void palOptions(struct cart *cart,
struct sqlConnection *conn, void (*addButtons)(),
char *extraVar)
/* output the options dialog (select MAF file, output options */
{
char *database = sqlGetDatabase(conn);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=POST>\n", cgiScriptName());
cartSaveSession(cart);
char *mafTable = outMafTableDrop(cart, conn);
char *numColumns = cartUsualString(cart, hgtaCGINumColumns, "");
printf("<BR><BR><B>Formatting options:</B><BR>\n");
jsMakeTrackingCheckBox(cart, hgtaCGIGeneExons, hgtaJSGeneExons, FALSE);
printf("Separate into exons<BR>");
jsMakeTrackingCheckBox(cart, hgtaCGIGeneNoTrans, hgtaJSGeneNoTrans, FALSE);
printf("Show nucleotides<BR>");
jsMakeTrackingCheckBox(cart, hgtaCGIGeneOutBlank, hgtaJSGeneOutBlank, FALSE);
printf("Output lines with just dashes<BR>");
jsMakeTrackingCheckBox(cart, hgtaCGIOutTable, hgtaJSOutTable, FALSE);
printf("Format output as table ");
jsMakeTrackingCheckBox(cart, hgtaCGITruncHeader, hgtaJSTruncHeader, FALSE);
printf("Truncate headers at ");
cgiMakeTextVar(hgtaCGINumColumns, numColumns, 2);
printf("characters (enter zero for no headers)<BR>");
printf("<BR>");
struct trackDb *maftdb = hTrackDbForTrack(database, mafTable);
/* get maf parent (if any) */
maftdb->parent = hCompositeTrackDbForSubtrack(database,maftdb);
wigMafSpeciesTable(cart, maftdb, mafTable, database);
addButtons();
cartSaveSession(cart);
hPrintf("</FORM>\n");
/* Hidden form - for benefit of javascript. */
{
static char *saveVars[32];
int varCount = ArraySize(curVars);
assert(varCount < (sizeof saveVars / sizeof(char *)));
memcpy(saveVars, curVars, varCount * sizeof(saveVars[0]));
if (extraVar != NULL)
{
assert(varCount + 1 < (sizeof saveVars / sizeof(char *)));
saveVars[varCount] = extraVar;
varCount++;
}
jsCreateHiddenForm(cart, cgiScriptName(), saveVars, varCount);
}
}
struct genoGraph *getDbGraphs(struct sqlConnection *conn)
/* Get graphs defined in database. Also use the composite settings if */
/* it's a subGraph. */
{
struct genoGraph *list = NULL, *gg;
struct sqlConnection *conn2 = hAllocConn(database);
struct sqlResult *sr;
char **row;
/* Get initial information from metaChromGraph table */
if (sqlTableExists(conn, "metaChromGraph"))
{
sr = sqlGetResult(conn, "select name,binaryFile from metaChromGraph where binaryFile!='composite'");
while ((row = sqlNextRow(sr)) != NULL)
{
char *table = row[0], *binaryFile = row[1];
AllocVar(gg);
gg->name = gg->shortLabel = gg->longLabel = cloneString(table);
gg->binFileName = cloneString(binaryFile);
slAddHead(&list, gg);
}
sqlFreeResult(&sr);
}
slReverse(&list);
/* Where possible fill in additional info from trackDb. */
for (gg = list; gg != NULL; gg = gg->next)
{
struct trackDb *tdb = hTrackDbForTrack(database, gg->name);
struct trackDb *compTdb = hCompositeTrackDbForSubtrack(database, tdb);
gg->isSubGraph = (compTdb != NULL) ? TRUE : FALSE;
gg->isComposite = FALSE;
if (tdb != NULL)
{
struct chromGraphSettings *cgs = NULL;
if (compTdb == NULL)
cgs = chromGraphSettingsGet(gg->name, conn2, tdb, cart);
else
cgs = chromGraphSettingsGet(compTdb->table, conn2, compTdb, cart);
gg->shortLabel = tdb->shortLabel;
gg->longLabel = tdb->longLabel;
gg->settings = cgs;
}
else
{
/* If we're here then there's an entry in metaChromGraph but not trackDb */
gg->settings = chromGraphSettingsGet(gg->name, NULL, NULL, NULL);
}
}
hFreeConn(&conn2);
slReverse(&list);
return list;
}
int palOutPredList(struct sqlConnection *conn, struct cart *cart,
struct genePred *list)
/* output a list of genePreds in pal format */
{
if (list == NULL)
return 0;
char *mafTable = cartString(cart, hgtaCGIGeneMafTable);
char *database = sqlGetDatabase(conn);
struct trackDb *maftdb = hTrackDbForTrack(database, mafTable);
struct wigMafSpecies *wmSpecies;
int groupCnt;
/* get maf parent (if any) */
maftdb->parent = hCompositeTrackDbForSubtrack(database,maftdb);
/* this queries the state of the getSpecies dialog */
wigMafGetSpecies(cart, maftdb, maftdb->track, database, &wmSpecies, &groupCnt);
/* since the species selection dialog doesn't list
* the reference species, we just automatically include
* it */
struct slName *includeList = slNameNew(database);
/* now make a list of all species that are on */
for(; wmSpecies; wmSpecies = wmSpecies->next)
{
if (wmSpecies->on)
{
struct slName *newName = slNameNew(wmSpecies->name);
slAddHead(&includeList, newName);
}
}
slReverse(&includeList);
boolean inExons = cartUsualBoolean(cart, hgtaCGIGeneExons , FALSE);
boolean noTrans = cartUsualBoolean(cart, hgtaCGIGeneNoTrans, FALSE);
boolean outBlank = cartUsualBoolean(cart, hgtaCGIGeneOutBlank, FALSE);
boolean outTable = cartUsualBoolean(cart, hgtaCGIOutTable, FALSE);
boolean truncHeader = cartUsualBoolean(cart, hgtaCGITruncHeader, FALSE);
int numCols = cartUsualInt(cart, hgtaCGINumColumns, 20);
unsigned options = 0;
if (inExons) options |= MAFGENE_EXONS;
if (noTrans) options |= MAFGENE_NOTRANS;
if (outBlank) options |= MAFGENE_OUTBLANK;
if (outTable) options |= MAFGENE_OUTTABLE;
if (!truncHeader)
numCols = -1;
/* send out the alignments */
int outCount = 0;
for( ; list ; list = list->next)
{
if (list->cdsStart != list->cdsEnd)
{
outCount++;
mafGeneOutPred(stdout, list, database, mafTable,
includeList, options, numCols);
}
}
slNameFreeList(&includeList);
return outCount;
}
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;
}
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());
}