e14906744b1316f4d4c2abc81b69168ac070d5ad
max
  Wed Feb 5 03:10:21 2020 -0800
adding note about precooked gtf files to table browser, refs #24810

diff --git src/hg/hgTables/mainPage.c src/hg/hgTables/mainPage.c
index b78cd71..1c93157 100644
--- src/hg/hgTables/mainPage.c
+++ src/hg/hgTables/mainPage.c
@@ -1,1022 +1,1040 @@
 /* mainPage - stuff to put up the first table browser page. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "htmshell.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "cartTrackDb.h"
 #include "textOut.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "web.h"
 #include "jsHelper.h"
 #include "hui.h"
 #include "hgColors.h"
 #include "trackDb.h"
 #include "grp.h"
 #include "hgTables.h"
 #include "joiner.h"
 #include "trackDb.h"
 #include "hubConnect.h"
 #include "trackHub.h"
 #include "hgConfig.h"
 
 
 static struct dyString *onChangeStart()
 /* Start up a javascript onChange command */
 {
 struct dyString *dy = jsOnChangeStart();
 jsDropDownCarryOver(dy, hgtaTrack);
 jsDropDownCarryOver(dy, hgtaGroup);
 jsTrackedVarCarryOver(dy, hgtaRegionType, "regionType");
 jsTextCarryOver(dy, hgtaRange);
 jsDropDownCarryOver(dy, hgtaOutputType);
 jsTextCarryOver(dy, hgtaOutFileName);
 return dy;
 }
 
 static char *onChangeClade()
 /* Return javascript executed when they change clade. */
 {
 struct dyString *dy = onChangeStart();
 jsDropDownCarryOver(dy, "clade");
 jsDropDownCarryOver(dy, hgtaTable);
 dyStringAppend(dy, " document.hiddenForm.org.value=0;");
 dyStringAppend(dy, " document.hiddenForm.db.value=0;");
 dyStringAppend(dy, " document.hiddenForm.position.value='';");
 return jsOnChangeEnd(&dy);
 }
 
 static char *onChangeOrg()
 /* Return javascript executed when they change organism. */
 {
 struct dyString *dy = onChangeStart();
 jsDropDownCarryOver(dy, "clade");
 jsDropDownCarryOver(dy, "org");
 jsDropDownCarryOver(dy, hgtaTable);
 dyStringAppend(dy, " document.hiddenForm.db.value=0;");
 dyStringAppend(dy, " document.hiddenForm.position.value='';");
 return jsOnChangeEnd(&dy);
 }
 
 static char *onChangeDb()
 /* Return javascript executed when they change database. */
 {
 struct dyString *dy = onChangeStart();
 jsDropDownCarryOver(dy, "clade");
 jsDropDownCarryOver(dy, "db");
 jsDropDownCarryOver(dy, hgtaTable);
 dyStringAppend(dy, " document.hiddenForm.position.value='';");
 return jsOnChangeEnd(&dy);
 }
 
 static char *onChangeGroupOrTrack()
 /* Return javascript executed when they change group. */
 {
 struct dyString *dy = onChangeStart();
 jsDropDownCarryOver(dy, "clade");
 jsDropDownCarryOver(dy, "db");
 jsDropDownCarryOver(dy, "org");
 dyStringPrintf(dy, " document.hiddenForm.%s.value=0;", hgtaTable);
 return jsOnChangeEnd(&dy);
 }
 
 static char *onChangeTable()
 /* Return javascript executed when they change group. */
 {
 struct dyString *dy = onChangeStart();
 jsDropDownCarryOver(dy, "clade");
 jsDropDownCarryOver(dy, "db");
 jsDropDownCarryOver(dy, "org");
 jsDropDownCarryOver(dy, hgtaTable);
 return jsOnChangeEnd(&dy);
 }
 
 void makeRegionButtonExtraHtml(char *val, char *selVal, char *extraHtml)
 /* Make region radio button including a little Javascript to save selection state
  * and optional extra html attributes. */
 {
 jsMakeTrackingRadioButtonExtraHtml(hgtaRegionType, "regionType", val, selVal, extraHtml);
 }
 
 void makeRegionButton(char *val, char *selVal)
 /* Make region radio button including a little Javascript
  * to save selection state. */
 {
 makeRegionButtonExtraHtml(val, selVal, NULL);
 }
 
 struct grp *showGroupField(char *groupVar, char *event, char *groupScript,
     struct sqlConnection *conn, boolean allTablesOk)
 /* Show group control. Returns selected group. */
 {
 struct grp *group, *groupList = fullGroupList;
 struct grp *selGroup = findSelectedGroup(groupList, groupVar);
 hPrintf("<B>group:</B>\n");
 hPrintf("<SELECT NAME=%s id='%s'>\n", groupVar, groupVar);
 jsOnEventById(event,groupVar,groupScript);
 for (group = groupList; group != NULL; group = group->next)
     {
     if (allTablesOk || differentString(group->name, "allTables"))
         hPrintf(" <OPTION VALUE=%s%s>%s\n", group->name,
                 (group == selGroup ? " SELECTED" : ""),
                 group->label);
     }
 hPrintf("</SELECT>\n");
 return selGroup;
 }
 
 static void addIfExists(struct hash *hash, struct slName **pList, char *name)
 /* Add name to tail of list if it exists in hash. */
 {
 if (hashLookup(hash, name))
     slNameAddTail(pList, name);
 }
 
 struct slName *getDbListForGenome()
 /* Get list of selectable databases. */
 {
 struct hash *hash = sqlHashOfDatabases();
 struct slName *dbList = NULL;
 addIfExists(hash, &dbList, database);
 addIfExists(hash, &dbList, "uniProt");
 addIfExists(hash, &dbList, "proteome");
 addIfExists(hash, &dbList, "go");
 addIfExists(hash, &dbList, "hgFixed");
 addIfExists(hash, &dbList, "visiGene");
 addIfExists(hash, &dbList, "ultra");
 return dbList;
 }
 
 char *findSelDb()
 /* Find user selected database (as opposed to genome database). */
 {
 struct slName *dbList = getDbListForGenome();
 char *selDb = cartUsualString(cart, hgtaTrack, NULL);
 if (!slNameInList(dbList, selDb))
     selDb = cloneString(dbList->name);
 slFreeList(&dbList);
 return selDb;
 }
 
 struct trackDb *showTrackField(struct grp *selGroup, char *trackVar, char *event, char *trackScript,
                                boolean disableNoGenome)
 /* Show track control. Returns selected track. */
 {
 struct trackDb *track, *selTrack = NULL;
 if (trackScript == NULL)
     trackScript = "";
 if (sameString(selGroup->name, "allTables"))
     {
     char *selDb = findSelDb();
     struct slName *dbList = getDbListForGenome(), *db;
     hPrintf("<B>database:</B>\n");
     hPrintf("<SELECT NAME=\"%s\" id='%s'>\n", trackVar, trackVar);
     jsOnEventById(event, trackVar, trackScript);
     for (db = dbList; db != NULL; db = db->next)
 	{
 	hPrintf(" <OPTION VALUE=%s%s>%s\n", db->name,
 		(sameString(db->name, selDb) ? " SELECTED" : ""),
 		db->name);
 	}
     hPrintf("</SELECT>\n");
     }
 else
     {
     boolean allTracks = sameString(selGroup->name, "allTracks");
     hPrintf("<B>track:</B>\n");
     hPrintf("<SELECT NAME=\"%s\" id='%s'>\n", trackVar, trackVar);
     jsOnEventById(event, trackVar, trackScript);
     if (allTracks)
         {
 	selTrack = findSelectedTrack(fullTrackList, NULL, trackVar);
 	slSort(&fullTrackList, trackDbCmpShortLabel);
 	}
     else
 	{
 	selTrack = findSelectedTrack(fullTrackList, selGroup, trackVar);
 	}
     boolean selTrackIsDisabled = FALSE;
     struct trackDb *firstEnabled = NULL;
     for (track = fullTrackList; track != NULL; track = track->next)
 	{
 	if (allTracks || sameString(selGroup->name, track->grp))
 	    {
 	    hPrintf(" <OPTION VALUE=\"%s\"", track->track);
             if (cartTrackDbIsNoGenome(database, track->table))
                 hPrintf(NO_GENOME_CLASS);
             if (disableNoGenome && isNoGenomeDisabled(database, track->table))
                 {
                 hPrintf(" DISABLED");
                 if (track == selTrack)
                     selTrackIsDisabled = TRUE;
                 }
             else if (firstEnabled == NULL)
                 firstEnabled = track;
             if (track == selTrack && !selTrackIsDisabled)
                 hPrintf(" SELECTED");
             hPrintf(">%s</OPTION>", track->shortLabel);
 	    }
 	}
     if (selTrackIsDisabled)
         selTrack = firstEnabled;
     hPrintf("</SELECT>\n");
     }
 hPrintf("\n");
 return selTrack;
 }
 
 char *unsplitTableName(char *table)
 /* Convert chr*_name to name */
 {
 if (startsWith("chr", table))
     {
     char *s = strrchr(table, '_');
     if (s != NULL)
         {
 	table = s + 1;
 	}
     }
 return table;
 }
 
 
 
 struct slName *tablesForDb(char *db)
 /* Find tables associated with database. */
 {
 boolean isGenomeDb = sameString(db, database);
 struct sqlConnection *conn = hAllocConn(db);
 struct slName *raw, *rawList = sqlListTables(conn);
 struct slName *cooked, *cookedList = NULL;
 struct hash *uniqHash = newHash(0);
 
 hFreeConn(&conn);
 for (raw = rawList; raw != NULL; raw = raw->next)
     {
     if (cartTrackDbIsAccessDenied(db, raw->name))
         continue;
     if (isGenomeDb)
 	{
 	/* Deal with tables split across chromosomes. */
 	char *root = unsplitTableName(raw->name);
 	if (cartTrackDbIsAccessDenied(db, root))
 	    continue;
 	if (!hashLookup(uniqHash, root))
 	    {
 	    hashAdd(uniqHash, root, NULL);
 	    cooked = slNameNew(root);
 	    slAddHead(&cookedList, cooked);
 	    }
 	}
     else
         {
 	char dbTable[256];
 	safef(dbTable, sizeof(dbTable), "%s.%s", db, raw->name);
 	cooked = slNameNew(dbTable);
 	slAddHead(&cookedList, cooked);
 	}
     }
 hashFree(&uniqHash);
 slFreeList(&rawList);
 slSort(&cookedList, slNameCmp);
 return cookedList;
 }
 
 char *showTableField(struct trackDb *track, char *varName, boolean useJoiner)
 /* Show table control and label. */
 {
 struct slName *name, *nameList = NULL;
 char *selTable;
 
 if (track == NULL)
     nameList = tablesForDb(findSelDb());
 else
     nameList = cartTrackDbTablesForTrack(database, track, useJoiner);
 
 /* Get currently selected table.  If it isn't in our list
  * then revert to first in list. */
 selTable = cartUsualString(cart, varName, nameList->name);
 if (!slNameInListUseCase(nameList, selTable))
     selTable = nameList->name;
 
 /* Print out label and drop-down list. */
 hPrintf("<B>table: </B>");
 hPrintf("<SELECT NAME=\"%s\" id='%s'>\n", varName, varName);
 jsOnEventById("change", varName, onChangeTable());
 struct trackDb *selTdb = NULL;
 for (name = nameList; name != NULL; name = name->next)
     {
     struct trackDb *tdb = NULL;
     if (track != NULL)
 	tdb = findTdbForTable(database,track,name->name, ctLookupName);
     hPrintf("<OPTION VALUE=\"%s\"", name->name);
     // Disable options for related tables that are noGenome -- if a non-positional table
     // is selected then we output its entire contents.
     if (cartTrackDbIsNoGenome(database, name->name) &&
         (track == NULL || differentString(track->table, name->name)))
         hPrintf(" DISABLED"NO_GENOME_CLASS);
     else if (sameString(selTable, name->name))
         {
         hPrintf(" SELECTED");
         selTdb = tdb;
         }
     if (tdb != NULL)
 	if ((curTrack == NULL) || differentWord(tdb->shortLabel, curTrack->shortLabel))
 	    hPrintf(">%s (%s)\n", tdb->shortLabel, name->name);
 	else
 	    hPrintf(">%s\n", name->name);
     else
 	hPrintf(">%s\n", name->name);
     }
 hPrintf("</SELECT>\n");
 if (!trackHubDatabase(database))
     {
     char *restrictDate = encodeRestrictionDateDisplay(database,selTdb);
     if (restrictDate)
 	{
 	hPrintf("<A HREF=\'%s\' TARGET=BLANK>restricted until:</A>&nbsp;%s",
 		    ENCODE_DATA_RELEASE_POLICY, restrictDate);
 	freeMem(restrictDate);
 	}
     }
 return selTable;
 }
 
 
 
 struct outputType
 /* Info on an output type. */
     {
     struct outputType *next;
     char *name;		/* Symbolic name of type. */
     char *label;	/* User visible label. */
     };
 
 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);
+hPrintf("<SELECT id='outputTypeDropdown' 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("<DIV style='display:none; opacity:0.9; border: 1px solid #EEE; margin: 2px; padding: 4px' id='gffNote'>"
+        "<b>Note:</b> Table Browser GTF files contain transcripts, but no gene identifiers or symbols.<br> "
+        "If you are looking for fully formatted "
+        "gene model files for use in genome analysis pipelines,<br>check the "
+        "<a href='https://hgdownload.soe.ucsc.edu/%s/bigZips/genes'>bigZips/genes</a> "
+        "directory on our download server.</DIV>", database);
+hPrintf(" ");
+
+jsInline("function checkGtfNote() {"
+    "if (document.getElementById('outputTypeDropdown').value==='gff') "
+    "    document.getElementById('gffNote').style.display=''; "
+    "else "
+    "    document.getElementById('gffNote').style.display='none'; "
+    "}"
+    "$(document).ready(checkGtfNote);\n"
+);
+jsOnEventById("change", "outputTypeDropdown", "checkGtfNote()");
+
 if (!cfgOptionBooleanDefault("hgta.disableSendOutput", FALSE))
     {
     hPrintf(" Send output to ");
     struct dyString *dy = dyStringNew(256);
     dyStringAppend(dy, 
 	"document.getElementById('checkboxGreat').checked=false;");
     if (isGenomeSpaceEnabled())
 	dyStringAppend(dy, 
 	      	  "document.getElementById('checkboxGenomeSpace').checked=false;");
     dyStringAppend(dy, 
 	      	  "return true;");
     cgiMakeCheckBoxWithId("sendToGalaxy", doGalaxy(), "checkboxGalaxy");
     jsOnEventById("click", "checkboxGalaxy", dy->string);
     hPrintf("<A HREF=\""GALAXY_URL_BASE"\" target=_BLANK>Galaxy</A>\n");
     nbSpaces(2);
     cgiMakeCheckBoxWithId("sendToGreat", doGreat(), "checkboxGreat");
     jsOnEventById("click", "checkboxGreat", "return onSelectGreat();");
     hPrintf(" <A HREF=\"http://great.stanford.edu\" target=_BLANK>GREAT</A>");
     if (isGenomeSpaceEnabled())
 	{
 	nbSpaces(2);
 	cgiMakeCheckBoxWithId("sendToGenomeSpace", doGenomeSpace(), "checkboxGenomeSpace");
 	jsOnEventById("click", "checkboxGenomeSpace", 
 	    "document.getElementById('checkboxGreat').checked=false;"
 	    "document.getElementById('checkboxGalaxy').checked=false; return true;");
 	hPrintf(" <A HREF=\"http://www.genomespace.org\" target=_BLANK>GenomeSpace</A>");
 	}
     }
 
 hPrintf("</TD></TR>\n");
 }
 
 struct outputType otAllFields = { NULL,	outPrimaryTable,"all fields from selected table", };
 struct outputType otSelected =  { NULL, outSelectedFields,
                                   "selected fields from primary and related tables",  };
 struct outputType otSequence =  { NULL, outSequence,    "sequence", };
 struct outputType otPal =       { NULL, outPalOptions,
                                   "CDS FASTA alignment from multiple alignment", };
 struct outputType otGff =         { NULL, outGff,         "GTF - gene transfer format &#40;limited&#41;", };
 struct outputType otBed =         { NULL, outBed,         "BED - browser extensible data", };
 struct outputType otCustomTrack = { NULL, outCustomTrack, "custom track", };
 struct outputType otHyperlinks =  { NULL, outHyperlinks,  "hyperlinks to Genome Browser", };
 struct outputType otWigData =     { NULL, outWigData,     "data points", };
 struct outputType otWigBed =      { NULL, outWigBed,      "bed format", };
 struct outputType otMaf =         { NULL, outMaf,         "MAF - multiple alignment format", };
 struct outputType otChromGraphData =      { NULL, outChromGraphData,       "data points", };
 struct outputType otMicroarrayNames =     { NULL, outMicroarrayNames,     "microarray names", };
 struct outputType otMicroarrayGroupings = { NULL, outMicroarrayGroupings, "microarray groupings", };
 
 static void showOutputTypeRow(boolean isWig, boolean isBedGr,
     boolean isPositional, boolean isMaf, boolean isChromGraphCt,
     boolean isPal, boolean isMicroarray, boolean isHalSnake)
 /* Print output line. */
 {
 struct outputType *otList = NULL, *otDefault = NULL;
 boolean bedifiedOnly = (anySubtrackMerge(database, curTable) || anyIntersection());
 
 hPrintf("<TR><TD><B>output format:</B>\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)
     {
     slAddTail(&otList, &otWigData);
     slAddTail(&otList, &otWigBed);
     slAddTail(&otList, &otCustomTrack);
     // hyperlinks output works for db-wiggle but not for bigWig
     }
 else if (isHalSnake)
     {
     slAddTail(&otList, &otMaf);
     }
 else if (isMaf)
     {
     slAddTail(&otList, &otMaf);
     if (! bedifiedOnly)
 	slAddTail(&otList, &otAllFields);
     }
 else if (isChromGraphCt)
     {
     slAddTail(&otList, &otChromGraphData);
     }
 else if (isMicroarray)
     {
     slAddTail(&otList, &otMicroarrayNames);
     slAddTail(&otList, &otAllFields);
     slAddTail(&otList, &otSelected);
     slAddTail(&otList, &otHyperlinks);
     }
 else if (isPositional)
     {
     if (! bedifiedOnly)
 	{
 	slAddTail(&otList, &otAllFields);
 	slAddTail(&otList, &otSelected);
 	}
     else
 	otDefault = &otBed;
     slAddTail(&otList, &otSequence);
     slAddTail(&otList, &otGff);
     if (isPal)
 	slAddTail(&otList, &otPal);
     slAddTail(&otList, &otBed);
     slAddTail(&otList, &otCustomTrack);
     slAddTail(&otList, &otHyperlinks);
     }
 else
     {
     slAddTail(&otList, &otAllFields);
     slAddTail(&otList, &otSelected);
     }
 showOutDropDown(otList, otDefault);
 }
 
 void nbSpaces(int count)
 /* Print some non-breaking spaces. */
 {
 int i;
 for (i=0; i<count; ++i)
     hPrintf("&nbsp;");
 }
 
 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, isHic = 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), "change", onChangeClade());
         nbSpaces(3);
         hPrintf("<B>genome:</B>\n");
         printGenomeListForCladeHtml(database, "change", onChangeOrg());
         }
     else
         {
         hPrintf("<TR><TD><B>genome:</B>\n");
         printGenomeListHtml(database, "change", onChangeOrg());
         }
     nbSpaces(3);
     hPrintf("<B>assembly:</B>\n");
     printAssemblyListHtml(database, "change", onChangeDb());
     hPrintf("</TD></TR>\n");
     }
 
 /* Print group and track line. */
     {
     hPrintf("<TR><TD>");
     selGroup = showGroupField(hgtaGroup, "change", onChangeGroupOrTrack(), conn, hAllowAllTables());
     nbSpaces(3);
     curTrack = showTrackField(selGroup, hgtaTrack, "change", 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("showMainCtlTbl_Ct", "document.customTrackForm.submit();return false;",
                    hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL);
 
     hPrintf(" ");
     if (hubConnectTableExists())
 	hOnClickButton("showMainCtlTbl_Hub", "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);
     isHic = isHicTable(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);
     }
 
 /* Table-specific options */
 if (isHicTable(curTable))
     hicMainPageConfig(cart, hTrackDbForTrack(database,curTable));
 
 /* Region line */
 {
 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("<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("&nbsp;<span"NO_GENOME_CLASS">genome (unavailable for selected track)</span>"
                 "&nbsp;");
         }
     else
         {
         makeRegionButton(hgtaRegionTypeGenome, regionType);
         hPrintf("&nbsp;genome&nbsp;");
         }
     if (doEncode)
         {
 	makeRegionButton(hgtaRegionTypeEncode, regionType);
 	hPrintf("&nbsp;ENCODE Pilot regions&nbsp;");
 	}
     makeRegionButton(hgtaRegionTypeRange, regionType);
     hPrintf("&nbsp;position&nbsp;");
     hPrintf("<INPUT TYPE=TEXT NAME=\"%s\" id='%s' SIZE=26 VALUE=\"%s\">\n",
     	hgtaRange, hgtaRange, range);
     jsOnEventById("focus", hgtaRange, 
 	jsRadioUpdate(hgtaRegionType, "regionType", "range"));
     cgiMakeButton(hgtaDoLookupPosition, "lookup");
     hPrintf("&nbsp;");
     if (userRegionsFileName() != NULL)
 	{
 	makeRegionButton(hgtaRegionTypeUserRegions, regionType);
 	hPrintf("&nbsp;defined regions&nbsp;");
 	cgiMakeButton(hgtaDoSetUserRegions, "change");
 	hPrintf("&nbsp;");
 	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("&nbsp;");
 	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 && !isHic);
 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("&nbsp;(with:&nbsp;&nbsp;%s)", tdb2->shortLabel);
 
 #ifdef NOT_YET
         /* debugging 	dbg	vvvvv	*/
         if (curTrack && curTrack->type)		/*	dbg	*/
             {
             hPrintf("<BR>&nbsp;(debug:&nbsp;'%s',&nbsp;'%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>&nbsp;");
     cgiMakeTextVar(hgtaOutFileName, fileName, 29);
     hPrintf("&nbsp;(leave blank to keep output in browser)</TD></TR>\n");
     hPrintf("<TR><TD>\n");
     hPrintf("<B>file type returned:&nbsp;</B>");
     cgiMakeRadioButton(hgtaCompressType, textOutCompressNone,
 	sameWord(textOutCompressNone, compressType));
     hPrintf("&nbsp;plain text&nbsp&nbsp");
     cgiMakeRadioButton(hgtaCompressType, textOutCompressGzip,
 	sameWord(textOutCompressGzip, compressType));
     hPrintf("&nbsp;gzip compressed");
     hPrintf("</TD></TR>\n");
     }
 
 hPrintf("</TABLE>\n");
 
 
 /* Submit buttons. */
     {
     hPrintf("<BR>\n");
     if (isWig || isBam || isVcf || isLongTabix || isHic)
 	{
 	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 || isHic)
 	    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());
 
 }
 
 static char *getGenomeSpaceText()
 /* fetch GenomeSpace text if enabled */
 {
 if (isGenomeSpaceEnabled())
     {
     return 
   "Send data to "
   "<A HREF=\"http://www.genomespace.org\" target=_BLANK>GenomeSpace</A> for use with diverse computational tools. ";
     }
 else
     {
     return "";
     }
 }
 
 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.soe.ucsc.edu/downloads.html\""
   ">Sequence and Annotation Downloads</A> page."
    , getGenomeSpaceText()
    );
 
 // When GREAT is selected, disable the other checkboxes and force output to BED
 jsInline(
     "function onSelectGreat() {\n"
     " document.getElementById('checkboxGalaxy').checked=false;\n");
 if (isGenomeSpaceEnabled())
     jsInline(
     " document.getElementById('checkboxGenomeSpace').checked=false;\n");
 jsInline(
     " document.getElementById('outBed').selected=true;\n"
     " return true;\n"
     "}\n");
 
 // Disable/enable noGenome tracks depending on whether region is genome.
 jsInline(
     "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");
 
 /* 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 doMainPage(struct sqlConnection *conn)
 /* Put up the first page user sees. */
 {
 htmlOpen("Table Browser");
 mainPageAfterOpen(conn);
 htmlClose();
 }