diff --git a/.gitignore b/.gitignore index 64e0e36..b67ce7c 100644 --- a/.gitignore +++ b/.gitignore @@ -3,5 +3,4 @@ # Server Submission(s) *.txt -*.htm *.tab diff --git a/README.md b/README.md old mode 100644 new mode 100755 diff --git a/cancer.html b/cancer.html index af22f87..04b2d05 100755 --- a/cancer.html +++ b/cancer.html @@ -205,9 +205,7 @@ We welcome any comments and/or suggestions that you may have regarding our software and server - please send an email directly to fathmm@biocompute.org.uk

+ - - - diff --git a/cgi-bin/results.cgi b/cgi-bin/results.cgi index 7f3b63a..88b5fba 100755 --- a/cgi-bin/results.cgi +++ b/cgi-bin/results.cgi @@ -90,6 +90,13 @@ if __name__ == '__main__': + + + + + + + - """ @@ -322,10 +327,8 @@ if __name__ == '__main__': We welcome any comments and/or suggestions that you may have regarding our software and server - please send an email directly to fathmm@biocompute.org.uk

+ - - - """ @@ -426,8 +429,6 @@ if __name__ == '__main__': - - """ @@ -552,8 +553,6 @@ if __name__ == '__main__': - - """ diff --git a/css/Data-Table.css b/css/Data-Table.css new file mode 100644 index 0000000..f43d686 --- /dev/null +++ b/css/Data-Table.css @@ -0,0 +1,178 @@ + +div.dataTables_length label { + float: left; + text-align: left; +} + +div.dataTables_length select { + width: 75px; +} + +div.dataTables_filter label { + float: right; +} + +div.dataTables_info { + padding-top: 8px; +} + +div.dataTables_paginate { + float: right; + margin: 0; +} + +table.table { + clear: both; + margin-bottom: 6px !important; + max-width: none !important; +} + +table.table thead .sorting, +table.table thead .sorting_asc, +table.table thead .sorting_desc, +table.table thead .sorting_asc_disabled, +table.table thead .sorting_desc_disabled { + cursor: pointer; + *cursor: hand; +} + +table.table thead .sorting { background: url('../img/sort_both.png') no-repeat center right; } +table.table thead .sorting_asc { background: url('../img/sort_asc.png') no-repeat center right; } +table.table thead .sorting_desc { background: url('../img/sort_desc.png') no-repeat center right; } + +table.table thead .sorting_asc_disabled { background: url('../img/sort_asc_disabled.png') no-repeat center right; } +table.table thead .sorting_desc_disabled { background: url('../img/sort_desc_disabled.png') no-repeat center right; } + +table.dataTable th:active { + outline: none; +} + +/* Scrolling */ +div.dataTables_scrollHead table { + margin-bottom: 0 !important; + border-bottom-left-radius: 0; + border-bottom-right-radius: 0; +} + +div.dataTables_scrollHead table thead tr:last-child th:first-child, +div.dataTables_scrollHead table thead tr:last-child td:first-child { + border-bottom-left-radius: 0 !important; + border-bottom-right-radius: 0 !important; +} + +div.dataTables_scrollBody table { + border-top: none; + margin-bottom: 0 !important; +} + +div.dataTables_scrollBody tbody tr:first-child th, +div.dataTables_scrollBody tbody tr:first-child td { + border-top: none; +} + +div.dataTables_scrollFoot table { + border-top: none; +} + + + + +/* + * TableTools styles + */ +.table tbody tr.active td, +.table tbody tr.active th { + background-color: #08C; + color: white; +} + +.table tbody tr.active:hover td, +.table tbody tr.active:hover th { + background-color: #0075b0 !important; +} + +.table-striped tbody tr.active:nth-child(odd) td, +.table-striped tbody tr.active:nth-child(odd) th { + background-color: #017ebc; +} + +table.DTTT_selectable tbody tr { + cursor: pointer; + *cursor: hand; +} + +div.DTTT .btn { + color: #333 !important; + font-size: 12px; +} + +div.DTTT .btn:hover { + text-decoration: none !important; +} + + +ul.DTTT_dropdown.dropdown-menu a { + color: #333 !important; /* needed only when demo_page.css is included */ +} + +ul.DTTT_dropdown.dropdown-menu li:hover a { + background-color: #0088cc; + color: white !important; +} + +/* TableTools information display */ +div.DTTT_print_info.modal { + height: 150px; + margin-top: -75px; + text-align: center; +} + +div.DTTT_print_info h6 { + font-weight: normal; + font-size: 28px; + line-height: 28px; + margin: 1em; +} + +div.DTTT_print_info p { + font-size: 14px; + line-height: 20px; +} + + + +/* + * FixedColumns styles + */ +div.DTFC_LeftHeadWrapper table, +div.DTFC_LeftFootWrapper table, +table.DTFC_Cloned tr.even { + background-color: white; +} + +div.DTFC_LeftHeadWrapper table { + margin-bottom: 0 !important; + border-top-right-radius: 0 !important; + border-bottom-left-radius: 0 !important; + border-bottom-right-radius: 0 !important; +} + +div.DTFC_LeftHeadWrapper table thead tr:last-child th:first-child, +div.DTFC_LeftHeadWrapper table thead tr:last-child td:first-child { + border-bottom-left-radius: 0 !important; + border-bottom-right-radius: 0 !important; +} + +div.DTFC_LeftBodyWrapper table { + border-top: none; + margin-bottom: 0 !important; +} + +div.DTFC_LeftBodyWrapper tbody tr:first-child th, +div.DTFC_LeftBodyWrapper tbody tr:first-child td { + border-top: none; +} + +div.DTFC_LeftFootWrapper table { + border-top: none; +} diff --git a/img/new.png b/img/new.png old mode 100644 new mode 100755 diff --git a/img/pubmed.png b/img/pubmed.png old mode 100644 new mode 100755 diff --git a/img/sort_asc.png b/img/sort_asc.png new file mode 100644 index 0000000..a88d797 Binary files /dev/null and b/img/sort_asc.png differ diff --git a/img/sort_asc_disabled.png b/img/sort_asc_disabled.png new file mode 100644 index 0000000..4e144cf Binary files /dev/null and b/img/sort_asc_disabled.png differ diff --git a/img/sort_both.png b/img/sort_both.png new file mode 100644 index 0000000..1867040 Binary files /dev/null and b/img/sort_both.png differ diff --git a/img/sort_desc.png b/img/sort_desc.png new file mode 100644 index 0000000..def071e Binary files /dev/null and b/img/sort_desc.png differ diff --git a/img/sort_desc_disabled.png b/img/sort_desc_disabled.png new file mode 100644 index 0000000..7824973 Binary files /dev/null and b/img/sort_desc_disabled.png differ diff --git a/index.html b/index.html index e51d540..b4b3707 100755 --- a/index.html +++ b/index.html @@ -141,8 +141,5 @@

Analyze Cancer-Associated Variants

- - - diff --git a/inherited.html b/inherited.html index 61da0c3..226dfa2 100755 --- a/inherited.html +++ b/inherited.html @@ -224,9 +224,7 @@ We welcome any comments and/or suggestions that you may have regarding our software and server - please send an email directly to fathmm@biocompute.org.uk

+ - - - diff --git a/js/Data-Table.js b/js/Data-Table.js new file mode 100644 index 0000000..d7075d4 --- /dev/null +++ b/js/Data-Table.js @@ -0,0 +1,158 @@ + +/* Set the defaults for DataTables initialisation */ +$.extend( true, $.fn.dataTable.defaults, { + "sDom": "<'row-fluid'<'span6'l><'span6'f>r>t<'row-fluid'<'span6'i><'span6'p>>", + "sPaginationType": "bootstrap", + "oLanguage": { + "sLengthMenu": "_MENU_ records per page" + } +} ); + + +/* Default class modification */ +$.extend( $.fn.dataTableExt.oStdClasses, { + "sWrapper": "dataTables_wrapper form-inline" +} ); + + +/* API method to get paging information */ +$.fn.dataTableExt.oApi.fnPagingInfo = function ( oSettings ) +{ + return { + "iStart": oSettings._iDisplayStart, + "iEnd": oSettings.fnDisplayEnd(), + "iLength": oSettings._iDisplayLength, + "iTotal": oSettings.fnRecordsTotal(), + "iFilteredTotal": oSettings.fnRecordsDisplay(), + "iPage": Math.ceil( oSettings._iDisplayStart / oSettings._iDisplayLength ), + "iTotalPages": Math.ceil( oSettings.fnRecordsDisplay() / oSettings._iDisplayLength ) + }; +}; + + +/* Bootstrap style pagination control */ +$.extend( $.fn.dataTableExt.oPagination, { + "bootstrap": { + "fnInit": function( oSettings, nPaging, fnDraw ) { + var oLang = oSettings.oLanguage.oPaginate; + var fnClickHandler = function ( e ) { + e.preventDefault(); + if ( oSettings.oApi._fnPageChange(oSettings, e.data.action) ) { + fnDraw( oSettings ); + } + }; + + $(nPaging).addClass('pagination').append( + '' + ); + var els = $('a', nPaging); + $(els[0]).bind( 'click.DT', { action: "previous" }, fnClickHandler ); + $(els[1]).bind( 'click.DT', { action: "next" }, fnClickHandler ); + }, + + "fnUpdate": function ( oSettings, fnDraw ) { + var iListLength = 5; + var oPaging = oSettings.oInstance.fnPagingInfo(); + var an = oSettings.aanFeatures.p; + var i, j, sClass, iStart, iEnd, iHalf=Math.floor(iListLength/2); + + if ( oPaging.iTotalPages < iListLength) { + iStart = 1; + iEnd = oPaging.iTotalPages; + } + else if ( oPaging.iPage <= iHalf ) { + iStart = 1; + iEnd = iListLength; + } else if ( oPaging.iPage >= (oPaging.iTotalPages-iHalf) ) { + iStart = oPaging.iTotalPages - iListLength + 1; + iEnd = oPaging.iTotalPages; + } else { + iStart = oPaging.iPage - iHalf + 1; + iEnd = iStart + iListLength - 1; + } + + for ( i=0, iLen=an.length ; i'+j+'') + .insertBefore( $('li:last', an[i])[0] ) + .bind('click', function (e) { + e.preventDefault(); + oSettings._iDisplayStart = (parseInt($('a', this).text(),10)-1) * oPaging.iLength; + fnDraw( oSettings ); + } ); + } + + // Add / remove disabled classes from the static elements + if ( oPaging.iPage === 0 ) { + $('li:first', an[i]).addClass('disabled'); + } else { + $('li:first', an[i]).removeClass('disabled'); + } + + if ( oPaging.iPage === oPaging.iTotalPages-1 || oPaging.iTotalPages === 0 ) { + $('li:last', an[i]).addClass('disabled'); + } else { + $('li:last', an[i]).removeClass('disabled'); + } + } + } + } +} ); + + +/* + * TableTools Bootstrap compatibility + * Required TableTools 2.1+ + */ +if ( $.fn.DataTable.TableTools ) { + // Set the classes that TableTools uses to something suitable for Bootstrap + $.extend( true, $.fn.DataTable.TableTools.classes, { + "container": "DTTT btn-group", + "buttons": { + "normal": "btn", + "disabled": "disabled" + }, + "collection": { + "container": "DTTT_dropdown dropdown-menu", + "buttons": { + "normal": "", + "disabled": "disabled" + } + }, + "print": { + "info": "DTTT_print_info modal" + }, + "select": { + "row": "active" + } + } ); + + // Have the collection use a bootstrap compatible dropdown + $.extend( true, $.fn.DataTable.TableTools.DEFAULTS.oTags, { + "collection": { + "container": "ul", + "button": "li", + "liner": "a" + } + } ); +} + + +/* Table initialisation */ +$(document).ready(function() { + $('#results').dataTable( { + "sDom": "<'row'<'span6'l><'span6'f>r>t<'row'<'span6'i><'span6'p>>", + "sPaginationType": "bootstrap", + "oLanguage": { + "sLengthMenu": "_MENU_ records per page" + } + } ); +} ); diff --git a/js/jquery.dataTables.min.js b/js/jquery.dataTables.min.js new file mode 100755 index 0000000..02694a4 --- /dev/null +++ b/js/jquery.dataTables.min.js @@ -0,0 +1,155 @@ +/* + * File: jquery.dataTables.min.js + * Version: 1.9.4 + * Author: Allan Jardine (www.sprymedia.co.uk) + * Info: www.datatables.net + * + * Copyright 2008-2012 Allan Jardine, all rights reserved. + * + * This source file is free software, under either the GPL v2 license or a + * BSD style license, available at: + * http://datatables.net/license_gpl2 + * http://datatables.net/license_bsd + * + * This source file is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY + * or FITNESS FOR A PARTICULAR PURPOSE. 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