PHP dirlist_dropdown Examples

Programming Language: PHP

Method/Function: dirlist_dropdown

Examples at hotexamples.com: 2

PHP dirlist_dropdown - 2 examples found. These are the top rated real world PHP examples of dirlist_dropdown extracted from open source projects. You can rate examples to help us improve the quality of examples.

Example #1

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File: view.php Project: BrendelGroup/xGDBvm

#$input_dirlist=dirlist_dropdown("", $dir2_dropdown, $dir3_dropdown, "$Input_Data_Path");// To prevent use of /xGDBvm/data for inputs, uncomment this line and comment out previous.
# display mount status (iPlant only)
$dir1_status = file_exists("/xGDBvm/admin/iplant") ? "<span class=\"normalfont\" style=\"font-weight:normal\">&nbsp; &nbsp;<a class='help-button' title='Mount status of /xGDBvm/data/' id='config_output_dir_mount'> {$dir1_mount} </a></span>" : "";
$dir2_status = file_exists("/xGDBvm/admin/iplant") ? "<span class=\"normalfont\" style=\"font-weight:normal\">&nbsp; &nbsp;<a class='help-button' title='Mount status of /xGDBvm/input/' id='config_input_datastore'> {$dir2_mount} </a></span>" : "";
# repeat mask directory and files
$dir4_dropdown = "{$inputDir}/repeatmask/";
$dir5_dropdown = "/xGDBvm/examples/repeatmask/";
$repmask_dirlist = filelist_dropdown($dir4_dropdown, $dir5_dropdown, "{$RepeatMask_File}");
//build dropdown for repeat mask dir(s)
# reference protein directory and files
$dir6_dropdown = "{$inputDir}/referenceprotein/";
$dir7_dropdown = "/xGDBvm/examples/referenceprotein/";
$refprot_dirlist = filelist_dropdown($dir6_dropdown, $dir7_dropdown, "{$CpGAT_ReferenceProt_File}");
//build dropdown for reference protein dir(s)
# update directory
$update_dirlist = dirlist_dropdown($Input_Data_Path, "", "", $Update_Data_Path);
//build dropdown for update dir(s)
#$update_dirlist=dirlist_dropdown($Input_Data_Path, $Update_Data_Path);
$display_block = "\n<div id=\"maincontentscontainer\" class=\"twocolumn configure {$background}\">\n\t<div style=\"text-align:right; margin:10px 150px -20px 0px\"></div>\n\t<div id=\"maincontents\" class=\"{$background}\">\n\t\t<div id=\"submenu\" class=\"bottommargin2\" style=\"background-color:#BBB; padding:0 0 3px 0;\twhite-space:nowrap\">\n\t\t\t<ul>\n\t\t\t\t<li>&nbsp; <span class=\"whitefont italic\" >Jump to: </span><img id='config_top_menu' title='Edit Help' class='help-button nudge2 smallerfont' src='/XGDB/images/help-icon.png' alt='?' /></li>\n\t\t\t\t<li><a href=\"#DatabaseDiv\">General Info</a></li>\n\t\t\t\t<li><a href=\"#InputDiv\">I/O</a></li>\n\t\t\t\t<li><a href=\"#TransAlignDiv\">Transcript</a></li>\n\t\t\t\t<li><a href=\"#ProtAlignDiv\">Protein</a></li>\n\t\t\t\t<li><a href=\"#CpGATDiv\">Gene Prediction</a></li>\n\t\t\t\t<li><a href=\"#UpdateDiv\">Update</a></li>\n\t\t\t\t<li><a href=\"#DefaultsDiv\">Other</a></li>\n\t\t\t\t<li><a href=\"#GenomeDiv\">Genome</a></li>\n\t\t\t\t<li><a href=\"#SegmentsDiv\">Scaffolds</a></li>\n\t\t\t\t<li><a href=\"#ModelsDiv\">Gene Models</a></li>\n\t\t\t\t<li><a href=\"#AlignmentsDiv\">Spliced Alignments</a></li>\n\t\t\t</ul>\n\t\t</div>\n\t\t\t<table class=\"topmargin2\" style=\"font-size:12px\" width=\"100%\">\n\t\t\t\t<!--tr><td>mode= {$mode}; display_load_archive={$display_load_archive}</td></tr-->\n\t\t\t\t<tr>\n\t\t\t\t\t<td width=\"80%\">\n\t\t<!-- PAGE TITLE HEADING H1 -->\t\t\t\n\t\t\t\t\t\t<h1 id=\"heading\" class=\"configure\"> \n\t\t\t\t\t\t\t<img alt=\"\" src=\"/XGDB/images/configure.png\" />\n\t\t\t\t\t\t\tGDB Configuration<img id='config_page' title='Here you can edit parameters or initiate data processing. Click ? for details.' class='help-button nudge1' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t<span class=\"edit_mode normalfont  {$edit} nowrap\"> \n\t\t\t\t\t\t\t\t&nbsp;&nbsp;Edit Mode&nbsp;<img id='config_edit_mode' title='Edit Help' class='help-button nudge1' src='/XGDB/images/help-icon.png' alt='?' />&nbsp;\n\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t<span class=\"options_mode normalfont {$options} nowrap\"> \n\t\t\t\t\t\t\t\t&nbsp;&nbsp;Options Mode&nbsp;<img id='config_options_mode' title='Allows user to Validate, Create, Update, Drop, or Abort. Click for more details.' class='help-button nudge1' src='/XGDB/images/help-icon.png' alt='?' />&nbsp;\n\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t<span class=\"lockout_mode normalfont {$lockout} nowrap\"> \n\t\t\t\t\t\t\t\t&nbsp;&nbsp;Lockout Mode - pipeline is running on {$locked_DBid} &nbsp;<img id='config_lockout_mode' title='No additional GDB processing until pipeline complete.' class='help-button nudge1' src='/XGDB/images/help-icon.png' alt='?' />&nbsp;\n\t\t\t\t\t\t\t</span>\t<!-- span class=\"normalfont\">Input: {$i_exists}; Output: {$o_exists}; GDB: {$g_exists};  Archive: {$a_exists}; ArchiveAll: {$aa_exists};</span-->\n\t\t\t\t\t\t\t<span class=\"process_notice largerfont\">{$alert}</span>\n\t\t\t\t\t\t\t<span class=\"darkgrayfont smallerfont\"> &nbsp; {$logged_in}</span>\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t</h1>\n\t\t\t\t\t</td>\n\t\t\t\t\t<td align = \"right\">\n\t\t\t\t\t\t<form style=\"display:inline\" method=\"post\" action=\"/XGDB/conf/navigate.php\" class=\"styled\">\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"Navigate\" value=\"Previous\" />\n\t\t\t\t\t\t\t<span class=\"{$nav}\">\n\t\t\t\t\t\t\t\t<input  style = \"margin:0\" id=\"prev\" type=\"submit\" class=\"submit\" value=\"&lt;Prev\"/>\n\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t</form>\n\t\t\t\t\t\t<form style=\"display:inline\" method=\"post\" action=\"/XGDB/conf/navigate.php\" class=\"styled\">\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"Navigate\" value=\"Next\" />\n\t\t\t\t\t\t\t<span class=\"{$nav}\">\n\t\t\t\t\t\t\t\t<input  style = \"margin:0\" id=\"next\" type=\"submit\" class=\"submit\" value=\"Next&gt;\" />\n\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t</form>\n\t\t\t\t\t\t<form method=\"post\" action=\"/XGDB/conf/load_archive.exec.php\" name=\"load_archive\" class=\"styled\">\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"action\" value=\"gdb_load_archive\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"ID\" value=\"{$ID}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"xgdb\" value=\"{$DBid}\" />\n\t\t\t\t\t\t\t<div class=\"nowrap {$display_load_archive}\">\n\t\t\t\t\t\t\t\t<select name=\"file\">\n\t\t\t\t\t\t\t\t\t{$archive_dirlist_display}\n\t\t\t\t\t\t\t\t</select>\n\t\t\t\t\t\t\t\t<input type=\"submit\" id=\"load_archive\" class=\"submit save_style {$display_load_archive}\" style=\"color:purple\" value=\"&nbsp;&nbsp;Load Config&nbsp;&nbsp;\"  onclick=\"return confirm('Really load this GDB archive config? It may take some time for large datasets. Then you will need to select Data Process Options -> Restore from Archive to complete the process.')\" />\n\t\t\t\t\t\t\t\t &nbsp;\n\t\t\t\t\t\t\t\t\t <img src='' id='config_load_archive' alt='save help' title='Click for more info' class='help-button nudge2' />\n\t\t\t\t\t\t\t\t &nbsp;\n\t\t\t\t\t\t\t</div>\n\t\t\t\t\t\t</form>\n\t\t\t\t\t</td>\n\t\t\t\t</tr>\n\t\t\t\t<tr>\n\t\t\t\t    <td>\n\t\t\t\t        <span class=\"normalfont indent1\" style=\"font-weight:normal\">&nbsp; {$dir1_status} &nbsp; {$dir2_status}</span>\n\t\t\t\t        \t\t\t\t\t&nbsp;\n\t\t\t\t\t\t\t\t\t\t    <span class=\"{$gth_class}\">\n                                                    GTH {$gth_valid}\n                                            </span>\n                                            &nbsp;\n\t\t\t\t\t\t\t\t\t\t    <span class=\"{$gm_class} \">\n                                                    GM {$gm_valid}\n                                            </span>\n                                            &nbsp;\n\t\t\t\t\t\t\t\t\t\t    <span class=\" {$vm_class}\">\n                                                    VM {$vm_valid}\n                                            </span>\n                                            &nbsp;\n\n                                            <img src='' id='config_status_flags' alt='save help' title='Click for more info' class='help-button nudge2' />\n\t\t\t\t    </td>\n\t\t\t\t</tr>\n\t\t\t</table>\n\t\t\n\t\t<div id=\"whatsthisdivfor\">\n\t\t\t\n\t\t<!-- GDB TITLE HEADING H1 -->\t\n\t\t\t<h1 style=\"border:1px solid #AAA\" class=\" {$Status} nowrap bottommargin2 topmargin1 indent1\"> \n\t\t\t\t {$DBid}: &nbsp; &ldquo;{$DBname}&rdquo;\n\t\t\t</h1>\n\t\t\t\n\t\t<!-- GDB STATUS HEADING TABLE (large font) -->\n\t\t<div style=\"margin-bottom:30px\">\n\t\t\t<table id=\"status_table\"><!-- to adjust gap in edit mode-->\n\t\t\t\t<tr>\n\t\t\t\t\t<td align=\"left\" width=\"auto\" >\n\t\t\t\t\t\t<span class=\"bigfont\" style=\"white-space:nowrap\"  >\n\t\t\t\t\t\t\t&nbsp;\n\t\t\t\t\t\t\t\tStatus:\n\t\t\t\t\t\t\t\t &nbsp;<span style=\"padding:5px; font-variant:small-caps; border:2px solid #AAA\" class= \"view hugefont bold {$Status}\">{$Status}</span>\n\t\t\t\t\t\t\t\t<img id='config_status' title='Click for more info' class='help-button nudge2' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t&nbsp;\n\t\t\t\t\t\t</span>\t\t\t\t\t\t\n\t\t\t\t\t</td>\n\t\t\t\t\t<td style=\"padding:0px 0 0 10px\">\n\t\t\t\t\t\t\t<span class=\"{$mode_message_style} {$mode_message_display}\">\n\t\t\t\t\t\t\t\t{$mode_message}\n\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t<span class=\"{$nav} normalfont\">\n\t\t\t\t\t\t\t\t{$database_message}\n\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t<span class=\"{$error} alertnotice largerfont\"> \n\t\t\t\t\t\t\t\tCannot create GDB! Configuration is incomplete.\n\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t {$warning_msg}\n\t\t\n\t\t\t\t\t</td>\n\t\t\t\t</tr>\n\t\t\t</table>\n\t\t</div>\t\n\t\t<!-- LIST OF VALID INPUT FILES, REFPRO FILES -->\n\t\t<div id=\"valid_inputs\">\n\t\t<table id=\"inputs_errors\">\n\t\t\t<tr>\n\t\t\t\t<td style=\"padding:0px 0 0 10px\"  valign=\"top\">\n\t\t\t\t\t<div id=\"input_list\" class=\"{$top_list_hide} {$locked}\">\n\t\t\t\t\t\t{$validList}\n\t\t\t\t\t</div><!-- end input list -->\n\t\t\t\t\t<div id=\"refpro_valid\" class=\"{$cpgat_row_hide} {$top_list_hide} {$locked}\">\n\t\t\t\t\t\t{$validRefPro}\n\t\t\t\t\t</div><!-- end refpro valid -->\n\t\t\t\t\t<div id=\"repmast_valid\" class=\"{$repmask_row_hide} {$top_list_hide} {$locked}\">\n\t\t\t\t\t\t{$validRepMask}\n\t\t\t\t\t</div><!-- end refpro list -->\n\t\t\t\t\t<div id=\"update_list\" class=\"{$conditional_update}\">\n\t\t\t\t\t\t{$validUpdateList}\n\t\t\t\t\t</div><!-- end validupdate list -->\n\t\t\t\t\t<div id=\"pipeline_errors\" class=\"{$conditional_current_locked}\">\n\t\t\t\t\t\t{$pipeline_errors_display}\n\t\t\t\t\t</div><!-- end pipeline_errors list -->\n\t\t\t\t\t<div id=\"input_errors\" class=\"{$display_development}\">\n\t\t\t\t\t\t{$input_errors_display}\n\t\t\t\t\t</div><!-- end input errors list -->\n\t\t\t\t\t<div id=\"input_results_2\" class=\"{$result_list_hide} {$locked}\">\n\t\t\t\t\t\t{$input_results_display}\n\t\t\t\t\t</div><!-- end input results -->\n\t\t\t\t\t<div id=\"update_results\" class=\"{$conditional_update}\">\n\t\t\t\t\t    {$update_results_display}\n\t\t\t\t\t</div><!-- end update results -->\n\t\t\t\t</td>\n\t\t\t</tr>\n\t\t</table>\n\t\t</div><!-- end valid_inputs -->\n\t\t<!-- LOGFILE DISPLAY TABLE (DURING LOCKED STATUS) -->\t\n\t\t\t<table class=\"tail_display {$tail_display}\">\n                <tbody>\n                    <tr>\n                        <td>\n                            <span class=\"nowrap largerfont\" style=\"color:purple\">\n                                Now processing: <br />\n                            </span>\n                            <a id='{$XGDB_DATADIR}{$DBid}/logs/Pipeline_procedure.log' name='{$ID}' title='Procedure log for {$DBid} (popup)' class='logfile-button smallerfont link'> \n                                Logfile <img style='margin-bottom:-5px' src='/XGDB/images/logfile-icon.png' alt='?' />\n                            </a>\n                            <a  id='{$XGDB_DATADIR}{$DBid}/logs/Pipeline_error.log' name='{$ID}' title='Error log for {$DBid} (popup)'  class='logfile-button smallerfont link'> \n                                Errors <img style='margin-bottom:-5px' src='/XGDB/images/logfile-icon.png' alt='?' />\n                            </a>\n                        </td>\n                        <td>\n                            <span class=\"normalfont\">{$tail_line1} <br /> {$tail_line2}</span>\n                        </td>\n                    </tr>\n\t\t\t\t</tbody>\n\t\t\t</table>\n\t\t\n\t\t<!-- DATA PROCESS OPTIONS: CREATE DROP ARCHIVE RESTORE ABORT forms -->\n\t\t\n\t\t<div>\n            <span class=\"{$conditional_edit} alertnotice normalfont\">Edit values and click 'Save Changes', or 'Cancel'. Note required fields (<span class=\"required\"></span>). 'Reset' restores original entries.</span>\t\t\t\t\t\t\n            <span class=\"{$conditional_edit_current} {$edit} {$current_class} alertnotice normalfont\">Edit values and click 'Save Changes', or 'Cancel'. Do not edit configuration parameters unless you are going to run a GDB 'Update'. </span>\n\t\t</div>\n\t\t\t<table style=\"font-size:12px\" class=\"topmargin2\" width=\"100%\">\n\t\t\t\t<tr>\n\t\t\t\t\t<td align=\"left\" width=\"54%\">\n\t\t\t\t\t    <span class=\"{$nav} instruction\">To <b>Validate, Create, Drop, Abort, Archive, or Restore</b>, click 'Options' button at right &rarr;</span>\n\t\t\t\t\t\t<span class=\"{$create} instruction\">To <b>CREATE a new xGDBvm database, {$DBid}, </b> make sure all necessary data files are in the Input directory,  \n\t\t\t\t\t\tthen click <span class=\"heading\">\"Create New Database\" </span> to start pipeline. Once complete (from less a minute to many hours, depending on genome size and number of alignments), the new genome will be added to the '<i>View</i>' menu.<br /><br /></span>\n\n\t\t\t\t\t\t<span class=\"{$restore} instruction\">To <b>RESTORE the selected archive</b>, click <span class=\"bold\" style=\"color:purple\">\"Restore from {$Restore_GDB} Archive\" </span> button.\n\t\t\t\t\t\t Once complete, the restored genome will be added to the '<i>View</i>' menu.</span>\n\n\t\t\t\t\t\t<span class=\"{$update} instruction\">\n\t\t\t\t\t\tTo <b>UPDATE</b> {$DBid}, make sure all necessary data files are in the Update directory and with valid filenames:\n\t\t\t\t\t\tThen click \"Update Database\" to start update pipeline. Once complete (from less a minute to many hours, depending on genome size and number of alignments), the updated genome will be displayed.\n\t\t\t\t\t\t<br /><br /></span>\t\n\t\t\t\t\t\t\n\t\t\t\t\t\t<span class=\"{$drop} instruction\">\n\t\t\t\t\t\t    To <b>DROP</b> (REMOVE) {$DBid}  and start over, click the \"Drop Database\" button at right. This will PERMANENTLY remove Output data for this GDB, but GDB Configuration and Input data are untouched.\n\t\t\t\t\t\t<br /><br /></span>\n\t\t\t\t\t\t\n                        <span class=\"{$drop} instruction\">\n                            To <b>ARCHIVE</b> {$DBid}, click the \"Archive Database\" button at right. All data and configurations will be saved to your attached data volume under <span class=\"plaintext\">{$dataDir}/ArchiveGDB_{$VM}/</span>. \n\t\t\t\t\t\t</span>\n\t\t\t\t\t\t<span  class=\"{$abort} instruction\">To ABORT {$DBid} when the pipeline has failed or you want to start over with this GDB, click 'Abort Process' to revert to Development Status. Click \"Cancel\" to return to configuration view.</span>\n\t\t\n\t\t\t\t\t</td>\n\t\t\t\n\t\t\t\t\t<td  align=\"right\" width=\"10%\">\n\t\t\t\t\t\t<form method=\"post\" action=\"/XGDB/conf/view.php?id={$ID}\" name=\"view_status_on\" class=\"styled\">\n\t\t\t\t\t\t\t<input id=\"cancel\" class=\"{$cancel} cancel_style submit\" type=\"submit\" value=\"&nbsp;&nbsp;Cancel&nbsp;&nbsp;\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"mode\" value=\"Cancel\" />\n\t\t\t\t\t\t</form>\t\n\t\t\t\n\t\t\t\t\t</td>\n\t\t\t\t\t<td align=\"right\" width=\"40%\">\n\t\t\t\t\t\t<form method=\"post\" name=\"create_drop\" action=\"/XGDB/conf/view.php?id={$ID}\" class=\"styled\">\n\t\t\t\t\t\t\t<input style=\"width:200px\"  id=\"options\" class=\" {$nav} options_style submit\" type=\"submit\" value=\"Data Process Options...\" />\n\t\t\t\t\t\t\t<img id='config_db_options' title='Search Help' class='help-button {$nav}' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"action\" value=\"options\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"mode\" value=\"{$mode}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$id}\" />\n\t\t\t\t\t\t</form>\n\n\t\t\t\t\t\t<form method=\"post\" action=\"/XGDB/conf/validate_files.php\" class=\"styled\">\n\t\t\t\t\t\t    <input type=\"hidden\" name=\"valid\" value=\"{$valid_post}\" />\n\t\t\t\t\t\t    <input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"xgdb\" value=\"{$DBid}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"inputdir\" value=\"{$validate_input}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"updatedir\" value=\"{$validate_update}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"refprotfile\" value=\"{$validate_refprot}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"repeatmaskfile\" value=\"{$validate_repmask}\" />\n\t\t\t\t\t\t\t<input class=\"{$validate} submit\"  id=\"create\" type=\"submit\" style=\"color:#488EC5; width:200px\"  value=\"Validate Input Data Files\" onclick=\"return confirm('Really validate datafiles? This may take a few minutes.')\" />\n\t\t\t\t\t\t\t<img id='config_file_contents_validation' title='Validate all input data files. Click for more details' class=\"help-button {$validate}\" src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t</form>\n\n\n\t\t\t\t\t\t<form method=\"post\" action=\"/XGDB/conf/create.php\" class=\"styled topmargin1\">\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"action\" value=\"update\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"valid\" value=\"{$valid_post}\" />\n\t\t\t\t\t\t\t<input id=\"update\" style=\"color:#01BFA9\" class=\"{$update} update_style submit\" type=\"submit\" value=\"Update {$DBid} Database\" onclick=\"return confirm('Really update this GDB?')\" />\n\t\t\t\t\t\t\t<img id='config_update_button' title='Process data and Update this database. Click for more details. ' class='help-button {$update}' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t</form>\n\n\t\t\t\t\t\t<form method=\"post\" action=\"/XGDB/conf/create.php\" class=\"styled topmargin1\">\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"action\" value=\"create\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"valid\" value=\"{$valid_post}\" />\n\t\t\t\t\t\t\t<input class=\"{$create} submit {$conditional_loggedin}\"  id=\"create\" type=\"submit\" value=\"Create New {$DBid} Database\" onclick=\"return confirm('Really create this GDB?')\" />\n\t\t\t\t\t\t\t<img id='config_create_db' title='Process Input data and create a new genome browser. Click for more details' class=\"help-button {$create} {$conditional_loggedin}\" src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t</form>\n\t\t\t\t\t\t<form method=\"post\" action=\"/XGDB/conf/drop.php\" class=\"styled topmargin1\">\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"action\" value=\"drop\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"valid\" value=\"{$valid_post}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"redirect\" value=\"view\" />\n\t\t\t\t\t\t\t<input style=\"width:200px\" id=\"drop\" class=\"{$drop} drop_style submit\"  type=\"submit\" value=\"Drop {$DBid} Database\" onclick=\"return confirm('Really drop this GDB?')\" />\n\t\t\t\t\t\t\t<img id='config_drop' title='Remove all data for this GDB. Click for more details.' class='help-button {$drop}' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t</form>\n\t\t\t\t\t\t<form method=\"post\" action=\"/XGDB/conf/drop.php\" class=\"styled\">\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"action\" value=\"abort\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"valid\" value=\"{$valid_post}\" />\n\t\t\t\t\t\t\t<input  id=\"abort\" class=\"{$abort} abort_style submit\"  type=\"submit\" value=\"Abort Process\" onclick=\"return confirm('Really abort this GDB?')\" />\n\t\t\t\t\t\t\t<img id='config_abort_option' title='Abort Help' class='help-button {$abort}' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t</form>\n\t\t\t\t\t\t<form method=\"post\" name=\"archive\" action=\"/XGDB/conf/archive_exec.php\" class=\"styled topmargin1\">\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"xgdb\" value=\"{$DBid}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"return\" value=\"view\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"valid\" value=\"{$valid_post}\" />\n\t\t\t\t\t\t\t\t<input type=\"hidden\" name=\"action\" value=\"archive_one\" />\n\t\t\t\t\t\t\t\t<input id=\"archive\" class=\"{$drop} submit\"  style=\"width: 200px\" type=\"submit\" value=\"Archive {$DBid} Database\" onclick=\"return confirm('Do you really want to archive? (This will not affect current xGDB data).')\"/>\n\t\t\t\t\t\t\t<img id='config_archive' title='Help with the Archive button' class='help-button {$drop}' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t</form>\n\t\t\t\t\t\t<form method=\"post\" name=\"restore\" action=\"/XGDB/conf/restore_exec.php\" class=\"styled\">\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"xgdb\" value=\"{$DBid}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"source_file\" value=\"{$Restore_From_File}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"action\" value=\"restore_one\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"valid\" value=\"{$valid_post}\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"return\" value=\"view\" />\n\t\t\t\t\t\t\t<input id=\"restore\" class=\"{$restore} submit\" style=\"color:#72028E\" type=\"submit\" value=\"Restore from {$Restore_GDB} Archive\" onclick=\"return confirm('Do you really want to restore to {$Archive_Date} version?')\"/>\n\t\t\t\t\t\t\t<img id=\"config_restore\" title=\"Help with the Restore button\" class=\"help-button {$restore}\" src=\"/XGDB/images/help-icon.png\" alt=\"?\" />\n\t\t\t\t\t\t</form>\n\t\t\t\t\t</td>\n\t\t\t\t</tr>\t\t\t\n\t\t\t</table>\n\t\t\n\t\t<!-- Mode Information, EDIT CLEAR BUTTONS (load this page) / FORM  -->\t\n\t\t\n\t\t\t<table style=\"font-size:12px\" width=\"100%\">\n\t\t\t\n\t\t\t\t<tr>\n\t\t\t\t\t<td width=\"60%\" align = \"left\" class=\"normalfont\">\n\t\t\t\t\t\t\t<span class= \"{$locked} {$nav} normalfont instruction\">To <b>modify this configuration</b>, click 'Edit' button at right &rarr;</span>\t\t\t\t\t\t\n\t\t\t\t\t</td>\n\t\t\t\t\t<td width=\"40%\" align = \"right\">\n\t\t\t\t\t\t<form method=\"post\" action=\"/XGDB/conf/view.php?id={$ID}\" name=\"edit_status_on\" class=\"styled\">\n\t\t\t\t\t\t\t<input style=\"width:200px\" id=\"edit\" class=\"{$locked} {$nav} edit_style submit\" type=\"submit\" name=\"mode\" value=\"Edit Configuration...\" />\n\t\t\t\t\t\t\t<img id='config_edit' title='Click for help with Edit this Configuration' class='help-button {$locked} {$nav}' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"mode\" value=\"Edit\" />\n\t\t\t\t\t\t</form>\n\t\t\t\t\t</td>\t\n\t\t\t  </tr>\n\t\t\t</table>\n\t\t<!-- CLEAR/CANCEL BUTTONS -->\t\n\t\t<table width=\"100%\">\n\t\t\t<tr>\n\t\t\t\t<td width=\"auto\">\n\t\t\t\t\t\t<form method=\"post\" name=\"clear_data\" action=\"/XGDB/conf/view.php?id={$ID}\" class=\"styled\">\n\t\t\t\t\t        <input id=\"clear\" class=\"{$conditional_edit} clear_style submit\" style=\"color:#FF8484\"  type=\"submit\" value=\"Clear\" onclick=\"return confirm('Do you really want to clear this configuration and start over? All saved values will be lost')\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"action\" value=\"Clear\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"mode\" value=\"Edit\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\t\t\t\t\t\t</form>\n\t\t\t\t</td>\n\t\t\t\n\t\t\t\t<td width=\"auto\">\n\t\t\t\t\n\t\t\t\t\t\t<!--form method=\"post\" name=\"clear_data\" action=\"/XGDB/conf/view.php\" class=\"styled\">\n\t\t\t\t\t\t\t<input class=\"{$conditional_edit} clear_style submit\" style=\"color:#999\"  type=\"submit\" value=\"Clear\"  />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"clear\" value=\"Clear\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"mode\" value=\"Edit\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\t\t\t\t\t\t</form -->\n\t\t\t\t</td>\n\t\t\t\t<td width=\"400px\" align=\"right\">\n\t\t\t\t\t\t<form method=\"post\" action=\"/XGDB/conf/view.php?id={$ID}\" name=\"view_status_on\" class=\"styled\">\n\t\t\t\t\t\t\t<input style=\"width:150px\" id=\"cancel2\" class=\"{$edit} cancel_style submit\" type=\"submit\" value=\"&nbsp;&nbsp;Cancel&nbsp;&nbsp;\" />\n\t\t\t\t\t\t\t<input type=\"hidden\" name=\"mode\" value=\"Cancel\" />\n\t\t\t\t\t\t</form>\n\t\t\t\t</td>\n\t\t\t</tr>\n\t\t</table>\n\t\t<!-- SAVE CONFIG DATA BUTTONS TABLE / FORM (through end of tables)-->\t\n\t\t<div id=\"big_form\">\n\t\t\t\t\t<!-- the big form -->\n\t\t\t\t\t<form method=\"post\" name=\"record_data\" action=\"/XGDB/conf/update.php\" class=\"styled topmargin1\">\n\t\t\t\t\t<input style=\"color:#999\" class=\"{$conditional_edit} reset_style submit\" type=\"reset\" value=\"Reset\" name=\"reset\" />\n\t\t\t\t\t<input style=\"width:150px; float:right\" id=\"save\" class=\"{$edit} save_style submit\" type=\"submit\" name=\"submit\" value=\"Save Changes\" />\n\t\t\t\t\t<input type=\"hidden\" name=\"id\" value=\"{$ID}\" />\n\n\t\t\t\t\t\n\t\t\t\n            <!-- MAIN CONFIG DATA TABLE / FORM DATA INPUTS -->\t\n                    <div id=\"GeneralDiv\" class=\"description \">\n                        <fieldset  class=\"bottommargin1 topmargin1 xgdb_log {$Status}\">\n                        <legend class=\"conf {$status_font_display}\"> &nbsp; General Information &nbsp;</legend>\n                        <table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\" >\n                            <colgroup>\n                                <col width =\"25%\" style=\"background-color: #DDD\" />\n                                <col width =\"75%\" />\n                            </colgroup>\n                            <tbody>\n                                <tr class=\"{$conditional_dev}\">\n                                    <td>\n                                        Data Volumes (GB free):\n                                    </td>\n                                    <td>\n                                        <div class=\"showhide\">\n                                            <p class=\"normalfont label\" style=\"cursor:pointer\" title=\"Show file validation\">\n                                                    <span class=\"normalfont\" style=\"color: #555\">\n                                                        Inputs: \n                                                    </span>\n                                                    <span class=\"bold\">\n                                                        {$validGB}\n                                                    </span>;\n                                                     &nbsp; Root:{$gb1_display}; &nbsp; Data:{$gb2_display}; &nbsp; Scratch:{$gb3_display};  &nbsp; MySQL:{$gb4_display}\n                                                    <span class=\"heading normalfont\">\n                                                        (click for details)\n                                                    </span>\n                                                </p>\n                                            <div class=\" hidden\" style=\"display: none;\">\n                                            <p>Based on <span class=\"bold\">{$validGB} GB</span> of input files, available space rated as <span class=\"checked\"> = adequate</span> or <span class=\"warning\">=not sufficient</span></p>\n                                                <ul class=\"bullet1\">\n                                                    <li><b>Output Files</b> are created under <span class=\"plaintext largerfont\">/{$dataDir}/</span>. Available disk space: {$gb2_display} GB</li>\n                                                    <li><b>Scratch</b> (temporary) files are created under <span class=\"plaintext largerfont\">/{$dataDir}/scratch/</span>. Available disk space: {$gb3_display} GB</li>\n                                                    <li><b>MySQL</b> (database) files are created under <span class=\"plaintext largerfont\">{$dataDir}/mysql/</span>. Available disk space: {$gb3_display} GB</li>\n                                                </ul>\n                                                <p> Refer to <a href=\"/XGDB/conf/volumes.php\">Data Volumes</a> page for more details.</p>\t\t\t\t\t\t\n                                            </div>\n                                        </div>\n                                    </td>\n                                </tr>\n                                <tr>\n                                    <td>\n                                        Database ID:\n                                    </td>\n                                    <td class=\"no_edit\">\n                                        {$DBid}\n                                    </td>\n                                </tr>\n                                <tr>\n                                    <td class=\"{$required}\" >Database Name:</td>\n                                    <td class=\"{$view} user_entry\">{$DBname}</td>\n                                    <td class=\"{$edit}\">\n                                        <input name=\"DBname\" size=\"50\" value=\"{$DBname}\" />\n                                    </td>\n                                </tr>\n                                <tr>\n                                    <td class=\"{$required}\">Organism: </td>\n                                    <td class=\"{$view} italic user_entry\">{$Organism}</td>\n                                    <td class=\"{$edit}\">\n                                        <input name=\"Organism\" size=\"35\" value=\"{$Organism}\" />\n                                    </td>\n                                </tr>\n                                <tr>\n                                    <td>Common Name: </td>\n                                    <td class=\"{$view} user_entry\">{$Common_Name}</td>\n                                    <td class=\"{$edit}\">\n                                        <input name=\"Common_Name\" size=\"35\" value=\"{$Common_Name}\" />\n                                    </td>\n                                </tr>\n                                <tr>\n                                    <td>Genome Type: </td>\n                                    <td class=\"{$view} user_entry\">{$Genome_Type}</td>\n                                    <td class=\"{$edit}\">\n                                            <select name=\"Genome_Type\">\n                                            <option selected=\"selected\">{$Genome_Type}</option>\n                                                <option>Chromosome</option>\n                                                <option>Scaffold</option>\n                                                <option>Chromosome/Scaffold</option>\n                                                <option>BAC</option>\n                                                <option>BAC/Scaffold</option>\n                                            </select>\n                                    </td>\n                                </tr>\n                                <tr>\n                                    <td>\n                                        GDB Status\n                                        <span class='{$display_current_only} smallerfont'>\n                                        </span>\n                                    </td>\n                                    <td class=\"{$view} no_edit\">\n                                        {$Status}\n                                    </td>\n                                    <td class=\"{$edit}\">\n                                            <select name=\"Status\">\n                                            <option selected=\"selected\">{$Status}</option>\n                                                {$Offline_option}\n                                                {$Current_option}\n                                            </select>\n                                    </td>\n\t\t\t\t\t\t\t\t</tr>\t\t\n\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t<td class=\"indent2\">Config Last Modified:</td>\n\t\t\t\t\t\t\t\t\t<td class=\"no_edit\">{$Config_Date}</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$display_current_only}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent2\">Database Created:</td>\n\t\t\t\t\t\t\t\t\t<td class=\"no_edit\">{$Create_Date}</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$display_current_only}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent2\">Database Updated:</td>\n\t\t\t\t\t\t\t\t\t<td class=\"no_edit\">{$Update_Date}</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$display_current_only}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent2\">Features: <img id='config_current_features' title='Feature Track totals for this GDB (click to view). Click ? for details.' class='help-button nudge1' src='/XGDB/images/help-icon.png' alt='?' /></td>\n\t\t\t\t\t\t\t\t\t<td class=\"no_edit\"><span style='color:#CF0C14'>{$feature_totals_string} </span> </td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$display_archive}\">\n\t\t\t\t\t\t\t\t\t<td>{$DBid} Archived: <img id='config_archive_file' title='Archive Help' class='help-button' src='/XGDB/images/help-icon.png' alt='?' /></td>\n\t\t\t\t\t\t\t\t\t<td class=\"no_edit\">{$Archive_Date} <b>File:</b> <span class=\"plaintext\">{$Archive_File}</span></td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$display_restore}\">\n\t\t\t\t\t\t\t\t\t<td>{$DBid} Restored: <img id='config_restore_file' title='Search Help' class='help-button' src='/XGDB/images/help-icon.png' alt='?' /></td>\n\t\t\t\t\t\t\t\t\t<td class=\"no_edit\">{$Restore_Date} <b>File:</b> <span class=\"plaintext\">{$Restore_Source}</span></td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$display_archive_all}\">\n\t\t\t\t\t\t\t\t\t<td>All GDB Archived</td>\n\t\t\t\t\t\t\t\t\t<td class=\"no_edit\">{$Archive_All_Date}</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$display_restore_all}\">\n\t\t\t\t\t\t\t\t\t<td>All GDB Restored:</td>\n\t\t\t\t\t\t\t\t\t<td class=\"no_edit\">{$Restore_All_Date}</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t</table>\n\t\t\t\t\t</fieldset>\n\t\t\t\t\t\n\t\t\t\t</div>\n\t\t\t\n\t\t\t\n\t\t\t\t<div id=\"InputDiv\" class=\"description \">\n\t\t\t\t\t<fieldset  class=\"bottommargin1 topmargin1 xgdb_log {$Status}\">\n\t\t\t\t\t<legend class=\"conf {$status_font_display}\"> <img src=\"/XGDB/images/input_output.png\" alt=\"\" /> &nbsp; Input / Output <img id='config_input_data' title='Search Help' class='help-button' src='/XGDB/images/help-icon.png' alt='?' /> &nbsp;</legend>\n\t\t\n\t\t\t\t\t<div class=\"bottommargin1\">\n\t\t\t\t\t\t<div class=\"heading {$edit}\">\n\t\t\t\t\t\t    <p class=\"instruction\">\n\t\t\t\t\t\t\t\tPlace all input data files in the Input Data Directory you specify below.<br /> \n\t\t\t\t\t\t\t\t<span class=\"heading indent1\"><b>Required</b>: <a id='config_data_decisions-gdna' title='Choosing genome data' class=\"help-button link\">Genome</a>,  <a id='config_data_decisions-transcr' title='Choosing transcript data' class=\"help-button link\">Transcript and/or Protein</a></span><br />\n\t\t\t\t\t\t\t\t<span class=\"heading indent1\"><b>Optional</b>: <a id='config_data_decisions-anno' title='Choosing annotation data' class=\"help-button link\">Gene predictions</a></span>\n\t\t\t\t\t\t        <br />\n\t\t\t\t\t\t        Your data files must have <span class=\"checked\">VALID</span> filenames and no <span class=\"warning\">permissions</span> problems in order to be processed -- <a id='config_file_names_brief' title='Search Help' class='help-button link' >Click here for details</a> \n\t\t\t\t\t\t\t</p>\n\t\t\t\t\t\t</div>\n\t\t\t\t\t</div>\n\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\" >\n\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t<col width =\"20%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t<col width =\"30%\" />\n\t\t\t\t\t\t\t<col width =\"50%\" />\n\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td class=\"{$required}\" >\n\t\t\t\t\t\t\t\t\t Input Data Directory <img id='config_input_dir' title='Input Data Help' class='help-button  nudge2' src='/XGDB/images/help-icon.png' alt='?' /> &nbsp;\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t<span class=\"{$conditional_view} user_entry plaintext\">\n\t\t\t\t\t\t\t\t\t\t{$Input_Data_Path}\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t<span class=\"{$conditional_edit}\">\n\t\t\t\t\t\t\t\t\t\t<!--input name=\"Input_Data_Path\" size=\"30\" value=\"{$Input_Data_Path}\" /-->\n\t\t\t\t\t\t\t\t\t\t<select name=\"Input_Data_Path\">\n\t\t\t\t\t\t\t\t\t\t\t{$input_dirlist}\n\t\t\t\t\t\t\t\t\t\t</select>\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t<div class=\"no_edit\">\n\t\t\t\t\t\t\t\t\t\t{$validList}\n\t\t\t\t\t\t\t\t\t</div>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td class=\"{$display_current_only}\">\n\t\t\t\t\t\t\t\t\t<span class=\"{$display_current_only}\">\n\t\t\t\t\t\t\t\t\t\tOutput Data <img id='config_output_dir_download' title='Output Data Help' class='help-button  nudge2' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td class=\"{$display_current_only}\">\n\t\t\t\t\t\t\t\t\t<span class=\"no_edit {$display_current_only} user_entry plaintext\">\n\t\t\t\t\t\t\t\t\t\t/xGDBvm/data/{$DBid}/data/\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td class=\"{$display_current_only}\">\n\t\t\t\t\t\t\t\t<a href=\"/XGDB/phplib/download.php?GDB={$DBid}&dir=download \">Download {$DBid} Outputs</a>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t<tr class=\"{$display_restore_gdb}\">\n\t\t\t\t\t\t\t\t<td class=\"{$display_current_only}\">\n\t\t\t\t\t\t\t\t\t<span class=\"{$display_current_only}\">\n\t\t\t\t\t\t\t\t\t\tArchive Data <img id='config_archive_output' title='Archive Output Help' class='help-button  nudge2' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td class=\"{$display_current_only}\">\n\t\t\t\t\t\t\t\t\t<span name=\"{$Restore_From_File}\" class=\"no_edit {$display_current_only} user_entry plaintext\">\n\t\t\t\t\t\t\t\t\t\t/xGDBvm/data/ArchiveGDB/\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td class=\"{$display_current_only}\">\n\t\t\t\t\t\t\t\t<a href=\"/XGDB/phplib/download.php?GDB={$DBid}&dir=Archive\">Download {$DBid} Archive</a>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t</table>\t\t\t\t\t\t\n\t\t\t\t\t</fieldset>\n\t\t\t\t</div>\n\t\t\t\n\t\t\t\t<div id=\"TransAlignDiv\" class=\"description \">\n\t\t\t\t\t<fieldset  class=\"bottommargin1 topmargin1 xgdb_log {$Status}\">\n\t\t\t\t\t<legend class=\"conf {$status_font_display}\"> <img src=\"/XGDB/images/transcripts_est.png\" alt=\"?\" /> &nbsp; Transcript Spliced Alignment  <span class=\"heading\"> (GeneSeqer) </span>  &nbsp;</legend>\n\t\t\t\t\t\t<div class=\"bottommargin1\"><span class=\"heading \"> This process will run automatically if <span class=\"plaintext\"> ~est.fa</span>, <span class=\"plaintext\">~cdna.fa</span> or <span class=\"plaintext\">~tsa.fa</span> files are provided. Repeat masking is advised for large genomes. </span></div>\n\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\" >\n\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t<tbody>\n\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t    GSQ Compute <img id='config_comp_res_gsq' title='Search Help' class='help-button' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t    <span class=\"{$conditional_view} user_entry\">\n\t\t\t\t\t\t\t\t        {$gsq_compres_display} <span class=\"normalfont {$conditional_gsq}\"> &nbsp;Job ID: {$gsq_jobs_display}</span>\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t    <span class=\"{$conditional_edit} normalfont\"> \n\t\t\t\t\t\t\t\t\t\t<input title =\"internal\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$GSQCompRes_Internal_checked} name=\"GSQ_CompResources\" value=\"Local\"  /> Local &nbsp; &nbsp;\n\t\t\t\t\t\t\t\t\t\t<span class=\" {$gsq_app_id_config}\"><input title =\"external\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$GSQCompRes_External_checked}  name=\"GSQ_CompResources\"  value=\"Remote\" /> Remote</span>\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\n\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t    GSQ Species Model:\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td  align = \"left\">\n\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t        {$Species_Model}\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry normalfont\">\n\t\t\t\t\t\t\t\t\t\t<input title =\"species_model\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Arabidopsis_checked}  name=\"Species_Model\" value=\"Arabidopsis\" /> Arabidopsis &nbsp; &nbsp;\n\t\t\t\t\t\t\t\t\t\t<input title =\"maize\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$maize_checked}  name=\"Species_Model\" value=\"maize\"  /> maize  &nbsp; &nbsp;\n\t\t\t\t\t\t\t\t\t\t<input title =\"rice\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$rice_checked}  name=\"Species_Model\" value=\"rice\" /> rice  &nbsp; &nbsp;\t\n\t\t\t\t\t\t\t\t\t\t<input title =\"Medicago\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Medicago_checked}  name=\"Species_Model\" value=\"Medicago\" /> Medicago\n\t\t\t\t\t\t\t\t\t\t<input title =\"Drosophila\" style=\"cursor:pointer\"  type=\"radio\" {$Drosophila_checked} name=\"Species_Model\" value=\"Drosophila\" /> Drosophila\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t    GSQ Alignment Stringency:\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t        {$Alignment_Stringency}\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry normalfont\">\n\t\t\t\t\t\t\t\t\t\t<input title =\"other\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Strict_Stringency_checked}  name=\"Alignment_Stringency\" value=\"Strict\" /> Strict &nbsp; &nbsp;\n\t\t\t\t\t\t\t\t\t\t<input title =\"other\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Moderate_Stringency_checked}  name=\"Alignment_Stringency\" value=\"Moderate\" /> Moderate &nbsp; &nbsp;\n\t\t\t\t\t\t\t\t\t\t<input title =\"other\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Low_Stringency_checked}  name=\"Alignment_Stringency\" value=\"Low\" /> Low &nbsp; &nbsp;\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t</tbody>\n\t\t\t\t\t</table>\n\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\" >\n\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t<td class=\"indent2 subhead\" colspan=\"3\" style=\"background:#EEE\">Repeat Mask Option:</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td  class=\"\">\n\t\t\t\t\t\t\t\t    Repeat Mask this Genome? <img id='config_repmask_option' alt='cpgat' title='Configure: Repeat Mask Option Help' class='help-button  nudge2' src='/XGDB/images/help-icon.png' />\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t        {$RepeatMask_Status}\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t    <span class=\"{$edit} normalfont\">\n\t\t\t\t\t\t\t\t\t\t<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$RepeatMask_Status_no_checked}  name=\"RepeatMask_Status\" value=\"\" /> No &nbsp;\n\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"Click make genome sequence repeats prior to GeneSeqer\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$RepeatMask_Status_yes_checked}  name=\"RepeatMask_Status\" value=\"Yes\" /> Yes &nbsp; &nbsp; &nbsp; \n\t\t\t\t\t\t\t\t\t\t<span class=\"heading\">(If Yes, specify <b>Repeat Mask Library</b> below)</span>\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\tRepeat Mask Library: <img id='config_repmask_file' title='Search Help' class='help-button' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry plaintext\">\n\t\t\t\t\t\t\t\t\t\t{$RepeatMask_File}\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t<span class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t<!--input name=\"RepeatMask_File\" size=\"40\" value=\"{$RepeatMask_File}\" /-->\n\t\t\t\t\t\t\t\t\t\t<select name=\"RepeatMask_File\">\n\t\t\t\t\t\t\t\t\t\t\t{$repmask_dirlist}\n\t\t\t\t\t\t\t\t\t\t</select>\t\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t</tbody>\n\t\t\t\t\t</table>\n\t\t\t\t\t</fieldset>\n\t\t\t\t</div>\n\t\t\t\n\t\t\t\t<div id=\"ProtAlignDiv\" class=\"description \">\n\t\t\t\t\t<fieldset  class=\"bottommargin1 topmargin1 xgdb_log {$Status}\">\n\t\t\t\t\t<legend class=\"conf {$status_font_display}\"> <img src=\"/XGDB/images/proteins.png\" alt=\"?\" /> &nbsp; Protein Spliced Alignment  <span class=\"heading\"> (GenomeThreader) </span> </legend>\n\t                <div class=\"bottommargin1\"><span class=\"heading \"> This process will run automatically if <span class=\"plaintext\"> ~prot.fa</span> files are provided. Repeat masking is not used for protein alignments. </span></div>\n\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\" >\n\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t    GTH Compute <img id='config_comp_res_gth' title='Search Help' class='help-button' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t    <span class=\"{$conditional_view} user_entry\">\n\t\t\t\t\t\t\t\t        {$gth_compres_display} <span class=\"normalfont {$conditional_gth}\">&nbsp;Job ID: {$gth_jobs_display}</span>\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t    <span class=\"{$conditional_edit} normalfont\"> \n\t\t\t\t\t\t\t\t\t\t<input title =\"internal\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$GTHCompRes_Internal_checked} name=\"GTH_CompResources\" value=\"Local\"  /> Local &nbsp; &nbsp;\n\t\t\t\t\t\t\t\t\t\t<span class=\"{$gth_app_id_config}\">\n\t\t\t\t\t\t\t\t\t\t    <input title =\"external\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$GTHCompRes_External_checked}  name=\"GTH_CompResources\"  value=\"Remote\" />\n\t\t\t\t\t\t\t\t\t\t    Remote\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t    GTH Species Model:\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t        {$Gth_Species_Model}\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry normalfont\">\n\t\t\t\t\t\t\t\t\t\t<input title =\"gth_arabidopsis\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$gth_arabidopsis_checked}  name=\"Gth_Species_Model\" value=\"arabidopsis\" /> arabidopsis &nbsp; &nbsp;\n\t\t\t\t\t\t\t\t\t\t<input title =\"gth_maize\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$gth_maize_checked}  name=\"Gth_Species_Model\" value=\"maize\"  /> maize  &nbsp; &nbsp;\n\t\t\t\t\t\t\t\t\t\t<input title =\"gth_rice\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$gth_rice_checked}  name=\"Gth_Species_Model\" value=\"rice\" /> rice  &nbsp; &nbsp;\t\n\t\t\t\t\t\t\t\t\t\t<input title =\"gth_medicago\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$gth_medicago_checked}  name=\"Gth_Species_Model\" value=\"medicago\" /> medicago\n\t\t\t\t\t\t\t\t                <input title =\"gth_drosophila\" style=\"cursor:pointer\"  type=\"radio\" {$gth_drosophila_checked} name=\"Gth_Species_Model\" value=\"drosophila\" /> drosophila\n\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t</tbody>\n\t\t\t\t\t</table>\n\t\t\t\t\t</fieldset>\n\t\t\t\t</div>\n\t\t\t\n\t\t\t\t<div id=\"CpGATDiv\" class=\"description \">\n\t\t\t\t\t<fieldset  class=\"bottommargin1 topmargin1 xgdb_log {$Status}\">\n\t\t\t\t\t<legend class=\"conf {$status_font_display} {$cpgat_legend_gray}\"> <img src=\"/XGDB/images/cpgatmodels.png\" alt=\"?\" />\n\t\t\t\t\t    &nbsp; Gene Prediction \n\t\t\t\t\t    <span class=\"heading\"> \n\t\t\t\t\t        (CpGAT)\n\t\t\t\t\t    </span> &nbsp;\n\t\t\t\t\t    <img id='config_cpgat_option' alt='cpgat' title='Search Help' class='help-button' src='/XGDB/images/help-icon.png' /> &nbsp;\n\t\t\t\t\t</legend>\n\t\t\t\t\t\t<div class=\"bottommargin1\">\n\t\t\t\t\t\t    <span class=\"heading\"> \n\t\t\t\t\t\t        (Optional) Running the CpGAT gene prediction tool requires transcript and/or protein spliced alignments. <br /> \n\t\t\t\t\t\t        For optimal results you should also provide a reference protein dataset (see below). <br />\n\t\t\t\t\t\t        <a id='{$XGDB_DATADIR}{$DBid}/logs/CpGAT_procedure.log' name=\"{$ID}\" title=\"CpGAT procedure log \"  class='logfile-button link smallerfont'> \n\t\t\t\t\t\t            View CpGAT Logfile <img style='margin-bottom:-5px' src='/XGDB/images/logfile-icon.png' alt='?' />\n\t\t\t\t\t\t        </a>\n\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t</div>\n\t\t\t\t\t\n\t\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\" >\n\t\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t\t<td  class=\"\">\n\t\t\t\t\t\t\t\t\t\t    <span class=\"bigfont\">\n\t\t\t\t\t\t\t\t\t\t        Predict genes?\n\t\t\t\t\t\t\t\t\t\t    </span> </td>\n\t\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t    <span class=\"{$view} \">\n\t\t\t\t\t\t\t\t\t\t        {$CpGAT_Status_Display} \n\t\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t\t    <span class=\"{$edit} normalfont\">\n\t\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$CpGAT_Status_none_checked}  name=\"CpGAT_Status\" value=\"\" /> No &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"Click to update data for this GDB\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$CpGAT_Status_Updateable_checked}  name=\"CpGAT_Status\" value=\"Yes\" /> Yes:\n\t\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t</table>\n\t\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\" >\n\t\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t\t<td class=\"indent2 subhead\" colspan=\"3\" style=\"background:#EEE\">Reference Protein Index:</td>\n\t\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\" style=\"background-color: #DDD\">\n\t\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t\tReference Protein Index:  <img id='config_cpgat_refprotein' title='Info on CpGAT reference proteins' class='help-button' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry plaintext\">\n\t\t\t\t\t\t\t\t\t\t\t\t{$CpGAT_ReferenceProt_File}\n\t\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t\t    <span class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t\t    <!--input name=\"CpGAT_ReferenceProt_File\" size=\"60\" value=\"{$CpGAT_ReferenceProt_File}\" /-->\n\t\t\t\t\t\t\t\t\t\t       <select name=\"CpGAT_ReferenceProt_File\">\n\t\t\t\t\t\t\t\t\t\t        \t{$refprot_dirlist}\n\t\t\t\t\t\t\t\t\t\t       </select>\t\n\t\t\t\t\t\t\t\t\t\t    </span>\n                                            <div class=\"no_edit normalfont\">\n                                                {$validRefPro}\n                                            </div>\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t</table>\n\t\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\">\n\t\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent2 subhead\" colspan=\"2\" style=\"background:#EEE\">\n\t\t\t\t\t\t\t\t\t\tGenefinders:\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1\">\n\t\t\t\t\t\t\t\t\t\tBGF:\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t{$CpGAT_BGF}\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"Skip\" style=\"cursor:pointer\" type=\"radio\"  {$Skip_BGF_checked}  name=\"CpGAT_BGF\" value=\"Skip\" /> (Skip) &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"Arabidopsis\" style=\"cursor:pointer\" type=\"radio\" {$Arabidopsis_BGF_checked}  name=\"CpGAT_BGF\" value=\"Arabidopsis\"  /> Arabidopsis  &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"maize\" style=\"cursor:pointer\" type=\"radio\"  {$maize_BGF_checked}  name=\"CpGAT_BGF\" value=\"maize\" /> maize &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"rice\" style=\"cursor:pointer\" type=\"radio\"  {$rice_BGF_checked}  name=\"CpGAT_BGF\" value=\"rice\" /> rice &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"Silkworm\" style=\"cursor:pointer\" type=\"radio\"   {$Silkworm_BGF_checked} name=\"CpGAT_BGF\" value=\"Silkworm\"  /> Silkworm  &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"soybean\" style=\"cursor:pointer\" type=\"radio\" {$soybean_BGF_checked}  name=\"CpGAT_BGF\" value=\"Arabidopsis\"  /> soybean  &nbsp; \n\t\t\t\t\t\t\t\t\t\t\t<input title =\"fruitfly\" style=\"cursor:pointer\"  type=\"radio\" {$Fruitfly_BGF_checked} name=\"CpGAT_BGF\" value=\"Fruitfly\" /> Fruitfly\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1\">\n\t\t\t\t\t\t\t\t\t    Augustus:\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t{$CpGAT_Augustus}\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"Skip\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Skip_Augustus_checked}  name=\"CpGAT_Augustus\" value=\"Skip\" /> (Skip) &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"maize\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$maize_Augustus_checked}  name=\"CpGAT_Augustus\" value=\"maize\" /> maize &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"tomato\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$tomato_Augustus_checked}  name=\"CpGAT_Augustus\" value=\"tomato\" /> tomato &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"arabidopsis\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$arabidopsis_Augustus_checked}  name=\"CpGAT_Augustus\" value=\"arabidopsis\"  /> arabidopsis  &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"chlamydomonas\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$chlamydomonas_Augustus_checked}  name=\"CpGAT_Augustus\" value=\"chlamydomonas\"  /> chlamydomonas  &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"fly\" style=\"cursor:pointer\"  type=\"radio\" {$fly_Augustus_checked} name=\"CpGAT_Augustus\" value=\"fly\" /> fly \n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1\">\n\t\t\t\t\t\t\t\t\t    GeneMark:\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t{$CpGAT_GeneMark}\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"Skip\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Skip_GeneMark_checked}  name=\"CpGAT_GeneMark\" value=\"Skip\" /> (Skip) &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"a_thaliana\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$a_thaliana_GeneMark_checked}  name=\"CpGAT_GeneMark\" value=\"a_thaliana\"  /> a_thaliana  &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"c_reinhardtii\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$c_reinhardtii_GeneMark_checked}  name=\"CpGAT_GeneMark\" value=\"c_reinhardtii\" /> c_reinhardtii &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"corn\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$corn_GeneMark_checked}  name=\"CpGAT_GeneMark\" value=\"corn\" /> corn &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"d_melanogaster\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$d_melanogaster_GeneMark_checked}  name=\"CpGAT_GeneMark\" value=\"d_melanogaster\" /> d_melanogaster &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"o_sativa\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$o_sativa_GeneMark_checked}  name=\"CpGAT_GeneMark\" value=\"o_sativa\" /> o_sativa &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"m_truncatula\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$m_truncatula_GeneMark_checked}  name=\"CpGAT_GeneMark\" value=\"m_truncatula\"  /> m_truncatula  &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"barley\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$barley_GeneMark_checked}  name=\"CpGAT_GeneMark\" value=\"barley\"  /> barley  &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"wheat\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$wheat_GeneMark_checked}  name=\"CpGAT_GeneMark\" value=\"wheat\"  /> wheat  &nbsp; \n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent2 subhead\" colspan=\"2\" style=\"background:#EEE\">\n\t\t\t\t\t\t\t\t\t    CpGAT Options:\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1\">\n\t\t\t\t\t\t\t\t\t    Skip Mask:\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t{$CpGAT_Skip_Mask} <img id='config_cpgat_option_skipmask' title='Do NOT mask genome before ab inito gene prediction (click for more info)' class='help-button' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$CpGAT_Skip_Mask_no_checked}  name=\"CpGAT_Skip_Mask\" value=\"\" /> No &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"Skip Repeat Mask for GTH\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$CpGAT_Skip_Mask_yes_checked}  name=\"CpGAT_Skip_Mask\" value=\"Yes\" /> Yes  &nbsp; &nbsp; &nbsp; <span class=\"heading\">(if No, specify <b>Repeat Mask Index</b> above, or leave blank to use default)</span>\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1\">\n\t\t\t\t\t\t\t\t\t    Relax UniRef: <img id='config_cpgat_option_relaxuniref' title='Allow gene models with no blast support from RefProt (click for more info)' class='help-button' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t    {$CpGAT_Relax_UniRef} \n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$CpGAT_Relax_UniRef_no_checked}  name=\"CpGAT_Relax_UniRef\" value=\"\" /> No &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"Relax Requirement for UniRef Blast Hit for GTH Output\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$CpGAT_Relax_UniRef_yes_checked}  name=\"CpGAT_Relax_UniRef\" value=\"Yes\" /> Yes\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1\">\n                                    Skip PASA: <img id='config_cpgat_options_skippasa' title='Do not run PASA to assemble spliced alignments (click for more info)' class='help-button' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t    {$CpGAT_Skip_PASA}\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$CpGAT_Skip_PASA_no_checked}  name=\"CpGAT_Skip_PASA\" value=\"\" /> No &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"Relax Requirement for UniRef Blast Hit for GTH Output\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$CpGAT_Skip_PASA_yes_checked}  name=\"CpGAT_Skip_PASA\" value=\"Yes\" /> Yes\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\tCpGAT Command String:  <img id='config_cpgat_parameters' title='Feature Track totals for this GDB (click to view). Click ? for details.' class='help-button nudge1' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t<span class=\"smallerfont\">\n\t\t\t\t\t\t\t\t\t\t\t{$CpGATparameter}\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent2 subhead\" colspan=\"2\" style=\"background:#EEE\">\n\t\t\t\t\t\t\t\t\t    Track Options:\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$cpgat_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1\">\n\t\t\t\t\t\t\t\t\t    Load Filtered Genes:  <img id='config_cpgat_filtergenes' title='Load ONLY genes with transcript evidence (click for more info)' class='help-button' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t    {$CpGAT_Filter_Genes}\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$edit} user_entry\"  align = \"left\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$CpGAT_Filter_Genes_no_checked}  name=\"CpGAT_Filter_Genes\" value=\"\" /> No &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"Relax Requirement for UniRef Blast Hit for GTH Output\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$CpGAT_Filter_Genes_yes_checked}  name=\"CpGAT_Filter_Genes\" value=\"Yes\" /> Yes\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t</table>\n\t\t\t\t\t</fieldset>\n\t\t\t\t</div><!-- end CpGAT div -->\n\t\t\t\n\t\t\t\t<div id=\"UpdateDiv\" class=\"description \">\n\t\t\t\t\t<fieldset  class=\"bottommargin1 topmargin1 xgdb_log {$Status}\">\n\t\t\t\t\t<legend class=\"conf {$status_font_display} {$update_legend_gray}\"><img alt=\"update\" src=\"/XGDB/images/update.png\" /> &nbsp;  Update Options <img id='config_update_option' title='Search Help' class='help-button' src='/XGDB/images/help-icon.png' alt='?' /> &nbsp; <span class=\"largerfont {$Update_Status} {$status_font_display}\">{$mode_message}</span>  <span class=\"heading {$edit}\"></span></legend>\n\t\t\n\t\t\t\t\t\t<div class=\"bottommargin1\"><span class=\"heading\">To configure for update, click 'Yes' below, enter Update Data Path and desired Update Action(s). Then 'Save' and click 'Data Process Options'</span></div>\n\t\t\t\t\t\t<table class=\"xgdb_log {$status_font_display} {$conditional_display}\"  border=\"0\" style=\"font-size:12px\" width=\"95%\">\n\t\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t\t<col width =\"20%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t<col width =\"80%\" />\n\t\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"{$update_legend_gray}\"><span class=\"largerfont\">Update this GDB?</span></td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$view} user_entry {$update_legend_gray}\">{$Update_Status_Display}</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Update_Status_none_checked}  name=\"Update_Status\" value=\"\" /> No &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"Click to update data for this GDB\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Update_Status_Updateable_checked}  name=\"Update_Status\" value=\"Update\" /> Yes &nbsp; &nbsp; <span class=\"heading\"> (If Yes, indicate path to update data files</span>)\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t</table>\n\t\t\t\t\t\t<table class=\"xgdb_log {$status_font_display} {$conditional_display}\"  border=\"0\" style=\"font-size:12px\" width=\"95%\">\n\t\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t\t<col width =\"20%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t<col width =\"40%\" />\n\t\t\t\t\t\t\t\t<col width =\"40%\" />\n\t\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\" indent2 subhead\" colspan=\"3\" style=\"background:#EEE\"> Update Data Path:</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide} {$conditional_display}\">\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t  Select Path: <img id='config_update_data' title='Search Help' class='help-button' src='/XGDB/images/help-icon.png' alt='?' /> &nbsp;\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry plaintext largerfont\">\n\t\t\t\t\t\t\t\t\t\t\t{$Update_Data_Path}\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t\t<!--input name=\"Update_Data_Path\" size=\"30\" value=\"{$Update_Data_Path}\" /-->\n\t\t\t\t\t\t\t\t\t\t<select name=\"Update_Data_Path\">\n\t\t\t\t\t\t\t\t\t\t\t{$update_dirlist}\n\t\t\t\t\t\t\t\t\t\t</select>\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td class=\"no_edit\">\n\t\t\t\t\t\t\t\t\t\t{$validUpdateList}\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\t\t\t\t\t\t\t\n\t\t\t\t\t\t    </tbody>\n\t\t\t\t\t\t</table>\n\t\t\t\t\t\t<table class=\"xgdb_log {$status_font_display} {$conditional_display}\"  border=\"0\" style=\"font-size:12px\" width=\"95%\">\n\t\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t\t<col width =\"20%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t<col width =\"40%\" />\n\t\t\t\t\t\t\t\t<col width =\"20%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t<col width =\"20%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\" indent2 subhead\" style=\"background:#EEE\">Track(s): <img id='config_update_tracks' title='Search Help' class='help-button' src='/XGDB/images/help-icon.png' alt='?' /> </td>\n\t\t\t\t\t\t\t\t\t<td style=\"background:#EEE\"><i>Update Action</i></td>\n\t\t\t\t\t\t\t\t\t<td style=\"background:#EEE\"><i>Required Files</i></td>\n\t\t\t\t\t\t\t\t\t<td style=\"background:#EEE\"><i>Optional Files</i></td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1 nowrap\">\n\t\t\t\t\t\t\t\t\t    Genome <img  alt=\"\" src=\"/XGDB/images/genomesegments.png\" /> \n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Update_Data_GSEG}\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$None_GSEG_checked}  name=\"Update_Data_GSEG\" value=\"\" /> None &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"append existing GSEG set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Append_GSEG_checked}  name=\"Update_Data_GSEG\" value=\"Append\" /> Append &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"replace existing GSEG set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$Replace_GSEG_checked}  name=\"Update_Data_GSEG\" value=\"Replace\"  /> Replace/New  &nbsp; \n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"genome segments\" class=\"plaintext grayfont\">~gdna.fa </span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1 nowrap\">\n\t\t\t\t\t\t\t\t\t    EST  <img  alt=\"\" src=\"/XGDB/images/transcripts_est.png\" /> \n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Update_Data_EST}\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$None_EST_checked}  name=\"Update_Data_EST\" value=\"\" /> None &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"append existing EST set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Append_EST_checked}  name=\"Update_Data_EST\" value=\"Append\" /> Append &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"replace existing EST set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$Replace_EST_checked}  name=\"Update_Data_EST\" value=\"Replace\"  /> Replace/New  &nbsp; \n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"fasta sequence file (required)\" class=\"plaintext grayfont\">~est.fa </span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"precomputed spliced alignments (optional)\" class=\"plaintext grayfont\">~est.gsq</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1 nowrap\">\n\t\t\t\t\t\t\t\t\t    cDNA  <img alt=\"?\" src=\"/XGDB/images/transcripts_cdna.png\" />\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Update_Data_cDNA}\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$None_cDNA_checked}  name=\"Update_Data_cDNA\" value=\"\" /> None &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"append existing cDNA set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Append_cDNA_checked}  name=\"Update_Data_cDNA\" value=\"Append\" /> Append &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"replace existing cDNA set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$Replace_cDNA_checked}  name=\"Update_Data_cDNA\" value=\"Replace\"  /> Replace/New  &nbsp; \n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"fasta sequence file (required)\" class=\"plaintext grayfont\">~cdna.fa  </span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"precomputed spliced alignments (optional)\" class=\"plaintext grayfont\">[~cdna.gsq] </span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1 nowrap\">\n\t\t\t\t\t\t\t\t\t    TSA   <img  alt=\"?\" src=\"/XGDB/images/transcripts_put.png\" /> \n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Update_Data_TrAssembly}\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$None_TrAssembly_checked}  name=\"Update_Data_TrAssembly\" value=\"\" /> None &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"append existing TrAssembly set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Append_TrAssembly_checked}  name=\"Update_Data_TrAssembly\" value=\"Append\" /> Append &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"replace existing TrAssembly set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$Replace_TrAssembly_checked}  name=\"Update_Data_TrAssembly\" value=\"Replace\"  /> Replace/New  &nbsp; \n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"fasta sequence file (required)\" class=\"plaintext grayfont\">~tsa.fa</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"precomputed spliced alignments (optional)\" class=\"plaintext grayfont\">~tsa.gsq</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1 nowrap\">\n\t\t\t\t\t\t\t\t\t    Protein  <img  alt=\"?\" src=\"/XGDB/images/proteins.png\" /> \n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Update_Data_Protein}\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$None_Protein_checked}  name=\"Update_Data_Protein\" value=\"\" /> None &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"append existing Protein set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Append_Protein_checked}  name=\"Update_Data_Protein\" value=\"Append\" /> Append &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"replace existing Protein set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$Replace_Protein_checked}  name=\"Update_Data_Protein\" value=\"Replace\"  /> Replace/New  &nbsp; \n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"fasta sequence file (required)\" class=\"plaintext grayfont\">~prot.fa </span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"precomputed spliced alignments (optional)\" class=\"plaintext grayfont\">~prot.gth</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1 nowrap\">\n\t\t\t\t\t\t\t\t\t    Genes 1 <img  alt=\"\" src=\"/XGDB/images/genemodels.png\" /> <br />\n\t\t\t\t\t\t\t\t\t    <span class=\"heading\">(precomputed)</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Update_Data_GeneModel}\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$None_GeneModel_checked}  name=\"Update_Data_GeneModel\" value=\"\" /> None &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"append existing Gene Model set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Append_GeneModel_checked}  name=\"Update_Data_GeneModel\" value=\"Append\" /> Append &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"replace existing Gene Model set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$Replace_GeneModel_checked}  name=\"Update_Data_GeneModel\" value=\"Replace\"  /> Replace/New &nbsp; \n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"precomputed Annotation models\" class=\"plaintext grayfont\">~annot.gff3 </span><br />\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"precomputed Annotation proteins\" class=\"plaintext grayfont\">~annot.pep.fa </span>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"precomputed Annotation mrna\" class=\"plaintext grayfont\">~annot.mrna.fa </span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\t\t\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1 nowrap\">\n\t\t\t\t\t\t\t\t\t    Genes 2 <img  alt=\"\" src=\"/XGDB/images/cpgatmodels.png\" /> <br />\n\t\t\t\t\t\t\t\t\t    <span class=\"heading\">(precomputed CpGAT)</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Update_Data_CpGATModel}\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$None_CpGATModel_checked}  name=\"Update_Data_CpGATModel\" value=\"\" /> None &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"append existing CpGATModel set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Append_CpGATModel_checked}  name=\"Update_Data_CpGATModel\" value=\"Append\" /> Append &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"replace existing CpGATModel set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$Replace_CpGATModel_checked}  name=\"Update_Data_CpGATModel\" value=\"Replace\"  /> Replace/New &nbsp; \n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"preomputed CpGAT models\" class=\"plaintext grayfont\">~cpgat.gff3 </span><br />\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"precomputed CpGAT proteins\" class=\"plaintext grayfont\">~cpgat.pep.fa </span>\n\t\t\t\t\t\t\t\t\t    <span style=\"cursor:pointer\" title=\"precomputed CpGAT mrna\" class=\"plaintext grayfont\">~cpgat.mrna.fa</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\t\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1\">Predict Genes <br />\n\t\t\t\t\t\t\t\t\t    <span class=\"heading\">\n\t\t\t\t\t\t\t\t\t        (CpGAT) <img  alt=\"\" src=\"/XGDB/images/cpgatmodels.png\" />\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Update_Data_CpGAT}\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry normalfont\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$None_CpGAT_checked}  name=\"Update_Data_CpGAT\" value=\"\" />\n\t\t\t\t\t\t\t\t\t\t\t    None &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"append existing CpGAT set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Append_CpGAT_checked}  name=\"Update_Data_CpGAT\" value=\"Append\" />\n\t\t\t\t\t\t\t\t\t\t\t    Append &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"replace existing CpGAT set\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$Replace_CpGAT_checked}  name=\"Update_Data_CpGAT\" value=\"Replace\"  />\n\t\t\t\t\t\t\t\t\t\t\t    Replace/New &nbsp;\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td class=\"indent1\" colspan=\"2\">\n\t\t\t\t\t\t\t\t\t    <span class=\"heading\">\n                                            NOTE: Make sure CpGAT is correctly configured under <span class=\"Current\">Gene Prediction</span>\n                                        </span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\" indent2 subhead\" colspan=\"4\" style=\"background:#EEE\"> Add Descriptions:</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent1\">\n\t\t\t\t\t\t\t\t\t    Add Gene Descriptions: <img id='config_update_descriptions' title='Search Help' class='help-button' src='/XGDB/images/help-icon.png' alt='?' />\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Update_Descriptions}\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"none\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$None_Descriptions_checked}  name=\"Update_Descriptions\" value=\"\" /> None &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t&nbsp;<input title =\"replace or add gene model descriptions\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\"  {$Precomputed_Descriptions_checked}  name=\"Update_Descriptions\" value=\"Precomputed\" /> Genes 1 <img  alt=\"\" src=\"/XGDB/images/genemodels_precomp.png\" /> &nbsp;\n\t\t\t\t\t\t\t\t\t\t\t<input title =\"replace or add CpGAT Descriptions\" style=\"cursor:pointer\" class=\"normalfont\" type=\"radio\" {$CpGAT_Descriptions_checked}  name=\"Update_Descriptions\" value=\"CpGAT\"  /> Genes 2 <img  alt=\"\" src=\"/XGDB/images/cpgatmodels_precomp.png\" />\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t    <td class=\"indent1\" colspan=\"2\">\n\t\t\t\t\t\t\t\t        <span class=\"plaintext grayfont\">~annot.desc.txt</span> or <span class=\"plaintext grayfont\">\n\t\t\t\t\t\t\t\t          ~cpgat.desc.txt\n\t\t\t\t\t\t\t\t        </span>\n\t\t\t\t\t\t\t\t    </td>\n\t\t\t\t\t\t\t\t</tr>\t\t\t\t\t\t\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td class=\"indent2 subhead\" colspan=\"4\" style=\"background:#EEE\">\n\t\t\t\t\t\t\t\t\t    Other Information:\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_row_hide}\">\n\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t    Update Comments:\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t<td colspan=\"3\">\n\t\t\t\t\t\t\t\t\t    <span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Update_Comments}\n\t\t\t\t\t\t\t\t\t    </span>\n\t\t\t\t\t\t\t\t\t    <span class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t    <textarea class=\"data_entry smallerfont\" rows=\"1\" name=\"Update_Comments\" cols=\"80\">{$Update_Comments}</textarea>\n\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr class=\"{$update_history_hide}\">\n\t\t\t\t\t\t\t\t\t<td>Update History:</td>\n\t\t\t\t\t\t\t\t\t<td class=\"no_edit {$display_current_only}\" colspan=\"3\">\n\t\t\t\t\t\t\t\t\t\t{$Update_History}\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\t\t\t\t\t\t\n\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t</table>\n\t\t\t\t\t</fieldset>\n\t\t\t\t</div>\n\t\t\t\n\t\t\t\t<div id=\"DefaultsDiv\" class=\"description \">\n\t\t\t\t\t<fieldset  class=\"bottommargin1 topmargin1 xgdb_log {$Status}\">\n\t\t\t\t\t<legend class=\"conf largerfont {$status_font_display}\"> &nbsp;<b>Other Settings</b> <span class=\"heading\"> (Display and yrGATE defaults for this genome)</span> &nbsp;</legend>\n\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\">\n\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td>Default Genome Segment: <img id='config_default_display' title='Search Help' class='help-button' src='/XGDB/images/help-icon.png' alt='?' /></td>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t\t{$Default_GSEG}\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t<span class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t<input name=\"Default_GSEG\" size=\"15\" value=\"{$Default_GSEG}\" />\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t<tr><td class=\"indent2\">Default Left Coordinate:</td><td class=\"{$view} user_entry\">{$Default_lpos}</td><td class=\"{$edit}\"><input name=\"Default_lpos\" size=\"15\" value=\"{$Default_lpos}\" /></td></tr>\n\t\t\t\t\t\t\t<tr><td class=\"indent2\">Default Right Coordinate:</td><td class=\"{$view} user_entry\">{$Default_rpos}</td><td class=\"{$edit}\"><input name=\"Default_rpos\" size=\"15\" value=\"{$Default_rpos}\" /></td></tr>\t\n\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td><span class=\"tip\" title=\"Click CpGAT to use as yrGATE reference annotation.\">yrGATE Ref. Annot. </span>  <img id='config_yrgate_ref' title='Configure: yrGATE Reference Help' class='help-button  nudge2' src='/XGDB/images/help-icon.png' alt='?' /></td>\n\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t\t{$yrGATE_Reference}\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t<span class=\"{$edit} user_entry\">\n\t\t\t\t\t\t\t\t\t\t<input title =\"yrGATE_Ref_pre\" style=\"cursor:pointer\"  type=\"radio\"  {$yrGATE_Ref_pre_checked}  name=\"yrGATE_Reference\" value=\"Precomputed\" /> Precomputed &nbsp;\n\t\t\t\t\t\t\t\t\t\t<input title =\"yrGATE_Ref_cpgat\" style=\"cursor:pointer\"  type=\"radio\" {$yrGATE_Ref_cpgat_checked}  name=\"yrGATE_Reference\" value=\"CpGAT\" /> CpGAT &nbsp;&nbsp;\n\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t</tbody>\n\t\t\t\t\t</table>\n\t\t\t\t</fieldset>\t\n\t\t\t\t</div>\t\n\t\t\t\t<div id=\"GenomeDiv\" class=\"description \">\n\t\t\t\t\t\n\t\t\t\t\t<span class=\"hugefont bold topmargin2\">Genome Information (optional)</span>\n\t\t\t\t\t\n\t\t\t\t\t<hr class=\"featuredivider bottommargin2\" />\n\t\t\t\t\t\n\t\t\t\t\t<fieldset  class=\"topmargin2 bottommargin1 xgdb_log {$Status}\">\n\t\t\t\t\t<legend class=\"conf largerfont {$status_font_display}\"> <img alt=\"\" src=\"/XGDB/images/DNA.png\" />&nbsp; Genome: <span class=\"heading {$edit}\"> (Optional)</span></legend>\n\t\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\"  border=\"0\" style=\"font-size:12px\" width=\"100%\">\n\t\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t<td>Genome Version:</td>\n\t\t\t\t\t\t\t\t<td class=\"{$view} user_entry\">{$Genome_Version}</td>\n\t\t\t\t\t\t\t\t<td class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t<input name=\"Genome_Version\" size=\"9\" value=\"{$Genome_Version}\" />\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t<td>Genome Source:</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$view} user_entry\">{$Genome_Source}</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t<input name=\"Genome_Source\" size=\"25\" value=\"{$Genome_Source}\" />\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t<td>Genome Source Link:</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$view} user_entry\"><pre><a href=\"{$Genome_Source_Link}\">{$Genome_Source_Link}</a></pre></td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t<input name=\"Genome_Source_Link\" size=\"60\" value=\"{$Genome_Source_Link}\" />\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t<td>Genome Comments:</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$view} user_entry\">{$Genome_Comments}</td>\n\t\t\t\t\t\t\t\t\t<td class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t<textarea class=\"data_entry smallerfont\" rows=\"1\" name=\"Genome_Comments\" cols=\"65\">{$Genome_Comments}</textarea>\n\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t</table>\n\t\t\t\t\t</fieldset>\t\n\t\t\t\t</div>\n\t\t\t\n\t\t\t\t<div id=\"SegmentsDiv\" class=\"description \">\n\t\t\t\t\t\t<fieldset  class=\"bottommargin1 xgdb_log {$Status}\">\n\t\t\t\t\t\t<legend class=\"conf largerfont {$status_font_display}\"> <img alt=\"\" src=\"/XGDB/images/genomesegments.png\" />&nbsp; Genome Segments: <span class=\"heading {$edit}\"> (record number of segments expected, and type)</span> &nbsp;</legend>\n\t\t\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\">\n\t\t\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t\t\t<tr class=\"no_edit\">\n\t\t\t\t\t\t\t\t\t    <td class=\"heading\">Genome Segments (Total) Detected:</td><td>{$gseg_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t    <td>Genome Segments Expected:</td><td class=\"{$view} user_entry\">{$Genome_Count}</td><td class=\"{$edit}\"><input name=\"Genome_Count\" size=\"5\" value=\"{$Genome_Count}\" /></td></tr>\n\t\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t    <td class=\"indent3\">Chromosomes:</td><td class=\"{$view} user_entry\">{$Chromosome_Count}</td><td class=\"{$edit}\"><input name=\"Chromosome_Count\" size=\"5\" value=\"{$Chromosome_Count}\" /></td></tr>\n\t\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t    <td class=\"indent3\">\n\t\t\t\t\t\t\t\t\t        Unlinked Chromosomes:\n\t\t\t\t\t\t\t\t\t    </td>\n\t\t\t\t\t\t\t\t\t    <td class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Unlinked_Chromosome_Count}\n\t\t\t\t\t\t\t\t\t    </td>\n\t\t\t\t\t\t\t\t\t    <td class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t        <input name=\"Unlinked_Chromosome_Count\" size=\"5\" value=\"{$Unlinked_Chromosome_Count}\" />\n\t\t\t\t\t\t\t\t\t    </td>\n\t\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t    <td class=\"indent3\">\n\t\t\t\t\t\t\t\t\t        Scaffolds:\n\t\t\t\t\t\t\t\t\t    </td>\n\t\t\t\t\t\t\t\t\t    <td class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$Scaffold_Count}\n\t\t\t\t\t\t\t\t\t    </td>\n\t\t\t\t\t\t\t\t\t    <td class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t        <input name=\"Scaffold_Count\" size=\"5\" value=\"{$Scaffold_Count}\" />\n\t\t\t\t\t\t\t\t\t    </td>\n\t\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t    <td class=\"indent3\">\n\t\t\t\t\t\t\t\t\t        BACs:\n\t\t\t\t\t\t\t\t\t    </td>\n\t\t\t\t\t\t\t\t\t    <td class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t        {$BAC_Count}\n\t\t\t\t\t\t\t\t\t    </td>\n\t\t\t\t\t\t\t\t\t    <td class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t        <input name=\"BAC_Count\" size=\"5\" value=\"{$BAC_Count}\" />\n\t\t\t\t\t\t\t\t\t    </td>\n\t\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t\t</table>\n\t\t\t\t\t\t</fieldset>\t\n\t\t\t\t</div>\n\t\t\t\n\t\t\t\t<div id=\"ModelsDiv\" class=\"description \">\n\t\t\t\t\t\t<fieldset  class=\"bottommargin1 xgdb_log {$Status}\">\n\t\t\t\t\t\t<legend class=\"conf largerfont {$status_font_display}\"> &nbsp;  Gene Models: <span class=\"heading {$edit}\"> (Optional)</span></legend>\n\t\t\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\">\n\t\t\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t\t\t<tr><td>Gene Model Version:</td><td class=\"{$view} user_entry\">{$GeneModel_Version}</td><td class=\"{$edit}\"><input name=\"GeneModel_Version\" size=\"9\" value=\"{$GeneModel_Version}\" /></td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td>Gene Model Source:</td><td class=\"{$view} user_entry\">{$GeneModel_Source}</td><td class=\"{$edit}\"><input name=\"GeneModel_Source\" size=\"25\" value=\"{$GeneModel_Source}\" /></td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td>Gene Model Link:</td><td class=\"{$view} user_entry\"><pre><a href=\"{$GeneModel_Link}\">{$GeneModel_Link}</a></pre></td><td class=\"{$edit}\"><input name=\"GeneModel_Link\" size=\"60\" value=\"{$GeneModel_Link}\" /></td></tr>\n\t\t\t\t\t\t\t\t\t<tr class=\"no_edit\"><td>Genome Segments Annotated:</td><td>{$anno_gseg_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr class=\"no_edit\"><td><img src=\"/XGDB/images/genemodels.png\" alt=\"\" /> Precomputed Gene Models:</td><td class=\"\">{$gene_anno_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr class=\"no_edit\"><td class=\"indent2\">Gene Loci:</td><td class=\"\">{$gene_loci_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr class=\"no_edit\"><td><img src=\"/XGDB/images/cpgatmodels.png\" alt=\"\" /> CpGAT Gene Models: </td><td class=\"\">{$cpgat_gene_anno_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr class=\"no_edit\"><td width=\"35\"> <img src=\"/XGDB/images/yrgatemodels.png\" alt=\"\" /> yrGATE Annotations: </td><td width=\"5\">{$yrgate_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td>GeneModel Comments:</td><td class=\"{$view} user_entry\">{$GeneModel_Comments}</td><td  class=\"{$edit}\"><textarea class=\"data_entry smallerfont\" rows=\"1\" name=\"GeneModel_Comments\" cols=\"65\">{$GeneModel_Comments}</textarea></td></tr>\n\t\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t\t</table>\n\t\t\t\t\t\t</fieldset>\t\n\t\t\t\t</div>\n\t\t\t\n\t\t\t\t<div id=\"AlignmentsDiv\" class=\"description \">\n\t\t\t\t\t\t<fieldset  class=\"bottommargin1 xgdb_log {$Status}\">\n\t\t\t\t\t\t<legend class=\"conf largerfont {$status_font_display}\"> &nbsp; Transcript Spliced Alignments: <span class=\"heading {$edit}\">(Optional)</span></legend>\n\t\t\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\">\n\t\t\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t\tAligned EST Species:\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$view} italic user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t\t{$EST_Align_sp}\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t\t\t<input name=\"EST_Align_sp\" size=\"35\" value=\"{$EST_Align_sp}\" />\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t\tAligned EST Version:\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t\t{$EST_Align_Version}\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t\t\t\t<input name=\"EST_Align_Version\" size=\"15\" value=\"{$EST_Align_Version}\" />\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent2 heading\">EST Count Total:</td><td>{$est_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent2 heading\"> <img src=\"/XGDB/images/transcripts_est.png\" alt=\"\" /> EST Alignments:</td><td>{$est_algn_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent3 heading\">Cognate:</td><td>{$est_cog_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent3 heading\">Non-cognate:</td><td>{$est_non_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t\t<td class=\"indent2 heading\">\n\t\t\t\t\t\t\t\t\t\t\tAligned EST Comments:\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t\t{$EST_Align_Comments}\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t\t\t<input name=\"EST_Align_Comments\" size=\"75\" value=\"{$EST_Align_Comments}\" />\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t\t<tr><td>Aligned cDNA Species:</td><td class=\"{$view} italic user_entry\">{$cDNA_Align_sp}</td><td class=\"{$edit}\"><input name=\"cDNA_Align_sp\" size=\"35\" value=\"{$cDNA_Align_sp}\" /></td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td>Aligned cDNA Version:</td><td class=\"{$view} user_entry\">{$cDNA_Align_Version}</td><td class=\"{$edit}\"><input name=\"cDNA_Align_Version\" size=\"15\" value=\"{$cDNA_Align_Version}\" /></td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent2 heading\">cDNA Count Total:</td><td class=\"\">{$cdna_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent2 heading\"> <img src=\"/XGDB/images/transcripts_cdna.png\" alt=\"?\" /> cDNA Alignments:</td><td>{$cdna_algn_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent3 heading\">Cognate:</td><td>{$cdna_cog_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent3 heading\">Non-cognate:</td><td>{$cdna_non_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t\t<td class=\"indent2 heading\">\n\t\t\t\t\t\t\t\t\t\t\tAligned cDNA Comments:\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t\t{$cDNA_Align_Comments}\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t\t\t<input name=\"cDNA_Align_Comments\" size=\"75\" value=\"{$cDNA_Align_Comments}\" />\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t</tr>\n\n\t\t\t\t\t\t\t\t\t<tr><td>Aligned TSA<span class=\"heading\">*</span> Species:</td><td class=\"{$view} italic user_entry\">{$PUT_Align_sp}</td><td class=\"{$edit}\"><input name=\"PUT_Align_sp\" size=\"35\" value=\"{$PUT_Align_sp}\" /></td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td>Aligned TSA<span class=\"heading\">*</span> Version:</td><td class=\"{$view} user_entry\">{$PUT_Align_Version}</td><td class=\"{$edit}\"><input name=\"PUT_Align_Version\" size=\"15\" value=\"{$PUT_Align_Version}\" /></td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent2\"> <img src=\"/XGDB/images/transcripts_put.png\" alt=\"?\" /> TSA<span class=\"heading\">*</span> Alignments:</td><td class=\"\">{$put_align_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t\t<td class=\"indent2 heading\">\n\t\t\t\t\t\t\t\t\t\t\tAligned TSA* Comments:\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t\t{$PUT_Align_Comments}\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t\t\t<input name=\"PUT_Align_Comments\" size=\"75\" value=\"{$PUT_Align_Comments}\" />\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t\t</table>\n\t\t\t\t\t\t\t<span class=\"heading\">*TSA = Transcript Sequence Assembly</span>\n\t\t\t\t\t\t</fieldset>\n\t\t\t\t\t\t\n\t\t\t\t\t\t<fieldset  class=\"bottommargin1 xgdb_log {$Status}\">\n\t\t\t\t\t\t\t<legend class=\"conf largerfont {$status_font_display}\"> &nbsp; Protein Alignments:  <span class=\"heading {$edit}\">(Optional)</span></legend>\n\t\t\t\t\t\t\t<table class=\"xgdb_log {$status_font_display}\" border=\"0\" style=\"font-size:12px\" width=\"100%\">\n\t\t\t\t\t\t\t\t<colgroup>\n\t\t\t\t\t\t\t\t\t<col width =\"25%\" style=\"background-color: #DDD\" />\n\t\t\t\t\t\t\t\t\t<col width =\"75%\" />\n\t\t\t\t\t\t\t\t</colgroup>\n\t\t\t\t\t\t\t\t<tbody>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent2\">Species:</td><td class=\"{$view} italic user_entry\">{$Prot_Align_sp}</td><td class=\"{$edit}\"><input name=\"Prot_Align_sp\" size=\"35\" value=\"{$Prot_Align_sp}\" /></td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent2\">Version:</td><td class=\"{$view} user_entry\">{$Prot_Align_Version}</td><td class=\"{$edit}\"><input name=\"Prot_Align_Version\" size=\"10\" value=\"{$Prot_Align_Version}\" /></td></tr>\n\t\t\t\t\t\t\t\t\t<tr>\n\t\t\t\t\t\t\t\t\t\t<td class=\"indent2 heading\">\n\t\t\t\t\t\t\t\t\t\t\tAligned Protein Comments:\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t\t<td>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$view} user_entry\">\n\t\t\t\t\t\t\t\t\t\t\t\t{$Prot_Align_Comments}\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t\t<span class=\"{$edit}\">\n\t\t\t\t\t\t\t\t\t\t\t\t<input name=\"Prot_Align_Comments\" size=\"75\" value=\"{$Prot_Align_Comments}\" />\n\t\t\t\t\t\t\t\t\t\t\t</span>\n\t\t\t\t\t\t\t\t\t\t</td>\n\t\t\t\t\t\t\t\t\t</tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent2 heading\">Protein Count Total:</td><td>{$prot_total}</td></tr>\n\t\t\t\t\t\t\t\t\t<tr><td class=\"indent2 heading\"> <img alt=\"?\" src=\"/XGDB/images/proteins.png\" />&nbsp; Protein Alignments:</td><td>{$prot_align_total}</td></tr>\n\t\t\t\t\t\t\t\t</tbody>\n\t\t\t\t\t\t\t</table>\n\t\t\t\t\t\t</fieldset>\n\t\t\t\t\t</div>\n\t\t\t\t</form>\n\t\t\t\t</div><!-- big_form-->\n\t\t\t</div><!-- whatsthisdivfor -->\n\t\t</div><!-- maincontents -->\n\t\t\t\t\t\t  <div style=\"clear:both; float:right\">\n\t\t\t\t\t\t\t<a href=\"http://validator.w3.org/check?uri=referer\"><img\n\t\t\t\t\t\t\t  src=\"http://www.w3.org/Icons/valid-xhtml10\" alt=\"Valid XHTML 1.0 Transitional\" height=\"15\" width=\"44\" /></a>\n\t\t\t\t\t\t  </div>\t\t\t\t\t\t\n</div> <!-- maincontentscontainer -->\n";
?>
	
						<div id="leftcolumncontainer">
							<div class="minicolumnleft">
							<?php 
include_once "/xGDBvm/XGDB/conf/leftmenu.inc.php";
?>
							</div>
						</div>

				<?php 
#	echo "<span class=\"heading\" >".$get_data." | ".$get_est_tot." | ".$get_est_algn." </span>";

Example #2

Show file

File: new.php Project: BrendelGroup/xGDBvm

    //flag for dir1 mount
}
# data input directory: e.g. /input/xgdbvm/ ($dir2)
$dir2_dropdown = "{$inputDir}";
// 1-26-16
if (file_exists("/xGDBvm/admin/iplant")) {
    // xGDBvm-iPlant only
    $df_dir2 = df_available($dir2_dropdown);
    // check if /input/ directory is fuse-mounted (returns array)
    #    $dir2_dropdown=($df_dir2[0]=="fuse"  || $df_dir2[0]=="irodsFs")?"$dir2_dropdown":""; //only show input dir if fuse-mounted DISABLED THIS REQUIREMENT 4/16/2014
    $dir2_mount = $df_dir2[0] == "fuse" || $df_dir2[0] == "irodsFs" ? "<span class=\"checked_mount\">DataStore mounted</span>" : "<span class=\"lightgrayfont\">DataStore not mounted</span>";
    //flag for dir1 mount
}
$dir3_dropdown = "/xGDBvm/examples/";
// TODO: move to sitedef.php
$input_dirlist = dirlist_dropdown("", $dir2_dropdown, $dir3_dropdown, "{$Input_Data_Path}");
//build dropdown for input dir(s). Note that access to dir1_dropdown (under /xGDBvm/data) is DISABLED -- this parameter is not sent.
# display mount status (iPlant only)
$dir1_status = file_exists("/xGDBvm/admin/iplant") ? "<span class=\"normalfont\" style=\"font-weight:normal\">&nbsp; &nbsp;<a class='help-button' title='Mount status of {$dataDir}' id='config_input_ebs'>  {$dir1_mount} </a></span>" : "";
$dir2_status = file_exists("/xGDBvm/admin/iplant") ? "<span class=\"normalfont\" style=\"font-weight:normal\">&nbsp; &nbsp;<a class='help-button' title='Mount status of /xGDBvm/input/' id='config_input_input'> {$dir2_mount} </a></span>" : "";
# repeat mask directory
$dir4_dropdown = "{$inputDir}/repeatmask/";
$dir5_dropdown = "/xGDBvm/examples/repeatmask/";
$repmask_dirlist = filelist_dropdown($dir4_dropdown, $dir5_dropdown, "{$RepeatMask_File}");
//build dropdown for input dir(s), to include /xGDBvm/input (preferred) or /xGDBvm/data
# reference protein directory and files
$dir6_dropdown = "{$inputDir}/referenceprotein/";
$dir7_dropdown = "/xGDBvm/examples/referenceprotein/";
$refprot_dirlist = filelist_dropdown($dir6_dropdown, $dir7_dropdown, "{$CpGAT_ReferenceProt_File}");
//build dropdown for reference protein dir(s)
# archive directory list (top of form, conditional, allows user to load an archive config set) #