Output format:\n");
if (isBedGr)
{
if (! bedifiedOnly)
{
slAddTail(&otList, &otAllFields);
slAddTail(&otList, &otSelected);
}
slAddTail(&otList, &otWigData);
slAddTail(&otList, &otWigBed);
slAddTail(&otList, &otCustomTrack);
slAddTail(&otList, &otHyperlinks);
}
else if (isWig)
{
@@ -645,43 +645,43 @@
isChromGraphCt = FALSE, isPal = FALSE, isArray = FALSE, isBam = FALSE, isVcf = FALSE, isHalSnake = FALSE,
isLongTabix = FALSE, isHic = FALSE;
boolean gotClade = hGotClade();
struct hTableInfo *hti = NULL;
hPrintf("\n");
int stepNumber = 1;
printStep(stepNumber++);
/* Print clade, genome and assembly line. */
{
if (gotClade)
{
- hPrintf("clade:\n");
+ hPrintf(" | Clade:\n");
printCladeListHtml(hGenome(database), "change", onChangeClade());
nbSpaces(3);
- hPrintf("genome:\n");
+ hPrintf("Genome:\n");
printGenomeListForCladeHtml(database, "change", onChangeOrg());
}
else
{
- hPrintf(" | genome:\n");
+ hPrintf(" | Genome:\n");
printGenomeListHtml(database, "change", onChangeOrg());
}
nbSpaces(3);
- hPrintf("assembly:\n");
+ hPrintf("Assembly:\n");
printAssemblyListHtml(database, "change", onChangeDb());
hPrintf(" | \n");
}
/* Print group and track line. */
{
hPrintf("");
selGroup = showGroupField(hgtaGroup, "change", onChangeGroupOrTrack(), conn, hAllowAllTables());
nbSpaces(3);
curTrack = showTrackField(selGroup, hgtaTrack, "change", onChangeGroupOrTrack(), FALSE);
nbSpaces(3);
hPrintf(" | \n");
}
/* Print table line. */
@@ -700,31 +700,31 @@
{
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, "data format description");
+ cgiMakeButton(hgtaDoSchema, "Data format description");
hPrintf("\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);
}
/* Table-specific options */
@@ -744,257 +744,257 @@
char *regionType;
if (cartVarExists(cart, "hgFind.matches")) // coming back from a search
regionType = cartUsualString(cart, hgtaRegionType, hgtaRegionTypeRange);
else
regionType = cartUsualString(cart, hgtaRegionType, hgtaRegionTypeGenome);
char *range = cartUsualString(cart, hgtaRange, "");
if (isPositional)
{
boolean doEncode = FALSE;
if (!trackHubDatabase(database))
doEncode = sqlTableExists(conn, "encodeRegions");
- hPrintf("region:\n");
+ hPrintf(" | Region:\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(" genome (unavailable for selected track)"
" ");
}
else
{
makeRegionButton(hgtaRegionTypeGenome, regionType);
- hPrintf(" genome ");
+ hPrintf(" Genome ");
}
if (doEncode)
{
makeRegionButton(hgtaRegionTypeEncode, regionType);
hPrintf(" ENCODE Pilot regions ");
}
makeRegionButton(hgtaRegionTypeRange, regionType);
- hPrintf(" position ");
+ hPrintf(" Position ");
hPrintf("\n",
hgtaRange, hgtaRange, range);
jsOnEventById("focus", hgtaRange,
jsRadioUpdate(hgtaRegionType, "regionType", "range"));
- cgiMakeButton(hgtaDoLookupPosition, "lookup");
+ cgiMakeButton(hgtaDoLookupPosition, "Lookup");
hPrintf(" ");
if (userRegionsFileName() != NULL)
{
makeRegionButton(hgtaRegionTypeUserRegions, regionType);
- hPrintf(" defined regions ");
- cgiMakeButton(hgtaDoSetUserRegions, "change");
+ hPrintf(" Defined regions ");
+ cgiMakeButton(hgtaDoSetUserRegions, "Change");
hPrintf(" ");
- cgiMakeButton(hgtaDoClearUserRegions, "clear");
+ cgiMakeButton(hgtaDoClearUserRegions, "Clear");
}
else
- cgiMakeButton(hgtaDoSetUserRegions, "define regions");
+ cgiMakeButton(hgtaDoSetUserRegions, "Define regions");
hPrintf(" | \n");
if (disableGenome) { // no need to check curTrack for NULL, disableGenome can only be set if curTable is set
hPrintf("");
char *noGenomeNote = trackDbSettingClosestToHome(curTrack, "noGenomeReason");
hPrintf("Note: This track is unavailable for genome-wide download. ");
if (noGenomeNote)
hPrintf("Reason: %s", noGenomeNote);
else
hPrintf("Usually, this is due to distribution restrictions of the source database or the size of the track. Please see the track documentation for more details. Contact us if you are still unable to access the data. ");
hPrintf(" | ");
}
}
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("identifiers (names/accessions):\n");
- cgiMakeButton(hgtaDoPasteIdentifiers, "paste list");
+ hPrintf(" | Identifiers (names/accessions):\n");
+ cgiMakeButton(hgtaDoPasteIdentifiers, "Paste list");
hPrintf(" ");
- cgiMakeButton(hgtaDoUploadIdentifiers, "upload list");
+ cgiMakeButton(hgtaDoUploadIdentifiers, "Upload list");
if (identifierFileName() != NULL)
{
hPrintf(" ");
- cgiMakeButton(hgtaDoClearIdentifiers, "clear list");
+ cgiMakeButton(hgtaDoClearIdentifiers, "Clear list");
}
hPrintf(" | \n");
}
}
/* button for option page here (median/log-ratio, etc) */
printStep(stepNumber++);
/* Filter line. */
{
-hPrintf("filter:\n");
+hPrintf(" | Filter:\n");
if (anyFilter())
{
- cgiMakeButton(hgtaDoFilterPage, "edit");
+ cgiMakeButton(hgtaDoFilterPage, "Edit");
hPrintf(" ");
- cgiMakeButton(hgtaDoClearFilter, "clear");
+ cgiMakeButton(hgtaDoClearFilter, "Clear");
if (isWig || isBedGr)
wigShowFilter(conn);
}
else
{
- cgiMakeButton(hgtaDoFilterPage, "create");
+ cgiMakeButton(hgtaDoFilterPage, "Create");
}
hPrintf(" | \n");
}
/* Composite track subtrack merge line. */
boolean canSubtrackMerge = (curTrack && tdbIsComposite(curTrack) && !isBam && !isVcf && !isLongTabix && !isHic);
if (canSubtrackMerge)
{
- hPrintf("subtrack merge:\n");
+ hPrintf(" | Subtrack merge:\n");
if (anySubtrackMerge(database, curTable))
{
- cgiMakeButton(hgtaDoSubtrackMergePage, "edit");
+ cgiMakeButton(hgtaDoSubtrackMergePage, "Edit");
hPrintf(" ");
- cgiMakeButton(hgtaDoClearSubtrackMerge, "clear");
+ cgiMakeButton(hgtaDoClearSubtrackMerge, "Clear");
}
else
{
- cgiMakeButton(hgtaDoSubtrackMergePage, "create");
+ cgiMakeButton(hgtaDoSubtrackMergePage, "Create");
}
hPrintf(" | \n");
}
/* Intersection line. */
if (isPositional)
{
if (anyIntersection())
{
- hPrintf("intersection with %s:\n",
+ hPrintf(" | Intersection with %s:\n",
cartString(cart, hgtaIntersectTable));
- cgiMakeButton(hgtaDoIntersectPage, "edit");
+ cgiMakeButton(hgtaDoIntersectPage, "Edit");
hPrintf(" ");
- cgiMakeButton(hgtaDoClearIntersect, "clear");
+ cgiMakeButton(hgtaDoClearIntersect, "Clear");
hPrintf(" | \n");
}
else if (canIntersect(database, curTable))
{
- hPrintf("intersection:\n");
- cgiMakeButton(hgtaDoIntersectPage, "create");
+ hPrintf(" | Intersection:\n");
+ cgiMakeButton(hgtaDoIntersectPage, "Create");
hPrintf(" | \n");
}
}
/* Correlation line. */
struct trackDb *tdb = findTdbForTable(database, curTrack, curTable, ctLookupName);
if (correlateTrackTableOK(tdb, curTable))
{
char *table2 = cartUsualString(cart, hgtaCorrelateTable, "none");
- hPrintf("correlation:\n");
+ hPrintf(" | Correlation:\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");
+ 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(" (debug: '%s', '%s(%s)')",
curTrack->type, tdb2->type, table2);
}
/* debugging debug ^^^^^ */
#endif
}
else
- cgiMakeButton(hgtaDoCorrelatePage, "create");
+ cgiMakeButton(hgtaDoCorrelatePage, "Create");
hPrintf(" | \n");
}
/* Print output type line. */
printStep(stepNumber++);
showOutputTypeRow(isWig, isBedGr, isPositional, isMaf, isChromGraphCt, isPal, isArray, isHalSnake);
/* Print output destination line. */
{
char *compressType = cartUsualString(cart, hgtaCompressType, textOutCompressNone);
char *fieldSep = cartUsualString(cart, hgtaOutSep, outTab);
char *fileName = cartUsualString(cart, hgtaOutFileName, "");
hPrintf("\n");
- hPrintf("output filename: ");
+ hPrintf("Output filename: ");
cgiMakeTextVar(hgtaOutFileName, fileName, 29);
hPrintf(" (add .csv extension if opening in Excel, leave blank to keep output in browser) | \n");
hPrintf("\n");
- hPrintf("output field separator: ");
+ hPrintf("Output field separator: ");
// tab or csv output
cgiMakeRadioButton(hgtaOutSep, outTab, sameWord(outTab, fieldSep));
hPrintf(" tsv (tab-separated)  ");
cgiMakeRadioButton(hgtaOutSep, outCsv, sameWord(outCsv, fieldSep));
hPrintf(" csv (for excel) ");
hPrintf(" | \n");
hPrintf("\n");
- hPrintf("file type returned: ");
+ hPrintf("File type returned: ");
cgiMakeRadioButton(hgtaCompressType, textOutCompressNone,
sameWord(textOutCompressNone, compressType));
- hPrintf(" plain text ");
+ hPrintf(" Plain text ");
cgiMakeRadioButton(hgtaCompressType, textOutCompressGzip,
sameWord(textOutCompressGzip, compressType));
- hPrintf(" gzip compressed");
+ hPrintf(" Gzip compressed");
hPrintf(" | \n");
}
hPrintf(" \n");
/* Submit buttons. */
{
hPrintf(" \n");
if (isWig || isBam || isVcf || isLongTabix || isHic)
{
char *name;
extern char *maxOutMenu[];
char *maxOutput = maxOutMenu[0];
@@ -1012,35 +1012,35 @@
" a very large file that contains the original data values (not"
" compressed into the wiggle format) -- see the Downloads page."
" ", maxOutput);
else if (isBam || isVcf || isLongTabix || isHic)
hPrintf(
"Note: to return more than %s lines, change the filter setting"
" (above). Please consider downloading the entire data from our Download pages."
" ", maxOutput);
}
else if (anySubtrackMerge(database, curTable) || anyIntersection())
{
hPrintf("Note: The all fields and selected fields output formats "
"are not available when a%s has been specified. ",
canSubtrackMerge ? " subtrack merge or intersection" : "n intersection");
}
- cgiMakeButton(hgtaDoTopSubmit, "get output");
+ cgiMakeButton(hgtaDoTopSubmit, "Get output");
hPrintf(" ");
if (isPositional || isWig)
{
- cgiMakeButton(hgtaDoSummaryStats, "summary/statistics");
+ cgiMakeButton(hgtaDoSummaryStats, "Summary/statistics");
hPrintf(" ");
}
#ifdef SOMETIMES
hPrintf(" ");
cgiMakeButton(hgtaDoTest, "test");
#endif /* SOMETIMES */
}
hPrintf("");
}
static char *getGenomeSpaceText()
/* fetch GenomeSpace text if enabled */
{
if (isGenomeSpaceEnabled())
|