int
main( int argc, char **argv ) {
signal( SIGPIPE, SIG_IGN );
const char * optStr = "ah";
rodsArguments_t myRodsArgs;
int status = parseCmdLineOpt( argc, argv, optStr, 0, &myRodsArgs );
if ( status < 0 ) {
printf( "Use -h for help\n" );
return 1;
}
if ( myRodsArgs.help == True ) {
usage();
return 0;
}
if ( myRodsArgs.all == True ) {
for ( unsigned int i = 0; i < sizeof( icmds ) / sizeof( icmds[0] ); ++i ) {
std::string myExe( icmds[i] );
myExe += " -h";
status = system( myExe.c_str() );
if ( status ) {
printf( "error %d running %s\n", status, myExe.c_str() );
}
}
return 0;
}
if ( argc == 1 ) {
printMainHelp();
}
else if ( argc == 2 ) {
for ( unsigned int i = 0; i < sizeof( icmds ) / sizeof( icmds[0] ); ++i ) {
if ( strcmp( argv[1], icmds[i] ) == 0 ) {
std::string myExe( icmds[i] );
myExe += " -h";
status = system( myExe.c_str() );
if ( status ) {
printf( "error %d running %s\n", status, myExe.c_str() );
}
return 0;
}
}
printf( "%s is not an iCommand\n", argv[1] );
}
return 0;
}
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 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();
}
