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);
}
}
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.cse.ucsc.edu/downloads.html\""
">Sequence and Annotation Downloads</A> page."
, getGenomeSpaceText()
);
hPrintf("<script type=\"text/javascript\">\n");
// When GREAT is selected, disable the other checkboxes and force output to BED
hPrintf("function onSelectGreat() {\n");
hPrintf("document.getElementById('checkboxGalaxy').checked=false;\n");
if (isGenomeSpaceEnabled())
hPrintf("document.getElementById('checkboxGenomeSpace').checked=false;\n");
hPrintf("document.getElementById('outBed').selected=true;\n");
hPrintf("return true;\n");
hPrintf("}\n");
// Disable/enable noGenome tracks depending on whether region is genome.
hPrintf("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"
"</script>\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 doIntersectMore(struct sqlConnection *conn)
/* Continue working in intersect page. */
{
struct trackDb *iTrack;
char *name = curTableLabel();
char *iName, *iTable;
char *onChange = onChangeEither();
char *op, *setting;
boolean wigOptions = (isWiggle(database, curTable) || isBedGraph(curTable));
// Note - bigWig is purposely left out of wigOptions. It supports more intersection options
// than wig does.
struct hTableInfo *hti1 = maybeGetHti(database, curTable, conn), *hti2 = NULL;
htmlOpen("Intersect with %s", name);
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=GET>\n", getScriptName());
cartSaveSession(cart);
hPrintf("<TABLE BORDER=0>\n");
/* Print group and track line. */
hPrintf("Select a group, track and table to intersect with:\n");
iTrack = showGroupTrackRow(hgtaNextIntersectGroup, onChange,
hgtaNextIntersectTrack, onChange, conn);
iName = iTrack->shortLabel;
hPrintf("<TR><TD>\n");
iTable = showTableField(iTrack, hgtaNextIntersectTable, FALSE);
hti2 = maybeGetHti(database, iTable, conn);
hPrintf("</TD></TR>\n");
hPrintf("</TABLE>\n");
if (!wigOptions)
{
if (hti1 && hti1->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the exons/blocks will be considered.\n", name);
if (hti2 && hti2->hasBlocks)
hPrintf("<BR>Note: %s has gene/alignment structure. "
"Only the bases covered by its exons/blocks will be "
"considered.\n", iName);
hPrintf("<H4>Intersect %s items with bases covered by %s:</H4>\n",
name, iName);
hPrintf("These combinations will maintain the names and "
"gene/alignment structure (if any) of %s: <P>\n",
name);
}
else
hPrintf("<P>\n");
op = cartUsualString(cart, hgtaNextIntersectOp, "any");
jsTrackingVar("op", op);
makeOpButton("any", op);
printf("All %s records that have any overlap with %s <BR>\n",
name, iName);
makeOpButton("none", op);
printf("All %s records that have no overlap with %s <BR>\n",
name, iName);
if (!wigOptions)
{
makeOpButton("more", op);
printf("All %s records that have at least ",
name);
setting = cartCgiUsualString(cart, hgtaNextMoreThreshold, "80");
cgiMakeTextVar(hgtaNextMoreThreshold, setting, 3);
printf(" %% overlap with %s <BR>\n", iName);
makeOpButton("less", op);
printf("All %s records that have at most ",
name);
setting = cartCgiUsualString(cart, hgtaNextLessThreshold, "80");
cgiMakeTextVar(hgtaNextLessThreshold, setting, 3);
printf(" %% overlap with %s <P>\n", iName);
}
else
{
/* keep javaScript onClick happy */
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextMoreThreshold\" VALUE=80>\n");
hPrintf("<input TYPE=HIDDEN NAME=\"hgta_nextLessThreshold\" VALUE=80>\n");
hPrintf(" <P>\n");
}
if (!wigOptions)
{
boolean bigWig = isBigWigTable(curTable);
hPrintf("<H4>Intersect bases covered by %s and/or %s:</H4>\n",
name, iName);
if (!bigWig)
hPrintf("These combinations will discard the names and "
"gene/alignment structure (if any) of %s and produce a simple "
"list of position ranges.<P>\n",
name);
makeOpButton("and", op);
printf("Base-pair-wise intersection (AND) of %s and %s <BR>\n",
name, iName);
makeOpButton("or", op);
printf("Base-pair-wise union (OR) of %s and %s <P>\n",
name, iName);
hPrintf("Check the following boxes to complement one or both tables. "
"To complement a table means to include a base pair in the "
"intersection/union if it is <I>not</I> included in the table."
"<P>\n");
if (!bigWig)
{
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable, "invertTable", FALSE);
printf("Complement %s before base-pair-wise intersection/union <BR>\n",
name);
}
jsMakeTrackingCheckBox(cart, hgtaNextInvertTable2, "invertTable2", FALSE);
printf("Complement %s before base-pair-wise intersection/union <P>\n",
iName);
}
else
{
/* keep javaScript onClick happy */
jsTrackingVar("op", op);
hPrintf("<SCRIPT>\n");
hPrintf("var invertTable=0;\n");
hPrintf("var invertTable2=0;\n");
hPrintf("</SCRIPT>\n");
hPrintf("(data track %s is not composed of gene records. Specialized intersection operations are not available.)<P>\n", name);
}
cgiMakeButton(hgtaDoIntersectSubmit, "submit");
hPrintf(" ");
cgiMakeButton(hgtaDoMainPage, "cancel");
hPrintf("</FORM>\n");
/* Hidden form - for benefit of javascript. */
{
static char *saveVars[32];
int varCount = ArraySize(nextVars);
memcpy(saveVars, nextVars, varCount * sizeof(saveVars[0]));
saveVars[varCount] = hgtaDoIntersectMore;
jsCreateHiddenForm(cart, getScriptName(), saveVars, varCount+1);
}
htmlClose();
}
void mainPageAfterOpen(struct sqlConnection *conn)
/* Put up main page assuming htmlOpen()/htmlClose()
* will happen in calling routine. */
{
hPrintf("%s",
"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\">GREAT</A>. 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.cse.ucsc.edu/downloads.html\""
">Sequence and Annotation Downloads</A> page."
);
hPrintf("<script type=\"text/javascript\">\n");
hPrintf("function onSelectGreat() {\n");
hPrintf("document.getElementById('checkboxGalaxy').checked=false;\n");
hPrintf("document.getElementById('outBed').selected=true;\n");
hPrintf("return true;\n");
hPrintf("}\n");
hPrintf("</script>\n");
/* Main form. */
hPrintf("<FORM ACTION=\"%s\" NAME=\"mainForm\" METHOD=%s>\n",
getScriptName(), cartUsualString(cart, "formMethod", "POST"));
cartSaveSession(cart);
jsWriteFunctions();
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());
cgiMakeHiddenVar(hgHubConnectCgiDestUrl, "../cgi-bin/hgTables");
cartSaveSession(cart);
hPrintf("</FORM>\n");
webNewSection("<A NAME=\"Help\"></A>Using the Table Browser\n");
printMainHelp();
}
