static void showOutDropDown(struct outputType *otList, struct outputType *otDefault)
/* Display output drop-down. */
{
struct outputType *ot;
char *outputType = cartUsualString(cart, hgtaOutputType, otList->name);
if (otDefault != NULL && otDefault != otList)
{
boolean otInOtList = FALSE;
for (ot = otList; ot != NULL; ot = ot->next)
if (sameString(ot->name, outputType))
{
otInOtList = TRUE;
break;
}
if (! otInOtList)
outputType = otDefault->name;
}
hPrintf("<SELECT NAME=\"%s\">", hgtaOutputType);
for (ot = otList; ot != NULL; ot = ot->next)
{
hPrintf(" <OPTION VALUE=%s", ot->name);
if (sameString(ot->name, outputType))
hPrintf(" SELECTED");
if (sameString(ot->name, outBed) || sameString(ot->name, outWigBed))
hPrintf(" id=\"outBed\"");
hPrintf(">%s\n", ot->label);
}
hPrintf("</SELECT>\n");
hPrintf(" ");
hPrintf(" Send output to ");
cgiMakeCheckBoxIdAndJS("sendToGalaxy", doGalaxy(),
"checkboxGalaxy",
"onclick=\"document.getElementById('checkboxGreat').checked=false; return true;\"");
hPrintf("<A HREF=\""GALAXY_URL_BASE"\" target=_BLANK>Galaxy</A>\n");
nbSpaces(2);
cgiMakeCheckBoxIdAndJS("sendToGreat", doGreat(),
"checkboxGreat",
"onclick=\"return onSelectGreat();\"");
hPrintf(" <A HREF=\"http://great.stanford.edu\" target=_BLANK>GREAT</A>");
hPrintf("</TD></TR>\n");
}
void showMainControlTable(struct sqlConnection *conn)
/* Put up table with main controls for main page. */
{
struct grp *selGroup;
boolean isWig = FALSE, isPositional = FALSE, isMaf = FALSE, isBedGr = FALSE,
isChromGraphCt = FALSE, isPal = FALSE, isArray = FALSE, isBam = FALSE, isVcf = FALSE, isHalSnake = FALSE, isLongTabix = FALSE;
boolean gotClade = hGotClade();
struct hTableInfo *hti = NULL;
hPrintf("<TABLE BORDER=0>\n");
/* Print clade, genome and assembly line. */
{
if (gotClade)
{
hPrintf("<TR><TD><B>clade:</B>\n");
printCladeListHtml(hGenome(database), onChangeClade());
nbSpaces(3);
hPrintf("<B>genome:</B>\n");
printGenomeListForCladeHtml(database, onChangeOrg());
}
else
{
hPrintf("<TR><TD><B>genome:</B>\n");
printGenomeListHtml(database, onChangeOrg());
}
nbSpaces(3);
hPrintf("<B>assembly:</B>\n");
printAssemblyListHtml(database, onChangeDb());
hPrintf("</TD></TR>\n");
}
/* Print group and track line. */
{
hPrintf("<TR><TD>");
selGroup = showGroupField(hgtaGroup, onChangeGroupOrTrack(), conn, hAllowAllTables());
nbSpaces(3);
curTrack = showTrackField(selGroup, hgtaTrack, onChangeGroupOrTrack(), FALSE);
nbSpaces(3);
boolean hasCustomTracks = FALSE;
struct trackDb *t;
for (t = fullTrackList; t != NULL; t = t->next)
{
if (isCustomTrack(t->table))
{
hasCustomTracks = TRUE;
break;
}
}
hOnClickButton("document.customTrackForm.submit();return false;",
hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL);
hPrintf(" ");
if (hubConnectTableExists())
hOnClickButton("document.trackHubForm.submit();return false;", "track hubs");
hPrintf("</TD></TR>\n");
}
/* Print table line. */
{
hPrintf("<TR><TD>");
curTable = showTableField(curTrack, hgtaTable, TRUE);
if (isHubTrack(curTable) || (strchr(curTable, '.') == NULL)) /* In same database */
{
hti = getHti(database, curTable, conn);
isPositional = htiIsPositional(hti);
}
isLongTabix = isLongTabixTable( curTable);
isBam = isBamTable( curTable);
isVcf = isVcfTable(curTable, NULL);
isWig = isWiggle(database, curTable);
if (isBigWigTable(curTable))
{
isPositional = TRUE;
isWig = TRUE;
}
isHalSnake = isHalTable( curTable);
isMaf = isMafTable(database, curTrack, curTable);
isBedGr = isBedGraph(curTable);
isArray = isMicroarray(curTrack, curTable);
struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
isPal = isPalCompatible(conn, tdb, curTable);
nbSpaces(1);
if (isCustomTrack(curTable))
{
isChromGraphCt = isChromGraph(tdb);
}
cgiMakeButton(hgtaDoSchema, "describe table schema");
hPrintf("</TD></TR>\n");
}
if (curTrack == NULL)
{
struct trackDb *tdb = hTrackDbForTrack(database, curTable);
struct trackDb *cTdb = hCompositeTrackDbForSubtrack(database, tdb);
if (cTdb)
curTrack = cTdb;
else
curTrack = tdb;
isMaf = isMafTable(database, curTrack, curTable);
}
/* Region line */
{
char *regionType = cartUsualString(cart, hgtaRegionType, hgtaRegionTypeGenome);
char *range = cartUsualString(cart, hgtaRange, "");
if (isPositional)
{
boolean doEncode = FALSE;
if (!trackHubDatabase(database))
doEncode = sqlTableExists(conn, "encodeRegions");
hPrintf("<TR><TD><B>region:</B>\n");
/* If regionType not allowed force it to "genome". */
if ((sameString(regionType, hgtaRegionTypeUserRegions) &&
userRegionsFileName() == NULL) ||
(sameString(regionType, hgtaRegionTypeEncode) && !doEncode))
regionType = hgtaRegionTypeGenome;
// Is "genome" is not allowed because of tdb 'tableBrowser noGenome'?
boolean disableGenome = ((curTrack && cartTrackDbIsNoGenome(database, curTrack->table)) ||
(curTable && cartTrackDbIsNoGenome(database, curTable)));
// If "genome" is selected but not allowed, force it to "range":
if (sameString(regionType, hgtaRegionTypeGenome) && disableGenome)
regionType = hgtaRegionTypeRange;
jsTrackingVar("regionType", regionType);
if (disableGenome)
{
makeRegionButtonExtraHtml(hgtaRegionTypeGenome, regionType, "DISABLED");
hPrintf(" <span"NO_GENOME_CLASS">genome (unavailable for selected track)</span>"
" ");
}
else
{
makeRegionButton(hgtaRegionTypeGenome, regionType);
hPrintf(" genome ");
}
if (doEncode)
{
makeRegionButton(hgtaRegionTypeEncode, regionType);
hPrintf(" ENCODE Pilot regions ");
}
makeRegionButton(hgtaRegionTypeRange, regionType);
hPrintf(" position ");
hPrintf("<INPUT TYPE=TEXT NAME=\"%s\" SIZE=26 VALUE=\"%s\" onFocus=\"%s\">\n",
hgtaRange, range, jsRadioUpdate(hgtaRegionType, "regionType", "range"));
cgiMakeButton(hgtaDoLookupPosition, "lookup");
hPrintf(" ");
if (userRegionsFileName() != NULL)
{
makeRegionButton(hgtaRegionTypeUserRegions, regionType);
hPrintf(" defined regions ");
cgiMakeButton(hgtaDoSetUserRegions, "change");
hPrintf(" ");
cgiMakeButton(hgtaDoClearUserRegions, "clear");
}
else
cgiMakeButton(hgtaDoSetUserRegions, "define regions");
hPrintf("</TD></TR>\n");
}
else
{
/* Need to put at least stubs of cgi variables in for JavaScript to work. */
jsTrackingVar("regionType", regionType);
cgiMakeHiddenVar(hgtaRange, range);
cgiMakeHiddenVar(hgtaRegionType, regionType);
}
/* Select identifiers line (if applicable). */
if (!isWig && getIdField(database, curTrack, curTable, hti) != NULL)
{
hPrintf("<TR><TD><B>identifiers (names/accessions):</B>\n");
cgiMakeButton(hgtaDoPasteIdentifiers, "paste list");
hPrintf(" ");
cgiMakeButton(hgtaDoUploadIdentifiers, "upload list");
if (identifierFileName() != NULL)
{
hPrintf(" ");
cgiMakeButton(hgtaDoClearIdentifiers, "clear list");
}
hPrintf("</TD></TR>\n");
}
}
/* microarray options */
/* button for option page here (median/log-ratio, etc) */
/* Filter line. */
{
hPrintf("<TR><TD><B>filter:</B>\n");
if (anyFilter())
{
cgiMakeButton(hgtaDoFilterPage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearFilter, "clear");
if (isWig || isBedGr)
wigShowFilter(conn);
}
else
{
cgiMakeButton(hgtaDoFilterPage, "create");
}
hPrintf("</TD></TR>\n");
}
/* Composite track subtrack merge line. */
boolean canSubtrackMerge = (curTrack && tdbIsComposite(curTrack) && !isBam && !isVcf && !isLongTabix);
if (canSubtrackMerge)
{
hPrintf("<TR><TD><B>subtrack merge:</B>\n");
if (anySubtrackMerge(database, curTable))
{
cgiMakeButton(hgtaDoSubtrackMergePage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearSubtrackMerge, "clear");
}
else
{
cgiMakeButton(hgtaDoSubtrackMergePage, "create");
}
hPrintf("</TD></TR>\n");
}
/* Intersection line. */
if (isPositional)
{
if (anyIntersection())
{
hPrintf("<TR><TD><B>intersection with %s:</B>\n",
cartString(cart, hgtaIntersectTable));
cgiMakeButton(hgtaDoIntersectPage, "edit");
hPrintf(" ");
cgiMakeButton(hgtaDoClearIntersect, "clear");
hPrintf("</TD></TR>\n");
}
else if (canIntersect(database, curTable))
{
hPrintf("<TR><TD><B>intersection:</B>\n");
cgiMakeButton(hgtaDoIntersectPage, "create");
hPrintf("</TD></TR>\n");
}
}
/* Correlation line. */
struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
if (correlateTrackTableOK(tdb, curTable))
{
char *table2 = cartUsualString(cart, hgtaCorrelateTable, "none");
hPrintf("<TR><TD><B>correlation:</B>\n");
if (differentWord(table2, "none") && strlen(table2) && ! isNoGenomeDisabled(database, table2))
{
struct grp *groupList = fullGroupList;
struct grp *selGroup = findSelectedGroup(groupList, hgtaCorrelateGroup);
struct trackDb *tdb2 = findSelectedTrack(fullTrackList, selGroup,hgtaCorrelateTrack);
if (tdbIsComposite(tdb2))
{
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(tdb2->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *subTdb = tdbRef->val;
if (sameString(table2, subTdb->table))
{
tdb2 = subTdb;
break;
}
}
slFreeList(&tdbRefList);
}
cgiMakeButton(hgtaDoCorrelatePage, "calculate");
cgiMakeButton(hgtaDoClearCorrelate, "clear");
if (tdb2 && tdb2->shortLabel)
hPrintf(" (with: %s)", tdb2->shortLabel);
#ifdef NOT_YET
/* debugging dbg vvvvv */
if (curTrack && curTrack->type) /* dbg */
{
hPrintf("<BR> (debug: '%s', '%s(%s)')",
curTrack->type, tdb2->type, table2);
}
/* debugging debug ^^^^^ */
#endif
}
else
cgiMakeButton(hgtaDoCorrelatePage, "create");
hPrintf("</TD></TR>\n");
}
/* Print output type line. */
showOutputTypeRow(isWig, isBedGr, isPositional, isMaf, isChromGraphCt, isPal, isArray, isHalSnake);
/* Print output destination line. */
{
char *compressType =
cartUsualString(cart, hgtaCompressType, textOutCompressNone);
char *fileName = cartUsualString(cart, hgtaOutFileName, "");
hPrintf("<TR><TD>\n");
hPrintf("<B>output file:</B> ");
cgiMakeTextVar(hgtaOutFileName, fileName, 29);
hPrintf(" (leave blank to keep output in browser)</TD></TR>\n");
hPrintf("<TR><TD>\n");
hPrintf("<B>file type returned: </B>");
cgiMakeRadioButton(hgtaCompressType, textOutCompressNone,
sameWord(textOutCompressNone, compressType));
hPrintf(" plain text  ");
cgiMakeRadioButton(hgtaCompressType, textOutCompressGzip,
sameWord(textOutCompressGzip, compressType));
hPrintf(" gzip compressed");
hPrintf("</TD></TR>\n");
}
hPrintf("</TABLE>\n");
/* Submit buttons. */
{
hPrintf("<BR>\n");
if (isWig || isBam || isVcf || isLongTabix)
{
char *name;
extern char *maxOutMenu[];
char *maxOutput = maxOutMenu[0];
if (isCustomTrack(curTable))
name=filterFieldVarName("ct", curTable, "_", filterMaxOutputVar);
else
name=filterFieldVarName(database,curTable, "_",filterMaxOutputVar);
maxOutput = cartUsualString(cart, name, maxOutMenu[0]);
if (isWig)
hPrintf(
"<I>Note: to return more than %s lines, change the filter setting"
" (above). The entire data set may be available for download as"
" a very large file that contains the original data values (not"
" compressed into the wiggle format) -- see the Downloads page."
"</I><BR>", maxOutput);
else if (isBam || isVcf || isLongTabix)
hPrintf(
"<I>Note: to return more than %s lines, change the filter setting"
" (above). Please consider downloading the entire data from our Download pages."
"</I><BR>", maxOutput);
}
else if (anySubtrackMerge(database, curTable) || anyIntersection())
{
hPrintf("<I>Note: The all fields and selected fields output formats "
"are not available when a%s has been specified.</I><BR>",
canSubtrackMerge ? " subtrack merge or intersection" : "n intersection");
}
cgiMakeButton(hgtaDoTopSubmit, "get output");
hPrintf(" ");
if (isPositional || isWig)
{
cgiMakeButton(hgtaDoSummaryStats, "summary/statistics");
hPrintf(" ");
}
#ifdef SOMETIMES
hPrintf(" ");
cgiMakeButton(hgtaDoTest, "test");
#endif /* SOMETIMES */
}
hPrintf("<P>"
"To reset <B>all</B> user cart settings (including custom tracks), \n"
"<A HREF=\"/cgi-bin/cartReset?destination=%s\">click here</A>.\n",
getScriptName());
}
