static void verifySubTracks(struct trackDb *tdbList, struct hash *compositeHash)
/* Verify subGroup relelated settings in subtracks, assisted by compositeHash */
{
struct trackDb *tdb;
for (tdb = tdbList; tdb != NULL; tdb = tdb->next)
{
struct slRef *child;
if (trackDbLocalSetting(tdb, "compositeTrack"))
{
struct slRef *childList = trackDbListGetRefsToDescendantLeaves(
tdb->subtracks);
verbose(2,"verifying %s child %p\n",tdb->track, childList);
for (child = childList; child != NULL; child = child->next)
{
struct trackDb *childTdb = child->val;
verbose(2, " checking child %s\n",childTdb->track);
/* Look for some ancestor in composite hash and set sgd to it. */
struct subGroupData *sgd = hashFindVal(compositeHash, tdb->track);
verbose(2, "looking for %s in compositeHash got %p\n",
tdb->track, sgd);
assert(sgd != NULL);
checkOneSubGroups(tdb->track, childTdb, sgd);
}
}
}
}
static void addTablesAccordingToTrackType(char *db, struct slName **pList, struct hash *uniqHash,
struct trackDb *track)
/* Parse out track->type and if necessary add some tables from it. */
{
struct slName *name;
char *trackDupe = cloneString(track->type);
if (trackDupe != NULL && trackDupe[0] != 0)
{
char *s = trackDupe;
char *type = nextWord(&s);
if (sameString(type, "wigMaf"))
{
static char *wigMafAssociates[] = {"frames", "summary"};
int i;
for (i=0; i<ArraySize(wigMafAssociates); ++i)
{
char *setting = wigMafAssociates[i];
char *table = trackDbSetting(track, setting);
if (table != NULL)
{
name = slNameNew(table);
slAddHead(pList, name);
hashAdd(uniqHash, table, NULL);
}
}
/* include conservation wiggle tables */
struct consWiggle *wig, *wiggles = wigMafWiggles(db, track);
slReverse(&wiggles);
for (wig = wiggles; wig != NULL; wig = wig->next)
{
name = slNameNew(wig->table);
slAddHead(pList, name);
hashAdd(uniqHash, wig->table, NULL);
}
}
if (track->subtracks)
{
struct slName *subList = NULL;
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(track->subtracks);
slSort(&tdbRefList, trackDbRefCmp);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *subTdb = tdbRef->val;
name = slNameNew(subTdb->table);
slAddTail(&subList, name);
hashAdd(uniqHash, subTdb->table, NULL);
}
pList = slCat(pList, subList);
}
}
freez(&trackDupe);
}
static void doOutWig(struct trackDb *track, char *table, struct sqlConnection *conn,
enum wigOutputType wigOutType)
{
struct region *regionList = getRegions(), *region;
int maxOut = 0, outCount, curOut = 0;
char *shortLabel = table, *longLabel = table;
if (track == NULL)
errAbort("Sorry, can't find necessary track information for %s. "
"If you reached this page by selecting \"All tables\" as the "
"group, please go back and select the same table via a regular "
"track group if possible.",
table);
maxOut = bigFileMaxOutput();
if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE))
fputs("#", stdout);
else
textOpen();
if (track != NULL)
{
if (!sameString(track->table, table) && track->subtracks != NULL)
{
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(track->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *tdb = tdbRef->val;
if (sameString(tdb->table, table))
{
track = tdb;
break;
}
}
slFreeList(&tdbRefList);
}
shortLabel = track->shortLabel;
longLabel = track->longLabel;
}
wigDataHeader(shortLabel, longLabel, NULL, wigOutType);
for (region = regionList; region != NULL; region = region->next)
{
int curMaxOut = maxOut - curOut;
if (anySubtrackMerge(database, table))
outCount = mergedWigOutRegion(table, conn, region, curMaxOut,
wigOutType);
else if (startsWithWord("bedGraph", track->type))
outCount = bedGraphOutRegion(table, conn, region, curMaxOut,
wigOutType);
else if (startsWithWord("mathWig", track->type))
outCount = mathWigOutRegion(track, table, conn, region, curMaxOut, wigOutType);
else if (startsWithWord("bigWig", track->type))
outCount = bigWigOutRegion(table, conn, region, curMaxOut, wigOutType);
else
outCount = wigOutRegion(table, conn, region, curMaxOut,
wigOutType, NULL, 0);
curOut += outCount;
if (curOut >= maxOut)
break;
}
if (curOut >= maxOut)
errAbort("Reached output limit of %d data values, please make region smaller,\n\tor set a higher output line limit with the filter settings.", curOut);
}
struct dataVector *mergedWigDataVector(char *table,
struct sqlConnection *conn, struct region *region)
/* Perform the specified subtrack merge wiggle-operation on table and
* all other selected subtracks and intersect if necessary. */
{
struct trackDb *tdb1 = hTrackDbForTrack(database, table);
struct trackTable *tt1 = trackTableNew(tdb1, table, conn);
struct dataVector *dataVector1 = dataVectorFetchOneRegion(tt1, region, conn);
struct trackDb *cTdb = hCompositeTrackDbForSubtrack(database, tdb1);
int numSubtracks = 1;
char *op = cartString(cart, hgtaSubtrackMergeWigOp);
boolean requireAll = cartBoolean(cart, hgtaSubtrackMergeRequireAll);
boolean useMinScore = cartBoolean(cart, hgtaSubtrackMergeUseMinScore);
float minScore = atof(cartString(cart, hgtaSubtrackMergeMinScore));
if (cTdb == NULL)
errAbort("mergedWigDataVector: could not find parent/composite trackDb "
"entry for subtrack %s", table);
if (dataVector1 == NULL)
{
return NULL;
}
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(cTdb->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
struct trackDb *sTdb = tdbRef->val;
if (isSubtrackMerged(sTdb->table) &&
! sameString(tdb1->table, sTdb->table) &&
hSameTrackDbType(tdb1->type, sTdb->type))
{
struct trackTable *tt2 = trackTableNew(sTdb, sTdb->table, conn);
struct dataVector *dataVector2 = dataVectorFetchOneRegion(tt2, region,
conn);
numSubtracks++;
if (dataVector2 == NULL)
{
if (requireAll)
{
freeDataVector(&dataVector1);
return NULL;
}
continue;
}
if (sameString(op, "average") || sameString(op, "sum"))
dataVectorSum(dataVector1, dataVector2, requireAll);
else if (sameString(op, "product"))
dataVectorProduct(dataVector1, dataVector2, requireAll);
else if (sameString(op, "min"))
dataVectorMin(dataVector1, dataVector2, requireAll);
else if (sameString(op, "max"))
dataVectorMax(dataVector1, dataVector2, requireAll);
else
errAbort("mergedWigOutRegion: unknown WigOp %s", op);
dataVectorFree(&dataVector2);
}
}
slFreeList(&tdbRefList);
if (sameString(op, "average"))
dataVectorNormalize(dataVector1, numSubtracks);
if (useMinScore)
dataVectorFilterMin(dataVector1, minScore);
intersectDataVector(table, dataVector1, region, conn);
return dataVector1;
}
char *describeSubtrackMerge(char *linePrefix)
/* Return a multi-line string that describes the specified subtrack merge,
* with each line beginning with linePrefix. */
{
struct dyString *dy = dyStringNew(512);
struct trackDb *primary = subTdbFind(curTrack,curTable), *tdb = NULL;
dyStringAppend(dy, linePrefix);
dyStringPrintf(dy, "Subtrack merge, primary table = %s (%s)\n",
curTable, primary->longLabel);
dyStringAppend(dy, linePrefix);
dyStringPrintf(dy, "Subtrack merge operation: ");
if (isWiggle(database, curTable) || isBedGraph(curTable) || isBigWigTable(curTable))
{
char *op = cartString(cart, hgtaSubtrackMergeWigOp);
dyStringPrintf(dy, "%s of %s and selected subtracks:\n", op, curTable);
}
else
{
char *op = cartString(cart, hgtaSubtrackMergeOp);
if (sameString(op, "any"))
dyStringPrintf(dy, "All %s records that have any overlap with "
"any other selected subtrack:\n",
curTable);
else if (sameString(op, "none"))
dyStringPrintf(dy, "All %s records that have no overlap with "
"any other selected subtrack:\n",
curTable);
else if (sameString(op, "more"))
{
dyStringPrintf(dy, "All %s records that have at least %s ",
curTable,
cartString(cart, hgtaNextSubtrackMergeMoreThreshold));
dyStringPrintf(dy, " %% overlap with any other selected subtrack:\n");
}
else if (sameString(op, "less"))
{
dyStringPrintf(dy, "All %s records that have at most %s ",
curTable,
cartString(cart, hgtaNextSubtrackMergeLessThreshold));
dyStringPrintf(dy, " %% overlap with any other selected subtrack:\n");
}
else if (sameString(op, "cat"))
dyStringPrintf(dy, "All %s records, as well as all records from "
"all other selected subtracks:\n", curTable);
else if (sameString(op, "and"))
dyStringPrintf(dy, "Base-pair-wise intersection (AND) of %s and "
"other selected subtracks:\n", curTable);
else if (sameString(op, "or"))
dyStringPrintf(dy, "Base-pair-wise union (OR) of %s and other "
"selected subtracks:\n",
curTable);
else
errAbort("describeSubtrackMerge: unrecognized op %s", op);
}
struct slRef *tdbRef, *tdbRefList = trackDbListGetRefsToDescendantLeaves(curTrack->subtracks);
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
tdb = tdbRef->val;
if (!sameString(tdb->table, curTable) &&
isSubtrackMerged(tdb->table) &&
sameString(tdb->type, primary->type))
{
dyStringAppend(dy, linePrefix);
dyStringPrintf(dy, " %s (%s)\n", tdb->table, tdb->longLabel);
}
}
return dyStringCannibalize(&dy);
}
struct bed *getRegionAsMergedBed(
char *db, char *table, /* Database and table. */
struct region *region, /* Region to get data for. */
char *filter, /* Filter to add to SQL where clause if any. */
struct hash *idHash, /* Restrict to id's in this hash if non-NULL. */
struct lm *lm, /* Where to allocate memory. */
int *retFieldCount) /* Number of fields. */
/* Return a bed list of all items in the given range in subtrack-merged table.
* Cleanup result via lmCleanup(&lm) rather than bedFreeList. */
{
if (! anySubtrackMerge(db, table))
return getRegionAsBed(db, table, region, filter, idHash, lm, retFieldCount);
else
{
struct hTableInfo *hti = getHtiOnDb(database, table);
int chromSize = hChromSize(database, region->chrom);
Bits *bits1 = NULL;
Bits *bits2 = NULL;
struct bed *bedMerged = NULL;
struct trackDb *subtrack = NULL;
char *primaryType = findTypeForTable(database,curTrack,table, ctLookupName);
char *op = cartString(cart, hgtaSubtrackMergeOp);
boolean isBpWise = (sameString(op, "and") || sameString(op, "or"));
double moreThresh = cartDouble(cart, hgtaSubtrackMergeMoreThreshold);
double lessThresh = cartDouble(cart, hgtaSubtrackMergeLessThreshold);
boolean firstTime = TRUE;
if (sameString(op, "cat"))
{
struct bed *bedList = getRegionAsBed(db, table, region, filter,
idHash, lm, retFieldCount);
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(curTrack->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
subtrack = tdbRef->val;
if (! sameString(curTable, subtrack->table) &&
isSubtrackMerged(subtrack->table) &&
sameString(subtrack->type, primaryType))
{
struct bed *bedList2 =
getRegionAsBed(db, subtrack->table, region, NULL,
idHash, lm, retFieldCount);
bedList = slCat(bedList, bedList2);
}
}
slFreeList(&tdbRefList);
return bedList;
}
bits1 = bitAlloc(chromSize+8);
bits2 = bitAlloc(chromSize+8);
/* If doing a base-pair-wise operation, then start with the primary
* subtrack's ranges in bits1, and AND/OR all the selected subtracks'
* ranges into bits1. If doing a non-bp-wise intersection, then
* start with all bits clear in bits1, and then OR selected subtracks'
* ranges into bits1. */
if (isBpWise)
{
struct lm *lm2 = lmInit(64*1024);
struct bed *bedList1 = getRegionAsBed(db, table, region, filter,
idHash, lm2, retFieldCount);
bedOrBits(bits1, chromSize, bedList1, hti->hasBlocks, 0);
lmCleanup(&lm2);
}
struct slRef *tdbRefList = trackDbListGetRefsToDescendantLeaves(curTrack->subtracks);
struct slRef *tdbRef;
for (tdbRef = tdbRefList; tdbRef != NULL; tdbRef = tdbRef->next)
{
subtrack = tdbRef->val;
if (! sameString(curTable, subtrack->table) &&
isSubtrackMerged(subtrack->table) &&
sameString(subtrack->type, primaryType))
{
struct hTableInfo *hti2 = getHtiOnDb(database, subtrack->table);
struct lm *lm2 = lmInit(64*1024);
struct bed *bedList2 =
getRegionAsBed(db, subtrack->table, region, NULL, idHash,
lm2, NULL);
if (firstTime)
firstTime = FALSE;
else
bitClear(bits2, chromSize);
bedOrBits(bits2, chromSize, bedList2, hti2->hasBlocks, 0);
if (sameString(op, "and"))
bitAnd(bits1, bits2, chromSize);
else
bitOr(bits1, bits2, chromSize);
lmCleanup(&lm2);
}
}
slFreeList(&tdbRefList);
if (isBpWise)
{
bedMerged = bitsToBed4List(bits1, chromSize, region->chrom, 1,
region->start, region->end, lm);
if (retFieldCount != NULL)
*retFieldCount = 4;
}
else
{
struct bed *bedList1 = getRegionAsBed(db, table, region, filter,
idHash, lm, retFieldCount);
bedMerged = filterBedByOverlap(bedList1, hti->hasBlocks, op,
moreThresh, lessThresh, bits1,
chromSize);
}
bitFree(&bits1);
bitFree(&bits2);
return bedMerged;
}
}
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());
}
