void oneTrackInit()
/* Set up global variables using cart settings and initialize libs. */
{
hPrintDisable();
database = cartUsualString(cart, "db", "ce4");
hSetDb(database);
organism = hOrganism(database);
withLeftLabels = FALSE; /* Left labels are not supported. */
withCenterLabels = cartUsualBoolean(cart, "centerLabels", FALSE);
withGuidelines = cartUsualBoolean(cart, "guidelines", FALSE);
revCmplDisp = cartUsualBooleanDb(cart, database, REV_CMPL_DISP, FALSE);
position = cartUsualString(cart, "position", "chrI:4001-5000");
hgParseChromRange(position, &chromName, &winStart, &winEnd);
insideX = 0; /* Left labels are not supported. */
insideWidth = cartUsualInt(cart, "pix", 640);
leftLabelX = 0;
leftLabelWidth = 0; /* Left labels are not supported. */
winBaseCount = winEnd - winStart;
basesPerPixel = ((float)winBaseCount) / ((float)insideWidth);
zoomedToCdsColorLevel = (winBaseCount <= insideWidth*3);
seqBaseCount = hChromSize(database, chromName);
initTl();
zoomedToBaseLevel = (winBaseCount <= insideWidth / tl.mWidth);
zoomedToCodonLevel = (ceil(winBaseCount/3) * tl.mWidth) <= insideWidth;
createHgFindMatchHash();
}

boolean checkGsReady()
/* check that GS requirements are met */
{
// check that the output file has been specified
char *fileName = cartUsualString(cart, hgtaOutFileName, "");
if (sameString(fileName,""))
    {
    cartRemove(cart, hgtaDoTopSubmit);
    showMissingOutputFileForm();
    return FALSE;
    }
// check login
// is the GS login token in the cart?
char *gsToken = cartUsualString(cart, "gsToken", NULL);
if (!gsToken)
    { 
    cartRemove(cart, hgtaDoTopSubmit);
    showGsLoginForm();
    return FALSE;
    }
else
    {   
    // check if the token still valid
    char *temp = getGsPersonalDirectory(gsToken);
    if (!temp)
	{
	cartRemove(cart, hgtaDoTopSubmit);
    	showGsLoginForm();
	return FALSE;
	}
    freeMem(temp);
    }
return TRUE; 
}

void doGsLogin(struct sqlConnection *conn)
/* Process user password post.
 * Log into GS 
 * if successful save gsToken 
 * else return to login page or to mainpage */
{
char *user = cloneString(cartUsualString(cart, hgtaGsUser, NULL));
char *password = cloneString(cartUsualString(cart, hgtaGsPassword, NULL));
// do not leave them in the cart
cartRemove(cart, hgtaGsUser);
cartRemove(cart, hgtaGsPassword);

if (!(user && password))
    errAbort("expecting GenomeSpace user and password");

char *gsToken = getAuthorizationToken(user, password);

if (gsToken)
    {
    cartSetString(cart, "gsToken", gsToken);
    }
else
    {
    cartRemove(cart, "gsToken");
    }

cartSetString(cart, hgtaDoTopSubmit, "get output");

}

void enumFilterOption(char *db, char *table, char *field, char *type,
		      char *logOp)
/* Print out a table row with filter constraint options for an enum/set.  */
{
char *name = NULL;
char **valMenu = NULL;
int valMenuSize = 0;

hPrintf("<TR VALIGN=BOTTOM align='left'><TD valign=top align='left'colspan=2> %s </TD>"
        "<TD valign=top>\n", field);
name = filterFieldVarName(db, table, field, filterDdVar);
cgiMakeDropListClassWithStyle(name, ddOpMenu, ddOpMenuSize,
                              cartUsualString(cart, name, ddOpMenu[0]),"normalText","width: 76px");
hPrintf("<TD valign=top>%s</TD><TD colspan=4 nowrap>\n", isSqlSetType(type) ? "include" : "match");
name = filterPatternVarName(db, table, field);
makeEnumValMenu(type, &valMenu, &valMenuSize);
if (logOp == NULL)
    logOp = "";
if (valMenuSize-1 > 2)
    {
    struct slName *defaults = cartOptionalSlNameList(cart, name);
    if (defaults == NULL)
	defaults = slNameNew("*");
    cgiMakeCheckboxGroup(name, valMenu, valMenuSize, defaults, 5);
    hPrintf("</TD><TD>%s </TD></TR>\n", logOp);
    }
else
    {
    cgiMakeDropList(name, valMenu, valMenuSize,cartUsualString(cart, name, valMenu[0]));
    hPrintf("&nbsp;%s </TD></TR>\n", logOp);
    }
}

void dispatch()
/* Look at input variables and figure out which page to show. */
{
    char *db, *organism;
    int maxSize = 4000;
    int minPerfect = 15;
    int minGood = 15;
    char *fPrimer = cartUsualString(cart, "wp_f", "");
    char *rPrimer = cartUsualString(cart, "wp_r", "");
    boolean flipReverse = cartUsualBoolean(cart, "wp_flipReverse", FALSE);
    struct pcrServer *serverList = getServerList();

    getDbAndGenome(cart, &db, &organism, oldVars);

    /* Get variables. */
    maxSize = cartUsualInt(cart, "wp_size", maxSize);
    minPerfect = cartUsualInt(cart, "wp_perfect", minPerfect);
    minGood = cartUsualInt(cart, "wp_good", minGood);
    if (minPerfect < 15)
        minPerfect = 15;
    if (minGood < minPerfect)
        minGood = minPerfect;

    /* Decide based on transient variables what page to put up.
     * By default put up get primer page. */
    if (isNotEmpty(fPrimer) && isNotEmpty(rPrimer) &&
            !cartVarExists(cart, "wp_showPage"))
    {
        struct pcrServer *server = NULL;
        struct targetPcrServer *targetServer = NULL;
        char *target = cartUsualString(cart, "wp_target", "genome");
        if (isEmpty(target) || sameString(target, "genome"))
            server = findServer(db, serverList);
        else
        {
            targetServer = getTargetServerList(db, target);
            if (targetServer == NULL)
                errAbort("Can't find targetPcr server for db=%s, target=%s",
                         db, target);
        }

        fPrimer = gfPcrMakePrimer(fPrimer);
        rPrimer = gfPcrMakePrimer(rPrimer);
        if (doPcr(server, targetServer, fPrimer, rPrimer,
                  maxSize, minPerfect, minGood, flipReverse))
            return;
    }
    doGetPrimers(db, organism, serverList,
                 fPrimer, rPrimer, maxSize, minPerfect, minGood, flipReverse);
}

static Color cgColorLikeHgGenome(struct track *tg, struct hvGfx *hvg)
/* Search the cart variables and use the colors corresponding to the hgGenome */
/* graph. */
{
Color ret;
struct hashEl *matchingCartSettings = NULL;
struct hashEl *el;
char cartGenomeWildStr[256];
char *graphCartVarName = NULL;
char *colorCartVarSetting = "black";
safef(cartGenomeWildStr, sizeof(cartGenomeWildStr), "hgGenome_graph_%s_*", database);
/* for ex. hgGenome_graph_hg18_1_1 */
matchingCartSettings = cartFindLike(cart, cartGenomeWildStr);
for (el = matchingCartSettings; el != NULL; el = el->next)
    {
    char *val = (char *)el->val;
    if (val && sameString(val, tg->track))
	{
	graphCartVarName = el->name;
	break;
	}
    }
if (graphCartVarName)
    {
    char *colorCartVarName = replaceChars(graphCartVarName, "_graph_", "_graphColor_");
    colorCartVarSetting = cartUsualString(cart, colorCartVarName, "black");
    freeMem(colorCartVarName);
    }
hashElFreeList(&matchingCartSettings);
ret = colorFromAscii(hvg, colorCartVarSetting);
return ret;
}

void doMiddle(struct cart *cart)
/* Write body of web page. */
{
struct trackDb *tdbList = NULL;
char *organism = NULL;
char *db = NULL;
getDbAndGenome(cart, &db, &organism, NULL);
char *chrom = cartUsualString(cart, "c", hDefaultChrom(db));
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));

// QUESTION: Do We need track list ???  trackHash ??? Can't we just get one track and no children
trackHash = trackHashMakeWithComposites(db,chrom,&tdbList,FALSE);

cartWebStart(cart, db, "Search for " FILE_SEARCH_WHAT " in the %s %s Assembly", 
             organism, hFreezeFromDb(db));

webIncludeResourceFile("HGStyle.css");
webIncludeResourceFile("jquery-ui.css");
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("ui.dropdownchecklist.js",NULL);
jsIncludeFile("utils.js",NULL);

// This line is needed to get the multi-selects initialized
jsIncludeFile("ddcl.js",NULL);
printf("<script type='text/javascript'>$(document).ready(function() "
       "{ findTracks.updateMdbHelp(0); });</script>\n");

doFileSearch(db,organism,cart,tdbList);


printf("<BR>\n");
webEnd();
}

static void addIfNonempty(struct hash *hash, char *cgiVar, char *trackVar)
/* If cgiVar exists and is non-empty, add it to ra. */
{
char *val = skipLeadingSpaces(cartUsualString(cart, cgiVar, ""));
if (val[0] != 0)
    hashAdd(hash, trackVar, val);
}

void doSetUserRegions(struct sqlConnection *conn)
/* Respond to set regions button. */
{
char *oldPasted = cartUsualString(cart, hgtaEnteredUserRegions, "");
char *db = cartOptionalString(cart, hgtaUserRegionsDb);
if (db && !sameString(db, database))
    oldPasted = "";
htmlOpen("Enter region definition\n");
hPrintf("<FORM ACTION=\"%s\" METHOD=POST "
    " ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE><TR><TD ALIGN=LEFT>\n");
hPrintf("Paste regions:");
hPrintf("</TD><TD ALIGN=RIGHT>");
hPrintf("Or upload file: <INPUT TYPE=FILE NAME=\"%s\">&nbsp;<BR>\n",
	hgtaEnteredUserRegionFile);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeTextArea(hgtaEnteredUserRegions, oldPasted, 10, 70);
hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
cgiMakeButton(hgtaDoSubmitUserRegions, "submit");
hPrintf("&nbsp;");
cgiMakeButton(hgtaDoClearSetUserRegionsText, "clear");
hPrintf("&nbsp;");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</TD></TR></TABLE>");
hPrintf("</FORM><BR>\n");
webIncludeHelpFile("hgTbUserRegionsHelp", FALSE);
htmlClose();
}

static void howRadioButton(char *how)
/* Put up a getSeqHow radio button. */
{
char *howName = getSeqHowVarName;
char *oldVal = cartUsualString(cart, howName, "protein");
cgiMakeRadioButton(howName, how, sameString(how, oldVal));
}

static void showWiggleMergeOptions()
/* Show subtrack merge operation options for wiggle/bedGraph tables. */
{
char *setting = cartUsualString(cart, hgtaNextSubtrackMergeWigOp, "average");
makeWigOpButton("average", setting);
printf("Average (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("sum", setting);
printf("Sum (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("product", setting);
printf("Product (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("min", setting);
printf("Minimum (at each position) of all selected subtracks' scores<BR>\n");
makeWigOpButton("max", setting);
printf("Maximum (at each position) of all selected subtracks' scores<P>\n");

cgiMakeCheckBox(hgtaNextSubtrackMergeRequireAll,
		cartUsualBoolean(cart, hgtaSubtrackMergeRequireAll, FALSE));
printf("Discard scores for positions at which one or more selected subtracks "
       "have no data.<BR>\n");
cgiMakeCheckBox(hgtaNextSubtrackMergeUseMinScore,
		cartUsualBoolean(cart, hgtaSubtrackMergeUseMinScore, FALSE));
printf("Discard scores less than \n");
setting = cartCgiUsualString(cart, hgtaNextSubtrackMergeMinScore, "0.0");
cgiMakeTextVar(hgtaNextSubtrackMergeMinScore, setting, 5);
printf(" after performing the above operation.<P>\n");
}

static char *getDbForGenome(char *genome, struct cart *cart)
/*
  Function to find the default database for the given Genome.
It looks in the cart first and then, if that database's Genome matches the
passed-in Genome, returns it. If the Genome does not match, it returns the default
database that does match that Genome.

param Genome - The Genome for which to find a database
param cart - The cart to use to first search for a suitable database name
return - The database matching this Genome type
*/
{

char *retDb = cartUsualString(cart, dbCgiName, NULL);

if ((retDb == NULL) || !hDbExists(retDb))
    {
    retDb = hDefaultDb();
    }

/* If genomes don't match, then get the default db for that genome */
if (differentWord(genome, hGenome(retDb)))
    {
    retDb = hDefaultDbForGenome(genome);
    }

return retDb;
}

void integerFilter(char *db, char *table, char *field, char *label,char *logOp)
/* Print out a filter constraint for an integer within a range. */
{
char *name;

hPrintf("<TR VALIGN=BOTTOM align='left'><TD> %s</TD><TD>is</TD><TD colspan=2>\n", label);
name = filterFieldVarName(db, table, field, filterCmpVar);
cgiMakeDropListClassWithStyle(name, cmpOpMenu, cmpOpMenuSize,
                              cartUsualString(cart, name, cmpOpMenu[0]),"normalText","width: 76px");
puts("</TD><TD>\n");
name = filterPatternVarName(db, table, field);
cgiMakeTextVar(name, cartUsualString(cart, name, "0"), 20);
if (logOp == NULL)
    logOp = "";
hPrintf("&nbsp;%s</TD></TR>\n", logOp);
}

static void doBigSelectPage(char *db, char *table)
/* Put up big field selection page. Assumes html page open already*/
{
struct joiner *joiner = allJoiner;
struct dbTable *dtList, *dt;
char dbTableBuf[256];

cartSetString(cart, hgtaFieldSelectTable, getDbTable(db, table));
if (strchr(table, '.'))
    htmlOpen("Select Fields from %s", table);
else
    htmlOpen("Select Fields from %s.%s", db, table);
hPrintf("<FORM NAME=\"mainForm\" ACTION=\"%s\" METHOD=%s>\n", cgiScriptName(),
	cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
cgiMakeHiddenVar(hgtaDatabase, db);
cgiMakeHiddenVar(hgtaTable, table);
dbOverrideFromTable(dbTableBuf, &db, &table);

showTableFields(db, table, TRUE);
dtList = extraTableList(selFieldLinkedTablePrefix());
showLinkedFields(dtList);
dt = dbTableNew(db, table);
slAddHead(&dtList, dt);
showLinkedTables(joiner, dtList, selFieldLinkedTablePrefix(),
	hgtaDoSelectFieldsMore, "allow selection from checked tables");

/* clean up. */
hPrintf("</FORM>");
cgiDown(0.9);
htmlClose();
joinerFree(&joiner);
}

static void doBigFilterPage(struct sqlConnection *conn, char *db, char *table)
/* Put up filter page on given db.table. */
{
struct joiner *joiner = allJoiner;
struct dbTable *dtList, *dt;
char dbTableBuf[256];

if (strchr(table, '.'))
    htmlOpen("Filter on Fields from %s", table);
else
    htmlOpen("Filter on Fields from %s.%s", db, table);

jsIncludeFile("jquery.js", NULL);
jsIncludeFile("utils.js", NULL);
commonCssStyles();

hPrintf("<FORM ACTION=\"%s\" METHOD=%s>\n", cgiScriptName(),
	cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
cgiMakeHiddenVar(hgtaDatabase, db);
cgiMakeHiddenVar(hgtaTable, table);
dbOverrideFromTable(dbTableBuf, &db, &table);

filterControlsForTable(db, table);
dtList = extraTableList(filterLinkedTablePrefix);
showLinkedFilters(dtList);
dt = dbTableNew(db, table);
slAddHead(&dtList, dt);
showLinkedTables(joiner, dtList, filterLinkedTablePrefix,
	hgtaDoFilterMore, "allow filtering using fields in checked tables");

hPrintf("</FORM>\n");
cgiDown(0.9);
htmlClose();
}

void stringFilterOption(char *db, char *table, char *field, char *logOp)
/* Print out a table row with filter constraint options for a string/char. */
{
char *name;

hPrintf("<TR VALIGN=BOTTOM align='left'><TD colspan=2> %s </TD><TD>\n", field);
name = filterFieldVarName(db, table, field, filterDdVar);
cgiMakeDropListClassWithStyle(name, ddOpMenu, ddOpMenuSize,
                              cartUsualString(cart, name, ddOpMenu[0]),"normalText","width: 76px");
hPrintf("</TD><TD>match </TD><TD>\n");
name = filterPatternVarName(db, table, field);
cgiMakeTextVarWithExtraHtml(name, cartUsualString(cart, name, "*"),140,NULL);
//cgiMakeTextVar(name, cartUsualString(cart, name, "*"), 20);
if (logOp == NULL)
    logOp = "";
hPrintf("&nbsp;%s </TD></TR>\n", logOp);
}

void advFilterAnyAllMenu(struct column *col, char *varName, 
	boolean defaultAny)
/* Make a drop-down menu with value all/any. */
{
char *var = advFilterNameI(col, varName);
char *val = cartUsualString(cart, var, anyAllMenu[defaultAny]);
cgiMakeDropList(var, anyAllMenu, ArraySize(anyAllMenu), val);
}

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\" %s>\n", 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;
}

static void showTableSortingLabelRow(struct fieldedTable *table, struct cart *cart, char *varPrefix,
    char *returnUrl)
/* Put up the label row with sorting fields attached.  ALso actually sort table.  */
{
/* Get order var */
char orderVar[256];
safef(orderVar, sizeof(orderVar), "%s_order", varPrefix);
char *orderFields = cartUsualString(cart, orderVar, "");

char pageVar[64];
safef(pageVar, sizeof(pageVar), "%s_page", varPrefix);

/* Print column labels */
int i;
for (i=0; i<table->fieldCount; ++i)
    {
    webPrintLabelCellStart();
    printf("<A class=\"topbar\" HREF=\"");
    printf("%s", returnUrl);
    printf("&%s=1", pageVar);
    printf("&%s=", orderVar);
    char *field = table->fields[i];
    if (!isEmpty(orderFields) && sameString(orderFields, field))
        printf("-");
    printf("%s", field);
    printf("\">");
    printf("%s", field);
    if (!isEmpty(orderFields))
        {
	char *s = orderFields;
	boolean isRev = (s[0] == '-');
	if (isRev)
	    ++s;
	if (sameString(field, s))
	    {
	    if (isRev)
	        printf("&uarr;");
	    else
	        printf("&darr;");
	    }
	}
    printf("</A>");
    webPrintLabelCellEnd();
    }

/* Sort on field */
if (!isEmpty(orderFields))
    {
    boolean doReverse = FALSE;
    char *field = orderFields;
    if (field[0] == '-')
        {
	field += 1;
	doReverse = TRUE;
	}
    fieldedTableSortOnField(table, field, doReverse);
    }
}

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);
    }

}