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(" %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();
}
void doMiddle(struct cart *cart)
/* Print out middle parts. */
{
char *old;
printf("<FORM ACTION=\"../cgi-bin/testCart\" METHOD=GET>\n");
cartSaveSession(cart, "testCart");
printf("<H3>Just a Test</H3>\n");
printf("<B>Filter:</B> ");
old = cartUsualString(cart, "filter", "red");
cgiMakeRadioButton("filter", "red", sameString(old, "red"));
printf("red ");
cgiMakeRadioButton("filter", "green", sameString(old, "green"));
printf("green ");
cgiMakeRadioButton("filter", "blue", sameString(old, "blue"));
printf("blue ");
cgiMakeButton("submit", "Submit");
printf("<BR>\n");
printf("<B>Font Attributes:</B> ");
cgiMakeCheckBox("fBold", cartUsualBoolean(cart, "fBold", FALSE, "testCart"));
printf("bold ");
cgiMakeCheckBox("fItalic", cartUsualBoolean(cart, "fItalic", FALSE, "testCart"));
printf("italic ");
cgiMakeCheckBox("fUnderline", cartUsualBoolean(cart, "fUnderline", FALSE, "testCart"));
printf("underline ");
printf("<BR>\n");
printf("</FORM>");
printf("<TT><PRE>");
cartDump(cart);
}
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 doMiddle(struct cart *theCart)
/* Set up globals and make web page */
{
cart = theCart;
char *db = cartUsualString(cart, "db", hDefaultDb());
cartWebStart(cart, db, "Public Sessions");
/* Not in a form; can't use cartSaveSession() to set up an hgsid input */
printf ("<script>var common = {hgsid:\"%s\"};</script>\n", cartSessionId(cart));
jsIncludeDataTablesLibs();
printf("<p>Sessions allow users to save snapshots of the Genome Browser "
"and its current configuration, including displayed tracks, position, "
"and custom track data. The Public Sessions tool allows users to easily "
"share those sessions that they deem interesting with the rest of the "
"world's researchers. You can add your own sessions to this list by "
"checking the appropriate box on the "
"<a href=\"../cgi-bin/hgSession?%s\">Session Management</a> page.</p>\n"
"<p>See the "
"<a href=\"../goldenPath/help/hgSessionHelp.html\">Sessions User's Guide</a> "
"for more information.\n</p>", cartSidUrlString(cart));
showGalleryTab();
cartWebEnd();
}
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\"> <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(" ");
cgiMakeButton(hgtaDoClearSetUserRegionsText, "clear");
hPrintf(" ");
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(" %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(" %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> %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("↑");
else
printf("↓");
}
}
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);
}
}
static int longRangeHeight(struct track *tg, enum trackVisibility vis)
/* calculate height of all the snakes being displayed */
{
if ( tg->visibility == tvDense)
return tl.fontHeight;
char buffer[1024];
safef(buffer, sizeof buffer, "%s.%s", tg->tdb->track, LONG_HEIGHT );
return tg->height = sqlUnsigned(cartUsualString(cart, buffer, LONG_DEFHEIGHT));
}
boolean advFilterOrLogic(struct column *col, char *varName,
boolean defaultOr)
/* Return TRUE if user has selected 'all' from any/all menu
* of given name. */
{
char *var = advFilterNameI(col, varName);
char *val = cartUsualString(cart, var, anyAllMenu[defaultOr]);
return sameWord(val, "any");
}
static void getUiState(struct cartJson *cj, struct hash *paramHash)
/* Write out JSON for hgGateway.js's uiState object using current cart settings. */
{
char *db = cartUsualString(cj->cart, "db", hDefaultDb());
char *position = cartUsualString(cart, "position", hDefaultPos(db));
char *hubUrl = NULL;
if (trackHubDatabase(db))
{
struct trackHub *hub = hubConnectGetHubForDb(db);
hubUrl = hub->url;
}
writeFindPositionInfo(cj->jw, db, hTaxId(db), hubUrl, position);
// If cart already has a pix setting, pass that along; otherwise the JS will
// set pix according to web browser window width.
int pix = cartUsualInt(cj->cart, "pix", 0);
if (pix)
jsonWriteNumber(cj->jw, "pix", pix);
}
static void getCladeOrgDbPos(struct cartJson *cj, struct hash *paramHash)
/* Get cart's current clade, org, db, position and geneSuggest track. */
{
jsonWriteObjectStart(cj->jw, "cladeOrgDb");
printCladeOrgDbTree(cj->jw);
char *db = cartString(cj->cart, "db");
jsonWriteString(cj->jw, "db", db);
char *org = cartUsualString(cj->cart, "org", hGenome(db));
jsonWriteString(cj->jw, "org", org);
char *clade = cartUsualString(cj->cart, "clade", hClade(org));
jsonWriteString(cj->jw, "clade", clade);
jsonWriteObjectEnd(cj->jw);
char *position = cartOptionalString(cj->cart, "position");
if (isEmpty(position))
position = hDefaultPos(db);
jsonWriteString(cj->jw, "position", position);
printGeneSuggestTrack(cj, db);
}
void doControls(struct sqlConnection *conn)
/* Put up controls pane. */
{
char *listSpec = cartUsualString(cart, hgpListSpec, "");
htmlSetBgColor(0xD0FFE0);
// resource file link wrapped in html
char * link = webTimeStampedLinkToResourceOnFirstCall("HGStyle.css",TRUE);
if (link)
htmlSetStyle(link);
htmStart(stdout, "do controls");
printf("<FORM ACTION=\"%s\" NAME=\"mainForm\" target=\"_parent\" METHOD=GET>\n",
hgVisiGeneCgiName());
cartSaveSession(cart);
printf("<TABLE WIDTH=100%%><TR>");
printf("<TD WIDTH=230 bgcolor=\"#"HG_COL_HOTLINKS"\">");
printf(" <B><A HREF=\"../index.html\" target=\"_parent\" class=\"topbar\">UCSC</A> ");
printf(" <A HREF=\"%s?%s=\" target=\"_parent\" class=\"topbar\">VisiGene</A></B> ",
hgVisiGeneCgiName(), hgpListSpec);
printf("</TD>");
printf("<TD>");
printf(" ");
cgiMakeTextVar(hgpListSpec, listSpec, 16);
cgiMakeButton(hgpDoSearch, "search");
printf("</TD>");
#ifdef SOON
printf("<TD>");
cgiMakeButton(hgpDoConfig, "configure");
printf("</TD>");
#endif /* SOON */
printf("<TD>");
printf("Zoom: ");
printf(
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmOut\" VALUE=\" out \""
" onclick=\"parent.image.bigImg.zoomer('out');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmIn\" VALUE=\" in \""
" onclick=\"parent.image.bigImg.zoomer('in');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmFull\" VALUE=\" full \""
" onclick=\"parent.image.bigImg.zoomer('full');return false;\"> "
"<INPUT TYPE=SUBMIT NAME=\"hgp_zmFit\" VALUE=\" fit \""
" onclick=\"parent.image.bigImg.zoomer('fit');return false;\"> "
"\n");
printf("</TD>");
printf("<TD ALIGN=Right>");
printf("<A HREF=\"../goldenPath/help/hgTracksHelp.html#VisiGeneHelp\" target=_parent>");
printf("Help");
printf("</A> ");
printf("</TD>");
printf("</TR></TABLE>");
printf("</FORM>\n");
htmlEnd();
}
void doDefault(struct sqlConnection *conn, boolean newSearch)
/* Put up default page - if there is no specific do variable. */
{
char *listSpec = cartUsualString(cart, hgpListSpec, "");
listSpec = skipLeadingSpaces(listSpec);
if (listSpec[0] == 0)
doInitialPage();
else
doFrame(conn, newSearch);
}
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;
}
static boolean keepThisLib(char *tissue, char *libId)
/* Tissue filtering code checks cart. */
{
char *tissueHl = cartUsualString(cart, "cgapSage.tissueHl", "All");
if (!tissue)
errAbort("NULL tissue or libId passed into keepThisLib()");
if (sameString(tissueHl, "All") || sameString(tissue, tissueHl))
return TRUE;
return FALSE;
}