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authorZachary Sloan2013-01-11 23:59:41 +0000
committerZachary Sloan2013-01-11 23:59:41 +0000
commit2b2970d167c5b555e0e0ad0b34b72f817c1fac91 (patch)
tree36fa8c708138fff03593e0f50cc933bcb62b5592 /web
parent1db9237a05fd27c80dc963db9916072594156198 (diff)
parentd39b691994a395c45fa242de6d64d12a5470af10 (diff)
downloadgenenetwork2-2b2970d167c5b555e0e0ad0b34b72f817c1fac91.tar.gz
Merge branch 'flask' of http://github.com/zsloan/genenetwork
Diffstat (limited to 'web')
-rwxr-xr-xweb/css/general_flask.css266
-rwxr-xr-xweb/javascript/header.js122
-rwxr-xr-x[-rw-r--r--]web/javascript/jqueryFunction.js2041
-rw-r--r--[-rwxr-xr-x]web/javascript/selectDatasetMenu.js0
-rwxr-xr-xweb/javascript/webqtl.js184
-rwxr-xr-xweb/webqtl/base/webqtlConfigLocal.py10
-rw-r--r--web/webqtl/base/webqtlTrait.py9
-rwxr-xr-xweb/webqtl/basicStatistics/updatedBasicStatisticsPage.py54
-rwxr-xr-xweb/webqtl/collection/ExportSelectionDetailInfoPage.py5
-rwxr-xr-xweb/webqtl/correlation/CorrelationPage.py171
-rwxr-xr-xweb/webqtl/maintainance/genSelectDatasetJS.py3
-rwxr-xr-xweb/webqtl/search/SearchResultPage.py6
-rwxr-xr-x[-rw-r--r--]web/webqtl/showTrait/DataEditingPage.py49
13 files changed, 1599 insertions, 1321 deletions
diff --git a/web/css/general_flask.css b/web/css/general_flask.css
new file mode 100755
index 00000000..d40fa267
--- /dev/null
+++ b/web/css/general_flask.css
@@ -0,0 +1,266 @@
+@import url(import.css);
+
+body
+{
+ font-family : verdana, geneva, lucida, 'lucida grande', arial, helvetica;
+ font-weight : Normal;
+}
+
+Blockquote {
+ margin : 14px 18px 14px 18px;
+}
+
+/********** All this font size stuff, etc. needs to be replaced/removed ********** /
+
+/*Font size*/
+.fs10 {font-size : 10px}
+.fs11 {font-size : 11px}
+.fs12 {font-size : 12px}
+.fs13 {font-size : 13px}
+.fs14 {font-size : 14px}
+.fs15 {font-size : 15px}
+.fs16 {font-size : 16px}
+.fs17 {font-size : 17px}
+
+/*Font Weight*/
+.fwb {font-weight : Bold}
+.fwn {font-weight : Normal}
+
+/*Font Style*/
+.fsI {font-style : Italic}
+
+/*Font family*/
+.ffv {font-family : verdana, geneva, lucida, 'lucida grande', arial, helvetica;}
+.ffl {font-family : lucida, verdana, 'lucida grande', helvetica, arial, geneva;}
+.ffmono {font-family : "CourierNew", Courier, mono;}
+
+/*Color*/
+.cr {color : #f00}
+.cg {color : #0f0}
+.cdg {color : darkgreen}
+.cb {color : #00f}
+.c222 {color : #222}
+.c999 {color : #999}
+.c00d {color : #00d}
+.cori {color : #CC9933}
+.crb {color : royalblue}
+.cw {color : #fff}
+.cbl {color : #000000}
+.cydull {color : #cfcf32}
+.cdefault {color : #503A7D}
+
+/*backColor*/
+.cbr {background-color : #f00}
+.cbg {background-color : #0f0}
+.cbdg {background-color : darkgreen}
+.cbb {background-color : #00f}
+.cb222 {background-color : #222}
+.cbg22t {background-color : #FF6}
+.cbg22c {background-color : #5CB3FF}
+.cbg2C {background-color : #1569C7}
+.cbg22a {background-color : #F66}
+.cbg22g {background-color : #CF9}
+.cb00d {background-color : #00d}
+.cb222 {background-color : #222}
+.cbeee {background-color : #eee}
+.cbori {background-color : #CC9933}
+.cbrb {background-color : royalblue}
+.cbdb {background-color : #2D2DB5}
+.cbw {background-color : #fff}
+.cbydull {background-color : #cfcf32}
+.cbrdull {background-color : #c33232}
+.cbgdull {background-color : #32c332}
+.cbbdull {background-color : #1569C7}
+.cbpdull {background-color : #c332c3}
+.cbccc {background-color : #ccc}
+.cbddf {background-color : #ddf}
+
+.nowrap {white-space: nowrap;}
+
+/*Table Cell*/
+.collap {border-collapse : collapse;}
+
+TH.header {
+ background-image: url(/images/bg.gif);
+ background-color: #4169E1;
+ cursor: pointer;
+ background-repeat: no-repeat;
+ background-position: center left;
+ padding-left: 20px;
+ margin-left: -1px;
+}
+TH.headerSortUp {
+ background-image: url(/images/desc.gif);
+ background-color: #4169E1;
+}
+TH.headerSortDown {
+ background-image: url(/images/asc.gif);
+ background-color: #4169E1;
+}
+
+TD, P {color : #222222; font-size : 13px}
+TD.b1 {border : 1px solid #999999; padding : 3px;}
+TH.b1 {border : 1px solid #999999; padding : 3px;}
+TD.bt1 {border-top : 1px solid #999999; padding : 3px;}
+TD.bb1 {border-bottom : 1px solid #999999; padding : 3px;}
+
+.b2 {border : 2px solid royalblue; padding : 3px;}
+
+.bd1 {border : 1px dashed #999999; padding : 6px;}
+
+TR.outlier, TD.outlier {background-color : yellow;}
+
+TR.alt td {
+ background: #e6e8fa;
+}
+
+TR.over td {
+ background: #82CFFD;
+}
+
+/*Table Row*/
+.toggleShowHide { color : #0000DD; cursor: pointer;}
+.invisible {display: none;}
+
+/*Link*/
+A.font_black:link {color: #000000; text-decoration : None}
+A.font_black:active {color: #000000; text-decoration : None}
+A.font_black:hover {color: #000000; text-decoration : None}
+A.font_black:visited {color: #000000; text-decoration : None}
+
+A {font-family : lucida, 'lucida grande', verdana, helvetica, arial, geneva;
+ font-weight : Bold; font-size : 13px; text-decoration : None}
+
+A:link, A:visited {color : #0000DD; text-decoration : None}
+
+A:active {color : #FF0000; text-decoration : None}
+
+A:hover {color : #FF0000; text-decoration : None}
+
+A.background_grey {background:#dddddd;padding:2;}
+
+A.non_bold {font-weight : Normal; color : #0000DD;}
+
+/*Border Style*/
+.solidBorder {border : 1px solid #CCCCCC; padding : 2px;}
+.doubleBorder {border : double #AAAAAA; padding : 2px;}
+
+/*Title style*/
+.title {font-weight:Bold; color:#222222; font-size:16px}
+
+.subtitle {font-family : lucida, verdana, 'lucida grande', helvetica, arial, geneva;
+ font-weight:Bold; font-size:14px; color:#000082}
+
+.sectionheader {font-family : arial, verdana, 'lucida grande', helvetica, lucida, geneva;
+ font-weight:Bold; font-size:14px; vertical-align: middle; display:block; color:#000000; background-color:#DDDDDD; line-height:24px; height:24px;}
+
+/*drop shadow*/
+#v3 .wrap1 {background:url(/images/shadow/shadow.gif) right bottom no-repeat;}
+#v3 .wrap2 {background:url(/images/shadow/corner_bl.gif) -12px 100% no-repeat;}
+#v3 .wrap3 {
+ padding:0 9px 9px 0;
+ background:url(/images/shadow/corner_tr.gif) 100% -12px no-repeat;}
+
+
+/*steal from google*/
+
+ .tabsTableBox {
+ width:100%;
+ border-spacing:0;
+ border-collapse:collapse;
+ margin-top:5px;
+ font-size:smaller;
+ text-align:center;
+ }
+ .tabsTableBox td {
+ padding-right:5px;
+ padding-left:5px;
+ padding-bottom:3px;
+ }
+
+/*For making the Custom Strain box in snpBrowser.py a default width, instead of looking weird always*/
+.customBoxWidth {
+ width: 143px;
+}
+ .selectedBox {
+ border-top:1px solid #676767;
+ border-right:1px solid #676767;
+ border-left:1px solid #676767;
+ width:80;
+ font-weight:bolder;
+ color:#3366cc;
+ font-size:12px;
+ }
+ .unselectedBox {
+ background-color:#dddddd;
+ border-top:1px solid #aaaaaa;
+ width:80;
+ border-right:1px solid #aaaaaa;
+ border-left:1px solid #aaaaaa;
+ border-bottom:1px solid #676767;
+ font-size:12px;
+ }
+
+ .spacerTabBox {
+ border-bottom:1px solid #676767;
+ width:5px;
+ }
+
+ .emptyTabBox {
+ border-bottom:1px solid #676767;
+ }
+
+/*For font color of 'Get Any' and 'Combined' in the main page*/
+.searchtip
+{
+color: #999999;
+}
+
+
+/*For font style and color of commands and keywords in the scriptable interface page*/
+.keywords
+{
+ font-family : "CourierNew", Courier, mono;
+ font-size : 15px;
+ color : #0000FF;
+ font-weight : Normal
+}
+
+/*For RIsample.html page*/
+.strains
+{
+ border:1px solid #999999;
+ border-top:1px solid #940;
+ border-bottom:1px solid #940;
+ padding:5;
+ background-color:#ddf;
+ font-family:verdana;
+}
+
+.values
+{
+ border:1px solid #999999;
+ border-top:1px solid #940;
+ border-bottom:1px solid #940;
+ padding:5;
+ background-color:#eee;
+ font-family:courier;
+}
+
+/*****************************************/
+
+/* Standard table cell */
+.std_cell
+{
+ border : 1px solid #999999;
+ color : #222;
+ font-size : 13px;
+ padding : 3px;
+}
+
+/*Input field used to enter sample values, SE, etc.*/
+.trait_value_input
+{
+ font-style : Italic
+}
+
diff --git a/web/javascript/header.js b/web/javascript/header.js
index 59fcacd8..65ba1bd6 100755
--- a/web/javascript/header.js
+++ b/web/javascript/header.js
@@ -1,62 +1,62 @@
-ctext = ''
-ctext += '<TD width=30 rowSpan=5>&nbsp;</TD>'
-ctext += '<TD bgColor=#ffffff NOWRAP="yes" width="100%" class="solidBorder">'
-ctext += ' <Table width= "100%" cellSpacing=0 cellPadding=0>'
-ctext += ' <TR>'
-ctext += ' <TD width= "100%" id="smallsize">'
-ctext += ' <a href="/">'
-ctext += ' <IMG src="/images/upload/GeneNet_Banner2009c.png" border="0">'
-ctext += ' </a>'
-ctext += ' </TD>'
-ctext += ' <TD valign="bottom">'
-ctext += ' <A HREF="http://www.touchgraph.com/TGGoogleBrowser.php?start=genenetwork.org&signed=false" target="_blank">'
-ctext += ' <IMG SRC="/images/upload/NetworkLogo.png" width="101" height="73" border="0">'
-ctext += ' </a>'
-ctext += ' </td>'
-ctext += ' <TD valign="bottom">'
-ctext += ' <IMG src="/images/webqtllogo2.gif" alt="WebQTL" border="0">'
-ctext += ' </TD>'
-ctext += ' </TR>'
-ctext += ' </Table>'
-ctext += '</TD>'
-ctext += '<TD width="30" rowSpan=5>&nbsp;</TD>'
-ctext += '</TR>'
-ctext += '<TR>'
-ctext += '<!--Home Help Search News Papers Policies Accounts Links-->'
-ctext += '<TD bgColor=#ddddff NOWRAP="yes" class="solidBorder">'
-ctext += '<table width="100%" cellSpacing=0 cellPadding=0 border=0>'
-ctext += '<tr>'
-ctext += '<td aligh=left NOWRAP="yes">'
-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
-ctext += '<Span Id= "menu_grp1" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp1\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp1\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
-ctext += '<Strong>Home</Strong></Span>'
-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
-ctext += '<Span Id= "menu_grp2" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp2\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp2\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
-ctext += '<Strong>Search</Strong></Span>'
-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
-ctext += '<Span Id= "menu_grp3" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp3\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp3\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
-ctext += '<Strong>Help</Strong></Span>'
-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
-ctext += '<Span Id= "menu_grp4" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp4\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp4\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
-ctext += '<A Href="/whats_new.html" style="font-size:12px;font-family:verdana;color:#0000ae">'
-ctext += '<Strong>News</Strong></A></Span>'
-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
-ctext += '<Span Id= "menu_grp5" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp5\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp5\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
-ctext += '<A Href="/reference.html" style="font-size:12px;font-family:verdana;color:#0000ae">'
-ctext += '<Strong>References</Strong></A></Span>'
-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
-ctext += '<Span Id= "menu_grp6" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp6\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp6\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
-ctext += '<Strong>Policies</Strong></Span>'
-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
-ctext += '<Span Id= "menu_grp8" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp8\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp8\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
-ctext += '<A Href="/links.html" style="font-size:12px;font-family:verdana;color:#0000ae">'
-ctext += '<Strong>Links</Strong></A></Span>'
-ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
-ctext += '</td>'
-ctext += '<td align="right" NOWRAP="yes">'
-ctext += '<!-- %s -->&nbsp;&nbsp;&nbsp;'
-ctext += '</td>'
-ctext += '</tr>'
-ctext += '</table>'
-ctext += '</TD>'
+ctext = ''
+ctext += '<TD width=30 rowSpan=5>&nbsp;</TD>'
+ctext += '<TD bgColor=#ffffff NOWRAP="yes" width="100%" class="solidBorder">'
+ctext += ' <Table width= "100%" cellSpacing=0 cellPadding=0>'
+ctext += ' <TR>'
+ctext += ' <TD width= "100%" id="smallsize">'
+ctext += ' <a href="/">'
+ctext += ' <IMG src="/images/upload/GeneNet_Banner2009c.png" border="0">'
+ctext += ' </a>'
+ctext += ' </TD>'
+ctext += ' <TD valign="bottom">'
+ctext += ' <A HREF="http://www.touchgraph.com/TGGoogleBrowser.php?start=genenetwork.org&signed=false" target="_blank">'
+ctext += ' <IMG SRC="/images/upload/NetworkLogo.png" width="101" height="73" border="0">'
+ctext += ' </a>'
+ctext += ' </td>'
+ctext += ' <TD valign="bottom">'
+ctext += ' <IMG src="/images/webqtllogo2.gif" alt="WebQTL" border="0">'
+ctext += ' </TD>'
+ctext += ' </TR>'
+ctext += ' </Table>'
+ctext += '</TD>'
+ctext += '<TD width="30" rowSpan=5>&nbsp;</TD>'
+ctext += '</TR>'
+ctext += '<TR>'
+ctext += '<!--Home Help Search News Papers Policies Accounts Links-->'
+ctext += '<TD bgColor=#ddddff NOWRAP="yes" class="solidBorder">'
+ctext += '<table width="100%" cellSpacing=0 cellPadding=0 border=0>'
+ctext += '<tr>'
+ctext += '<td aligh=left NOWRAP="yes">'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp1" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp1\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp1\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>Home</Strong></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp2" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp2\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp2\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>Search</Strong></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp3" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp3\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp3\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>Help</Strong></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp4" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp4\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp4\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<A Href="/whats_new.html" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>News</Strong></A></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp5" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp5\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp5\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<A Href="/reference.html" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>References</Strong></A></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp6" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp6\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp6\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>Policies</Strong></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '<Span Id= "menu_grp8" onmouseover="A_MENUS[0].onmouseover(grpObj[\'menu_grp8\'])" onmouseout="A_MENUS[0].onmouseout(grpObj[\'menu_grp8\'])" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<A Href="/links.html" style="font-size:12px;font-family:verdana;color:#0000ae">'
+ctext += '<Strong>Links</Strong></A></Span>'
+ctext += '&nbsp;&nbsp;&nbsp;|&nbsp;&nbsp;&nbsp;'
+ctext += '</td>'
+ctext += '<td align="right" NOWRAP="yes">'
+ctext += '<!-- %s -->&nbsp;&nbsp;&nbsp;'
+ctext += '</td>'
+ctext += '</tr>'
+ctext += '</table>'
+ctext += '</TD>'
document.write(ctext) \ No newline at end of file
diff --git a/web/javascript/jqueryFunction.js b/web/javascript/jqueryFunction.js
index 5e6641cd..e612098b 100644..100755
--- a/web/javascript/jqueryFunction.js
+++ b/web/javascript/jqueryFunction.js
@@ -1,80 +1,75 @@
/*
jquery part
*/
-
/*
used by index (base/indexBody.py)
*/
-
-$(document).ready(function(){
+$(document).ready(function () {
options_visible = 0; //Whether advanced options are being shown
-
$('tr .advanced_option').hide();
- $('.toggle_advanced').click(function(){
+ $('.toggle_advanced').click(function () {
$('tr .advanced_option').toggle();
-
- if (options_visible = 0) {
- $('.full_search_td').css('display','none;');
- $('.search_td').css('display','inline');
- options_visible = 1;
- }
- else {
- if ($('#type_menu.type_menu').val() = 'Hippocampus'){
- $('.search_td').css('display','none;');
- $('.full_search_td').css('display','inline');
- }
- options_visible = 0;
- }
+
+ if (options_visible = 0) {
+ $('.full_search_td').css('display', 'none;');
+ $('.search_td').css('display', 'inline');
+ options_visible = 1;
+ } else {
+ if ($('#type_menu.type_menu').val() = 'Hippocampus') {
+ $('.search_td').css('display', 'none;');
+ $('.full_search_td').css('display', 'inline');
+ }
+ options_visible = 0;
+ }
});
- $('#full_search').click(function(){
+ $('#full_search').click(function () {
gene_symbol = $('input[name=keyword]').val();
scriptable_interface_url = 'http://alexandria.uthsc.edu:89/webqtl/main.py?cmd=sch&gene=' + gene_symbol;
- window.open(scriptable_interface_url,'_self');
+ window.open(scriptable_interface_url, '_self');
});
});
-$('select.type_menu').live('change', function() {
+$('select.type_menu').live('change', function () {
var trait_type = $('select.type_menu option:selected').val();
- $('#tissue').val(trait_type);
- $('#tissue').trigger('change');
+ $('#tissue').val(trait_type);
+ $('#tissue').trigger('change');
});
/*
used by CorrelationPage.py, AddToSelectionPage.py, and SearchResultPage.py
*/
-$(document).ready(function(){
- $('img[name=addselect], img[name=networkgraph], img[name=corrmatrix], img[name=partialCorr], img[name=comparecorr], img[name=mintmap], img[name=heatmap]').click(function(){
- if ($('input[name=searchResult]:checked').length < 1){
- for (i=0; i<10; i++){
- $('input[name=searchResult]:eq('+i+')').attr('checked',true);
+$(document).ready(function () {
+ $('img[name=addselect], img[name=networkgraph], img[name=corrmatrix], img[name=partialCorr], img[name=comparecorr], img[name=mintmap], img[name=heatmap]').click(function () {
+ if ($('input[name=searchResult]:checked').length < 1) {
+ for (i = 0; i < 10; i++) {
+ $('input[name=searchResult]:eq(' + i + ')').attr('checked', true);
}
}
});
- $('img[name=addselect]').click(function(){
- addRmvSelection($('input[name=RISet]').val(), document.getElementsByName('showDatabase'+ $('input[name=RISet]').val())[0], 'addToSelection');
+ $('img[name=addselect]').click(function () {
+ addRmvSelection($('input[name=RISet]').val(), document.getElementsByName('showDatabase' + $('input[name=RISet]').val())[0], 'addToSelection');
});
- $('.toggleShowHide').click(function(){
+ $('.toggleShowHide').click(function () {
var className = '.extra_options';
- if ($(className).css('display') == 'none'){
- var less = 'less';
- $('input[name=showHideOptions]').val(less);
+ if ($(className).css('display') == 'none') {
+ var less = 'less';
+ $('input[name=showHideOptions]').val(less);
$(className).show();
$('input[name=options]').val('Fewer Options');
var display = $('input[name=options]').css('display')
- $(display).val('block');
- }
- else {
- var more = 'more';
- $('input[name=showHideOptions]').val(more);
- $(className).hide();
- $('input[name=options]').val('More Options');
- var display = $('input[name=showHideOptions]').css('display')
- $(display).val('block');
+ $(display).val('block');
+ } else {
+ var more = 'more';
+ $('input[name=showHideOptions]').val(more);
+ $(className).hide();
+ $('input[name=options]').val('More Options');
+ var display = $('input[name=showHideOptions]').css('display')
+ $(display).val('block');
}
});
});
@@ -83,82 +78,91 @@ $(document).ready(function(){
used by AddToSelectionPage.py
*/
function validateTraitNumber() {
- var checkBoxes = $('.checkallbox');
- if (checkBoxes.filter(":checked").length < 2) {
- alert("Please select at least two traits.");
- return false;
- }
- else {
- return true;
- }
+ var checkBoxes = $('.checkallbox');
+ if (checkBoxes.filter(":checked").length < 2) {
+ alert("Please select at least two traits.");
+ return false;
+ } else {
+ return true;
+ }
}
/*
used by TextSearchPage.py
*/
-$(document).ready(function(){
-
- $('.add_traits').click(function(){
- $('input[name=searchResult]').each(function(){
- if ($(this).is(':checked')){
- groupName = $(this).parents().next().next().children('[href]').text();
- addORrmv = 'addToSelection';
- thisForm = $('form[name=showDatabase]');
- addRmvSelection_allGroups(groupName, thisForm, addORrmv);
- }
- });
- });
-
- function addRmvSelection_allGroups(groupName, thisForm, addORrmv){
- thisForm.attr('target',groupName);
- thisForm.children('input[name=FormID]:hidden').val(addORrmv);
- thisForm.children('input[name=RISet]:hidden').val(groupName);
- var newWindow = open("",thisForm.attr('target'),"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
- thisForm.submit();
- }
-
- $('.tab_content').hide(); //Hide all tab content
- $('div.tab_container').each(function(){
- $(this).parent('td').find('div.tab_container:first').find('div.tab_content:first').show();
- });
- $('ul.tabs').each(function(){
- $(this).find('li:first').addClass('active');
- });
- $('ul.tabs:first').find('li:first').show();
- $('.tab_container:first').find('.tab_content:first').show();
-
- //On Click Event
- $('ul.tabs li').click(function() {
- $('ul.tabs').find('li').removeClass('last_viewed');
- if($(this).parent('ul.tabs').next('div.tab_container').attr('id').indexOf('stats') != 1){
- $(this).addClass('last_viewed');
- }
- $(this).parent('ul.tabs').find('li').removeClass('active');
- $(this).addClass('active');
- $(this).parent('ul.tabs').next('div.tab_container').find('.tab_content').hide();
- var activeTab = $(this).find('a').attr('href');
- if ($.browser.msie)
- {$(activeTab).show();}
- else
- {$(activeTab).fadeIn();} //Fade in the active ID content
-
- return false;
- });
+$(document).ready(function () {
+
+ $('.add_traits').click(function () {
+ $('input[name=searchResult]').each(function () {
+ if ($(this).is(':checked')) {
+ groupName = $(this).parents().next().next().children('[href]').text();
+ addORrmv = 'addToSelection';
+ thisForm = $('form[name=showDatabase]');
+ addRmvSelection_allGroups(groupName, thisForm, addORrmv);
+ }
+ });
+ });
+
+ function addRmvSelection_allGroups(groupName, thisForm, addORrmv) {
+ thisForm.attr('target', groupName);
+ thisForm.children('input[name=FormID]:hidden').val(addORrmv);
+ thisForm.children('input[name=RISet]:hidden').val(groupName);
+ var newWindow = open("", thisForm.attr('target'), "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
+ thisForm.submit();
+ }
+
+ $('.tab_content').hide(); //Hide all tab content
+ $('div.tab_container').each(function () {
+ $(this).parent('td').find('div.tab_container:first').find('div.tab_content:first').show();
+ });
+ $('ul.tabs').each(function () {
+ $(this).find('li:first').addClass('active');
+ });
+ $('ul.tabs:first').find('li:first').show();
+ $('.tab_container:first').find('.tab_content:first').show();
+
+ //On Click Event
+ $('ul.tabs li').click(function () {
+ $('ul.tabs').find('li').removeClass('last_viewed');
+ if ($(this).parent('ul.tabs').next('div.tab_container').attr('id').indexOf('stats') != 1) {
+ $(this).addClass('last_viewed');
+ }
+ $(this).parent('ul.tabs').find('li').removeClass('active');
+ $(this).addClass('active');
+ $(this).parent('ul.tabs').next('div.tab_container').find('.tab_content').hide();
+ var activeTab = $(this).find('a').attr('href');
+ if ($.browser.msie) {
+ $(activeTab).show();
+ } else {
+ $(activeTab).fadeIn();
+ } //Fade in the active ID content
+ return false;
+ });
});
/*
used by DataEditingPage.py
*/
-$(document).ready(function() {
+$(document).ready(function () {
+
+ // ZS: This checks the number of columns in order to determine which column to not sort; in this case the plus-minus symbol shouldn't be sortable
+ $('#sortable1,#sortable2').find('th').each(function () {
+ if ($(this).text() == 'SE') {
+ $.tablesorter.defaults.headers = {
+ 3: {
+ sorter: false
+ }
+ };
+ return false;
+ }
+ });
+
+ if ($('#sortable1,#sortable2').find('.outlier').size() > 0) {
+ $('input[name=sample_method]:eq(1)').attr('checked','checked');
+ $('input[name=tissue_method]:eq(1)').attr('checked','checked');
+ }
- // ZS: This checks the number of columns in order to determine which column to not sort; in this case the plus-minus symbol shouldn't be sortable
- $('#sortable1,#sortable2').find('th').each(function() {
- if ($(this).text() == 'SE'){
- $.tablesorter.defaults.headers = { 3: {sorter: false} };
- return false;
- }
- });
/*
ZS: This segment is called by tablesorter.js; it determines where to get the text used when sorting, based on the type of cell.
@@ -167,949 +171,922 @@ $(document).ready(function() {
This segment is repeated twice. Ideally this wouldn't be the case, but I can't find a way to reuse the inner textExtraction function.
*/
- //ZS: Defining these here, so they don't need to be searched for in the DOM for every single node
- primaryTable = $("#sortable1");
- otherTable = $("#sortable2");
-
- primaryValueHeader = primaryTable.find('th:contains("Value"):eq(0)');
- primarySEHeader = primaryTable.find('th:contains("SE"):eq(0)');
- otherValueHeader = otherTable.find('th:contains("Value"):eq(1)');
- otherSEHeader = otherTable.find('th:contains("SE"):eq(1)');
-
- $("#sortable1").tablesorter({
- textExtraction: function(node) {
- if ((node.children[0] == "[object HTMLInputElement]" && node.children[0].type == "text") || (/\S/.test(node.id))) {
- cellId = node.id;
- thisCell = $('#'+cellId).children(':eq(0)')
- valueClassNames = thisCell.attr('class').split(/\s+/);
- capitalized_column_name = cellId.split('_')[0].charAt(0).toUpperCase() + cellId.split('_')[0].slice(1);
- value = valueClassNames[valueClassNames.length - 1];
- newValue = thisCell.val();
-
- if (newValue == 'x' || value == '9999' || value == '-9999') {
- valueType = cellId.split('_')[0];
- if (valueType == 'value'){
- header = primaryValueHeader;
- } else {
- header = primarySEHeader;
- }
-
- if (header.hasClass('headerSortUp')){
- sort_order = 'desc';
- } else if (header.hasClass('headerSortDown')){
- sort_order = 'asc';
- } else {
- sort_order = 'desc';
- }
-
- if (sort_order == 'desc') {
- value = 9999;
- thisCell.removeClass(value).addClass('9999');
- } else if (sort_order == 'asc'){
- value = -9999;
- thisCell.removeClass(value).addClass('-9999');
- } else {
- value = 9999;
- thisCell.removeClass(value).addClass('9999');
- }
- }
-
- text = value;
- }
-
- else {
- if (node.textContent) {
- text = node.textContent;
- } else {
- if (node.childNodes[0] && node.childNodes[0].hasChildNodes()) {
- text = node.childNodes[0].innerHTML;
- } else {
- text = node.innerText;
- }
- }
- }
- return text
- }
- });
-
- $("#sortable2").tablesorter({
- textExtraction: function(node) {
- if ((node.children[0] == "[object HTMLInputElement]" && node.children[0].type == "text") || (/\S/.test(node.id))) {
- cellId = node.id;
- thisCell = $('#'+cellId).children(':eq(0)')
- valueClassNames = thisCell.attr('class').split(/\s+/);
- capitalized_column_name = cellId.split('_')[0].charAt(0).toUpperCase() + cellId.split('_')[0].slice(1);
- value = valueClassNames[valueClassNames.length - 1];
- newValue = thisCell.val();
-
- if (newValue == 'x' || value == '9999' || value == '-9999') {
- valueType = cellId.split('_')[0];
- if (valueType == 'value'){
- header = otherValueHeader;
- } else {
- header = otherSEHeader;
- }
-
- if (header.hasClass('headerSortUp')){
- sort_order = 'desc';
- } else if (header.hasClass('headerSortDown')){
- sort_order = 'asc';
- } else {
- sort_order = 'desc';
- }
-
- if (sort_order == 'desc') {
- value = 9999;
- thisCell.removeClass(value).addClass('9999');
- } else if (sort_order == 'asc'){
- value = -9999;
- thisCell.removeClass(value).addClass('-9999');
- } else {
- value = 9999;
- thisCell.removeClass(value).addClass('9999');
- }
- }
-
- text = value;
- }
-
- else {
- if (node.textContent) {
- text = node.textContent;
- } else {
- if (node.childNodes[0] && node.childNodes[0].hasChildNodes()) {
- text = node.childNodes[0].innerHTML;
- } else {
- text = node.innerText;
- }
- }
- }
- return text
- }
- });
+ //ZS: Defining these here, so they don't need to be searched for in the DOM for every single node
+ primaryTable = $("#sortable1");
+ otherTable = $("#sortable2");
+
+ primaryValueHeader = primaryTable.find('th:contains("Value"):eq(0)');
+ primarySEHeader = primaryTable.find('th:contains("SE"):eq(0)');
+ otherValueHeader = otherTable.find('th:contains("Value"):eq(1)');
+ otherSEHeader = otherTable.find('th:contains("SE"):eq(1)');
+
+ $("#sortable1").tablesorter({
+ textExtraction: function (node) {
+ if ((node.children[0] == "[object HTMLInputElement]" && node.children[0].type == "text") || (/\S/.test(node.id))) {
+ cellId = node.id;
+ thisCell = $('#' + cellId).children(':eq(0)')
+ valueClassNames = thisCell.attr('class').split(/\s+/);
+ capitalized_column_name = cellId.split('_')[0].charAt(0).toUpperCase() + cellId.split('_')[0].slice(1);
+ value = valueClassNames[valueClassNames.length - 1];
+ newValue = thisCell.val();
+
+ if (newValue == 'x' || value == '9999' || value == '-9999') {
+ valueType = cellId.split('_')[0];
+ if (valueType == 'value') {
+ header = primaryValueHeader;
+ } else {
+ header = primarySEHeader;
+ }
+
+ if (header.hasClass('headerSortUp')) {
+ sort_order = 'desc';
+ } else if (header.hasClass('headerSortDown')) {
+ sort_order = 'asc';
+ } else {
+ sort_order = 'desc';
+ }
+
+ if (sort_order == 'desc') {
+ value = 9999;
+ thisCell.removeClass(value).addClass('9999');
+ } else if (sort_order == 'asc') {
+ value = -9999;
+ thisCell.removeClass(value).addClass('-9999');
+ } else {
+ value = 9999;
+ thisCell.removeClass(value).addClass('9999');
+ }
+ }
-/*
+ text = value;
+ } else {
+ if (node.textContent) {
+ text = node.textContent;
+ } else {
+ if (node.childNodes[0] && node.childNodes[0].hasChildNodes()) {
+ text = node.childNodes[0].innerHTML;
+ } else {
+ text = node.innerText;
+ }
+ }
+ }
+ return text
+ }
+ });
+
+ $("#sortable2").tablesorter({
+ textExtraction: function (node) {
+ if ((node.children[0] == "[object HTMLInputElement]" && node.children[0].type == "text") || (/\S/.test(node.id))) {
+ cellId = node.id;
+ thisCell = $('#' + cellId).children(':eq(0)')
+ valueClassNames = thisCell.attr('class').split(/\s+/);
+ capitalized_column_name = cellId.split('_')[0].charAt(0).toUpperCase() + cellId.split('_')[0].slice(1);
+ value = valueClassNames[valueClassNames.length - 1];
+ newValue = thisCell.val();
+
+ if (newValue == 'x' || value == '9999' || value == '-9999') {
+ valueType = cellId.split('_')[0];
+ if (valueType == 'value') {
+ header = otherValueHeader;
+ } else {
+ header = otherSEHeader;
+ }
+
+ if (header.hasClass('headerSortUp')) {
+ sort_order = 'desc';
+ } else if (header.hasClass('headerSortDown')) {
+ sort_order = 'asc';
+ } else {
+ sort_order = 'desc';
+ }
+
+ if (sort_order == 'desc') {
+ value = 9999;
+ thisCell.removeClass(value).addClass('9999');
+ } else if (sort_order == 'asc') {
+ value = -9999;
+ thisCell.removeClass(value).addClass('-9999');
+ } else {
+ value = 9999;
+ thisCell.removeClass(value).addClass('9999');
+ }
+ }
+
+ text = value;
+ } else {
+ if (node.textContent) {
+ text = node.textContent;
+ } else {
+ if (node.childNodes[0] && node.childNodes[0].hasChildNodes()) {
+ text = node.childNodes[0].innerHTML;
+ } else {
+ text = node.innerText;
+ }
+ }
+ }
+ return text
+ }
+ });
+
+ /*
ZS: When the user changes the value in the text field, the new value is added as a class. This is because
$('input[type=text]').val() gets the value attribute, which is always the default value, instead of the
value property (which can be changed)
*/
- var thisTable = $('#sortable1,#sortable2');
-
- thisTable.bind("update propertychange keyup input paste", function(e){
-
- var target = e.target;
- $target = $(target);
-
- if (target.nodeName.toLowerCase() == 'input'){
- thisClassNames = $target.attr('class').split(/\s+/);
- valueClass = thisClassNames[thisClassNames.length - 1];
- newValue = $target.val();
- thisParent = $target.parent('td');
- thisParentId = thisParent.attr('id');
-
- $target.removeClass(valueClass);
-
- if (newValue == 'x'){
- thisParent.parent('tr').addClass('blocked');
- } else {
- $('#'+thisParentId).children('input.valueField:eq(0)').addClass(newValue);
- }
- }
- });
-
- ////////////////////////////////////
- // Initially close tabs
- ////////////////////////////////////
-
- thisForm = $('form[name="dataInput"]');
-
- $('#sectionbody2').hide();
- $('#sectionbody3').hide();
- $('#sectionbody4').hide();
-
- $('#title1').click(function() {
- $('#sectionbody1').toggle();
- return false;
- });
- $('#title2').click(function() {
- $('#sectionbody2').toggle();
- return false;
- });
- $('#title3').click(function() {
- $('#sectionbody3').toggle();
- return false;
- });
- $('#title4').click(function() {
- $('#sectionbody4').toggle();
- return false;
- });
- $('#title5').click(function() {
- $('#sectionbody5').toggle();
- return false;
- });
-
-
-
- //////////////////////////////////////////////////////////////
- // Switch out + and - icon when you click each section header
- //////////////////////////////////////////////////////////////
-
- var expand_html = "<span class=\"expand_container\">&nbsp;&nbsp;<IMG src=\"/images/Expand.gif\" alt=\"Expand\"></span>";
- var contract_html = "<span class=\"contract_container\">&nbsp;&nbsp;<IMG src=\"/images/Contract.gif\" alt=\"Contract\"></span>";
-
- $('#title2, #title3, #title4').prepend(expand_html).addClass('1');
-
- $('#title1, #title5').prepend(contract_html).addClass('0');
-
- for(i=1;i<=5;i++){
- $('#title'+i).click(function(){
- if ($(this).hasClass('0')) {
- $(this).find('span').replaceWith(expand_html);
- $(this).removeClass('0');
- $(this).addClass('1');
- }
- else {
- $(this).find('span').replaceWith(contract_html);
- $(this).removeClass('1');
- $(this).addClass('0');
- }
- });
- }
-
- // Exclude cases by attributes
-
- $('div.attribute_values:first').css('display', 'inline'); //Display the dropdown menu with the first attribute's distinct values
-
- $('select[name=exclude_menu]').change(function(){
- $('div.attribute_values').css('display', 'none'); //clear all other menus when a new attribute is selected
- attribute = $(this).val();
- //attribute = $('select[name=exclude_menu]').val();
- menu = $('div.attribute_values').find('[name=\''+attribute+'\']');
- menu.parent().css('display', 'inline');
- });
-
- primary_row_count = $('#primary').find('tr').length - 1;
- other_row_count = $('#other').find('tr').length - 1;
-
- if (primary_row_count >= other_row_count) {
- row_count = primary_row_count;
- }
- else {
- row_count = other_row_count;
- }
-
- $('div.attribute_values').children('select').change(function(){
- exclude_value = $(this).val();
- });
-});
-
-$(window).load(function(){
-
- //ZS: These are needed in a few places; looping through rows by index is faster than doing a "find" search
- numPrimaryRows = $('#sortable1').find('tr').length;
- numOtherRows = $('#sortable2').find('tr').length;
-
-
-///////////////////////////////
-//Basic Statistics
-///////////////////////////////
-
- /////////////////////////////////////////////////////////////////
- // Hide unselected Basic Statistics tabs (when just BXD strains
- // are selected, hide the results for all strains/non-BXD)
- /////////////////////////////////////////////////////////////////
-
- $('#stats_tabs1').hide();
- $('#stats_tabs2').hide();
-
- $('#sectionbody2').find('select[name=stats_mdp]').change(function(){
- selected = $('#sectionbody2').find('select[name=stats_mdp] option:selected').val();
- for (i=0;i<=2;i++){
- $('#stats_tabs'+i).hide();
- }
- $('#stats_tabs'+selected).show();
- });
-
- ////////////////////////////////////////////////////////////////////////
- // Select the same tab across each sample group (when a Box Plot is
- // selected for BXD, switching to Non-BXD will also display a Box Plot)
- ////////////.///////////////////////////////////////////////////////////
-
- var $tabs1 = $('#stats_tabs0').tabs();
- var $tabs2 = $('#stats_tabs1').tabs();
- var $tabs3 = $('#stats_tabs2').tabs();
-
- $tabs1.tabs({
- show: function(event, ui) {
- var selected = $tabs1.tabs('option','selected');
- $tabs2.tabs('select',selected);
- $tabs3.tabs('select',selected);
- }
- });
- $tabs2.tabs({
- show: function(event, ui) {
- var selected = $tabs2.tabs('option','selected');
- $tabs1.tabs('select',selected);
- $tabs3.tabs('select',selected);
- }
- });
- $tabs3.tabs({
- show: function(event, ui) {
- var selected = $tabs3.tabs('option','selected');
- $tabs1.tabs('select',selected);
- $tabs2.tabs('select',selected);
- }
- });
-
-
-///////////////////////////////
-//Calculate Correlations
-///////////////////////////////
-
- $('#sectionbody3').find('input[name="sample_corr"]').click(function() {
- dbValue = $('select[name=database1] option:selected').val();
- $('input[name=database]').val(dbValue);
- criteriaValue = $('select[name=criteria1] option:selected').val();
- $('input[name=criteria]').val(criteriaValue);
- MDPValue = $('select[name=MDPChoice1] option:selected').val();
- $('input[name=MDPChoice]').val(MDPValue);
-
- methodValue = $('input[name=sample_method]:checked').val();
-
- //This simple method can be used now that 'method' is defaulted to None instead of ''
- if (methodValue == "1"){
- $('input[name=method]').val('1');
- }
- else{
- $('input[name=method]').val('2');
- }
-
- dataEditingFunc(this.form,'correlation');
- });
-
- $('#sectionbody3').find('input[name="lit_corr"]').click(function() {
- dbValue = $('select[name=database2] option:selected').val();
- $('input[name=database]').val(dbValue);
- criteriaValue = $('select[name=criteria2] option:selected').val();
- $('input[name=criteria]').val(criteriaValue);
- MDPValue = $('select[name=MDPChoice2] option:selected').val();
- $('input[name=MDPChoice]').val(MDPValue);
-
- $('input[name=method]').val('3');
-
- dataEditingFunc(this.form,'correlation');
- });
-
- $('#sectionbody3').find('input[name="tiss_corr"]').click(function() {
- dbValue = $('select[name=database3] option:selected').val();
- $('input[name=database]').val(dbValue);
- criteriaValue = $('select[name=criteria3] option:selected').val();
- $('input[name=criteria]').val(criteriaValue);
- MDPValue = $('select[name=MDPChoice3] option:selected').val();
- $('input[name=MDPChoice]').val(MDPValue);
-
- methodValue = $('input[name=tissue_method]:checked').val();
-
- if (methodValue == "4"){
- $('input[name=method]').val('4');
- }
- else{
- $('input[name=method]').val('5');
- }
- dataEditingFunc(this.form,'correlation');
- });
-
-///////////////////////////////
-//Mapping Tools
-///////////////////////////////
-
- $('#sectionbody4').find('input[name=interval]').click(function() {
- chrValue = $('select[name=chromosomes1] option:selected').val();
- $('input[name=chromosomes]').val(chrValue);
- scaleValue = $('select[name=scale1] option:selected').val();
- $('input[name=scale]').val(scaleValue);
- $('input[name=controlLocus]').val('');
-
- //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
- permValue = $('input[name=permCheck1]:checked').val();
- $('input[name=permCheck]').val(permValue);
-
- bootValue = $('input[name=bootCheck1]:checked').val();
- $('input[name=bootCheck]').val(bootValue);
-
- if ($('input[name=parentsf14regression1]:checked').length > 0){
- $('input[name=parentsf14regression]').val('on');
- } else {
- $('input[name=parentsf14regression]').val('off');
- }
-
- varValue = $('input[name=applyVarianceSE1]:checked').val();
- $('input[name=applyVarianceSE]').val(varValue);
-
- dataEditingFunc(this.form,'intervalMap');
- });
-
- var tiptext = "e.g., rs12345";
- controlLocus = $('#sectionbody4').find('input[name=controlLocus]');
-
- if(controlLocus.val() == '' || controlLocus == tiptext) {
- controlLocus.addClass('searchtip').val(tiptext);
- }
-
- controlLocus.focus(function(e) {
- if(controlLocus.val() == tiptext) {
- controlLocus.val('');
- }
- controlLocus.removeClass('searchtip');
- });
-
- controlLocus.blur(function(e) {
- if(controlLocus.val() == '') {
- controlLocus.addClass('searchtip').val(tiptext);
- } else if(controlLocus.val() == tiptext) {
- controlLocus.addClass('searchtip');
- } else {
- controlLocus.removeClass('searchtip');
- }
- });
-
- $('#sectionbody4').find('input[name=composite]').click(function() {
- chrValue = $('select[name=chromosomes2] option:selected').val();
- $('input[name=chromosomes]').val(chrValue);
- scaleValue = $('select[name=scale2] option:selected').val();
- $('input[name=scale]').val(scaleValue);
- controlValue = controlLocus.val();
- if (controlValue != tiptext){
- controlLocus.val(controlValue);
- }
- else{
- controlLocus.val('');
- }
-
- //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
- permValue = $('input[name=permCheck2]:checked').val();
- $('input[name=permCheck]').val(permValue);
-
- bootValue = $('input[name=bootCheck2]:checked').val();
- $('input[name=bootCheck]').val(bootValue);
-
- if ($('input[name=parentsf14regression3]:checked').length > 0){
- $('input[name=parentsf14regression]').val('on');
- } else {
- $('input[name=parentsf14regression]').val('off');
- }
-
- dataEditingFunc(this.form,'intervalMap');
-
- });
-
- $('#sectionbody4').find('input[name=marker]').click(function() {
- //Changed the way parentsValue is acquired; before it was $(____).is(':checked');
- if ($('input[name=parentsf14regression2]:checked').length > 0){
- $('input[name=parentsf14regression]').val('on');
- } else {
- $('input[name=parentsf14regression]').val('off');
- }
-
- varValue = $('input[name=applyVarianceSE2]:checked').val();
- $('input[name=applyVarianceSE]').val(varValue);
-
- dataEditingFunc(this.form,'markerRegression');
- });
-
-///////////////////////////////
-//Review and Edit Data
-///////////////////////////////
-
- $('input[name=excludeGroup]').click(function(){
- for (i = 1;i <= Math.max(primary_row_count,other_row_count)-1; i++){
- valueExists = 0;
- $('#Primary_'+i+',#Other_'+i).children().each(function(){
- if ($(this).text() == exclude_value) {
- $('#Primary_'+i+',#Other_'+i).addClass('blocked').find('input[type=text]').val('x');
- valueExists = 1;
- return false;
- }
- });
- }
- });
-
- $('.update').click(function(){
- windowName = 'formTarget' + (new Date().getTime());
- newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=0,directories=1,width=900");
- document.dataInput.target = windowName;
- document.dataInput.submitID.value = "basicStatistics";
-
- primaryData = getTraitData()[0];
- otherData = getTraitData()[1];
- allData = getTraitData()[2];
-
- if (otherData[0].length > 0) {
- if ($('select[name="stats_mdp"] option:selected').val() == 0) {
- document.dataInput.strainNames.value = allData[0].toString();
- document.dataInput.strainVals.value = allData[1].toString();
- document.dataInput.strainVars.value = allData[2].toString();
- }
- else if ($('select[name="stats_mdp"] option:selected').val() == 1) {
- document.dataInput.strainNames.value = primaryData[0].toString();
- document.dataInput.strainVals.value = primaryData[1].toString();
- document.dataInput.strainVars.value = primaryData[2].toString();
- }
- else {
- document.dataInput.strainNames.value = otherData[0].toString();
- document.dataInput.strainVals.value = otherData[1].toString();
- document.dataInput.strainVars.value = otherData[2].toString();
- }
- }
- else {
- document.dataInput.strainNames.value = allData[0].toString();
- document.dataInput.strainVals.value = allData[1].toString();
- document.dataInput.strainVars.value = allData[2].toString();
- }
-
- document.dataInput.submit();
- });
-
- $('input[name="export"]').click(function(){
- windowName = 'formTarget' + (new Date().getTime());
- newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=0,directories=1,width=900");
- document.dataInput.target = windowName;
- document.dataInput.submitID.value = "exportData";
-
- primaryData = getTraitData()[0];
- otherData = getTraitData()[1];
-
- document.dataInput.strainNames.value = primaryData[0].toString();
- document.dataInput.strainVals.value = primaryData[1].toString();
- document.dataInput.strainVars.value = primaryData[2].toString();
-
- document.dataInput.otherStrainNames.value = otherData[0].toString();
- document.dataInput.otherStrainVals.value = otherData[1].toString();
- document.dataInput.otherStrainVars.value = otherData[2].toString();
-
- attribute_names = new Array();
- $('#primary,#other').find('th.attribute_name').each(function(){
- attribute_names.push($(this).val().toString());
- });
-
- primary_attribute_values = ""; //This string will be structured as a dictionary with a set of values for each attribute; it will be parsed in the ExportPage class
- other_attribute_values = "";
-
- attr_counter = 1; // Counter for each different attribute
- row_counter = 1; // Counter for each value for each attribute
- while (attr_counter <= attribute_names.length){
- attribute_name = $('#primary,#other').find('th.attribute_name:eq('+ (attr_counter-1).toString() + ')').text();
- primary_row_count = $('#primary').find('tr').length - 1;
- other_row_count = $('#other').find('tr').length - 1;
-
- primary_attribute_values += attribute_name + " : ";
- other_attribute_values += attribute_name + " : ";
-
- primary_value_string = ""; //This string of values (in the format 'a,b,c', etc) will be appended to the primary_attribute_values string
- for (row_counter = 1;row_counter <= numPrimaryRows; row_counter++){
- value = $('#primary_attribute'+attr_counter.toString()+'_sample'+row_counter.toString()).text();
- if (row_counter == primary_row_count) {
- primary_value_string += (value + " / ");
- }
- else{
- primary_value_string += (value + ",");
- }
- }
-
- primary_attribute_values += primary_value_string;
-
- other_value_string = ""; //This string of values (in the format 'a,b,c', etc) will be appended to the other_attribute_values string
- for (row_counter = 1;row_counter <= numOtherRows; row_counter++){
- value = $('#other_attribute'+attr_counter.toString()+'_sample'+row_counter.toString()).text();
- if (row_counter == other_row_count) {
- other_value_string += (value + " / ");
- }
- else{
- other_value_string += (value + ",");
- }
- }
- other_attribute_values += other_value_string;
- attr_counter += 1
- }
-
- document.dataInput.extra_attributes.value = primary_attribute_values;
- document.dataInput.other_extra_attributes.value = other_attribute_values;
-
- document.dataInput.submit();
- });
-
- var thisTable = $('#sortable1,#sortable2'); //ZS: variable representing each table, because it's used often
-
- thisTable.find('input[name="selectCheck"]').click(function(){
- if($(this).is(':checked')){
- $(this).parent("").parent("").children("td").css("background-color", "yellow");
- }
- else{
- if(!($(this).parent().parent().hasClass('outlier'))){
- $(this).parent().parent().children("td").css("background-color", "white");
- }
- }
- });
-
- $('input[name=resetButton]').click(function(){
-
- //ZS: Reset "hide no value" and "hide outliers"
- $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
- $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
- noValShown = 1;
- outliersShown = 1;
-
- for (i=1;i<=numPrimaryRows-1;i++){
- var thisRow = $('#Primary_'+i);
- if (thisRow.is('.invisible')){
- thisRow.removeClass('invisible');
- }
- if (thisRow.is('.blocked')){
- thisRow.removeClass('blocked');
- }
- if (thisRow.is(':not(.outlier)')){
- thisRow.css("background-color", "white");
- }
-
- var thisValueField = thisRow.find('.valueField');
-
- var originalValue = thisValueField[0].defaultValue;
- var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
-
- if (thisValueField.length > 1){
- var originalValue = thisValueField[1].defaultValue;
- var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
- }
- }
- for (i=1;i<=numOtherRows-1;i++){
- var thisRow = $('#Other_'+i);
- if (thisRow.is('.invisible')){
- thisRow.removeClass('invisible')
- }
- if (thisRow.is('.blocked')){
- thisRow.removeClass('blocked');
- }
- if (thisRow.is(':not(.outlier)')){
- thisRow.css("background-color", "white");
- }
-
- var thisValueField = thisRow.find('.valueField');
-
- var originalValue = thisValueField[0].defaultValue;
- var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
-
- if (thisValueField.length > 1){
- var originalValue = thisValueField[1].defaultValue;
- var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
- }
- }
- });
-
- var tiptext2 = "e.g., 4, 6-30, 43";
- var blockField = $('#showHideOptions').find('input[name=removeField]'); //ZS: Field where user inputs the index of the samples he/she wants to block; created variable because it's used often
-
- if(blockField.val() == '' || blockField.val() == tiptext2) {
- blockField.addClass('searchtip');
- blockField.val(tiptext2);
- }
-
- blockField.focus(function(e) {
- if(blockField.val() == tiptext2) {
- blockField.val('');
- }
- blockField.removeClass('searchtip');
- });
-
- blockField.blur(function(e) {
- if(blockField.val() == '') {
- blockField.addClass('searchtip');
- blockField.val(tiptext2);
- } else if(blockField.val() == tiptext2) {
- blockField.addClass('searchtip');
- } else {
- blockField.removeClass('searchtip');
- }
- });
-
- var noValShown = new Boolean(1);
- var outliersShown = new Boolean(1);
-
- $('#showHideOptions').bind('click', function(e){
- var target = e.target;
- $target = $(target);
-
- if (target.name === 'blockSamples'){
- if (blockField.val() == tiptext2){
- blockField.val('')
- }
- blockedText = blockField.val();
- blockedTextSplit = new Array();
- blockedItems = new Array();
-
- blockedTextSplit = blockedText.split(/\,/);
-
- for (i=0;i<=blockedTextSplit.length-1;i++) {
- var item = blockedTextSplit[i];
- if(item.indexOf('-') != -1){
- subArray = new Array();
- subArray = item.split('-');
- num1 = parseInt(subArray[0]);
- num2 = parseInt(subArray[1]);
- for (j=num1;j<=num2;j=j+1){
- blockedItems.push(j);
- }
- }
- else if(!(isNaN(item))) {
- blockedItems.push(item);
- }
- }
-
- for (i=0;i<=blockedItems.length-1;i++) {
- item = blockedItems[i];
- if ($('select[name=block_method]').val() == '0') {
- var thisRow = $('#Other_'+item);
- }
- else {
- var thisRow = $('#Primary_'+item);
- }
-
- if (thisRow.is('.novalue')) {
- continue;
- }
- else {
- thisRow.addClass('blocked').find('input.valueField').val('x');
- }
-
- //First look at value cell
- var thisCell = thisRow.find('input:eq(1)');
- var thisClassNames = thisCell.attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- var header = thisRow.parents('table.tablesorter').find('th.header:contains("Value"):eq(0)');
- if (header.hasClass('headerSortUp')){
- thisCell.removeClass(valueClass).addClass('-9999');
- } else if (header.hasClass('headerSortDown')){
- thisCell.removeClass(valueClass).addClass('9999');
- } else {
- thisCell.removeClass(valueClass).addClass('-9999');
- }
-
- //Check if there is an SE column
- if (thisRow.find('input.valueField').length > 1) {
- var thisCell = thisRow.find('input:eq(2)');
- var thisClassNames = thisCell.attr('class').split(/\s+/);
- var valueClass = thisClassNames[thisClassNames.length-1];
- var header = thisRow.parents('table.tablesorter').find('th.header:contains("SE"):eq(0)');
- if (header.hasClass('headerSortUp')){
- thisCell.removeClass(valueClass).addClass('-9999');
- } else if (header.hasClass('headerSortDown')){
- thisCell.removeClass(valueClass).addClass('9999');
- } else {
- thisCell.removeClass(valueClass).addClass('-9999');
- }
- }
- }
- }
-
- else if (target.name === 'showHideNoValue'){
- if (noValShown) {
- $('#showHideOptions').find('input[name=showHideNoValue]').val(' Show No Value ');
- for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
- if (i<=numPrimaryRows-1) {
- var thisRow = $('#Primary_'+i);
- if (thisRow.is('.novalue:visible') || thisRow.is('.blocked:visible')){
- jQuery(thisRow).addClass('invisible');
- }
- }
- if (i<=numOtherRows-1){
- var thisOtherRow = $('#Other_'+i);
- if (thisOtherRow.is('.novalue:visible') || thisOtherRow.is('.blocked:visible')){
- if (thisOtherRow.is(':visible')){
- jQuery(thisOtherRow).addClass('invisible');
- }
- }
- }
- }
- noValShown = 0;
- }
- else {
- $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
- for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
- if (i<=numPrimaryRows-1) {
- var thisRow = $('#Primary_'+i);
- if (thisRow.is('.novalue') || thisRow.is('.blocked')){
- jQuery(thisRow).removeClass('invisible');
- if (!(outliersShown)) {
- if (thisRow.is('.outlier:visible')){
- jQuery(thisRow).addClass('invisible');
- }
- }
- }
- }
- if (i<=numOtherRows-1){
- var thisOtherRow = $('#Other_'+i);
- if (thisOtherRow.is('.novalue') || thisOtherRow.is('.blocked')){
- jQuery(thisOtherRow).removeClass('invisible');
- if (!(outliersShown)) {
- if (thisOtherRow.is('.outlier:visible')){
- jQuery(thisOtherRow).addClass('invisible');
- }
- }
- }
- }
- }
- noValShown = 1;
- }
- }
-
- else if (target.name === 'showHideOutliers'){
- if (outliersShown){
- $('#showHideOptions').find('input[name=showHideOutliers]').val(' Show Outliers ');
- for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
- if (i<=numPrimaryRows-1) {
- thisRow = $('#Primary_'+i);
- if (thisRow.is('.outlier:visible') && (!(thisRow.is('.invisible')))) {
- thisRow.addClass('invisible')
- }
- }
- if (i<=numOtherRows-1) {
- thisOtherRow = $('#Other_'+i);
- if (thisOtherRow.is('.outlier:visible') && (!(thisOtherRow.is('.invisible')))) {
- thisOtherRow.addClass('invisible')
- }
- }
- }
- outliersShown = 0;
- }
- else {
- $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
- for (i=1;i<=Math.max(numPrimaryRows,numOtherRows)-1;i++) {
- if (i<=numPrimaryRows-1) {
- thisRow = $('#Primary_'+i);
- if (thisRow.is('.outlier') && (!(thisRow.is(':visible')))) {
- if (!(noValShown)) {
- if (thisRow.is('.blocked')){
- continue;
- }
- }
- jQuery(thisRow).removeClass('invisible')
- }
- }
- if (i<=numOtherRows-1) {
- thisOtherRow = $('#Other_'+i);
- if (thisOtherRow.is('.outlier') && (!(thisOtherRow.is(':visible')))) {
- if (!(noValShown)) {
- if (thisOtherRow.is('.blocked')){
- continue;
- }
- }
- jQuery(thisOtherRow).removeClass('invisible')
- }
- }
- }
- outliersShown = 1;
- }
- }
- return false;
- });
-});
-
-function getTraitData(){
- primary_row_count = $('#sortable1').find('tr').length - 1;
- other_row_count = $('#sortable2').find('tr').length - 1;
-
- primaryStrainNames = new Array();
- primaryVals = new Array();
- primaryVars = new Array();
-
- allStrainNames = new Array();
- allVals = new Array();
- allVars = new Array();
-
- for (i = 1;i <= primary_row_count; i++){
- thisRow = $('#Primary_'+i);
- strainName = thisRow.find('span:first').text();
- primaryStrainNames.push(strainName);
- allStrainNames.push(strainName);
- strainVal = thisRow.find('input:eq(1)').val();
- primaryVals.push(strainVal);
- allVals.push(strainVal);
- strainVar = ''; // Just to initialize it in case there is no var
- strainVar = thisRow.find('input:eq(2)').val();
- primaryVars.push(strainVar);
- allVars.push(strainVar);
- }
-
- otherStrainNames = new Array();
- otherVals = new Array();
- otherVars = new Array();
-
- for (j = 1;j <= other_row_count; j++){
- thisRow = $('#Other_'+j)
- strainName = thisRow.find('span:first').text();
- otherStrainNames.push(strainName);
- strainVal = thisRow.find('input:eq(1)').val();
- otherVals.push(strainVal);
- strainVar = ''; // Just to initialize it in case there is no var
- strainVar = thisRow.find('input:eq(2)').val();
- otherVars.push(strainVar);
-
- if (jQuery.inArray(strainName, allStrainNames) == -1) {
- allStrainNames.push(strainName);
- allVals.push(strainVal);
- allVars.push(strainVar);
- }
- }
-
- primaryData = [primaryStrainNames, primaryVals, primaryVars];
- otherData = [otherStrainNames, otherVals, otherVars];
- allData = [allStrainNames, allVals, allVars];
-
- return [primaryData, otherData, allData];
-}
+ var thisTable = $('#sortable1,#sortable2');
+ thisTable.bind("update propertychange keyup input paste", function (e) {
-/*
-used by networkGraphPageBody.py
-*/
+ var target = e.target;
+ $target = $(target);
-//Default to plain text + symbol for the "Export Graph File" button
-$('input[name=exportGraphFile]').live('click', function() { window.open($('input[name=exportFilename]').val() + "_plain_symbol.txt") });
+ if (target.nodeName.toLowerCase() == 'input') {
+ thisClassNames = $target.attr('class').split(/\s+/);
+ valueClass = thisClassNames[thisClassNames.length - 1];
+ newValue = $target.val();
+ thisParent = $target.parent('td');
+ thisParentId = thisParent.attr('id');
+
+ $target.removeClass(valueClass);
+
+ if (newValue == 'x') {
+ thisParent.parent('tr').addClass('blocked');
+ } else {
+ $('#' + thisParentId).children('input.valueField:eq(0)').addClass(newValue);
+ }
+ }
+ });
+
+ ////////////////////////////////////
+ // Initially close tabs
+ ////////////////////////////////////
+ thisForm = $('form[name="dataInput"]');
+
+ $('#sectionbody2').hide();
+ $('#sectionbody3').hide();
+ $('#sectionbody4').hide();
+
+ $('#title1').click(function () {
+ $('#sectionbody1').toggle();
+ return false;
+ });
+ $('#title2').click(function () {
+ $('#sectionbody2').toggle();
+ return false;
+ });
+ $('#title3').click(function () {
+ $('#sectionbody3').toggle();
+ return false;
+ });
+ $('#title4').click(function () {
+ $('#sectionbody4').toggle();
+ return false;
+ });
+ $('#title5').click(function () {
+ $('#sectionbody5').toggle();
+ return false;
+ });
-function changeFormat(graphName){
- var graphFormat = $('#exportFormat').val();
- var traitType = $('#traitType').val();
- $('input[name=exportGraphFile]').die('click');
- if (graphFormat=="xgmml"){
- if (traitType=="symbol"){
- var graphFile = graphName+ "_xgmml_symbol.txt";
- $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ //////////////////////////////////////////////////////////////
+ // Switch out + and - icon when you click each section header
+ //////////////////////////////////////////////////////////////
+ var expand_html = "<span class=\"expand_container\">&nbsp;&nbsp;<IMG src=\"/images/Expand.gif\" alt=\"Expand\"></span>";
+ var contract_html = "<span class=\"contract_container\">&nbsp;&nbsp;<IMG src=\"/images/Contract.gif\" alt=\"Contract\"></span>";
+
+ $('#title2, #title3, #title4').prepend(expand_html).addClass('1');
+
+ $('#title1, #title5').prepend(contract_html).addClass('0');
+
+ for (i = 1; i <= 5; i++) {
+ $('#title' + i).click(function () {
+ if ($(this).hasClass('0')) {
+ $(this).find('span').replaceWith(expand_html);
+ $(this).removeClass('0');
+ $(this).addClass('1');
+ } else {
+ $(this).find('span').replaceWith(contract_html);
+ $(this).removeClass('1');
+ $(this).addClass('0');
+ }
+ });
+ }
+
+ // Exclude cases by attributes
+ $('div.attribute_values:first').css('display', 'inline'); //Display the dropdown menu with the first attribute's distinct values
+ $('select[name=exclude_menu]').change(function () {
+ $('div.attribute_values').css('display', 'none'); //clear all other menus when a new attribute is selected
+ attribute = $(this).val();
+ //attribute = $('select[name=exclude_menu]').val();
+ menu = $('div.attribute_values').find('[name=\'' + attribute + '\']');
+ menu.parent().css('display', 'inline');
+ });
+
+ primary_row_count = $('#primary').find('tr').length - 1;
+ other_row_count = $('#other').find('tr').length - 1;
+
+ if (primary_row_count >= other_row_count) {
+ row_count = primary_row_count;
+ } else {
+ row_count = other_row_count;
+ }
+
+ $('div.attribute_values').children('select').change(function () {
+ exclude_value = $(this).val();
+ });
+});
+
+$(window).load(function () {
+
+ //ZS: These are needed in a few places; looping through rows by index is faster than doing a "find" search
+ numPrimaryRows = $('#sortable1').find('tr').length;
+ numOtherRows = $('#sortable2').find('tr').length;
+
+
+ ///////////////////////////////
+ //Basic Statistics
+ ///////////////////////////////
+ /////////////////////////////////////////////////////////////////
+ // Hide unselected Basic Statistics tabs (when just BXD strains
+ // are selected, hide the results for all strains/non-BXD)
+ /////////////////////////////////////////////////////////////////
+ $('#stats_tabs1').hide();
+ $('#stats_tabs2').hide();
+
+ $('#sectionbody2').find('select[name=stats_mdp]').change(function () {
+ selected = $('#sectionbody2').find('select[name=stats_mdp] option:selected').val();
+ for (i = 0; i <= 2; i++) {
+ $('#stats_tabs' + i).hide();
+ }
+ $('#stats_tabs' + selected).show();
+ });
+
+ ////////////////////////////////////////////////////////////////////////
+ // Select the same tab across each sample group (when a Box Plot is
+ // selected for BXD, switching to Non-BXD will also display a Box Plot)
+ ////////////.///////////////////////////////////////////////////////////
+ var $tabs1 = $('#stats_tabs0').tabs();
+ var $tabs2 = $('#stats_tabs1').tabs();
+ var $tabs3 = $('#stats_tabs2').tabs();
+
+ $tabs1.tabs({
+ show: function (event, ui) {
+ var selected = $tabs1.tabs('option', 'selected');
+ $tabs2.tabs('select', selected);
+ $tabs3.tabs('select', selected);
+ }
+ });
+ $tabs2.tabs({
+ show: function (event, ui) {
+ var selected = $tabs2.tabs('option', 'selected');
+ $tabs1.tabs('select', selected);
+ $tabs3.tabs('select', selected);
+ }
+ });
+ $tabs3.tabs({
+ show: function (event, ui) {
+ var selected = $tabs3.tabs('option', 'selected');
+ $tabs1.tabs('select', selected);
+ $tabs2.tabs('select', selected);
+ }
+ });
+
+
+ ///////////////////////////////
+ //Calculate Correlations
+ ///////////////////////////////
+ $('#sectionbody3').find('input[name="sample_corr"]').click(function () {
+ dbValue = $('select[name=database1] option:selected').val();
+ $('input[name=database]').val(dbValue);
+ criteriaValue = $('select[name=criteria1] option:selected').val();
+ $('input[name=criteria]').val(criteriaValue);
+ MDPValue = $('select[name=MDPChoice1] option:selected').val();
+ $('input[name=MDPChoice]').val(MDPValue);
+
+ methodValue = $('input[name=sample_method]:checked').val();
+
+ //This simple method can be used now that 'method' is defaulted to None instead of ''
+ if (methodValue == "1") {
+ $('input[name=method]').val('1');
+ } else {
+ $('input[name=method]').val('2');
+ }
+
+ dataEditingFunc(this.form, 'correlation');
+ });
+
+ $('#sectionbody3').find('input[name="lit_corr"]').click(function () {
+ dbValue = $('select[name=database2] option:selected').val();
+ $('input[name=database]').val(dbValue);
+ criteriaValue = $('select[name=criteria2] option:selected').val();
+ $('input[name=criteria]').val(criteriaValue);
+ MDPValue = $('select[name=MDPChoice2] option:selected').val();
+ $('input[name=MDPChoice]').val(MDPValue);
+
+ $('input[name=method]').val('3');
+
+ dataEditingFunc(this.form, 'correlation');
+ });
+
+ $('#sectionbody3').find('input[name="tiss_corr"]').click(function () {
+ dbValue = $('select[name=database3] option:selected').val();
+ $('input[name=database]').val(dbValue);
+ criteriaValue = $('select[name=criteria3] option:selected').val();
+ $('input[name=criteria]').val(criteriaValue);
+ MDPValue = $('select[name=MDPChoice3] option:selected').val();
+ $('input[name=MDPChoice]').val(MDPValue);
+
+ methodValue = $('input[name=tissue_method]:checked').val();
+
+ if (methodValue == "4") {
+ $('input[name=method]').val('4');
+ } else {
+ $('input[name=method]').val('5');
+ }
+ dataEditingFunc(this.form, 'correlation');
+ });
+
+ ///////////////////////////////
+ //Mapping Tools
+ ///////////////////////////////
+ $('#sectionbody4').find('input[name=interval]').click(function () {
+ chrValue = $('select[name=chromosomes1] option:selected').val();
+ $('input[name=chromosomes]').val(chrValue);
+ scaleValue = $('select[name=scale1] option:selected').val();
+ $('input[name=scale]').val(scaleValue);
+ $('input[name=controlLocus]').val('');
+
+ //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
+ permValue = $('input[name=permCheck1]:checked').val();
+ $('input[name=permCheck]').val(permValue);
+
+ bootValue = $('input[name=bootCheck1]:checked').val();
+ $('input[name=bootCheck]').val(bootValue);
+
+ if ($('input[name=parentsf14regression1]:checked').length > 0) {
+ $('input[name=parentsf14regression]').val('on');
+ } else {
+ $('input[name=parentsf14regression]').val('off');
+ }
+
+ varValue = $('input[name=applyVarianceSE1]:checked').val();
+ $('input[name=applyVarianceSE]').val(varValue);
+
+ dataEditingFunc(this.form, 'intervalMap');
+ });
+
+ var tiptext = "e.g., rs12345";
+ controlLocus = $('#sectionbody4').find('input[name=controlLocus]');
+
+ if (controlLocus.val() == '' || controlLocus == tiptext) {
+ controlLocus.addClass('searchtip').val(tiptext);
+ }
+
+ controlLocus.focus(function (e) {
+ if (controlLocus.val() == tiptext) {
+ controlLocus.val('');
+ }
+ controlLocus.removeClass('searchtip');
+ });
+
+ controlLocus.blur(function (e) {
+ if (controlLocus.val() == '') {
+ controlLocus.addClass('searchtip').val(tiptext);
+ } else if (controlLocus.val() == tiptext) {
+ controlLocus.addClass('searchtip');
+ } else {
+ controlLocus.removeClass('searchtip');
+ }
+ });
+
+ $('#sectionbody4').find('input[name=composite]').click(function () {
+ chrValue = $('select[name=chromosomes2] option:selected').val();
+ $('input[name=chromosomes]').val(chrValue);
+ scaleValue = $('select[name=scale2] option:selected').val();
+ $('input[name=scale]').val(scaleValue);
+ controlValue = controlLocus.val();
+ if (controlValue != tiptext) {
+ controlLocus.val(controlValue);
+ } else {
+ controlLocus.val('');
+ }
+
+ //Changed the way permValue, bootValue, and parentsValue are acquired; before it was $(____).is(':checked');
+ permValue = $('input[name=permCheck2]:checked').val();
+ $('input[name=permCheck]').val(permValue);
+
+ bootValue = $('input[name=bootCheck2]:checked').val();
+ $('input[name=bootCheck]').val(bootValue);
+
+ if ($('input[name=parentsf14regression3]:checked').length > 0) {
+ $('input[name=parentsf14regression]').val('on');
+ } else {
+ $('input[name=parentsf14regression]').val('off');
+ }
+
+ dataEditingFunc(this.form, 'intervalMap');
+
+ });
+
+ $('#sectionbody4').find('input[name=marker]').click(function () {
+ //Changed the way parentsValue is acquired; before it was $(____).is(':checked');
+ if ($('input[name=parentsf14regression2]:checked').length > 0) {
+ $('input[name=parentsf14regression]').val('on');
+ } else {
+ $('input[name=parentsf14regression]').val('off');
+ }
+
+ varValue = $('input[name=applyVarianceSE2]:checked').val();
+ $('input[name=applyVarianceSE]').val(varValue);
+
+ dataEditingFunc(this.form, 'markerRegression');
+ });
+
+ ///////////////////////////////
+ //Review and Edit Data
+ ///////////////////////////////
+ $('input[name=excludeGroup]').click(function () {
+ for (i = 1; i <= Math.max(primary_row_count, other_row_count) - 1; i++) {
+ valueExists = 0;
+ $('#Primary_' + i + ',#Other_' + i).children().each(function () {
+ if ($(this).text() == exclude_value) {
+ $('#Primary_' + i + ',#Other_' + i).addClass('blocked').find('input[type=text]').val('x');
+ valueExists = 1;
+ return false;
}
- else if (traitType=="name"){
- var graphFile = graphName+ "_xgmml_name.txt";
- $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ });
+ }
+ });
+
+ $('.update').click(function () {
+ windowName = 'formTarget' + (new Date().getTime());
+ var windowHeight; // windowHeight and windowWidth are used to place the window in the center of the screen
+ var windowWidth;
+ windowHeight = (window.screen.height/2) - (350 + 10)
+ windowWidth = (window.screen.width/2) - (450 + 50)
+ newWindow = open("",windowName,"menubar=1,toolbar=1,resizable=1,left=" + windowWidth + ",top=" + windowHeight + ",screenX=" + windowWidth + ",screenY=" + windowHeight + ",status=1,scrollbars=0,directories=1");
+
+ document.dataInput.target = windowName;
+ document.dataInput.submitID.value = "basicStatistics";
+
+ primaryData = getTraitData()[0];
+ otherData = getTraitData()[1];
+ allData = getTraitData()[2];
+
+ if (otherData[0].length > 0) {
+ if ($('select[name="stats_mdp"] option:selected').val() == 0) {
+ document.dataInput.strainNames.value = allData[0].toString();
+ document.dataInput.strainVals.value = allData[1].toString();
+ document.dataInput.strainVars.value = allData[2].toString();
+ } else if ($('select[name="stats_mdp"] option:selected').val() == 1) {
+ document.dataInput.strainNames.value = primaryData[0].toString();
+ document.dataInput.strainVals.value = primaryData[1].toString();
+ document.dataInput.strainVars.value = primaryData[2].toString();
+ } else {
+ document.dataInput.strainNames.value = otherData[0].toString();
+ document.dataInput.strainVals.value = otherData[1].toString();
+ document.dataInput.strainVars.value = otherData[2].toString();
+ }
+ } else {
+ document.dataInput.strainNames.value = allData[0].toString();
+ document.dataInput.strainVals.value = allData[1].toString();
+ document.dataInput.strainVars.value = allData[2].toString();
+ }
+
+ document.dataInput.submit();
+ });
+
+ $('input[name="export"]').click(function () {
+ windowName = 'formTarget' + (new Date().getTime());
+ newWindow = open("", windowName, "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=0,directories=1,width=900");
+ document.dataInput.target = windowName;
+ document.dataInput.submitID.value = "exportData";
+
+ primaryData = getTraitData()[0];
+ otherData = getTraitData()[1];
+
+ document.dataInput.strainNames.value = primaryData[0].toString();
+ document.dataInput.strainVals.value = primaryData[1].toString();
+ document.dataInput.strainVars.value = primaryData[2].toString();
+
+ document.dataInput.otherStrainNames.value = otherData[0].toString();
+ document.dataInput.otherStrainVals.value = otherData[1].toString();
+ document.dataInput.otherStrainVars.value = otherData[2].toString();
+
+ attribute_names = new Array();
+ $('#primary,#other').find('th.attribute_name').each(function () {
+ attribute_names.push($(this).val().toString());
+ });
+
+ primary_attribute_values = ""; //This string will be structured as a dictionary with a set of values for each attribute; it will be parsed in the ExportPage class
+ other_attribute_values = "";
+
+ attr_counter = 1; // Counter for each different attribute
+ row_counter = 1; // Counter for each value for each attribute
+ while (attr_counter <= attribute_names.length) {
+ attribute_name = $('#primary,#other').find('th.attribute_name:eq(' + (attr_counter - 1).toString() + ')').text();
+ primary_row_count = $('#primary').find('tr').length - 1;
+ other_row_count = $('#other').find('tr').length - 1;
+
+ primary_attribute_values += attribute_name + " : ";
+ other_attribute_values += attribute_name + " : ";
+
+ primary_value_string = ""; //This string of values (in the format 'a,b,c', etc) will be appended to the primary_attribute_values string
+ for (row_counter = 1; row_counter <= numPrimaryRows; row_counter++) {
+ value = $('#primary_attribute' + attr_counter.toString() + '_sample' + row_counter.toString()).text();
+ if (row_counter == primary_row_count) {
+ primary_value_string += (value + " / ");
+ } else {
+ primary_value_string += (value + ",");
}
+ }
+
+ primary_attribute_values += primary_value_string;
+
+ other_value_string = ""; //This string of values (in the format 'a,b,c', etc) will be appended to the other_attribute_values string
+ for (row_counter = 1; row_counter <= numOtherRows; row_counter++) {
+ value = $('#other_attribute' + attr_counter.toString() + '_sample' + row_counter.toString()).text();
+ if (row_counter == other_row_count) {
+ other_value_string += (value + " / ");
+ } else {
+ other_value_string += (value + ",");
+ }
+ }
+ other_attribute_values += other_value_string;
+ attr_counter += 1
+ }
+
+ document.dataInput.extra_attributes.value = primary_attribute_values;
+ document.dataInput.other_extra_attributes.value = other_attribute_values;
+
+ document.dataInput.submit();
+ });
+
+ var thisTable = $('#sortable1,#sortable2'); //ZS: variable representing each table, because it's used often
+ thisTable.find('input[name="selectCheck"]').click(function () {
+ if ($(this).is(':checked')) {
+ $(this).parent("").parent("").children("td").css("background-color", "yellow");
+ } else {
+ if (!($(this).parent().parent().hasClass('outlier'))) {
+ $(this).parent().parent().children("td").css("background-color", "white");
+ }
}
+ });
- else if (graphFormat=="plain"){
- if (traitType=="symbol"){
- var graphFile = graphName+ "_plain_symbol.txt";
- $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ $('input[name=resetButton]').click(function () {
+
+ //ZS: Reset "hide no value" and "hide outliers"
+ $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
+ $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
+ noValShown = 1;
+ outliersShown = 1;
+
+ for (i = 1; i <= numPrimaryRows - 1; i++) {
+ var thisRow = $('#Primary_' + i);
+ if (thisRow.is('.invisible')) {
+ thisRow.removeClass('invisible');
+ }
+ if (thisRow.is('.blocked')) {
+ thisRow.removeClass('blocked');
+ }
+ if (thisRow.is(':not(.outlier)')) {
+ thisRow.css("background-color", "white");
+ }
+
+ var thisValueField = thisRow.find('.valueField');
+
+ var originalValue = thisValueField[0].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+
+ if (thisValueField.length > 1) {
+ var originalValue = thisValueField[1].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+ }
+ }
+ for (i = 1; i <= numOtherRows - 1; i++) {
+ var thisRow = $('#Other_' + i);
+ if (thisRow.is('.invisible')) {
+ thisRow.removeClass('invisible')
+ }
+ if (thisRow.is('.blocked')) {
+ thisRow.removeClass('blocked');
+ }
+ if (thisRow.is(':not(.outlier)')) {
+ thisRow.css("background-color", "white");
+ }
+
+ var thisValueField = thisRow.find('.valueField');
+
+ var originalValue = thisValueField[0].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(1)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ thisRow.find('input:eq(1)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+
+ if (thisValueField.length > 1) {
+ var originalValue = thisValueField[1].defaultValue;
+ var thisClassNames = thisRow.find('input:eq(2)').attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ thisRow.find('input:eq(2)').removeClass(valueClass).addClass(originalValue).val(originalValue);
+ }
+ }
+ });
+
+ var tiptext2 = "e.g., 4, 6-30, 43";
+ var blockField = $('#showHideOptions').find('input[name=removeField]'); //ZS: Field where user inputs the index of the samples he/she wants to block; created variable because it's used often
+ if (blockField.val() == '' || blockField.val() == tiptext2) {
+ blockField.addClass('searchtip');
+ blockField.val(tiptext2);
+ }
+
+ blockField.focus(function (e) {
+ if (blockField.val() == tiptext2) {
+ blockField.val('');
+ }
+ blockField.removeClass('searchtip');
+ });
+
+ blockField.blur(function (e) {
+ if (blockField.val() == '') {
+ blockField.addClass('searchtip');
+ blockField.val(tiptext2);
+ } else if (blockField.val() == tiptext2) {
+ blockField.addClass('searchtip');
+ } else {
+ blockField.removeClass('searchtip');
+ }
+ });
+
+ var noValShown = new Boolean(1);
+ var outliersShown = new Boolean(1);
+
+ $('#showHideOptions').bind('click', function (e) {
+ var target = e.target;
+ $target = $(target);
+
+ if (target.name === 'blockSamples') {
+ if (blockField.val() == tiptext2) {
+ blockField.val('')
+ }
+ blockedText = blockField.val();
+ blockedTextSplit = new Array();
+ blockedItems = new Array();
+
+ blockedTextSplit = blockedText.split(/\,/);
+
+ for (i = 0; i <= blockedTextSplit.length - 1; i++) {
+ var item = blockedTextSplit[i];
+ if (item.indexOf('-') != -1) {
+ subArray = new Array();
+ subArray = item.split('-');
+ num1 = parseInt(subArray[0]);
+ num2 = parseInt(subArray[1]);
+ for (j = num1; j <= num2; j = j + 1) {
+ blockedItems.push(j);
+ }
+ } else if (!(isNaN(item))) {
+ blockedItems.push(item);
+ }
+ }
+
+ for (i = 0; i <= blockedItems.length - 1; i++) {
+ item = blockedItems[i];
+ if ($('select[name=block_method]').val() == '0') {
+ var thisRow = $('#Other_' + item);
+ } else {
+ var thisRow = $('#Primary_' + item);
+ }
+
+ if (thisRow.is('.novalue')) {
+ continue;
+ } else {
+ thisRow.addClass('blocked').find('input.valueField').val('x');
+ }
+
+ //First look at value cell
+ var thisCell = thisRow.find('input:eq(1)');
+ var thisClassNames = thisCell.attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ var header = thisRow.parents('table.tablesorter').find('th.header:contains("Value"):eq(0)');
+ if (header.hasClass('headerSortUp')) {
+ thisCell.removeClass(valueClass).addClass('-9999');
+ } else if (header.hasClass('headerSortDown')) {
+ thisCell.removeClass(valueClass).addClass('9999');
+ } else {
+ thisCell.removeClass(valueClass).addClass('-9999');
+ }
+
+ //Check if there is an SE column
+ if (thisRow.find('input.valueField').length > 1) {
+ var thisCell = thisRow.find('input:eq(2)');
+ var thisClassNames = thisCell.attr('class').split(/\s+/);
+ var valueClass = thisClassNames[thisClassNames.length - 1];
+ var header = thisRow.parents('table.tablesorter').find('th.header:contains("SE"):eq(0)');
+ if (header.hasClass('headerSortUp')) {
+ thisCell.removeClass(valueClass).addClass('-9999');
+ } else if (header.hasClass('headerSortDown')) {
+ thisCell.removeClass(valueClass).addClass('9999');
+ } else {
+ thisCell.removeClass(valueClass).addClass('-9999');
+ }
+ }
+ }
+ } else if (target.name === 'showHideNoValue') {
+ if (noValShown) {
+ $('#showHideOptions').find('input[name=showHideNoValue]').val(' Show No Value ');
+ for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
+ if (i <= numPrimaryRows - 1) {
+ var thisRow = $('#Primary_' + i);
+ if (thisRow.is('.novalue:visible') || thisRow.is('.blocked:visible')) {
+ jQuery(thisRow).addClass('invisible');
+ }
+ }
+ if (i <= numOtherRows - 1) {
+ var thisOtherRow = $('#Other_' + i);
+ if (thisOtherRow.is('.novalue:visible') || thisOtherRow.is('.blocked:visible')) {
+ if (thisOtherRow.is(':visible')) {
+ jQuery(thisOtherRow).addClass('invisible');
+ }
+ }
+ }
+ }
+ noValShown = 0;
+ } else {
+ $('#showHideOptions').find('input[name=showHideNoValue]').val(' Hide No Value ');
+ for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
+ if (i <= numPrimaryRows - 1) {
+ var thisRow = $('#Primary_' + i);
+ if (thisRow.is('.novalue') || thisRow.is('.blocked')) {
+ jQuery(thisRow).removeClass('invisible');
+ if (!(outliersShown)) {
+ if (thisRow.is('.outlier:visible')) {
+ jQuery(thisRow).addClass('invisible');
+ }
+ }
+ }
+ }
+ if (i <= numOtherRows - 1) {
+ var thisOtherRow = $('#Other_' + i);
+ if (thisOtherRow.is('.novalue') || thisOtherRow.is('.blocked')) {
+ jQuery(thisOtherRow).removeClass('invisible');
+ if (!(outliersShown)) {
+ if (thisOtherRow.is('.outlier:visible')) {
+ jQuery(thisOtherRow).addClass('invisible');
+ }
+ }
+ }
+ }
}
- else if (traitType=="name"){
- var graphFile = graphName+ "_plain_name.txt";
- $('input[name=exportGraphFile]').live('click', function() { window.open(graphFile) });
+ noValShown = 1;
+ }
+ } else if (target.name === 'showHideOutliers') {
+ if (outliersShown) {
+ $('#showHideOptions').find('input[name=showHideOutliers]').val(' Show Outliers ');
+ for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
+ if (i <= numPrimaryRows - 1) {
+ thisRow = $('#Primary_' + i);
+ if (thisRow.is('.outlier:visible') && (!(thisRow.is('.invisible')))) {
+ thisRow.addClass('invisible')
+ }
+ }
+ if (i <= numOtherRows - 1) {
+ thisOtherRow = $('#Other_' + i);
+ if (thisOtherRow.is('.outlier:visible') && (!(thisOtherRow.is('.invisible')))) {
+ thisOtherRow.addClass('invisible')
+ }
+ }
+ }
+ outliersShown = 0;
+ } else {
+ $('#showHideOptions').find('input[name=showHideOutliers]').val(' Hide Outliers ');
+ for (i = 1; i <= Math.max(numPrimaryRows, numOtherRows) - 1; i++) {
+ if (i <= numPrimaryRows - 1) {
+ thisRow = $('#Primary_' + i);
+ if (thisRow.is('.outlier') && (!(thisRow.is(':visible')))) {
+ if (!(noValShown)) {
+ if (thisRow.is('.blocked')) {
+ continue;
+ }
+ }
+ jQuery(thisRow).removeClass('invisible')
+ }
+ }
+ if (i <= numOtherRows - 1) {
+ thisOtherRow = $('#Other_' + i);
+ if (thisOtherRow.is('.outlier') && (!(thisOtherRow.is(':visible')))) {
+ if (!(noValShown)) {
+ if (thisOtherRow.is('.blocked')) {
+ continue;
+ }
+ }
+ jQuery(thisOtherRow).removeClass('invisible')
+ }
+ }
}
+ outliersShown = 1;
+ }
+ }
+ return false;
+ });
+});
+
+function getTraitData() {
+ primary_row_count = $('#sortable1').find('tr').length - 1;
+ other_row_count = $('#sortable2').find('tr').length - 1;
+
+ primaryStrainNames = new Array();
+ primaryVals = new Array();
+ primaryVars = new Array();
+
+ allStrainNames = new Array();
+ allVals = new Array();
+ allVars = new Array();
+
+ for (i = 1; i <= primary_row_count; i++) {
+ thisRow = $('#Primary_' + i);
+ strainName = thisRow.find('span:first').text();
+ primaryStrainNames.push(strainName);
+ allStrainNames.push(strainName);
+ strainVal = thisRow.find('input:eq(1)').val();
+ primaryVals.push(strainVal);
+ allVals.push(strainVal);
+ strainVar = ''; // Just to initialize it in case there is no var
+ strainVar = thisRow.find('input:eq(2)').val();
+ primaryVars.push(strainVar);
+ allVars.push(strainVar);
+ }
+
+ otherStrainNames = new Array();
+ otherVals = new Array();
+ otherVars = new Array();
+
+ for (j = 1; j <= other_row_count; j++) {
+ thisRow = $('#Other_' + j)
+ strainName = thisRow.find('span:first').text();
+ otherStrainNames.push(strainName);
+ strainVal = thisRow.find('input:eq(1)').val();
+ otherVals.push(strainVal);
+ strainVar = ''; // Just to initialize it in case there is no var
+ strainVar = thisRow.find('input:eq(2)').val();
+ otherVars.push(strainVar);
+
+ if (jQuery.inArray(strainName, allStrainNames) == -1) {
+ allStrainNames.push(strainName);
+ allVals.push(strainVal);
+ allVars.push(strainVar);
}
+ }
+
+ primaryData = [primaryStrainNames, primaryVals, primaryVars];
+ otherData = [otherStrainNames, otherVals, otherVars];
+ allData = [allStrainNames, allVals, allVars];
+
+ return [primaryData, otherData, allData];
}
+/*
+used by networkGraphPageBody.py
+*/
+
+//Default to plain text + symbol for the "Export Graph File" button
+$('input[name=exportGraphFile]').live('click', function () {
+ window.open($('input[name=exportFilename]').val() + "_plain_symbol.txt")
+});
+
+function changeFormat(graphName) {
+ var graphFormat = $('#exportFormat').val();
+ var traitType = $('#traitType').val();
+
+ $('input[name=exportGraphFile]').die('click');
+
+ if (graphFormat == "xgmml") {
+ if (traitType == "symbol") {
+ var graphFile = graphName + "_xgmml_symbol.txt";
+ $('input[name=exportGraphFile]').live('click', function () {
+ window.open(graphFile)
+ });
+ } else if (traitType == "name") {
+ var graphFile = graphName + "_xgmml_name.txt";
+ $('input[name=exportGraphFile]').live('click', function () {
+ window.open(graphFile)
+ });
+ }
+ } else if (graphFormat == "plain") {
+ if (traitType == "symbol") {
+ var graphFile = graphName + "_plain_symbol.txt";
+ $('input[name=exportGraphFile]').live('click', function () {
+ window.open(graphFile)
+ });
+ } else if (traitType == "name") {
+ var graphFile = graphName + "_plain_name.txt";
+ $('input[name=exportGraphFile]').live('click', function () {
+ window.open(graphFile)
+ });
+ }
+ }
+} \ No newline at end of file
diff --git a/web/javascript/selectDatasetMenu.js b/web/javascript/selectDatasetMenu.js
index bb910a5b..bb910a5b 100755..100644
--- a/web/javascript/selectDatasetMenu.js
+++ b/web/javascript/selectDatasetMenu.js
diff --git a/web/javascript/webqtl.js b/web/javascript/webqtl.js
index 19ecf3b7..536e7d26 100755
--- a/web/javascript/webqtl.js
+++ b/web/javascript/webqtl.js
@@ -38,16 +38,16 @@ function makeTree(thisForm, nnn){
j += 1;
}
}
-
+
var windowName = 'formTarget' + (new Date().getTime());
var newWindow = open("", windowName,"width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
var html = "";
if (j > 0)
- {
+ {
var waithtml1 ="<Blockquote class='title' id='red'>Your list of "+j+" transcripts is being exported to the Gene Ontology Tree Machine for analysis. This window will soon be replaced with the main GOTM results.</Blockquote>";
}
else
- {
+ {
var waithtml1 ="<Blockquote class='title' id='red'>Your should select at least one transcript to export to the Gene Ontology Tree Machine for analysis.</Blockquote>";
}
html += waithtml1;
@@ -152,7 +152,11 @@ function showDatabase3(formName, Database,ProbeSetID,CellID){
document[formName].database.value = Database;
document[formName].ProbeSetID.value = ProbeSetID;
document[formName].CellID.value = CellID;
- document[formName].submit();
+ console.log("formName:", formName)
+ console.log("document[formName]:", document[formName])
+ console.log("submit turned off for debugging")
+ console.log("showDatabase3 is deprecated for the flask version of this site")
+ //document[formName].submit();
}
@@ -188,10 +192,10 @@ function showTrait(fmName){
var thisForm = getForm(fmName);
if (thisForm == null || showTrait.arguments.length < 2)
return;
-
+
windowName = genNewWin();
thisForm.target = windowName;
-
+
thisForm.FormID.value = "showDatabase";
thisForm.ProbeSetID.value = showTrait.arguments[1];
if (showTrait.arguments.length > 2)
@@ -205,10 +209,10 @@ function showCateGraph(fmName){
var thisForm = getForm(fmName);
if (thisForm == null || showCateGraph.arguments.length < 2)
return;
-
+
windowName = genNewWin();
thisForm.target = windowName;
-
+
thisForm.FormID.value = "showCategoryGraph";
thisForm.interval1.value = showCateGraph.arguments[1];
thisForm.interval2.value = showCateGraph.arguments[2];
@@ -219,22 +223,22 @@ function showCorrPlot(fmName){
var thisForm = getForm(fmName);
if (thisForm == null || showCorrPlot.arguments.length < 2)
return;
-
+
windowName = genNewWin();
thisForm.target = windowName;
-
+
thisForm.FormID.value = "showCorrelationPlot";
thisForm.ProbeSetID.value = showCorrPlot.arguments[1];
if (showCorrPlot.arguments.length > 2)
thisForm.CellID.value = showCorrPlot.arguments[2];
else
thisForm.CellID.value = "";
-
+
thisForm.X_geneSymbol.value = null;
thisForm.Y_geneSymbol.value = null;
thisForm.submit();
-
+
}
@@ -242,12 +246,12 @@ function showCorrPlotThird(fmName){
var thisForm = getForm(fmName);
if (thisForm == null || showCorrPlotThird.arguments.length < 3)
return;
-
+
windowName = genNewWin();
thisForm.target = windowName;
-
+
var olddb = thisForm.database.value;
-
+
thisForm.FormID.value = "showCorrelationPlot";
thisForm.database.value = showCorrPlotThird.arguments[1];
thisForm.ProbeSetID.value = showCorrPlotThird.arguments[2];
@@ -284,15 +288,15 @@ function ODE(thisForm, script){
var windowName = 'formTarget' + (new Date().getTime());
var newWindow = open("", windowName, "width=900,menubar=0,toolbar=1,resizable=1,status=1,scrollbars=1");
var html = "";
- if (j == 0){
+ if (j == 0){
j = length;
trait_list2 = trait_list_all;
correlation2 = correlation_all;
llid_list2 = llid_list_all;
}
-
+
var waithtml1 ="<Blockquote class='title' id='red'>Your list of "+j+" transcripts is being exported to the ODE for analysis. This window will soon be replaced with the results.</Blockquote>";
-
+
html += waithtml1;
newWindow.document.write(html);
newWindow.document.close();
@@ -302,14 +306,14 @@ function ODE(thisForm, script){
thisForm.correlation.value = correlation2.join(',');
thisForm.id_value.value = thisForm.correlation.value;
thisForm.llid_list.value = llid_list2.join(',');
-
+
// ODE
-
+
thisForm.idtype.value = thisForm.id_type.value;
thisForm.species.value = thisForm.org.value;
thisForm.list.value = thisForm.id_list.value;
thisForm.client.value = "genenetwork";
-
+
thisForm.target = windowName;
var oldaction = thisForm.action;
thisForm.action = script;
@@ -318,13 +322,13 @@ function ODE(thisForm, script){
}
}
*/
-// 02/12/2009
+// 02/12/2009
// Lei Yan
/*scripts in the Dataediting form*/
function dataEditingFunc(thisForm,submitIdValue){
-
+
windowName = 'formTarget' + (new Date().getTime());
if (thisForm.FormID.value!='secondRegression'){
@@ -336,7 +340,7 @@ function dataEditingFunc(thisForm,submitIdValue){
}
else if (submitIdValue == "addRecord"){
- windowName = thisForm.RISet.value;
+ windowName = thisForm.RISet.value;
var name = thisForm.identification.value;
if (name != ""){
}
@@ -352,7 +356,7 @@ function dataEditingFunc(thisForm,submitIdValue){
newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
thisForm.target = windowName;
- newWindow.focus();
+ newWindow.focus();
thisForm.submitID.value = submitIdValue;
thisForm.submit();
}
@@ -394,7 +398,7 @@ function addRmvSelection(windowName, thisForm, addORrmv){
thisForm.target = windowName;
thisForm.FormID.value = addORrmv;
thisForm.submit();
- newWindow.focus();
+ newWindow.focus();
}
function batchSelection(thisForm){
@@ -424,7 +428,7 @@ function showTop10(formName, submitIdValue){
if ((submitIdValue == "markerRegression")||(submitIdValue == "compositeRegression")){
thisForm.topten.value = "topten";
}
-
+
thisForm.submitID.value = submitIdValue;
thisForm.submit();
}
@@ -441,12 +445,12 @@ function showIndividualChromosome(formName, submitIdValue, ii){
}
if (match == 0)
return;
-
+
windowName = 'formTarget' + (new Date().getTime());
newWindow = open("",windowName,"menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900");
newWindow.focus();
thisForm.target = windowName;
-
+
if (submitIdValue == "showIntMap"){
thisForm.chromosomes.value = ii;
}
@@ -529,10 +533,10 @@ function dataWindow(form){
}
-function xchange() {
+function xchange() {
var select = document.crossChoice.RISet;
var value = select.options[select.selectedIndex].value;
-
+
if (value !="BDAI") return;
document.crossChoice.variance.checked = false;
}
@@ -580,97 +584,97 @@ function crossinfo2(){
function checkWidth(){
var width = document.getElementsByName('plotSize')[0].value
-
+
if (width < 600) {
alert("Plot size is too small - setting size to 600")
document.getElementsByName('plotSize')[0].value = 600
- }
+ }
}
function changeLineColor(){
var lineColor = document.getElementsByName('lineColorSel')[0].value
-
+
document.getElementsByName('lineColor')[0].value = lineColor
}
function changeLineSize(){
var lineSize = document.getElementsByName('lineSizeSel')[0].value
-
+
document.getElementsByName('lineSize')[0].value = lineSize
}
function changeIdColor(){
var idColor = document.getElementsByName('idColorSel')[0].value
-
+
document.getElementsByName('idColor')[0].value = idColor
}
function changeIdFont(){
var idFont = document.getElementsByName('idFontSel')[0].value
-
+
document.getElementsByName('idFont')[0].value = idFont
}
function changeIdSize(){
var idSize = document.getElementsByName('idSizeSel')[0].value
-
+
document.getElementsByName('idSize')[0].value = idSize
}
function changeSymbolColor(){
var symbolColor = document.getElementsByName('colorSel')[0].value
-
+
document.getElementsByName('symbolColor')[0].value = symbolColor
}
function changeSymbol(){
var symbol = document.getElementsByName('symbolSel')[0].value
-
+
document.getElementsByName('symbol')[0].value = symbol
}
function changeFilled(){
var filled = document.getElementsByName('fillSel')[0].value
-
+
document.getElementsByName('filled')[0].value = filled
}
function changeSize(){
var symbolSize = document.getElementsByName('sizeSel')[0].value
-
+
document.getElementsByName('symbolSize')[0].value = symbolSize
}
-function checkAll(thisForm){
+function checkAll(thisForm){
var length = thisForm.searchResult.length;
for(var i = 0; i < length; i++)
{
thisForm.searchResult[i].checked = true;
highlight(thisForm.searchResult[i]);
}
-}
+}
-function checkNone(thisForm){
+function checkNone(thisForm){
var length = thisForm.searchResult.length;
for(var i = 0; i < length; i++)
{
thisForm.searchResult[i].checked = false;
highlight(thisForm.searchResult[i]);
}
-}
+}
-function checkInvert(thisForm){
+function checkInvert(thisForm){
var length = thisForm.searchResult.length;
for(var i = 0; i < length; i++)
{
thisForm.searchResult[i].checked = !(thisForm.searchResult[i].checked);
highlight(thisForm.searchResult[i]);
}
-}
+}
/*Not used anymore*/
-function checkTraits2(thisForm){
+function checkTraits2(thisForm){
var length = thisForm.searchResult.length;
var category = thisForm.selectmenu.value;
for(var i = 0; i < length; i++)
@@ -720,18 +724,18 @@ function checkTraits2(thisForm){
else
{}
}
-}
+}
function checkNumeric(field,limit,resetvalue,compares,fdname)
{
- pattern = /^-?[0-9]*\.?[0-9]*$/;
+ pattern = /^-?[0-9]*\.?[0-9]*$/;
if(pattern.test(field.value)==false)
{
alert("Not numeric in " + fdname);
field.value = resetvalue;
}
- else
+ else
{
if (compares == 'gthan') {
if(field.value > limit)
@@ -748,7 +752,7 @@ function checkNumeric(field,limit,resetvalue,compares,fdname)
}
}
-function checkTraits(thisForm){
+function checkTraits(thisForm){
var length = thisForm.searchResult.length;
var andor = thisForm.selectandor.value;
var gthan = parseFloat(thisForm.selectgt.value);
@@ -780,7 +784,7 @@ function checkTraits(thisForm){
}
-function checkPM(thisForm){
+function checkPM(thisForm){
var length = thisForm.searchResult.length;
for(var i = 0; i < length; i++)
{
@@ -792,8 +796,8 @@ function checkPM(thisForm){
{thisForm.searchResult[i].checked = false;}
highlight(thisForm.searchResult[i]);
}
-}
-function checkMM(thisForm){
+}
+function checkMM(thisForm){
var length = thisForm.searchResult.length;
for(var i = 0; i < length; i++)
{
@@ -804,14 +808,14 @@ function checkMM(thisForm){
{thisForm.searchResult[i].checked = false;}
highlight(thisForm.searchResult[i]);
}
-}
+}
-function directPermuAlert(thisForm){
- if (thisForm.directPermuCheckbox.checked){
- alert("Interaction permutation will take long time to compute.\n Check this box only when necessary.");
+function directPermuAlert(thisForm){
+ if (thisForm.directPermuCheckbox.checked){
+ alert("Interaction permutation will take long time to compute.\n Check this box only when necessary.");
}
-}
+}
function cliqueDatabase(pid){
var windowName = 'clique';
@@ -869,7 +873,7 @@ function snpbrowser_function_refresh() {
for (var i=1; i<document.newSNPPadding.exonfunction.length; i++) {
document.newSNPPadding.exonfunction.options[i].selected=false;
}
- }
+ }
}
function snpbrowser_domain_refresh() {
@@ -889,7 +893,7 @@ function showHideOptions() {
var options = document.getElementById("options");
var showOptions = document.getElementsByName("showOptions")[0];
var optionsButton = document.getElementsByName("optionsButton")[0];
-
+
if (showOptions.value == '0') {
showOptions.value = '1';
optionsButton.value = "Hide Options";
@@ -898,22 +902,22 @@ function showHideOptions() {
showOptions.value = '0';
optionsButton.value = "Show Options";
}
-
- options.style.display = (options.style.display != 'none' ? 'none' : '' );
+
+ options.style.display = (options.style.display != 'none' ? 'none' : '' );
}
function editPCAName(thisForm) {
var pcaTraits = document.getElementsByName("searchResult");
-
+
var nameArray = new Array();
-
+
for (j=1; j<=pcaTraits.length; j++){
var traitName = "pcaTrait" + String(j);
var pcaTrait = document.getElementById(traitName).childNodes[0].innerHTML;
var editID = "editName" + String(j);
var editName = document.getElementsByName(editID)[0].value;
var originalName = pcaTrait.split(":")[3];
-
+
if (editName.length < 1) {
nameArray.push(originalName);
}
@@ -921,13 +925,13 @@ function editPCAName(thisForm) {
nameArray.push(editName);
}
}
-
+
var newNames = nameArray.join(",");
-
+
thisForm.newNames.value = newNames;
thisForm.searchResult = thisForm.oldSearchResult;
thisForm.FormID.value = "corMatrix";
-
+
thisForm.submit();
}
@@ -950,7 +954,7 @@ function unknownChipError(chipName){
}
/*
-Used by PartialCorrInputPage.py,
+Used by PartialCorrInputPage.py,
*/
function validateTrait(thisForm, inputRadioNames, type, method)
{
@@ -1029,7 +1033,7 @@ function validateTrait(thisForm, inputRadioNames, type, method)
}
}
-
+
}
/*
@@ -1044,7 +1048,7 @@ function changeView(i, Chr_Mb_list){
newWindow = open('',windowName,'menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900');
document.changeViewForm.target = windowName;
document.changeViewForm.chromosomes.selectedIndex = i+1;
- document.changeViewForm.startMb.value = '0.000000';
+ document.changeViewForm.startMb.value = '0.000000';
document.changeViewForm.endMb.value = Chr_Mb_list[i];
document.changeViewForm.graphWidth.value = 1280;
document.changeViewForm.submit();
@@ -1076,7 +1080,7 @@ used by networkGraphPageBody.py
function changeFormat(graphName){
var graphFormat = document.getElementById('exportFormat').value;
var traitType = document.getElementById('traitType').value;
-
+
if (graphFormat=="xgmml"){
if (traitType=="symbol"){
var graphname = graphName+ "_xgmml_symbol.txt";
@@ -1087,7 +1091,7 @@ function changeFormat(graphName){
document.getElementById('exportGraphFile').onclick = function() { window.open(graphname) };
}
}
-
+
else if (graphFormat=="plain")
{
if (traitType=="symbol")
@@ -1102,7 +1106,7 @@ function changeFormat(graphName){
}
}
-}
+}
/*
@@ -1126,13 +1130,13 @@ function set_customStrains_cookie() {
}
/*
-* moved from beta2.js
-*/
+* moved from beta2.js
+*/
function centerIntervalMapOnRange2(chr, start, stop, form) {
var oldindex = form.chromosomes.selectedIndex;
var oldstart = form.startMb.value;
var oldend = form.endMb.value;
-
+
for (var i = 1; i < form.chromosomes.length; i++){
if(form.chromosomes.options[i].text == chr){
form.chromosomes.selectedIndex = i;
@@ -1145,12 +1149,12 @@ function centerIntervalMapOnRange2(chr, start, stop, form) {
form.chromosomes.selectedIndex = oldindex;
form.startMb.value = oldstart;
form.endMb.value = oldend;
-
+
}
/*
-* moved from index3.html
-*/
+* moved from index3.html
+*/
String.prototype.trim = function(){
return this.replace(/(^\s*)|(\s*$)/g, "");
@@ -1282,13 +1286,13 @@ function showTissueCorrPlot(fmName,geneSymbol1, geneSymbol2,rank){
var thisForm = getForm(fmName);
if (thisForm == null || showTissueCorrPlot.arguments.length < 3)
return;
-
+
if (rank){
thisForm.rankOrder.value = rank;
}else{
thisForm.rankOrder.value = 0;
}
-
+
windowName = genNewWin();
thisForm.target = windowName;
@@ -1302,7 +1306,7 @@ function showTissueCorrPlot(fmName,geneSymbol1, geneSymbol2,rank){
if(typeof(thisForm.ProbeSetID2) !== 'undefined'){
thisForm.ProbeSetID2.value = 'none';
}
- thisForm.submit();
+ thisForm.submit();
}
/* Used by MarkerRegressionPage.py */
@@ -1317,7 +1321,7 @@ function validatePvalue(thisForm){
{
alert("Please enter numeric value.");
thisForm.pValue.focus();
- }
+ }
else if (pValue <0){
alert("Please enter the valid P-Value.");
thisForm.pValue.focus();
@@ -1327,7 +1331,7 @@ function validatePvalue(thisForm){
}
-
+
}
@@ -1338,9 +1342,9 @@ function showTissueAbbr(fmName,shortname, fullname){
thisForm.FormID.value = 'tissueAbbreviation';
thisForm.shortTissueName.value=shortname;
thisForm.fullTissueName.value=fullname;
-
+
thisForm.submit();
thisForm.FormID.value = 'showCorrelationPlot';
thisForm.target =''
-
+
}
diff --git a/web/webqtl/base/webqtlConfigLocal.py b/web/webqtl/base/webqtlConfigLocal.py
index dc86bb10..1f986aa7 100755
--- a/web/webqtl/base/webqtlConfigLocal.py
+++ b/web/webqtl/base/webqtlConfigLocal.py
@@ -3,15 +3,15 @@
#########################################
MYSQL_SERVER = 'localhost'
-DB_NAME = 'db_webqtl'
-DB_USER = 'webqtl'
+DB_NAME = 'db_webqtl_zas1024'
+DB_USER = 'webqtlupd'
DB_PASSWD = 'webqtl'
MYSQL_UPDSERVER = 'localhost'
-DB_UPDNAME = 'db_webqtl'
-DB_UPDUSER = 'webqtl'
+DB_UPDNAME = 'db_webqtl_zas1024'
+DB_UPDUSER = 'webqtlupd'
DB_UPDPASSWD = 'webqtl'
-GNROOT = '/gnshare/gn/'
+GNROOT = '/home/zas1024/gn/'
PythonPath = '/usr/bin/python'
PIDDLE_FONT_PATH = '/usr/lib/python2.4/site-packages/piddle/truetypefonts/'
diff --git a/web/webqtl/base/webqtlTrait.py b/web/webqtl/base/webqtlTrait.py
index f5051e45..2469504f 100644
--- a/web/webqtl/base/webqtlTrait.py
+++ b/web/webqtl/base/webqtlTrait.py
@@ -9,6 +9,10 @@ from dbFunction import webqtlDatabaseFunction
from utility import webqtlUtil
+from __future__ import print_function, division
+
+from pprint import pformat as pf
+
class webqtlTrait:
"""
Trait class defines a trait in webqtl, can be either Microarray,
@@ -215,6 +219,9 @@ class webqtlTrait:
def retrieveData(self, strainlist=[]):
assert self.db and self.cursor
+ debug_file = open("/home/zas1024/gn/web/traitlist_debug.txt", "w")
+ debug_file.write("strianlist is:" + strainlist + "\n")
+
if self.db.type == 'Temp':
query = '''
SELECT
@@ -341,6 +348,8 @@ class webqtlTrait:
#end if
else:
pass
+
+ debug_file.write("self.data is:", pf(self.data) + "\n")
def keys(self):
return self.__dict__.keys()
diff --git a/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py b/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py
index 156dafe7..ab7ed07d 100755
--- a/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py
+++ b/web/webqtl/basicStatistics/updatedBasicStatisticsPage.py
@@ -63,9 +63,9 @@ class updatedBasicStatisticsPage(templatePage):
thisValFull = [strain_names[i], this_strain_val, this_strain_var]
vals.append(thisValFull)
- stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-5", Class="stats_tab"),
+ stats_tab_list = [HT.Href(text="Basic Table", url="#statstabs-1", Class="stats_tab"),HT.Href(text="Probability Plot", url="#statstabs-2", Class="stats_tab"),
HT.Href(text="Bar Graph (by name)", url="#statstabs-3", Class="stats_tab"), HT.Href(text="Bar Graph (by rank)", url="#statstabs-4", Class="stats_tab"),
- HT.Href(text="Box Plot", url="#statstabs-2", Class="stats_tab")]
+ HT.Href(text="Box Plot", url="#statstabs-5", Class="stats_tab")]
stats_tabs = HT.List(stats_tab_list)
stats_container = HT.Div(id="stats_tabs", Class="ui-tabs")
@@ -73,7 +73,7 @@ class updatedBasicStatisticsPage(templatePage):
stats_script_text = """$(function() { $("#stats_tabs").tabs();});""" #Javascript enabling tabs
- table_div = HT.Div(id="statstabs-1")
+ table_div = HT.Div(id="statstabs-1", style="height:320px;width:740px;overflow:scroll;")
table_container = HT.Paragraph()
statsTable = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
@@ -86,16 +86,21 @@ class updatedBasicStatisticsPage(templatePage):
table_div.append(table_container)
stats_container.append(table_div)
- boxplot_div = HT.Div(id="statstabs-2")
- boxplot_container = HT.Paragraph()
- boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
- boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals)
- boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left")))
- boxplot_container.append(boxplot)
- boxplot_div.append(boxplot_container)
- stats_container.append(boxplot_div)
+ normalplot_div = HT.Div(id="statstabs-2", style="height:540px;width:740px;overflow:scroll;")
+ normalplot_container = HT.Paragraph()
+ normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
+ plotTitle = fd.formdata.getvalue("normalPlotTitle","")
+ normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains)
+ normalplot.append(HT.TR(HT.TD(normalplot_img)))
+ normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \
+ normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(),
+ "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot",
+ target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary"))))
+ normalplot_container.append(normalplot)
+ normalplot_div.append(normalplot_container)
+ stats_container.append(normalplot_div)
- barName_div = HT.Div(id="statstabs-3")
+ barName_div = HT.Div(id="statstabs-3", style="height:540px;width:740px;overflow:scroll;")
barName_container = HT.Paragraph()
barName = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
barName_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="name")
@@ -104,7 +109,7 @@ class updatedBasicStatisticsPage(templatePage):
barName_div.append(barName_container)
stats_container.append(barName_div)
- barRank_div = HT.Div(id="statstabs-4")
+ barRank_div = HT.Div(id="statstabs-4", style="height:540px;width:740px;overflow:scroll;")
barRank_container = HT.Paragraph()
barRank = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
barRank_img = BasicStatisticsFunctions.plotBarGraph(identification=fd.identification, RISet=fd.RISet, vals=vals, type="rank")
@@ -112,20 +117,15 @@ class updatedBasicStatisticsPage(templatePage):
barRank_container.append(barRank)
barRank_div.append(barRank_container)
stats_container.append(barRank_div)
-
- normalplot_div = HT.Div(id="statstabs-5")
- normalplot_container = HT.Paragraph()
- normalplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
- plotTitle = fd.formdata.getvalue("normalPlotTitle","")
- normalplot_img = BasicStatisticsFunctions.plotNormalProbability(vals=vals, RISet=fd.RISet, title=plotTitle, specialStrains=specialStrains)
- normalplot.append(HT.TR(HT.TD(normalplot_img)))
- normalplot.append(HT.TR(HT.TD(HT.BR(),HT.BR(),"This plot evaluates whether data are \
- normally distributed. Different symbols represent different groups.",HT.BR(),HT.BR(),
- "More about ", HT.Href(url="http://en.wikipedia.org/wiki/Normal_probability_plot",
- target="_blank", text="Normal Probability Plots"), " and more about interpreting these plots from the ", HT.Href(url="/glossary.html#normal_probability", target="_blank", text="glossary"))))
- normalplot_container.append(normalplot)
- normalplot_div.append(normalplot_container)
- stats_container.append(normalplot_div)
+
+ boxplot_div = HT.Div(id="statstabs-5", style="height:540px;width:740px;overflow:scroll;")
+ boxplot_container = HT.Paragraph()
+ boxplot = HT.TableLite(cellspacing=0, cellpadding=0, width="100%")
+ boxplot_img, boxplot_link = BasicStatisticsFunctions.plotBoxPlot(vals)
+ boxplot.append(HT.TR(HT.TD(boxplot_img, HT.P(), boxplot_link, align="left")))
+ boxplot_container.append(boxplot)
+ boxplot_div.append(boxplot_container)
+ stats_container.append(boxplot_div)
stats_cell.append(stats_container)
stats_script.append(stats_script_text)
diff --git a/web/webqtl/collection/ExportSelectionDetailInfoPage.py b/web/webqtl/collection/ExportSelectionDetailInfoPage.py
index 69f293b2..7238c797 100755
--- a/web/webqtl/collection/ExportSelectionDetailInfoPage.py
+++ b/web/webqtl/collection/ExportSelectionDetailInfoPage.py
@@ -128,7 +128,10 @@ class ExportSelectionDetailInfoPage(templatePage):
count = count + 1
except:
pass
- mean = sum/count
+ if count == 0:
+ mean = 0
+ else:
+ mean = sum/count
text[-1].append(mean)
text[-1] += testval
if len(text[0]) < 255 or len(text) < 255:
diff --git a/web/webqtl/correlation/CorrelationPage.py b/web/webqtl/correlation/CorrelationPage.py
index ce8b8165..72e53f1d 100755
--- a/web/webqtl/correlation/CorrelationPage.py
+++ b/web/webqtl/correlation/CorrelationPage.py
@@ -91,7 +91,7 @@ class Trait(object):
#ZS: This takes the list of values of the trait our selected trait is being correlated against and removes the values of the samples our trait has no value for
#There's probably a better way of dealing with this, but I'll have to ask Christian
- updated_raw_values = []
+ updated_raw_values = []
updated_values = []
for i in range(len(values)):
if values[i] != "None":
@@ -120,7 +120,7 @@ class Trait(object):
ZValue = ZValue*sqrt(self.overlap-3)
self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-
+
#XZ, 01/14/2009: This method is for parallel computing only.
#XZ: It is supposed to be called when "Genetic Correlation, Pearson's r" (method 1)
@@ -151,7 +151,7 @@ def get_correlation_method_key(form_data):
#XZ, 09/28/2008: if user select "2", then display 2, 3 and 5.
#XZ, 09/28/2008: if user select "3", then display 1, 3 and 4.
#XZ, 09/28/2008: if user select "4", then display 1, 3 and 4.
- #XZ, 09/28/2008: if user select "5", then display 2, 3 and 5.
+ #XZ, 09/28/2008: if user select "5", then display 2, 3 and 5.
method = form_data.formdata.getvalue("method")
if method not in ["1", "2", "3" ,"4", "5"]:
@@ -172,7 +172,7 @@ def get_custom_trait(form_data, cursor):
return None
-#XZ, 09/18/2008: get the information such as value, variance of the input strain names from the form.
+#XZ, 09/18/2008: get the information such as value, variance of the input strain names from the form.
def get_sample_data(form_data):
if form_data.allstrainlist:
mdpchoice = form_data.formdata.getvalue('MDPChoice')
@@ -194,8 +194,8 @@ def get_sample_data(form_data):
strainlist = form_data.allstrainlist
#XZ, 09/18/2008: put the trait data into dictionary form_data.allTraitData
form_data.readData(form_data.allstrainlist)
- else:
- mdpchoice = None
+ else:
+ mdpchoice = None
strainlist = form_data.strainlist
#XZ, 09/18/2008: put the trait data into dictionary form_data.allTraitData
form_data.readData()
@@ -267,7 +267,7 @@ class CorrelationPage(templatePage):
CORRELATION_METHODS = {"1" : "Genetic Correlation (Pearson's r)",
"2" : "Genetic Correlation (Spearman's rho)",
"3" : "SGO Literature Correlation",
- "4" : "Tissue Correlation (Pearson's r)",
+ "4" : "Tissue Correlation (Pearson's r)",
"5" : "Tissue Correlation (Spearman's rho)"}
RANK_ORDERS = {"1": 0, "2": 1, "3": 0, "4": 0, "5": 1}
@@ -338,7 +338,7 @@ class CorrelationPage(templatePage):
# We will not get Tissue Correlations if there is no gene symbol because there is nothing to look against
self.trait_symbol = myTrait.symbol
-
+
#XZ, 12/12/2008: if the species is rat or human, translate the geneid to mouse geneid
self.input_trait_mouse_gene_id = self.translateToMouseGeneID(self.species, self.gene_id)
@@ -347,7 +347,7 @@ class CorrelationPage(templatePage):
self.tissue_probeset_freeze_id = 1
traitList = self.correlate(vals)
-
+
_log.info("Done doing correlation calculation")
############################################################################################################################################
@@ -356,12 +356,12 @@ class CorrelationPage(templatePage):
mainfmName = webqtlUtil.genRandStr("fm_")
form = HT.Form(cgi= os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), enctype='multipart/form-data', name= mainfmName, submit=HT.Input(type='hidden'))
- hddn = {'FormID': 'showDatabase',
+ hddn = {'FormID': 'showDatabase',
'ProbeSetID': '_',
- 'database': self.target_db_name,
- 'databaseFull': self.db.fullname,
- 'CellID': '_',
- 'RISet': fd.RISet,
+ 'database': self.target_db_name,
+ 'databaseFull': self.db.fullname,
+ 'CellID': '_',
+ 'RISet': fd.RISet,
'identification': fd.identification}
if myTrait:
@@ -400,7 +400,7 @@ class CorrelationPage(templatePage):
##############
# Excel file #
- ##############
+ ##############
filename= webqtlUtil.genRandStr("Corr_")
xlsUrl = HT.Input(type='button', value = 'Download Table', onClick= "location.href='/tmp/%s.xls'" % filename, Class='button')
# Create a new Excel workbook
@@ -432,7 +432,7 @@ class CorrelationPage(templatePage):
heatmap = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'heatmap');" % mainfmName)
heatmap_img = HT.Image("/images/heatmap2_final.jpg", name='mintmap', alt="QTL Heat Map and Clustering", title="QTL Heatmap and Clustering", style="border:none;")
heatmap.append(heatmap_img)
- partialCorr = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'partialCorrInput');" % mainfmName)
+ partialCorr = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'partialCorrInput');" % mainfmName)
partialCorr_img = HT.Image("/images/partial_correlation_final.jpg", name='partialCorr', alt="Partial Correlation", title="Partial Correlation", style="border:none;")
partialCorr.append(partialCorr_img)
addselect = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (fd.RISet, mainfmName))
@@ -454,7 +454,7 @@ class CorrelationPage(templatePage):
selectandor.append(('AND','and'))
selectandor.append(('OR','or'))
selectandor.selected.append('AND')
-
+
#External analysis tools
GCATButton = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'GCAT');" % mainfmName)
@@ -473,8 +473,8 @@ setTimeout('openWebGestalt()', 2000);
function openWebGestalt(){
var thisForm = document['WebGestalt'];
makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
-}
- """ % (mainfmName, len(traitList)))
+}
+ """ % (mainfmName, len(traitList)))
'''
self.cursor.execute('SELECT GeneChip.GO_tree_value FROM GeneChip, ProbeFreeze, ProbeSetFreeze WHERE GeneChip.Id = ProbeFreeze.ChipId and ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and ProbeSetFreeze.Name = "%s"' % self.db.name)
@@ -484,15 +484,15 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
GO_tree_value = result[0]
if GO_tree_value:
-
+
WebGestalt = HT.Href(url="#redirect", onClick="databaseFunc(document.getElementsByName('%s')[0], 'GOTree');" % mainfmName)
- WebGestalt_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none")
- WebGestalt.append(WebGestalt_img)
-
+ WebGestalt_img = HT.Image("/images/webgestalt_icon_final.jpg", name="webgestalt", alt="Gene Set Analysis Toolkit", title="Gene Set Analysis Toolkit", style="border:none")
+ WebGestalt.append(WebGestalt_img)
+
hddnWebGestalt = {
'id_list':'',
'correlation':'',
- 'id_value':'',
+ 'id_value':'',
'llid_list':'',
'id_type':GO_tree_value,
'idtype':'',
@@ -512,7 +512,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
hddnWebGestalt['org'] = 'Mus musculus'
else:
hddnWebGestalt['org'] = ''
-
+
for key in hddnWebGestalt.keys():
form.append(HT.Input(name=key, value=hddnWebGestalt[key], type='hidden'))
@@ -523,11 +523,11 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
containerTable = HT.TableLite(cellSpacing=0,cellPadding=0,width="90%",border=0, align="Left")
-
+
if not GO_tree_value:
optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="480", height="80", border=0, align="Left")
optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(addselect), HT.TD(GCATButton), HT.TD(ODE), align="left"))
- optionsTable.append(HT.TR(HT.TD("&nbsp;"*1,"Select"), HT.TD("Deselect"), HT.TD("&nbsp;"*1,"Invert"), HT.TD("&nbsp;"*3,"Add"), HT.TD("Gene Set"), HT.TD("&nbsp;"*2,"GCAT")))
+ optionsTable.append(HT.TR(HT.TD("&nbsp;"*1,"Select"), HT.TD("Deselect"), HT.TD("&nbsp;"*1,"Invert"), HT.TD("&nbsp;"*3,"Add"), HT.TD("Gene Set"), HT.TD("&nbsp;"*2,"GCAT")))
else:
optionsTable = HT.TableLite(cellSpacing=2, cellPadding=0,width="560", height="80", border=0, align="Left")
optionsTable.append(HT.TR(HT.TD(selectall), HT.TD(reset), HT.TD(selectinvert), HT.TD(addselect), HT.TD(GCATButton), HT.TD(ODE), HT.TD(WebGestalt), align="left"))
@@ -548,11 +548,11 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
fewerOptions = HT.Input(type='button',name='options',value='Fewer Options', onClick="",Class="toggle")
"""
- if (fd.formdata.getvalue('showHideOptions') == 'less'):
+ if (fd.formdata.getvalue('showHideOptions') == 'less'):
containerTable.append(HT.TR(HT.TD("&nbsp;"), height="10"), HT.TR(HT.TD(HT.Div(fewerOptions, Class="toggleShowHide"))))
containerTable.append(HT.TR(HT.TD("&nbsp;")))
- else:
- containerTable.append(HT.TR(HT.TD("&nbsp;"), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))
+ else:
+ containerTable.append(HT.TR(HT.TD("&nbsp;"), height="10"), HT.TR(HT.TD(HT.Div(moreOptions, Class="toggleShowHide"))))
containerTable.append(HT.TR(HT.TD("&nbsp;")))
"""
@@ -566,8 +566,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
tblobj = {}
if self.db.type=="Geno":
-
- containerTable.append(HT.TR(HT.TD(xlsUrl, height=40)))
+ containerTable.append(HT.TR(HT.TD(xlsUrl, height=60)))
pageTable.append(HT.TR(HT.TD(containerTable)))
@@ -579,7 +578,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
corrScript = HT.Script(language="Javascript")
corrScript.append("var corrArray = new Array();")
- tblobj['body'], worksheet, corrScript = self.getTableBodyForGeno(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript)
+ tblobj['body'], worksheet, corrScript = self.getTableBodyForGeno(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript)
workbook.close()
objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
@@ -604,15 +603,15 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
containerTable.append(HT.TR(HT.TD(xlsUrl, height=40)))
pageTable.append(HT.TR(HT.TD(containerTable)))
-
+
tblobj['header'], worksheet = self.getTableHeaderForPublish(method=self.method, worksheet=worksheet, newrow=newrow, headingStyle=headingStyle)
newrow += 1
sortby = self.getSortByValue( calculationMethod = self.method )
-
+
corrScript = HT.Script(language="Javascript")
corrScript.append("var corrArray = new Array();")
-
+
tblobj['body'], worksheet, corrScript = self.getTableBodyForPublish(traitList=traitList, formName=mainfmName, worksheet=worksheet, newrow=newrow, corrScript=corrScript, species=self.species)
workbook.close()
@@ -650,7 +649,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
workbook.close()
objfile = open('%s.obj' % (webqtlConfig.TMPDIR+filename), 'wb')
cPickle.dump(tblobj, objfile)
- objfile.close()
+ objfile.close()
#XZ: here is the table of traits
div = HT.Div(webqtlUtil.genTableObj(tblobj=tblobj, file=filename, sortby=sortby, tableID = "sortable", addIndex = "1", hiddenColumns=["Gene ID","Homologene ID"]), corrScript, Id="sortable")
@@ -708,11 +707,11 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
if self.species == 'human':
heatmap = ""
-
+
form.append(HT.Input(name='ShowStrains',type='hidden', value =1),
HT.Input(name='ShowLine',type='hidden', value =1),
info, HT.BR(), pageTable, HT.BR())
-
+
TD_LR.append(corrHeading, form, HT.P())
@@ -745,7 +744,7 @@ makeWebGestaltTree(thisForm, '%s', %d, 'edag_only.php');
sortby = ("Tissue r", "down")
elif calculationMethod == "5":
sortby = ("Tissue rho", "down")
-
+
return sortby
@@ -808,7 +807,7 @@ Resorting this table <br>
def getStrainIds(self, species=None, strains=[]):
StrainIds = []
for item in strains:
- self.cursor.execute('''SELECT Strain.Id FROM Strain, Species WHERE
+ self.cursor.execute('''SELECT Strain.Id FROM Strain, Species WHERE
Strain.Name="%s" and Strain.SpeciesId=Species.Id and Species.name = "%s" ''' % (item, species))
Id = self.cursor.fetchone()[0]
StrainIds.append(Id)
@@ -855,16 +854,16 @@ Resorting this table <br>
#XZ, 12/16/2008: the input geneid is of mouse type
def checkSymbolForTissueCorr(self, tissueProbeSetFreezeId=0, symbol=""):
- q = "SELECT 1 FROM TissueProbeSetXRef WHERE TissueProbeSetFreezeId=%s and Symbol='%s' LIMIT 1" % (tissueProbeSetFreezeId,symbol)
+ q = "SELECT 1 FROM TissueProbeSetXRef WHERE TissueProbeSetFreezeId=%s and Symbol='%s' LIMIT 1" % (tissueProbeSetFreezeId,symbol)
self.cursor.execute(q)
try:
x = self.cursor.fetchone()
if x: return True
else: raise
except: return False
-
-
+
+
def fetchAllDatabaseData(self, species, GeneId, GeneSymbol, strains, db, method, returnNumber, tissueProbeSetFreezeId):
StrainIds = []
@@ -879,9 +878,9 @@ Resorting this table <br>
nnn += 1
oridata = []
- #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId
+ #XZ, 09/24/2008: build one temporary table that only contains the records associated with the input GeneId
tempTable = None
- if GeneId and db.type == "ProbeSet":
+ if GeneId and db.type == "ProbeSet":
if method == "3":
tempTable = self.getTempLiteratureTable(species=species, input_species_geneid=GeneId, returnNumber=returnNumber)
@@ -892,7 +891,7 @@ Resorting this table <br>
temp = []
StrainIdstep = StrainIds[step*25:min(len(StrainIds), (step+1)*25)]
for item in StrainIdstep: temp.append('T%s.value' % item)
-
+
if db.type == "Publish":
query = "SELECT PublishXRef.Id, "
dataStartPos = 1
@@ -910,12 +909,12 @@ Resorting this table <br>
# as we would not have litCorr data.
if method == "3":
- query = "SELECT %s.Name, %s.value," % (db.type,tempTable)
- dataStartPos = 2
+ query = "SELECT %s.Name, %s.value," % (db.type,tempTable)
+ dataStartPos = 2
if method == "4" or method == "5":
- query = "SELECT %s.Name, %s.Correlation, %s.PValue," % (db.type,tempTable, tempTable)
- dataStartPos = 3
-
+ query = "SELECT %s.Name, %s.Correlation, %s.PValue," % (db.type,tempTable, tempTable)
+ dataStartPos = 3
+
query += string.join(temp,', ')
query += ' FROM (%s, %sXRef, %sFreeze)' % (db.type, db.type, db.type)
if method == "3":
@@ -925,8 +924,8 @@ Resorting this table <br>
#XZ, 03/04/2009: Xiaodong changed Data to %sData and changed parameters from %(item,item, db.type,item,item) to %(db.type, item,item, db.type,item,item)
for item in StrainIdstep:
query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(db.type, item,item, db.type,item,item)
-
- if method == "3":
+
+ if method == "3":
query += "WHERE ProbeSet.GeneId IS NOT NULL AND %s.value IS NOT NULL AND %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s' and %s.Id = %sXRef.%sId order by %s.Id" % (tempTable,db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type)
if method == "4" or method == "5":
query += "WHERE ProbeSet.Symbol IS NOT NULL AND %s.Correlation IS NOT NULL AND %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s' and %s.Id = %sXRef.%sId order by %s.Id" % (tempTable,db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type)
@@ -939,7 +938,7 @@ Resorting this table <br>
for item in StrainIdstep:
query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(db.type, item,item, db.type,item,item)
query += "WHERE %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Name = '%s' and %s.Id = %sXRef.%sId order by %s.Id" % (db.type, db.type, db.type, db.type, db.name, db.type, db.type, db.type, db.type)
-
+
self.cursor.execute(query)
results = self.cursor.fetchall()
oridata.append(results)
@@ -971,17 +970,17 @@ Resorting this table <br>
- # XZ, 09/20/2008: This function creates TEMPORARY TABLE tmpTableName_2 and return its name.
+ # XZ, 09/20/2008: This function creates TEMPORARY TABLE tmpTableName_2 and return its name.
# XZ, 09/20/2008: It stores top literature correlation values associated with the input geneId.
# XZ, 09/20/2008: Attention: In each row, the input geneId is always in column GeneId1.
#XZ, 12/16/2008: the input geneid can be of mouse, rat or human type
def getTempLiteratureTable(self, species, input_species_geneid, returnNumber):
# according to mysql the TEMPORARY TABLE name should not have to be unique because
- # it is only available to the current connection. This program will be invoked via command line, but if it
+ # it is only available to the current connection. This program will be invoked via command line, but if it
# were to be invoked over mod_python this could cuase problems. mod_python will keep the connection alive
# in its executing threads ( i think) so there is a potential for the table not being dropped between users.
#XZ, 01/29/2009: To prevent the potential risk, I generate random table names and drop the tables after use them.
-
+
# the 'input_species_geneid' could be rat or human geneid, need to translate it to mouse geneid
translated_mouse_geneid = self.translateToMouseGeneID (species, input_species_geneid)
@@ -1022,7 +1021,7 @@ Resorting this table <br>
translated_species_geneid = record[0]
if translated_species_geneid:
- self.cursor.execute( 'INSERT INTO %s (GeneId1, GeneId2, value) VALUES (%d,%d,%f)' % (tmpTableName_2, int(input_species_geneid),int(translated_species_geneid), float(lit_corr_alue)) )
+ self.cursor.execute( 'INSERT INTO %s (GeneId1, GeneId2, value) VALUES (%d,%d,%f)' % (tmpTableName_2, int(input_species_geneid),int(translated_species_geneid), float(lit_corr_alue)) )
counter = counter + 1
#pay attention to the number
@@ -1054,9 +1053,9 @@ Resorting this table <br>
symbolCorrList.sort(cmpTissCorrAbsoluteValue)
symbolCorrList = symbolCorrList[0 : 2*returnNumber]
-
+
tmpTableName = webqtlUtil.genRandStr(prefix="TOPTISSUE")
-
+
q1 = 'CREATE TEMPORARY TABLE %s (Symbol varchar(100) PRIMARY KEY, Correlation float, PValue float)' % tmpTableName
self.cursor.execute(q1)
@@ -1166,7 +1165,7 @@ Resorting this table <br>
return traitList
def get_trait(self, cached, vals):
-
+
if cached:
_log.info("Using the fast method because the file exists")
lit_corrs = {}
@@ -1194,7 +1193,7 @@ Resorting this table <br>
#XZ: The new method uses all strains stored in variable dataset_strains to create a new variable
#XZ: _newvals. _newvals has the same length as dataset_strains. The items in _newvals is in
#XZ: the same order of items in dataset_strains. The value of each item in _newvals is either
- #XZ: the value of correspinding strain in _vals or 'None'.
+ #XZ: the value of correspinding strain in _vals or 'None'.
new_vals = []
for name in cached_sample_names:
if name in self.sample_names:
@@ -1211,13 +1210,13 @@ Resorting this table <br>
data_start = 1
for line in datasetFile:
raw_trait = webqtlUtil.readLineCSV(line)
- trait = Trait.from_csv(raw_trait, data_start)
+ trait = Trait.from_csv(raw_trait, data_start)
trait.lit_corr = lit_corrs.get(trait.name)
trait.tissue_corr, trait.p_tissue = tissue_corrs.get(trait.name, (None, None))
traits.append(trait)
return traits, new_vals
-
+
else:
_log.info("Using the slow method for correlation")
@@ -1318,7 +1317,7 @@ Resorting this table <br>
#the top ones always have p value 0. So comparing p values actually does nothing.
#In addition, for the tissue data in our database, the N is always the same.
#So it's safe to compare with tissue corr statistic value.
- #That's the same as literature corr.
+ #That's the same as literature corr.
#if self.method in [METHOD_LIT, METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK] and self.gene_id:
# traits.sort(webqtlUtil.cmpLitCorr)
#else:
@@ -1348,13 +1347,13 @@ Resorting this table <br>
# NL, 07/19/2010
# js function changed, add a new parameter rankOrder for js function 'showTissueCorrPlot'
db_trait.RANK_ORDER = self.RANK_ORDERS[self.method]
-
+
#XZ, 26/09/2008: Method is 4 or 5. Have fetched tissue corr, but no literature correlation yet.
if self.method in TISSUE_METHODS:
db_trait.tissueCorr = trait.tissue_corr
db_trait.tissuePValue = trait.p_tissue
addTissueCorr = True
-
+
#XZ, 26/09/2008: Method is 3, Have fetched literature corr, but no tissue corr yet.
elif self.method == METHOD_LIT:
@@ -1374,13 +1373,13 @@ Resorting this table <br>
trait_list.append(db_trait)
if addLiteratureCorr:
- trait_list = self.getLiteratureCorrelationByList(self.input_trait_mouse_gene_id,
+ trait_list = self.getLiteratureCorrelationByList(self.input_trait_mouse_gene_id,
self.species, trait_list)
if addTissueCorr:
trait_list = self.getTissueCorrelationByList(
- primaryTraitSymbol = self.trait_symbol,
+ primaryTraitSymbol = self.trait_symbol,
traitList = trait_list,
- TissueProbeSetFreezeId = TISSUE_MOUSE_DB,
+ TissueProbeSetFreezeId = TISSUE_MOUSE_DB,
method=self.method)
return trait_list
@@ -1446,7 +1445,7 @@ Resorting this table <br>
if myTrait:
if method in ["1","2"]: #genetic correlation
- info = HT.Paragraph("Values of Record %s in the " % myTrait.getGivenName(), HT.Href(text=myTrait.db.fullname,url=webqtlConfig.INFOPAGEHREF % myTrait.db.name,target="_blank", Class="fwn"),
+ info = HT.Paragraph("Values of Record %s in the " % myTrait.getGivenName(), HT.Href(text=myTrait.db.fullname,url=webqtlConfig.INFOPAGEHREF % myTrait.db.name,target="_blank", Class="fwn"),
" database were compared to all %d records in the " % self.record_count, HT.Href(text=db.fullname,url=webqtlConfig.INFOPAGEHREF % target_db_name,target="_blank", Class="fwn"),
' database. The top %d correlations ranked by the %s are displayed.' % (returnNumber,methodDict[method]),
' You can resort this list using the small arrowheads in the top row.')
@@ -1498,7 +1497,7 @@ Resorting this table <br>
titleStyle = workbook.add_format(align = 'left', bold = 0, size=14, border = 1, border_color="gray")
##Write title Info
- # Modified by Hongqiang Li
+ # Modified by Hongqiang Li
worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
worksheet.write([1, 0], "Citations: Please see %s/reference.html" % webqtlConfig.PORTADDR, titleStyle)
worksheet.write([2, 0], "Trait : %s" % identification, titleStyle)
@@ -1568,7 +1567,7 @@ Resorting this table <br>
tr = []
trId = str(thisTrait)
-
+
corrScript.append('corrArray["%s"] = {corr:%1.4f};' % (trId, thisTrait.corr))
tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class="fs12 fwn ffl b1 c222"), text=trId))
@@ -1616,7 +1615,7 @@ Resorting this table <br>
tblobj_header = []
if method in ["1","3","4"]:
- tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0),
+ tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0),
THCell(HT.TD('Record',HT.BR(), 'ID',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Record ID", idx=1),
THCell(HT.TD('Phenotype', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Phenotype", idx=2),
THCell(HT.TD('Authors', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Authors", idx=3),
@@ -1626,7 +1625,7 @@ Resorting this table <br>
THCell(HT.TD(HT.Href(
text = HT.Span('Sample',HT.BR(), 'r', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"),
target = '_blank',
- url = "/correlationAnnotation.html#genetic_r"),
+ url = "/correlationAnnotation.html#genetic_r"),
Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample r", idx=7),
THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=8),
THCell(HT.TD(HT.Href(
@@ -1639,7 +1638,7 @@ Resorting this table <br>
worksheet.write([newrow, ncol], item, headingStyle)
worksheet.set_column([ncol, ncol], 2*len(item))
else:
- tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0),
+ tblobj_header = [[THCell(HT.TD(' ', Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), sort=0),
THCell(HT.TD('Record',HT.BR(), 'ID',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Record ID", idx=1),
THCell(HT.TD('Phenotype', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Phenotype", idx=2),
THCell(HT.TD('Authors', HT.BR(),HT.BR(), Class="fs13 fwb ffl b1 cw cbrb", nowrap="on"), text="Authors", idx=3),
@@ -1649,7 +1648,7 @@ Resorting this table <br>
THCell(HT.TD(HT.Href(
text = HT.Span('Sample',HT.BR(), 'rho', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"),
target = '_blank',
- url = "/correlationAnnotation.html#genetic_rho"),
+ url = "/correlationAnnotation.html#genetic_rho"),
Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample rho", idx=7),
THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=8),
THCell(HT.TD(HT.Href(
@@ -1674,7 +1673,7 @@ Resorting this table <br>
tr = []
trId = str(thisTrait)
-
+
corrScript.append('corrArray["%s"] = {corr:%1.4f};' % (trId, thisTrait.corr))
tr.append(TDCell(HT.TD(HT.Input(type="checkbox", Class="checkbox", name="searchResult",value=trId, onClick="highlight(this)"), nowrap="on", Class="fs12 fwn ffl b1 c222"), text=trId))
@@ -1757,7 +1756,7 @@ Resorting this table <br>
tr.append(TDCell(HT.TD(repr,nowrap='ON', Class="fs12 fwn ffl b1 c222", align='right'),repr,thisTrait.corrPValue))
tblobj_body.append(tr)
-
+
for ncol, item in enumerate([thisTrait.name, PhenotypeString, thisTrait.authors, thisTrait.year, thisTrait.pubmed_id, LRS_score_repr, LRS_location_repr, thisTrait.corr, thisTrait.nOverlap, thisTrait.corrPValue]):
worksheet.write([newrow, ncol], item)
newrow += 1
@@ -1783,7 +1782,7 @@ Resorting this table <br>
THCell(HT.TD(HT.Href(
text = HT.Span('Sample',HT.BR(), 'r', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"),
target = '_blank',
- url = "/correlationAnnotation.html#genetic_r"),
+ url = "/correlationAnnotation.html#genetic_r"),
Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample r", idx=10),
THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=11),
THCell(HT.TD(HT.Href(
@@ -1825,7 +1824,7 @@ Resorting this table <br>
THCell(HT.TD(HT.Href(
text = HT.Span('Sample',HT.BR(), 'rho', HT.Sup(' ?', style="color:#f00"),HT.BR(), Class="fs13 fwb ffl cw"),
target = '_blank',
- url = "/correlationAnnotation.html#genetic_rho"),
+ url = "/correlationAnnotation.html#genetic_rho"),
Class="fs13 fwb ffl b1 cw cbrb", nowrap='ON'), text="Sample rho", idx=10),
THCell(HT.TD('N',HT.BR(),'Cases',HT.BR(), Class="fs13 fwb ffl b1 cw cbrb"), text="N Cases", idx=11),
THCell(HT.TD(HT.Href(
@@ -1885,17 +1884,17 @@ Resorting this table <br>
#XZ, 12/08/2008: probeset name
tr.append(TDCell(HT.TD(HT.Href(text=thisTrait.name,url="javascript:showTrait('%s', '%s')" % (formName,thisTrait.name), Class="fs12 fwn"), Class="fs12 fwn b1 c222"), thisTrait.name, thisTrait.name.upper()))
- #XZ, 12/08/2008: gene id
+ #XZ, 12/08/2008: gene id
if thisTrait.geneid:
tr.append(TDCell(None, thisTrait.geneid, val=999))
else:
- tr.append(TDCell(None, thisTrait.geneid, val=999))
-
+ tr.append(TDCell(None, thisTrait.geneid, val=999))
+
#XZ, 12/08/2008: homologene id
if thisTrait.homologeneid:
tr.append(TDCell("", thisTrait.homologeneid, val=999))
else:
- tr.append(TDCell("", thisTrait.homologeneid, val=999))
+ tr.append(TDCell("", thisTrait.homologeneid, val=999))
#XZ, 12/08/2008: gene symbol
tr.append(TDCell(HT.TD(symbolurl, Class="fs12 fwn b1 c222 fsI"),thisTrait.symbol, thisTrait.symbol.upper()))
diff --git a/web/webqtl/maintainance/genSelectDatasetJS.py b/web/webqtl/maintainance/genSelectDatasetJS.py
index bc88beec..d03cc7af 100755
--- a/web/webqtl/maintainance/genSelectDatasetJS.py
+++ b/web/webqtl/maintainance/genSelectDatasetJS.py
@@ -27,6 +27,9 @@
# created by Ning Liu 07/01/2010
# This script is to generate selectDatasetMenu.js file for cascade menu in the main search page http://www.genenetwork.org/.
# This script will be run automatically every one hour or manually when database has been changed .
+
+from __future__ import print_function, division
+
import sys, os
current_file_name = __file__
diff --git a/web/webqtl/search/SearchResultPage.py b/web/webqtl/search/SearchResultPage.py
index 029a54c4..d62bb449 100755
--- a/web/webqtl/search/SearchResultPage.py
+++ b/web/webqtl/search/SearchResultPage.py
@@ -14,7 +14,7 @@ from htmlgen import HTMLgen2 as HT
from base import webqtlConfig
from utility.THCell import THCell
from utility.TDCell import TDCell
-from base.webqtlDataset import webqtlDataset
+from base.data_set import DataSet
from base.webqtlTrait import webqtlTrait
from base.templatePage import templatePage
from utility import webqtlUtil
@@ -65,12 +65,12 @@ class SearchResultPage(templatePage):
InbredSet where PublishFreeze.Name not like 'BXD300%' and InbredSet.Id =
PublishFreeze.InbredSetId""")
results = self.cursor.fetchall()
- self.database = map(lambda x: webqtlDataset(x[0], self.cursor), results)
+ self.database = map(lambda x: DataSet(x[0], self.cursor), results)
self.databaseCrosses = map(lambda x: x[1], results)
self.databaseCrossIds = map(lambda x: x[2], results)
self.singleCross = False
else:
- self.database = map(lambda x: webqtlDataset(x, self.cursor), self.database)
+ self.database = map(lambda x: DataSet(x, self.cursor), self.database)
#currently, webqtl wouldn't allow multiple crosses
#for other than multiple publish db search
#so we can use the first database as example
diff --git a/web/webqtl/showTrait/DataEditingPage.py b/web/webqtl/showTrait/DataEditingPage.py
index f38b9880..c240d8a0 100644..100755
--- a/web/webqtl/showTrait/DataEditingPage.py
+++ b/web/webqtl/showTrait/DataEditingPage.py
@@ -280,13 +280,13 @@ class DataEditingPage(templatePage):
if snpurl:
snpBrowserButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % snpurl)
- snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="addselect", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;")
+ snpBrowserButton_img = HT.Image("/images/snp_icon.jpg", name="snpbrowser", alt=" View SNPs and Indels ", title=" View SNPs and Indels ", style="border:none;")
snpBrowserButton.append(snpBrowserButton_img)
snpBrowserText = "SNPs"
#XZ: Show GeneWiki for all species
geneWikiButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE) + "?FormID=geneWiki&symbol=%s" % thisTrait.symbol))
- geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="addselect", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;")
+ geneWikiButton_img = HT.Image("/images/genewiki_icon.jpg", name="genewiki", alt=" Write or review comments about this gene ", title=" Write or review comments about this gene ", style="border:none;")
geneWikiButton.append(geneWikiButton_img)
geneWikiText = 'GeneWiki'
@@ -295,7 +295,7 @@ class DataEditingPage(templatePage):
if _Species in ("mouse", "rat", "human"):
similarUrl = "%s?cmd=sch&gene=%s&alias=1&species=%s" % (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.symbol, _Species)
similarButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % similarUrl)
- similarButton_img = HT.Image("/images/find_icon.jpg", name="addselect", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;")
+ similarButton_img = HT.Image("/images/find_icon.jpg", name="similar", alt=" Find similar expression data ", title=" Find similar expression data ", style="border:none;")
similarButton.append(similarButton_img)
similarText = "Find"
else:
@@ -416,13 +416,15 @@ class DataEditingPage(templatePage):
UTHSC_BLAT_URL = ""
if UCSC_BLAT_URL:
- verifyButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
- verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="addselect", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
+ verifyButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UCSC_BLAT_URL)
+ verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ",
+ title=" Check probe locations at UCSC ", style="border:none;")
verifyButton.append(verifyButtonImg)
verifyText = 'Verify'
if UTHSC_BLAT_URL:
- rnaseqButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
- rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="addselect", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
+ rnaseqButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % UTHSC_BLAT_URL)
+ rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ",
+ title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
rnaseqButton.append(rnaseqButtonImg)
rnaseqText = 'RNA-seq'
tSpan.append(HT.BR())
@@ -442,8 +444,8 @@ class DataEditingPage(templatePage):
if probeResult[0] > 0:
probeurl = "%s?FormID=showProbeInfo&database=%s&ProbeSetID=%s&CellID=%s&RISet=%s&incparentsf1=ON" \
% (os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE), thisTrait.db, thisTrait.name, thisTrait.cellid, fd.RISet)
- probeButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % probeurl)
- probeButton_img = HT.Image("/images/probe_icon.jpg", name="addselect", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;")
+ probeButton = HT.Href(url="#", onClick="javascript:openNewWin('%s'); return false;" % probeurl)
+ probeButton_img = HT.Image("/images/probe_icon.jpg", name="probe", alt=" Check sequence of probes ", title=" Check sequence of probes ", style="border:none;")
probeButton.append(probeButton_img)
probeText = "Probes"
@@ -590,10 +592,24 @@ class DataEditingPage(templatePage):
url="http://string.embl.de/newstring_cgi/show_link_summary.pl?identifier=%s" \
% thisTrait.symbol,Class="fs14 fwn", \
title="Protein interactions: known and inferred"), style=linkStyle), "&nbsp;"*2)
- if thisTrait.geneid:
+ if thisTrait.symbol:
+ #ZS: The "species scientific" converts the plain English species names we're using to their scientific names, which are needed for PANTHER's input
+ #We should probably use the scientific name along with the English name (if not instead of) elsewhere as well, given potential non-English speaking users
+ if _Species == "mouse":
+ species_scientific = "Mus%20musculus"
+ elif _Species == "rat":
+ species_scientific = "Rattus%20norvegicus"
+ elif _Species == "human":
+ species_scientific = "Homo%20sapiens"
+ elif _Species == "drosophila":
+ species_scientific = "Drosophila%20melanogaster"
+ else:
+ species_scientific = "all"
+
+ species_scientific
tSpan.append(HT.Span(HT.Href(text= 'PANTHER',target="mainFrame", \
- url="http://www.pantherdb.org/genes/gene.do?acc=%s" \
- % thisTrait.geneid,Class="fs14 fwn", \
+ url="http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=%s&listType=1&fieldValue=%s" \
+ % (species_scientific, thisTrait.symbol),Class="fs14 fwn", \
title="Gene and protein data resources from Celera-ABI"), style=linkStyle), "&nbsp;"*2)
else:
pass
@@ -755,12 +771,13 @@ class DataEditingPage(templatePage):
UCSC_BLAT_URL = ""
UTHSC_BLAT_URL = ""
if UCSC_BLAT_URL:
- verifyButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
- verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="addselect", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
+ #verifyButton = HT.Href(url="#", onClick="openNewWin('%s')" % UCSC_BLAT_URL)
+ verifyButton = HT.Href(url="#")
+ verifyButtonImg = HT.Image("/images/verify_icon.jpg", name="verify", alt=" Check probe locations at UCSC ", title=" Check probe locations at UCSC ", style="border:none;")
verifyButton.append(verifyButtonImg)
verifyText = "Verify"
- rnaseqButton = HT.Href(url="#redirect", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
- rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="addselect", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
+ rnaseqButton = HT.Href(url="#", onClick="openNewWin('%s')" % UTHSC_BLAT_URL)
+ rnaseqButtonImg = HT.Image("/images/rnaseq_icon.jpg", name="rnaseq", alt=" View probes, SNPs, and RNA-seq at UTHSC ", title=" View probes, SNPs, and RNA-seq at UTHSC ", style="border:none;")
rnaseqButton.append(rnaseqButtonImg)
rnaseqText = "RNA-seq"