqSims(struct cloneInfo *ci)
/* print similarity information for RefSeqs */
{
webNewSection("RefSeq CDS isoform similarity of %s clone %s",
cdnaInfoDbName(ci), ci->acc);
webPrintLinkTableStart();
webPrintLabelCell("RefSeq");
webPrintLabelCell("Position");
webPrintLabelCell("Similarity");
struct geneSim *gs;
for (gs = ci->refSeqs->genes; gs != NULL; gs = gs->next)
prRefSeqSim(ci, gs);
webPrintLinkTableEnd();
printf("This table compares the similarity of the BLAT genomic alignments of "
"the CDS of this %s clone with alignment of RefSeq mRNA CDSs. This is a metric "
"of the similarity of the exon structure of the mRNAs, rather than a measure of their "
"nucleotide sequence similarity.", cdnaInfoDbName(ci));
}
static void prMiscDiffs(struct sqlConnection *conn, char *acc)
/* print any gbMiscDiff rows for the accession */
{
struct gbMiscDiff *gmds = NULL, *gmd;
if (sqlTableExists(conn, "gbMiscDiff"))
gmds = sqlQueryObjs(conn, (sqlLoadFunc)gbMiscDiffLoad, sqlQueryMulti,
"select * from gbMiscDiff where acc=\"%s\"", acc);
webNewSection("NCBI Clone Validation");
if (gmds != NULL)
{
unsigned miscDiffFlds = getMiscDiffFields(gmds);
webPrintLinkTableStart();
prMiscDiffHdr(miscDiffFlds);
for (gmd = gmds; gmd != NULL; gmd = gmd->next)
prMiscDiff(gmd, miscDiffFlds);
webPrintLinkTableEnd();
}
else
printf("<EM>No clone discrepancies annotated</EM><BR><BR>\n");
}
void growthConditionSection(struct sqlConnection *conn, char *conditionTable)
/* Print out growth condition information. */
{
struct sqlResult *sr;
char query[256], **row;
webNewSection("Description of Growth Conditions");
sqlSafef(query, sizeof(query), "select * from %s order by name", conditionTable);
sr = sqlGetResult(conn, query);
printf("<UL>");
while ((row = sqlNextRow(sr)) != NULL)
{
struct growthCondition gc;
growthConditionStaticLoad(row, &gc);
printf("<LI>");
printf("<A NAME=\"GC_%s\"></A>", gc.name);
printf("%s - <I>%s</I> %s\n", gc.name, gc.shortLabel, gc.longLabel);
}
printf("</UL>");
sqlFreeResult(&sr);
}
static void prSeqLinks(struct sqlConnection *conn, struct cloneInfo *ci)
/* print table of sequence links */
{
webNewSection("Sequences");
webPrintLinkTableStart();
webPrintLinkCellStart();
hgcAnchorSomewhere("htcDisplayMrna", ci->acc, ci->pslTbl, seqName);
printf("mRNA</a>");
webPrintLinkCellEnd();
webPrintLinkCellStart();
hgcAnchorSomewhere("htcTranslatedMRna", ci->acc, ci->pslTbl, seqName);
printf("Protein</A><br>");
webPrintLinkCellEnd();
webPrintLinkCellStart();
hgcAnchorSomewhere("htcGeneInGenome", ci->acc, ci->gpTbl, seqName);
printf("Genomic</A>");
webPrintLinkCellEnd();
webPrintLinkTableNewRow();
webPrintLinkCellStart();
hgcAnchorSomewhere("htcDisplayMrna", ci->acc, ci->gpTbl, seqName);
printf("Reference genome mRNA</A>");
webPrintLinkCellEnd();
#if BROKEN
// FIXME: doesn't work when genePred table is not the track; not that important
webPrintLinkCellStart();
hgcAnchorSomewhereTbl("htcTranslatedPredMRna", ci->acc, ci->pslTbl, seqName, ci->gpTbl);
printf("Reference genome protein</A>");
webPrintLinkCellEnd();
webFinishPartialLinkTable(1, 2, 3);
#else
webFinishPartialLinkTable(1, 1, 3);
#endif
webPrintLinkTableEnd();
}
boolean doPcr(struct pcrServer *server, struct targetPcrServer *targetServer,
char *fPrimer, char *rPrimer,
int maxSize, int minPerfect, int minGood, boolean flipReverse)
/* Do the PCR, and show results. */
{
struct errCatch *errCatch = errCatchNew();
boolean ok = FALSE;
hgBotDelay();
if (flipReverse)
reverseComplement(rPrimer, strlen(rPrimer));
if (errCatchStart(errCatch))
{
struct gfPcrInput *gpi;
AllocVar(gpi);
gpi->fPrimer = fPrimer;
gpi->rPrimer = rPrimer;
if (server != NULL)
doQuery(server, gpi, maxSize, minPerfect, minGood);
if (targetServer != NULL)
doTargetQuery(targetServer, gpi, maxSize, minPerfect, minGood);
ok = TRUE;
}
errCatchEnd(errCatch);
if (errCatch->gotError)
warn("%s", errCatch->message->string);
errCatchFree(&errCatch);
if (flipReverse)
reverseComplement(rPrimer, strlen(rPrimer));
webNewSection("Primer Melting Temperatures");
printf("<TT>");
printf("<B>Forward:</B> %4.1f C %s<BR>\n", oligoTm(fPrimer, 50.0, 50.0), fPrimer);
printf("<B>Reverse:</B> %4.1f C %s<BR>\n", oligoTm(rPrimer, 50.0, 50.0), rPrimer);
printf("</TT>");
printf("The temperature calculations are done assuming 50 mM salt and 50 nM annealing "
"oligo concentration. The code to calculate the melting temp comes from "
"<A HREF=\"http://frodo.wi.mit.edu/primer3/input.htm\" target=_blank>"
"Primer3</A>.");
return ok;
}
void doSearchTracks(struct group *groupList)
{
if (!advancedJavascriptFeaturesEnabled(cart))
{
warn("Requires advanced javascript features.");
return;
}
struct group *group;
char *groups[128];
char *labels[128];
int numGroups = 1;
groups[0] = ANYLABEL;
labels[0] = ANYLABEL;
char *currentTab = cartUsualString(cart, TRACK_SEARCH_CURRENT_TAB, "simpleTab");
char *nameSearch = cartOptionalString(cart, TRACK_SEARCH_ON_NAME);
#ifdef TRACK_SEARCH_ON_TYPE
char *typeSearch = cartOptionalString(cart, TRACK_SEARCH_ON_TYPE);
#else///ifndef TRACK_SEARCH_ON_TYPE
char *typeSearch = NULL;
#endif///def TRACK_SEARCH_ON_TYPE
char *descSearch;
char *groupSearch = cartOptionalString(cart, TRACK_SEARCH_ON_GROUP);
boolean doSearch = sameString(cartOptionalString(cart, TRACK_SEARCH), "Search") || cartUsualInt(cart, TRACK_SEARCH_PAGER, -1) >= 0;
struct sqlConnection *conn = hAllocConn(database);
boolean metaDbExists = sqlTableExists(conn, "metaDb");
int numMetadataSelects, tracksFound = 0;
int numMetadataNonEmpty = 0;
char **mdbVar = NULL;
char **mdbVal = NULL;
#ifdef ONE_FUNC
struct hash *parents = newHash(4);
#endif///def ONE_FUNC
boolean simpleSearch;
struct trix *trix;
char trixFile[HDB_MAX_PATH_STRING];
char **descWords = NULL;
int descWordCount = 0;
boolean searchTermsExist = FALSE;
int cols;
char buf[512];
if(sameString(currentTab, "simpleTab"))
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_SIMPLE);
simpleSearch = TRUE;
freez(&nameSearch);
#ifdef TRACK_SEARCH_ON_TYPE
freez(&typeSearch);
#endif///def TRACK_SEARCH_ON_TYPE
freez(&groupSearch);
}
else
{
descSearch = cartOptionalString(cart, TRACK_SEARCH_ON_DESCR);
simpleSearch = FALSE;
}
if(descSearch)
stripChar(descSearch, '"');
trackList = getTrackList(&groupList, -2); // global
makeGlobalTrackHash(trackList);
// NOTE: This is necessary when container cfg by '*' results in vis changes
// This will handle composite/view override when subtrack specific vis exists, AND superTrack reshaping.
parentChildCartCleanup(trackList,cart,oldVars); // Subtrack settings must be removed when composite/view settings are updated
getSearchTrixFile(database, trixFile, sizeof(trixFile));
trix = trixOpen(trixFile);
slSort(&groupList, gCmpGroup);
for (group = groupList; group != NULL; group = group->next)
{
groupTrackListAddSuper(cart, group);
if (group->trackList != NULL)
{
groups[numGroups] = cloneString(group->name);
labels[numGroups] = cloneString(group->label);
numGroups++;
if (numGroups >= ArraySize(groups))
internalErr();
}
}
safef(buf, sizeof(buf),"Search for Tracks in the %s %s Assembly", organism, hFreezeFromDb(database));
webStartWrapperDetailedNoArgs(cart, database, "", buf, FALSE, FALSE, FALSE, FALSE);
hPrintf("<div style='max-width:1080px;'>");
hPrintf("<form action='%s' name='%s' id='%s' method='get'>\n\n", hgTracksName(),TRACK_SEARCH_FORM,TRACK_SEARCH_FORM);
cartSaveSession(cart); // Creates hidden var of hgsid to avoid bad voodoo
safef(buf, sizeof(buf), "%lu", clock1());
cgiMakeHiddenVar("hgt_", buf); // timestamps page to avoid browser cache
hPrintf("<input type='hidden' name='db' value='%s'>\n", database);
hPrintf("<input type='hidden' name='%s' id='currentTab' value='%s'>\n", TRACK_SEARCH_CURRENT_TAB, currentTab);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_DEL_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_ADD_ROW);
hPrintf("<input type='hidden' name='%s' value=''>\n",TRACK_SEARCH_PAGER);
hPrintf("<div id='tabs' style='display:none; %s'>\n"
"<ul>\n"
"<li><a href='#simpleTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Search</B></a></li>\n"
"<li><a href='#advancedTab'><B style='font-size:.9em;font-family: arial, Geneva, Helvetica, san-serif;'>Advanced</B></a></li>\n"
"</ul>\n"
"<div id='simpleTab' style='max-width:inherit;'>\n",cgiBrowser()==btIE?"width:1060px;":"max-width:inherit;");
hPrintf("<table style='width:100%%; font-size:.9em;'><tr><td colspan='2'>");
hPrintf("<input type='text' name='%s' id='simpleSearch' class='submitOnEnter' value='%s' style='max-width:1000px; width:100%%;' onkeyup='findTracksSearchButtonsEnable(true);'>\n",
TRACK_SEARCH_SIMPLE,descSearch == NULL ? "" : descSearch);
if (simpleSearch && descSearch)
searchTermsExist = TRUE;
hPrintf("</td></tr><td style='max-height:4px;'></td></tr></table>");
//hPrintf("</td></tr></table>");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
hPrintf("</div>\n");
// Advanced tab
hPrintf("<div id='advancedTab' style='width:inherit;'>\n"
"<table cellSpacing=0 style='width:inherit; font-size:.9em;'>\n");
cols = 8;
// Track Name contains
hPrintf("<tr><td colspan=3></td>");
hPrintf("<td nowrap><b style='max-width:100px;'>Track Name:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='nameSearch' class='submitOnEnter' value='%s' onkeyup='findTracksSearchButtonsEnable(true);' style='min-width:326px; font-size:.9em;'>",
TRACK_SEARCH_ON_NAME, nameSearch == NULL ? "" : nameSearch);
hPrintf("</td></tr>\n");
// Description contains
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>");
hPrintf("<td><b style='max-width:100px;'>Description:</b></td>");
hPrintf("<td align='right'>contains</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
hPrintf("<input type='text' name='%s' id='descSearch' value='%s' class='submitOnEnter' onkeyup='findTracksSearchButtonsEnable(true);' style='max-width:536px; width:536px; font-size:.9em;'>",
TRACK_SEARCH_ON_DESCR, descSearch == NULL ? "" : descSearch);
hPrintf("</td></tr>\n");
if (!simpleSearch && descSearch)
searchTermsExist = TRUE;
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td><b style='max-width:100px;'>Group:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
cgiMakeDropListFull(TRACK_SEARCH_ON_GROUP, labels, groups, numGroups, groupSearch, "class='groupSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (!simpleSearch && groupSearch)
searchTermsExist = TRUE;
#ifdef TRACK_SEARCH_ON_TYPE
// Track Type is (drop down)
hPrintf("<tr><td colspan=2></td><td align='right'>and </td>\n");
hPrintf("<td nowrap><b style='max-width:100px;'>Data Format:</b></td>");
hPrintf("<td align='right'>is</td>\n");
hPrintf("<td colspan='%d'>", cols - 4);
char **formatTypes = NULL;
char **formatLabels = NULL;
int formatCount = getFormatTypes(&formatLabels, &formatTypes);
cgiMakeDropListFull(TRACK_SEARCH_ON_TYPE, formatLabels, formatTypes, formatCount, typeSearch, "class='typeSearch' style='min-width:40%; font-size:.9em;'");
hPrintf("</td></tr>\n");
if (!simpleSearch && typeSearch)
searchTermsExist = TRUE;
#endif///def TRACK_SEARCH_ON_TYPE
// Metadata selects require careful accounting
if(metaDbExists)
numMetadataSelects = printMdbSelects(conn, cart, simpleSearch, &mdbVar, &mdbVal, &numMetadataNonEmpty, cols);
else
numMetadataSelects = 0;
hPrintf("</table>\n");
hPrintf("<input type='submit' name='%s' id='searchSubmit' value='search' style='font-size:.8em;'>\n", TRACK_SEARCH);
hPrintf("<input type='button' name='clear' value='clear' class='clear' style='font-size:.8em;' onclick='findTracksClear();'>\n");
hPrintf("<input type='submit' name='submit' value='cancel' class='cancel' style='font-size:.8em;'>\n");
//hPrintf("<a target='_blank' href='../goldenPath/help/trackSearch.html'>help</a>\n");
hPrintf("</div>\n</div>\n");
hPrintf("</form>\n");
hPrintf("</div>"); // Restricts to max-width:1000px;
if(descSearch != NULL && !strlen(descSearch))
descSearch = NULL;
if(groupSearch != NULL && sameString(groupSearch, ANYLABEL))
groupSearch = NULL;
if(typeSearch != NULL && sameString(typeSearch, ANYLABEL))
typeSearch = NULL;
if(!isEmpty(descSearch))
{
char *tmp = cloneString(descSearch);
char *val = nextWord(&tmp);
struct slName *el, *descList = NULL;
int i;
while (val != NULL)
{
slNameAddTail(&descList, val);
descWordCount++;
val = nextWord(&tmp);
}
descWords = needMem(sizeof(char *) * descWordCount);
for(i = 0, el = descList; el != NULL; i++, el = el->next)
descWords[i] = strLower(el->name);
}
if (doSearch && simpleSearch && descWordCount <= 0)
doSearch = FALSE;
if(doSearch)
{
// Now search
struct slRef *tracks = NULL;
if(simpleSearch)
tracks = simpleSearchForTracksstruct(trix,descWords,descWordCount);
else
tracks = advancedSearchForTracks(conn,groupList,descWords,descWordCount,nameSearch,typeSearch,descSearch,groupSearch,numMetadataNonEmpty,numMetadataSelects,mdbVar,mdbVal);
// Sort and Print results
enum sortBy sortBy = cartUsualInt(cart,TRACK_SEARCH_SORT,sbRelevance);
tracksFound = slCount(tracks);
if(tracksFound > 1)
findTracksSort(&tracks,simpleSearch,sortBy);
displayFoundTracks(cart,tracks,tracksFound,sortBy);
}
hFreeConn(&conn);
webNewSection("About Track Search");
if(metaDbExists)
hPrintf("<p>Search for terms in track names, descriptions, groups, and ENCODE "
"metadata. If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
else
hPrintf("<p>Search for terms in track descriptions, groups, and names. "
"If multiple terms are entered, only tracks with all terms "
"will be part of the results.");
hPrintf("<BR><a target='_blank' href='../goldenPath/help/trackSearch.html'>more help</a></p>\n");
webEndSectionTables();
}
void doSummaryStatsWiggle(struct sqlConnection *conn)
/* Put up page showing summary stats for wiggle track. */
{
// grab the right trackDb for the current table. The curTrack variable
// has the composite trackDb in it
struct trackDb *track = hTrackDbForTrack(database, curTable);
char *table = curTable;
struct region *region, *regionList = getRegions();
char *regionName = getRegionName();
long long regionSize = 0;
long long gapTotal = 0;
long startTime = 0, wigFetchTime = 0;
char splitTableOrFileName[HDB_MAX_TABLE_STRING];
struct customTrack *ct = NULL;
boolean isCustom = FALSE;
struct wiggleDataStream *wds = NULL;
unsigned long long valuesMatched = 0;
int regionCount = 0;
int regionsDone = 0;
unsigned span = 0;
char *dataConstraint;
double ll = 0.0;
double ul = 0.0;
boolean hasConstraint = FALSE;
char *table2 = NULL;
boolean fullGenome = FALSE;
boolean statsHeaderDone = FALSE;
boolean gotSome = FALSE;
char *shortLabel = table;
long long statsItemCount = 0; /* global accumulators for overall */
int statsSpan = 0; /* stats summary on a multiple region */
double statsSumData = 0.0; /* output */
double statsSumSquares = 0.0; /* " " */
double lowerLimit = INFINITY; /* " " */
double upperLimit = -1.0 * INFINITY; /* " " */
startTime = clock1000();
if (track != NULL)
shortLabel = track->shortLabel;
/* Count the regions, when only one, we can do more stats */
for (region = regionList; region != NULL; region = region->next)
++regionCount;
htmlOpen("%s (%s) Wiggle Summary Statistics", shortLabel, table);
if (anySubtrackMerge(database, curTable))
hPrintf("<P><EM><B>Note:</B> subtrack merge is currently ignored on this "
"page (not implemented yet). Statistics shown here are only for "
"the primary table %s (%s).</EM>", shortLabel, table);
fullGenome = fullGenomeRegion();
WIG_INIT; /* ct, isCustom, hasConstraint, wds and table2 are set here */
for (region = regionList; region != NULL; region = region->next)
{
struct bed *intersectBedList = NULL;
int operations;
++regionsDone;
if (table2)
intersectBedList = bedTable2(conn, region, table2);
operations = wigFetchStats;
#if defined(NOT)
/* can't do the histogram now, that operation times out */
if (1 == regionCount)
operations |= wigFetchAscii;
#endif
wds->setChromConstraint(wds, region->chrom);
if (fullGenome)
wds->setPositionConstraint(wds, 0, 0);
else
wds->setPositionConstraint(wds, region->start, region->end);
if (hasConstraint)
wds->setDataConstraint(wds, dataConstraint, ll, ul);
/* depending on what is coming in on regionList, we may need to be
* smart about how often we call getData for these custom tracks
* since that is potentially a large file read each time.
*/
if (isCustom)
{
if (ct->dbTrack)
{
struct sqlConnection *trashConn = hAllocConn(CUSTOM_TRASH);
struct trackDb *tdb = findTdbForTable(database, curTrack, table, ctLookupName);
span = minSpan(trashConn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, tdb);
wds->setSpanConstraint(wds, span);
valuesMatched = getWigglePossibleIntersection(wds, region,
CUSTOM_TRASH, table2, &intersectBedList,
splitTableOrFileName, operations);
hFreeConn(&trashConn);
}
else
{
valuesMatched = getWigglePossibleIntersection(wds, region, NULL,
table2, &intersectBedList, splitTableOrFileName, operations);
/* XXX We need to properly get the smallest span for custom tracks */
/* This is not necessarily the correct answer here */
if (wds->stats)
span = wds->stats->span;
else
span = 1;
}
}
else
{
if (hFindSplitTable(database, region->chrom, table, splitTableOrFileName, sizeof splitTableOrFileName, NULL))
{
span = minSpan(conn, splitTableOrFileName, region->chrom,
region->start, region->end, cart, track);
wds->setSpanConstraint(wds, span);
valuesMatched = getWigglePossibleIntersection(wds, region,
database, table2, &intersectBedList, splitTableOrFileName,
operations);
if (intersectBedList)
span = 1;
}
}
/* when doing multiple regions, we need to print out each result as
* it happens to keep the connection open to the browser and
* prevent any timeout since this could take a while.
* (worst case test is quality track on panTro1)
*/
if (wds->stats)
statsItemCount += wds->stats->count;
if (wds->stats && (regionCount > 1) && (valuesMatched > 0))
{
double sumData = wds->stats->mean * wds->stats->count;
double sumSquares;
if (wds->stats->count > 1)
sumSquares = (wds->stats->variance * (wds->stats->count - 1)) +
((sumData * sumData)/wds->stats->count);
else
sumSquares = sumData * sumData;
/* global accumulators for overall summary */
statsSpan = wds->stats->span;
statsSumData += sumData;
statsSumSquares += sumSquares;
if (wds->stats->lowerLimit < lowerLimit)
lowerLimit = wds->stats->lowerLimit;
if ((wds->stats->lowerLimit + wds->stats->dataRange) > upperLimit)
upperLimit = wds->stats->lowerLimit + wds->stats->dataRange;
if (statsHeaderDone)
wds->statsOut(wds, database, "stdout", TRUE, TRUE, FALSE, TRUE);
else
{
wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, TRUE);
statsHeaderDone = TRUE;
}
wds->freeStats(wds);
gotSome = TRUE;
}
if ((regionCount > MAX_REGION_DISPLAY) &&
(regionsDone >= MAX_REGION_DISPLAY))
{
hPrintf("<TR><TH ALIGN=CENTER COLSPAN=12> Can not display more "
"than %d regions, <BR> would take too much time </TH></TR>\n",
MAX_REGION_DISPLAY);
break; /* exit this for loop */
}
} /*for (region = regionList; region != NULL; region = region->next) */
if (hasConstraint)
freeMem(dataConstraint); /* been cloned into wds */
if (1 == regionCount)
{
statsPreamble(wds, regionList->chrom, regionList->start, regionList->end,
span, valuesMatched, table2);
/* 3 X TRUE = sort results, html table output, with header,
* the FALSE means close the table after printing, no more rows to
* come. The case in the if() statement was already taken care of
* in the statsPreamble() printout. No need to do that again.
*/
if ( ! ((valuesMatched == 0) && table2) )
wds->statsOut(wds, database, "stdout", TRUE, TRUE, TRUE, FALSE);
regionSize = basesInRegion(regionList,0);
gapTotal = gapsInRegion(conn, regionList,0);
}
else
{ /* this is a bit of a kludge here since these printouts are done in the
* library source wigDataStream.c statsOut() function and
* this is a clean up of that. That function should be
* pulled out of there and made independent and more
* versatile.
*/
long long realSize;
double variance;
double stddev;
/* Too expensive to lookup the numbers for thousands of regions */
regionSize = basesInRegion(regionList,MAX_REGION_DISPLAY);
gapTotal = gapsInRegion(conn, regionList,MAX_REGION_DISPLAY);
realSize = regionSize - gapTotal;
/* close the table which was left open in the loop above */
if (!gotSome)
hPrintf("<TR><TH ALIGN=CENTER COLSPAN=12> No data found matching this request </TH></TR>\n");
hPrintf("<TR><TH ALIGN=LEFT> SUMMARY: </TH>\n");
hPrintf("\t<TD> </TD>\n"); /* chromStart */
hPrintf("\t<TD> </TD>\n"); /* chromEnd */
hPrintf("\t<TD ALIGN=RIGHT> ");
printLongWithCommas(stdout, statsItemCount);
hPrintf(" </TD>\n" );
hPrintf("\t<TD ALIGN=RIGHT> %d </TD>\n", statsSpan);
hPrintf("\t<TD ALIGN=RIGHT> ");
printLongWithCommas(stdout, statsItemCount*statsSpan);
hPrintf(" (%.2f%%) </TD>\n",
100.0*(double)(statsItemCount*statsSpan)/(double)realSize);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", lowerLimit);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", upperLimit);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", upperLimit - lowerLimit);
if (statsItemCount > 0)
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", statsSumData/statsItemCount);
else
hPrintf("\t<TD ALIGN=RIGHT> 0.0 </TD>\n");
stddev = 0.0;
variance = 0.0;
if (statsItemCount > 1)
{
variance = (statsSumSquares -
((statsSumData * statsSumData)/(double) statsItemCount)) /
(double) (statsItemCount - 1);
if (variance > 0.0)
stddev = sqrt(variance);
}
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", variance);
hPrintf("\t<TD ALIGN=RIGHT> %g </TD>\n", stddev);
hPrintf("</TR>\n");
wigStatsTableHeading(stdout, TRUE);
hPrintf("</TABLE></TD></TR></TABLE></P>\n");
}
#if defined(NOT)
/* can't do the histogram now, that operation times out */
/* Single region, we can do the histogram */
if ((valuesMatched > 1) && (1 == regionCount))
{
float *valuesArray = NULL;
size_t valueCount = 0;
struct histoResult *histoGramResult;
/* convert the ascii data listings to one giant float array */
valuesArray = wds->asciiToDataArray(wds, valuesMatched, &valueCount);
/* histoGram() may return NULL if it doesn't work */
histoGramResult = histoGram(valuesArray, valueCount,
NAN, (unsigned) 0, NAN, (float) wds->stats->lowerLimit,
(float) (wds->stats->lowerLimit + wds->stats->dataRange),
(struct histoResult *)NULL);
printHistoGram(histoGramResult, TRUE); /* TRUE == html output */
freeHistoGram(&histoGramResult);
wds->freeAscii(wds);
wds->freeArray(wds);
}
#endif
wds->freeStats(wds);
wiggleDataStreamFree(&wds);
wigFetchTime = clock1000() - startTime;
webNewSection("Region and Timing Statistics");
hTableStart();
stringStatRow("region", regionName);
numberStatRow("bases in region", regionSize);
numberStatRow("bases in gaps", gapTotal);
floatStatRow("load and calc time", 0.001*wigFetchTime);
wigFilterStatRow(conn);
stringStatRow("intersection", cartUsualString(cart, hgtaIntersectTable, "off"));
hTableEnd();
htmlClose();
} /* void doSummaryStatsWiggle(struct sqlConnection *conn) */
void showSchemaBam(char *table, struct trackDb *tdb)
/* Show schema on bam. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(database);
char *fileName = bamFileName(table, conn, NULL);
struct asObject *as = bamAsObj();
hPrintf("<B>Database:</B> %s", database);
hPrintf(" <B>Primary Table:</B> %s<br>", table);
hPrintf("<B>BAM File:</B> %s", fileName);
hPrintf("<BR>\n");
hPrintf("<B>Format description:</B> %s<BR>", as->comment);
hPrintf("See the <A HREF=\"%s\" target=_blank>SAM Format Specification</A> for more details<BR>\n",
"http://samtools.sourceforge.net/SAM1.pdf");
/* Put up table that describes fields. */
hTableStart();
hPrintf("<TR><TH>field</TH>");
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
struct asColumn *col;
int colCount = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
hPrintf("<TD>%s</TD></TR>", col->comment);
++colCount;
}
hTableEnd();
/* Put up another section with sample rows. */
webNewSection("Sample Rows");
hTableStart();
/* Print field names as column headers for example */
hPrintf("<TR>");
int colIx = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TH>%s</TH>", col->name);
++colIx;
}
hPrintf("</TR>\n");
/* Fetch sample rows. */
samfile_t *fh = bamOpen(fileName, NULL);
struct lm *lm = lmInit(0);
struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, 10, lm);
/* Print sample lines. */
char *row[SAMALIGNMENT_NUM_COLS];
char numBuf[BAM_NUM_BUF_SIZE];
for (sam=samList; sam != NULL; sam = sam->next)
{
samAlignmentToRow(sam, numBuf, row);
hPrintf("<TR>");
for (colIx=0; colIx<colCount; ++colIx)
{
hPrintf("<TD>");
xmlEscapeStringToFile(row[colIx], stdout);
hPrintf("</TD>");
}
hPrintf("</TR>\n");
}
hTableEnd();
printTrackHtml(tdb);
/* Clean up and go home. */
bamClose(&fh);
lmCleanup(&lm);
freeMem(fileName);
hFreeConn(&conn);
}
void doSummaryStatsBed(struct sqlConnection *conn)
/* Put up page showing summary stats for track that is in database
* or that is bed-format custom. */
{
struct bed *bedList = NULL;
struct region *regionList = getRegions(), *region;
char *regionName = getRegionName();
long long regionSize = 0, gapTotal = 0, realSize = 0;
long startTime, midTime, endTime;
long loadTime = 0, calcTime = 0, freeTime = 0;
struct covStats *itemCovList = NULL, *blockCovList = NULL, *cov;
int itemCount = 0;
struct hTableInfo *hti = getHti(database, curTable, conn);
int minScore = BIGNUM, maxScore = -BIGNUM;
long long sumScores = 0;
boolean hasBlocks = hti->hasBlocks;
boolean hasScore = (hti->scoreField[0] != 0);
int fieldCount;
htmlOpen("%s (%s) Summary Statistics", curTableLabel(), curTable);
for (region = regionList; region != NULL; region = region->next)
{
struct lm *lm = lmInit(64*1024);
startTime = clock1000();
bedList = cookedBedList(conn, curTable, region, lm, &fieldCount);
if (fieldCount < 12)
hasBlocks = FALSE;
if (fieldCount < 5)
hasScore = FALSE;
midTime = clock1000();
loadTime += midTime - startTime;
if (bedList != NULL)
{
itemCount += slCount(bedList);
regionSize += region->end - region->start;
cov = calcSpanOverRegion(region, bedList);
slAddHead(&itemCovList, cov);
if (hasBlocks)
{
cov = calcBlocksOverRegion(region, bedList);
slAddHead(&blockCovList, cov);
}
if (hti->scoreField[0] != 0)
{
struct bed *bed;
for (bed = bedList; bed != NULL; bed = bed->next)
{
int score = bed->score;
if (score < minScore) minScore = score;
if (score > maxScore) maxScore = score;
sumScores += score;
}
}
}
endTime = clock1000();
calcTime += endTime - midTime;
lmCleanup(&lm);
bedList = NULL;
freeTime += clock1000() - endTime;
}
regionSize = basesInRegion(regionList, 0);
gapTotal = gapsInRegion(conn, regionList, 0);
realSize = regionSize - gapTotal;
hTableStart();
startTime = clock1000();
numberStatRow("item count", itemCount);
if (itemCount > 0)
{
cov = covStatsSum(itemCovList);
percentStatRow("item bases", cov->basesCovered, realSize);
percentStatRow("item total", cov->sumBases, realSize);
numberStatRow("smallest item", cov->minBases);
numberStatRow("average item", round((double)cov->sumBases/cov->itemCount));
numberStatRow("biggest item", cov->maxBases);
}
if (hasBlocks && itemCount > 0)
{
cov = covStatsSum(blockCovList);
hPrintf("<TR><TD>block count</TD><TD ALIGN=RIGHT>");
printLongWithCommas(stdout, cov->itemCount);
hPrintf("</TD></TR>\n");
percentStatRow("block bases", cov->basesCovered, realSize);
percentStatRow("block total", cov->sumBases, realSize);
numberStatRow("smallest block", cov->minBases);
numberStatRow("average block", round((double)cov->sumBases/cov->itemCount));
numberStatRow("biggest block", cov->maxBases);
}
if (hasScore != 0 && itemCount > 0 && sumScores != 0)
{
numberStatRow("smallest score", minScore);
numberStatRow("average score", round((double)sumScores/itemCount));
numberStatRow("biggest score", maxScore);
}
hTableEnd();
/* Show region and time stats part of stats page. */
webNewSection("Region and Timing Statistics");
hTableStart();
stringStatRow("region", regionName);
numberStatRow("bases in region", regionSize);
numberStatRow("bases in gaps", gapTotal);
floatStatRow("load time", 0.001*loadTime);
floatStatRow("calculation time", 0.001*calcTime);
floatStatRow("free memory time", 0.001*freeTime);
stringStatRow("filter", (anyFilter() ? "on" : "off"));
stringStatRow("intersection", (anyIntersection() ? "on" : "off"));
hTableEnd();
covStatsFreeList(&itemCovList);
covStatsFreeList(&blockCovList);
htmlClose();
}
void configPageSetTrackVis(int vis)
/* Do config page after setting track visibility. If vis is -2, then visibility
* is unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc. */
{
char *groupTarget;
struct track *trackList;
struct track *ideoTrack;
struct group *groupList;
configInitTrackList(vis, &groupTarget, &trackList, &ideoTrack, &groupList);
struct dyString *title = dyStringNew(0);
dyStringPrintf(title, "Configure Image");
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(),
cartUsualString(cart, "formMethod", "POST"));
webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE);
cartSaveSession(cart);
hPrintf("<INPUT TYPE=HIDDEN NAME=\"hgTracksConfigPage\" VALUE=\"\">");
/* do not want all the submit buttons named the same thing, this one is: */
cgiMakeButton("topSubmit", "submit");
// 3 column table
hPrintf("<TABLE style=\"border:0px; \">\n");
hPrintf("<TR><TD>image width:");
hPrintf("<TD style=\"text-align: right\">");
hIntVar("pix", tl.picWidth, 4);
hPrintf("<TD>pixels</TR>");
hPrintf("<TR><TD>label area width:");
hPrintf("<TD style=\"text-align: right\">");
hIntVar("hgt.labelWidth", leftLabelWidthChars, 2);
hPrintf("<TD>characters<TD></TR>");
hPrintf("<TR><TD>text size:");
hPrintf("<TD style=\"text-align: right\">");
textSizeDropDown();
hPrintf("</TD>");
if (trackLayoutInclFontExtras())
{
hPrintf("<TD>");
char *defaultStyle = cartUsualString(cart, "fontType", "medium");
cartMakeRadioButton(cart, "fontType", "medium", defaultStyle);
hPrintf(" medium ");
cartMakeRadioButton(cart, "fontType", "fixed", defaultStyle);
hPrintf(" fixed ");
cartMakeRadioButton(cart, "fontType", "bold", defaultStyle);
hPrintf(" bold ");
hPrintf(" ");
hPrintf("</TD>");
}
hPrintf("</TR>");
themeDropDown(cart);
hTableStart();
if (ideoTrack != NULL)
{
hPrintf("<TR><TD>");
hCheckBox("ideogram", cartUsualBoolean(cart, "ideogram", TRUE));
hPrintf("</TD><TD>");
hPrintf("Display chromosome ideogram above main graphic");
hPrintf("</TD></TR>\n");
}
hPrintf("<TR><TD>");
hCheckBox("guidelines", cartUsualBoolean(cart, "guidelines", TRUE));
hPrintf("</TD><TD>");
hPrintf("Show light blue vertical guidelines, or light red vertical window separators in multi-region view");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("leftLabels", cartUsualBoolean(cart, "leftLabels", TRUE));
hPrintf("</TD><TD>");
hPrintf("Display labels to the left of items in tracks");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("centerLabels", cartUsualBoolean(cart, "centerLabels", TRUE));
hPrintf("</TD><TD>");
hPrintf("Display description above each track");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("trackControlsOnMain", cartUsualBoolean(cart, "trackControlsOnMain", TRUE));
hPrintf("</TD><TD>");
hPrintf("Show track controls under main graphic");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("nextItemArrows", cartUsualBoolean(cart, "nextItemArrows", FALSE));
hPrintf("</TD><TD>");
hPrintf("Next/previous item navigation");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("nextExonArrows", cartUsualBoolean(cart, "nextExonArrows", TRUE));
hPrintf("</TD><TD>");
hPrintf("Next/previous exon navigation");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("exonNumbers", cartUsualBoolean(cart, "exonNumbers", TRUE));
hPrintf("</TD><TD>");
hPrintf("Show exon numbers");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("enableHighlightingDialog", cartUsualBoolean(cart, "enableHighlightingDialog", TRUE));
hPrintf("</TD><TD>");
hPrintf("Enable highlight with drag-and-select "
"(if unchecked, drag-and-select always zooms to selection)");
hPrintf("</TD></TR>\n");
hTableEnd();
cgiDown(0.9);
char buf[256];
char *freeze = hFreezeFromDb(database);
if (freeze == NULL)
safef(buf, sizeof buf, "Configure Tracks on %s %s: %s",
organization, browserName, trackHubSkipHubName(organism));
else if (stringIn(database, freeze))
safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s",
organization, browserName, trackHubSkipHubName(organism), freeze);
else
safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s (%s)",
organization, browserName, trackHubSkipHubName(organism), freeze, trackHubSkipHubName(database));
webNewSection("%s",buf);
hPrintf("Tracks: ");
if (isSearchTracksSupported(database,cart))
{
cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT);
hPrintf(" ");
}
cgiMakeButtonWithMsg(configHideAll, "hide all","Hide all tracks in this genome assembly");
hPrintf(" ");
cgiMakeButtonWithMsg(configShowAll, "show all","Show all tracks in this genome assembly");
hPrintf(" ");
cgiMakeButtonWithMsg(configDefaultAll, "default","Display only default tracks");
hPrintf(" Groups: ");
hButtonWithOnClick("hgt.collapseGroups", "collapse all", "Collapse all track groups",
"return vis.expandAllGroups(false)");
hPrintf(" ");
hButtonWithOnClick("hgt.expandGroups", "expand all", "Expand all track groups",
"return vis.expandAllGroups(true)");
hPrintf("<div style='margin-top:.2em; margin-bottom:.9em;'>Control track and group visibility "
"more selectively below.</div>");
trackConfig(trackList, groupList, groupTarget, vis);
dyStringFree(&title);
freez(&groupTarget);
webEndSectionTables();
hPrintf("</FORM>");
}
void mainPageAfterOpen(struct sqlConnection *conn)
/* Put up main page assuming htmlOpen()/htmlClose()
* will happen in calling routine. */
{
hPrintf(
"Use this program to retrieve the data associated with a track in text "
"format, to calculate intersections between tracks, and to retrieve "
"DNA sequence covered by a track. For help in using this application "
"see <A HREF=\"#Help\">Using the Table Browser</A> for a description "
"of the controls in this form, the "
"<A HREF=\"../goldenPath/help/hgTablesHelp.html\">User's Guide</A> for "
"general information and sample queries, and the OpenHelix Table Browser "
"<A HREF=\"http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28\" "
"TARGET=_blank>tutorial</A> for a narrated presentation of the software "
"features and usage. "
"For more complex queries, you may want to use "
"<A HREF=\""GALAXY_URL_BASE"\" target=_BLANK>Galaxy</A> or "
"our <A HREF=\"../goldenPath/help/mysql.html\">public "
"MySQL server</A>. "
"To examine the biological function of your set through annotation "
"enrichments, send the data to "
"<A HREF=\"http://great.stanford.edu\" target=_BLANK>GREAT</A>. "
"%s"
"Refer to the "
"<A HREF=\"../goldenPath/credits.html\">Credits</A> page for the list of "
"contributors and usage restrictions associated with these data. "
"All tables can be downloaded in their entirety from the "
"<A HREF=\"http://hgdownload.cse.ucsc.edu/downloads.html\""
">Sequence and Annotation Downloads</A> page."
, getGenomeSpaceText()
);
hPrintf("<script type=\"text/javascript\">\n");
// When GREAT is selected, disable the other checkboxes and force output to BED
hPrintf("function onSelectGreat() {\n");
hPrintf("document.getElementById('checkboxGalaxy').checked=false;\n");
if (isGenomeSpaceEnabled())
hPrintf("document.getElementById('checkboxGenomeSpace').checked=false;\n");
hPrintf("document.getElementById('outBed').selected=true;\n");
hPrintf("return true;\n");
hPrintf("}\n");
// Disable/enable noGenome tracks depending on whether region is genome.
hPrintf("function maybeDisableNoGenome() {\n"
" var regionTypeSelected = $('input[name=\"hgta_regionType\"]:checked').val();\n"
" var regionIsGenome = (regionTypeSelected === 'genome');\n"
" var $noGenomeOptions = $('select[name=\"hgta_track\"] option.hgtaNoGenome');\n"
" $noGenomeOptions.attr('disabled', regionIsGenome)\n"
" .css('color', regionIsGenome ? '' : 'black');\n"
"}\n"
"$(document).ready(function() {\n"
// once when the page loads, and every time the user changes the region type:
" maybeDisableNoGenome();\n"
" $('input[name=\"hgta_regionType\"]').change(maybeDisableNoGenome);\n"
"});\n"
"</script>\n");
/* Main form. */
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n",
getScriptName(), cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
jsInit();
showMainControlTable(conn);
hPrintf("</FORM>\n");
/* Hidden form - for benefit of javascript. */
{
static char *saveVars[] = {
"clade", "org", "db", hgtaGroup, hgtaTrack, hgtaTable, hgtaRegionType,
hgtaRange, hgtaOutputType, hgtaOutFileName};
jsCreateHiddenForm(cart, getScriptName(), saveVars, ArraySize(saveVars));
}
/* Hidden form for jumping to custom tracks CGI. */
hPrintf("<FORM ACTION='%s' NAME='customTrackForm'>", hgCustomName());
cartSaveSession(cart);
hPrintf("</FORM>\n");
/* Hidden form for jumping to track hub manager CGI. */
hPrintf("<FORM ACTION='%s' NAME='trackHubForm'>", hgHubConnectName());
cartSaveSession(cart);
hPrintf("</FORM>\n");
webNewSection("<A NAME=\"Help\"></A>Using the Table Browser\n");
printMainHelp();
cartFlushHubWarnings();
}
void askForSeq(char *organism, char *db)
/* Put up a little form that asks for sequence.
* Call self.... */
{
struct serverTable *serve = NULL;
/* JavaScript to update form when org changes */
char *onChangeText = "onchange=\""
"document.mainForm.changeInfo.value='orgChange';"
"document.mainForm.submit();\"";
char *userSeq = NULL;
serve = findServer(db, FALSE);
printf(
"<FORM ACTION=\"../cgi-bin/hgBlat\" METHOD=\"POST\" ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n"
"<H2>BLAT Search Genome</H2>\n");
cartSaveSession(cart);
puts("\n");
puts("<INPUT TYPE=HIDDEN NAME=changeInfo VALUE=\"\">\n");
puts("<TABLE BORDER=0 WIDTH=80>\n<TR>\n");
printf("<TD ALIGN=CENTER>Genome:</TD>");
printf("<TD ALIGN=CENTER>Assembly:</TD>");
printf("<TD ALIGN=CENTER>Query type:</TD>");
printf("<TD ALIGN=CENTER>Sort output:</TD>");
printf("<TD ALIGN=CENTER>Output type:</TD>");
printf("<TD ALIGN=CENTER> </TD>");
printf("</TR>\n<TR>\n");
printf("<TD ALIGN=CENTER>\n");
printBlatGenomeListHtml(db, onChangeText);
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
printBlatAssemblyListHtml(db);
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
cgiMakeDropList("type", typeList, ArraySize(typeList), NULL);
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
cgiMakeDropList("sort", sortList, ArraySize(sortList), cartOptionalString(cart, "sort"));
printf("</TD>\n");
printf("<TD ALIGN=CENTER>\n");
cgiMakeDropList("output", outputList, ArraySize(outputList), cartOptionalString(cart, "output"));
printf("</TD>\n");
printf("</TR>\n<TR>\n");
userSeq = cartUsualString(cart, "userSeq", "");
printf("<TD COLSPAN=5 ALIGN=CENTER>\n");
printf("<TEXTAREA NAME=userSeq ROWS=14 COLS=80>%s</TEXTAREA>\n", userSeq);
printf("</TD>\n");
printf("</TR>\n<TR>\n");
printf("<TD COLSPAN=5 ALIGN=CENTER>\n");
printf("<INPUT TYPE=SUBMIT NAME=Submit VALUE=submit>\n");
printf("<INPUT TYPE=SUBMIT NAME=Lucky VALUE=\"I'm feeling lucky\">\n");
printf("<INPUT TYPE=SUBMIT NAME=Clear VALUE=clear>\n");
printf("</TD>\n");
printf("</TR>\n<TR>\n");
puts("<TD COLSPAN=5 WIDTH=\"100%\">\n"
"Paste in a query sequence to find its location in the\n"
"the genome. Multiple sequences may be searched \n"
"if separated by lines starting with '>' followed by the sequence name.\n"
"</TD>\n"
"</TR>\n"
);
puts("<TR><TD COLSPAN=5 WIDTH=\"100%\">\n");
puts("<BR><B>File Upload:</B> ");
puts("Rather than pasting a sequence, you can choose to upload a text file containing "
"the sequence.<BR>");
puts("Upload sequence: <INPUT TYPE=FILE NAME=\"seqFile\">");
puts(" <INPUT TYPE=SUBMIT Name=Submit VALUE=\"submit file\"><P>\n");
printf("%s",
"<P>Only DNA sequences of 25,000 or fewer bases and protein or translated \n"
"sequence of 10000 or fewer letters will be processed. Up to 25 sequences\n"
"can be submitted at the same time. The total limit for multiple sequence\n"
"submissions is 50,000 bases or 25,000 letters.\n</P>");
if (hgPcrOk(db))
printf("<P>For locating PCR primers, use <A HREF=\"../cgi-bin/hgPcr?db=%s\">In-Silico PCR</A>"
" for best results instead of BLAT.</P>", db);
puts("</TD></TR></TABLE>\n");
printf("</FORM>\n");
webNewSection("About BLAT");
printf(
"<P>BLAT on DNA is designed to\n"
"quickly find sequences of 95%% and greater similarity of length 25 bases or\n"
"more. It may miss more divergent or shorter sequence alignments. It will find\n"
"perfect sequence matches of 20 bases.\n"
"BLAT on proteins finds sequences of 80%% and greater similarity of length 20 amino\n"
"acids or more. In practice DNA BLAT works well on primates, and protein\n"
"blat on land vertebrates."
);
printf("%s",
"\n</P><P>BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome\n"
"in memory. The index consists of all overlapping 11-mers stepping by 5 except for\n"
"those heavily involved in repeats. The index takes up about\n"
"2 gigabytes of RAM. RAM can be further reduced to less than 1 GB by increasing step size to 11.\n"
"The genome itself is not kept in memory, allowing\n"
"BLAT to deliver high performance on a reasonably priced Linux box.\n"
"The index is used to find areas of probable homology, which are then\n"
"loaded into memory for a detailed alignment. Protein BLAT works in a similar\n"
"manner, except with 4-mers rather than 11-mers. The protein index takes a little\n"
"more than 2 gigabytes.</P>\n"
"<P>BLAT was written by <A HREF=\"mailto:[email protected]\">Jim Kent</A>.\n"
"Like most of Jim's software, interactive use on this web server is free to all.\n"
"Sources and executables to run batch jobs on your own server are available free\n"
"for academic, personal, and non-profit purposes. Non-exclusive commercial\n"
"licenses are also available. See the \n"
"<A HREF=\"http://www.kentinformatics.com\" TARGET=_blank>Kent Informatics</A>\n"
"website for details.</P>\n"
"\n"
"<P>For more information on the graphical version of BLAT, click the Help \n"
"button on the top menu bar");
if (hIsGsidServer())
printf(". </P> \n");
else
printf(" or see the Genome Browser <A HREF=\"../FAQ/FAQblat.html\">FAQ</A>. </P> \n");
}
void showSchemaBigBed(char *table, struct trackDb *tdb)
/* Show schema on bigBed. */
{
/* Figure out bigBed file name and open it. Get contents for first chromosome as an example. */
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(database);
char *fileName = bigBedFileName(table, conn);
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct bbiChromInfo *chromList = bbiChromList(bbi);
struct lm *lm = lmInit(0);
struct bigBedInterval *ivList = getNElements(bbi, chromList, lm, 10);
/* Get description of columns, making it up from BED records if need be. */
struct asObject *as = bigBedAsOrDefault(bbi);
hPrintf("<B>Database:</B> %s", database);
hPrintf(" <B>Primary Table:</B> %s<br>", table);
hPrintf("<B>Big Bed File:</B> %s", fileName);
if (bbi->version >= 2)
{
hPrintf("<BR><B>Item Count:</B> ");
printLongWithCommas(stdout, bigBedItemCount(bbi));
}
hPrintf("<BR>\n");
hPrintf("<B>Format description:</B> %s<BR>", as->comment);
/* Put up table that describes fields. */
hTableStart();
hPrintf("<TR><TH>field</TH>");
if (ivList != NULL)
hPrintf("<TH>example</TH>");
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
struct asColumn *col;
int colCount = 0;
char *row[bbi->fieldCount];
char startBuf[16], endBuf[16];
if (ivList != NULL)
{
char *dupeRest = lmCloneString(lm, ivList->rest); /* Manage rest-stomping side-effect */
bigBedIntervalToRow(ivList, chromList->name, startBuf, endBuf, row, bbi->fieldCount);
ivList->rest = dupeRest;
}
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
if (ivList != NULL)
hPrintf("<TD>%s</TD>", row[colCount]);
hPrintf("<TD>%s</TD></TR>", col->comment);
++colCount;
}
/* If more fields than descriptions put up minimally helpful info (at least has example). */
for ( ; colCount < bbi->fieldCount; ++colCount)
{
hPrintf("<TR><TD><TT>column%d</TT></TD>", colCount+1);
if (ivList != NULL)
hPrintf("<TD>%s</TD>", row[colCount]);
hPrintf("<TD>n/a</TD></TR>\n");
}
hTableEnd();
if (ivList != NULL)
{
/* Put up another section with sample rows. */
webNewSection("Sample Rows");
hTableStart();
/* Print field names as column headers for example */
hPrintf("<TR>");
int colIx = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TH>%s</TH>", col->name);
++colIx;
}
for (; colIx < colCount; ++colIx)
hPrintf("<TH>column%d</TH>", colIx+1);
hPrintf("</TR>\n");
/* Print sample lines. */
struct bigBedInterval *iv;
for (iv=ivList; iv != NULL; iv = iv->next)
{
bigBedIntervalToRow(iv, chromList->name, startBuf, endBuf, row, bbi->fieldCount);
hPrintf("<TR>");
for (colIx=0; colIx<colCount; ++colIx)
{
writeHtmlCell(row[colIx]);
}
hPrintf("</TR>\n");
}
hTableEnd();
}
printTrackHtml(tdb);
/* Clean up and go home. */
lmCleanup(&lm);
bbiFileClose(&bbi);
freeMem(fileName);
hFreeConn(&conn);
}
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();
}
void configPageSetTrackVis(int vis)
/* Do config page after setting track visibility. If vis is -2, then visibility
* is unchanged. If -1 then set visibility to default, otherwise it should
* be tvHide, tvDense, etc. */
{
struct dyString *title = dyStringNew(0);
char *groupTarget = NULL;
struct track *trackList = NULL;
struct track *ideoTrack = NULL;
struct group *groupList = NULL;
withPriorityOverride = cartUsualBoolean(cart, configPriorityOverride, FALSE);
/* Get track list and group them. */
ctList = customTracksParseCart(database, cart, &browserLines, &ctFileName);
trackList = getTrackList(&groupList, vis);
/* The ideogram for some reason is considered a track.
* We don't really want to process it as one though, so
* we see if it's there, and if necessary remove it. */
ideoTrack = chromIdeoTrack(trackList);
if (ideoTrack != NULL)
removeTrackFromGroup(ideoTrack);
/* Fetch group to change on if any from CGI,
* and remove var so it doesn't get used again. */
groupTarget = cloneString(cartUsualString(cart, configGroupTarget, ""));
cartRemove(cart, configGroupTarget);
if (sameString(groupTarget, "none"))
freez(&groupTarget);
dyStringPrintf(title, "Configure Image");
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n", hgTracksName(),
cartUsualString(cart, "formMethod", "POST"));
webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE);
cartSaveSession(cart);
hPrintf("<INPUT TYPE=HIDDEN NAME=\"hgTracksConfigPage\" VALUE=\"\">");
/* do not want all the submit buttons named the same thing, this one is: */
cgiMakeButton("topSubmit", "submit");
// 3 column table
hPrintf("<TABLE style=\"border:0px; \">\n");
hPrintf("<TR><TD>image width:");
hPrintf("<TD style=\"text-align: right\">");
hIntVar("pix", tl.picWidth, 4);
hPrintf("<TD>pixels</TR>");
hPrintf("<TR><TD>label area width:");
hPrintf("<TD style=\"text-align: right\">");
hIntVar("hgt.labelWidth", leftLabelWidthChars, 2);
hPrintf("<TD>characters<TD></TR>");
hPrintf("<TR><TD>text size:");
hPrintf("<TD style=\"text-align: right\">");
textSizeDropDown();
hPrintf("<TD>");
if (trackLayoutInclFontExtras())
{
char *defaultStyle = cartUsualString(cart, "fontType", "medium");
cartMakeRadioButton(cart, "fontType", "medium", defaultStyle);
hPrintf(" medium ");
cartMakeRadioButton(cart, "fontType", "fixed", defaultStyle);
hPrintf(" fixed ");
cartMakeRadioButton(cart, "fontType", "bold", defaultStyle);
hPrintf(" bold ");
hPrintf(" ");
}
hPrintf("<TR><BR>");
hTableStart();
if (ideoTrack != NULL)
{
hPrintf("<TR><TD>");
hCheckBox("ideogram", cartUsualBoolean(cart, "ideogram", TRUE));
hPrintf("</TD><TD>");
hPrintf("Display chromosome ideogram above main graphic");
hPrintf("</TD></TR>\n");
}
hPrintf("<TR><TD>");
hCheckBox("guidelines", cartUsualBoolean(cart, "guidelines", TRUE));
hPrintf("</TD><TD>");
hPrintf("Show light blue vertical guidelines");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("leftLabels", cartUsualBoolean(cart, "leftLabels", TRUE));
hPrintf("</TD><TD>");
hPrintf("Display labels to the left of items in tracks");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("centerLabels", cartUsualBoolean(cart, "centerLabels", TRUE));
hPrintf("</TD><TD>");
hPrintf("Display description above each track");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("trackControlsOnMain", cartUsualBoolean(cart, "trackControlsOnMain", TRUE));
hPrintf("</TD><TD>");
hPrintf("Show track controls under main graphic");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("nextItemArrows", cartUsualBoolean(cart, "nextItemArrows", FALSE));
hPrintf("</TD><TD>");
hPrintf("Next/previous item navigation");
hPrintf("</TD></TR>\n");
hPrintf("<TR><TD>");
hCheckBox("nextExonArrows", cartUsualBoolean(cart, "nextExonArrows", TRUE));
hPrintf("</TD><TD>");
hPrintf("Next/previous exon navigation");
hPrintf("</TD></TR>\n");
#ifdef PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("<TR><TD>");
char *javascript="onClick=\"document.mainForm.hgTracksConfigPage.value='configure';document.mainForm.submit();\"";
hCheckBoxJS(configPriorityOverride,
cartUsualBoolean(cart, configPriorityOverride , FALSE), javascript);
hPrintf("</TD><TD>");
hPrintf("Enable track re-ordering");
hPrintf("</TD></TR>\n");
#endif///def PRIORITY_CHANGES_IN_CONFIG_UI
hPrintf("<TR><TD>");
hCheckBox("enableAdvancedJavascript", advancedJavascriptFeaturesEnabled(cart));
hPrintf("</TD><TD>");
hPrintf("Enable advanced javascript features");
hPrintf("</TD></TR>\n");
hTableEnd();
char *freeze = hFreezeFromDb(database);
char buf[128];
if (stringIn(database, freeze))
safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s",
organization, browserName, organism, freeze);
else
safef(buf, sizeof buf, "Configure Tracks on %s %s: %s %s (%s)",
organization, browserName, organism, freeze, database);
webNewSection(buf);
hPrintf("Tracks: ");
if(isSearchTracksSupported(database,cart))
{
cgiMakeButtonWithMsg(TRACK_SEARCH, TRACK_SEARCH_BUTTON,TRACK_SEARCH_HINT);
hPrintf(" ");
}
cgiMakeButtonWithMsg(configHideAll, "hide all","Hide all tracks in this genome assembly");
hPrintf(" ");
cgiMakeButtonWithMsg(configShowAll, "show all","Show all tracks in this genome assembly");
hPrintf(" ");
cgiMakeButtonWithMsg(configDefaultAll, "default","Display only default tracks");
hPrintf(" Groups: ");
hButtonWithOnClick("hgt.collapseGroups", "collapse all", "Collapse all track groups", "return setAllTrackGroupVisibility(false)");
hPrintf(" ");
hButtonWithOnClick("hgt.expandGroups", "expand all", "Expand all track groups", "return setAllTrackGroupVisibility(true)");
hPrintf("<P STYLE=\"margin-top:5;\">Control track and group visibility more selectively below.<P>");
trackConfig(trackList, groupList, groupTarget, vis);
dyStringFree(&title);
freez(&groupTarget);
webEndSectionTables();
hPrintf("</FORM>");
}
static void showLinkedTables(struct joiner *joiner, struct dbTable *inList,
char *varPrefix, char *buttonName, char *buttonText)
/* Print section with list of linked tables and check boxes to turn them
* on. */
{
struct dbTable *outList = NULL, *out, *in;
char dtName[256];
struct hash *uniqHash = newHash(0);
struct hash *inHash = newHash(8);
/* Build up list of tables we link to in outList. */
for (in = inList; in != NULL; in = in->next)
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(in->db);
struct joinerPair *jpList, *jp;
/* Keep track of tables in inList. */
safef(dtName, sizeof(dtName), "%s.%s", inList->db, inList->table);
hashAdd(inHash, dtName, NULL);
/* First table in input is not allowed in output. */
if (in == inList)
hashAdd(uniqHash, dtName, NULL);
/* Scan through joining information and add tables,
* avoiding duplicate additions. */
jpList = joinerRelate(joiner, in->db, in->table);
for (jp = jpList; jp != NULL; jp = jp->next)
{
safef(dtName, sizeof(dtName), "%s.%s",
jp->b->database, jp->b->table);
if (!hashLookup(uniqHash, dtName) &&
!cartTrackDbIsAccessDenied(jp->b->database, jp->b->table))
{
hashAdd(uniqHash, dtName, NULL);
out = dbTableNew(jp->b->database, jp->b->table);
slAddHead(&outList, out);
}
}
joinerPairFreeList(&jpList);
hFreeConn(&conn);
}
slSort(&outList, dbTableCmp);
/* Print html. */
if (outList != NULL)
{
webNewSection("Linked Tables");
hTableStart();
for (out = outList; out != NULL; out = out->next)
{
struct sqlConnection *conn = hAllocConn(out->db);
struct asObject *asObj = asForTable(conn, out->table);
char *var = dbTableVar(varPrefix, out->db, out->table);
hPrintf("<TR>");
hPrintf("<TD>");
cgiMakeCheckBox(var, varOn(var));
hPrintf("</TD>");
hPrintf("<TD>%s</TD>", out->db);
hPrintf("<TD>%s</TD>", out->table);
hPrintf("<TD>");
if (asObj != NULL)
hPrintf("%s", asObj->comment);
else
hPrintf(" ");
hPrintf("</TD>");
hPrintf("</TR>");
hFreeConn(&conn);
}
hTableEnd();
hPrintf("<BR>");
cgiMakeButton(buttonName, buttonText);
}
}