void printMainHelp()
/* Put up main page help info. */
{
hPrintf(
"This section provides brief line-by-line descriptions of the Table \n"
"Browser controls. For more information on using this program, see the \n"
"<A HREF=\"../goldenPath/help/hgTablesHelp.html\" TARGET=_blank>Table \n"
"Browser User's Guide</A>.\n"
" <UL>\n"
" <LI><B>clade: </B>Specifies which clade the organism is in.</LI>\n"
" \n"
" <LI><B>genome: </B>Specifies which organism data to use.</LI>\n"
" \n"
" <LI><B>assembly: </B>Specifies which version of the organism's genome\n"
" sequence to use.</LI>\n"
" \n"
" <LI><B>group: </B>Selects the type of tracks to be displayed in \n"
" the <em>track</em> list. The options correspond to the track groupings\n"
" shown in the Genome Browser. Select 'All Tracks' for an alphabetical list\n"
" of all available tracks in all groups. Select 'All Tables' to see all tables\n"
" including those not associated with a track.</LI>\n"
" \n"
" <LI><B>database: </B> (with "All Tables" group option) Determines \n"
" which database should be used for options in table menu.</LI>\n"
" \n"
" <LI><B>track: </B>Selects the annotation track data to work with. This \n"
" list displays all tracks belonging to the group specified in the \n"
" <em>group</em> list. </LI>\n"
" \n"
" <LI><B>table: </B>Selects the SQL table data to use. This list shows \n"
" all tables associated with the track specified in the <em>track</em> \n"
" list.</LI>\n"
" \n"
" <LI><B>describe table schema: </B>Displays schema information for the \n"
" tables associated with the selected track.</LI>\n"
" \n"
" <LI><B>region: </B>Restricts the query to a\n"
" particular chromosome or region. Select <em>genome</em> to apply the \n"
" query to the entire genome or <em>ENCODE</em> to examine only the \n"
" ENCODE Pilot regions.\n"
" To limit the query to a specific position, type a \n"
" chromosome name, e.g. <em>chrX</em>, or a chromosome coordinate \n"
" range, such as chrX:100000-200000, or a gene name or other id in \n"
" the text box.\n"
" You can select multiple genomic regions by clicking the "define regions" \n"
" button and entering up to 1,000 regions in a 3- or 4-field <a \n"
" href=\"../FAQ/FAQformat.html#format1\">BED</a> file \n"
" format.</LI>\n"
" \n"
" <LI><B>lookup:</B> Press this button after typing in a gene name or \n"
" other id in the position text box to look up the chromosome position\n"
" \n"
" <LI><B>identifiers</B> (selected tracks only)<B>: </B>Restricts the \n"
" output to table data that match a list of identifiers, for\n"
" instance RefSeq accessions for the RefSeq track. If no identifiers \n"
" are entered, all table data within the specified region will be \n"
" displayed.</LI>\n"
" \n"
" <LI><B>filter: </B>Restricts the query to only those items that\n"
" match certain criteria, e.g. genes with a single exon. Click the \n"
" <em>Create</em> button to add a filter, the <em>Edit</em> button to \n"
" modify an existing filter, or the <em>Clear</em> button to remove an \n"
" existing filter.</LI>\n"
" \n"
" <LI><B>intersection </B> (selected tracks only)<B>: </B>Combines the output \n"
" of two queries into a \n"
" single set of data based on specific join criteria. For example, this \n"
" can be used to find all SNPs that intersect with RefSeq coding \n"
" regions. The intersection can be configured to retain the \n"
" existing alignment structure of the table with a specified amount of \n"
" overlap, or discard the structure in favor of a simple list of position\n"
" ranges using a base-pair intersection or union of the two data sets. \n"
" The button functionalities are similar to those of the <em>filter</em>\n"
" option.</LI> \n"
" <LI><B>output: </B>Specifies the output format (not all options are \n"
" available for some tracks). Formats include:\n"
" <UL>\n"
" <LI><em><B>all fields from selected table</B></em> - data from the selected table\n"
" displayed in a tab-separated format suitable \n"
" for import into spreadsheets and relational databases. The ASCII \n"
" format may be read in any web browser or text editor.\n"
" <LI><em><B>selected fields from primary and related tables</B></em> - user-selected \n"
" set of tab-separated fields \n"
" from the selected table and (optionally) other related tables as well. \n"
" <LI><em><B>sequence</B></em> - DNA (or protein sequence, in some cases) \n"
" associated with the table.</LI>\n"
" <LI><em><B>BED</B></em> - positions of data items in a standard\n"
" UCSC Browser format.</LI>\n"
" \n"
" <LI><em><B>GTF</B></em> - positions of all data items in a standard\n"
" gene prediction format. (Both BED and GTF formats can be\n"
" used as the basis for custom tracks).</LI>\n"
" \n"
" <LI><em><B>CDS FASTA alignment from multiple alignment</B></em> \n"
" - FASTA alignments of the CDS regions of a gene prediction track \n"
" using any of the multiple alignment tracks for the current database. \n"
" Output sequence can be in either nucleotide-space or translated to \n"
" protein-space. Available only for genePred tracks.</LI>\n"
" \n"
" <LI><em><B>custom track</B></em> - customized Genome Browser annotation \n"
" track based on the results of the query.</LI>\n"
" \n"
" <LI><em><B>hyperlinks to Genome Browser</B></em> - returns a page full of\n"
" hyperlinks to the UCSC Genome Browser, one for each item in the table.</LI>\n"
" \n"
" <LI><em><B>data points</B></em> - the data points that make up a graph \n"
" (aka wiggle) track.</LI>\n"
" \n"
" <LI><em><B>MAF</B></em> - multiple alignments in MAF format</LI>\n"
" \n"
" </UL>\n"
" </LI>\n"
" \n"
" <LI><B>Send output to Galaxy:</B> displays results of query in \n"
" <A HREF=\""GALAXY_URL_BASE"\">Galaxy</A>, a framework for \n"
" interactive genome analysis.\n"
" <LI><B>Send output to GREAT:</B> displays the functional enrichments of the \n"
" query results in <A HREF=\"http://great.stanford.edu\">GREAT</A>, a tool for\n"
" analysis of the biological function of cis-regulatory regions.\n"
"%s"
" <LI><B>file type returned: </B>When a filename is entered in the \n"
" "output file" text box, specifies the format of the output file:\n"
" <UL>\n"
" <LI><em><B>plain text</B></em> - data is in ASCII format\n"
" \n"
" <LI><em><B>gzip compressed</B></em> - data is compressed in gzip format\n"
" \n"
" </UL>\n"
" </LI>\n"
" <LI><B>get output: </B>Submits a data query based on the specified \n"
" parameters and returns the output.</LI>\n"
" \n"
" <LI><B>summary/statistics: </B>Displays statistics about the data \n"
" specified by the parameters.</LI>\n"
" \n"
" </UL>\n"
, getGenomeSpaceText()
);
}
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();
}