Template:TestClassification

{{ var subnav;
var navhtml;
var uniprot = args.uniprotId; var dropicon='<span class="dropicon">v</span>';
var topselect;
var uniprothtml;
var pfamhtml;
var kegghtml;
var cathhtml; var scophtml; var interprohtml; var stringhtml; var seedhtml;
if (args.uniprotId && args.uniprotId != '') { var namemap = { 'xsi': 'http://pfam.sanger.ac.uk/'}; var docerr = web.xml('http://pfam.sanger.ac.uk//protein/'..args.uniprotId..'?output=xml');
var strctn = xml.format(docerr, 'plain'); if (string.contains(strctn, 'No valid UniProt accession or ID')) { let uniprothtml =('<li class="'..'Uniprot'..topselect..'"><span><b>'..'Uniprot</b>'..dropicon..'</span><ul>'..'No valid UniProt accession or ID'..'</ul></li>'); let pfamhtml = ''; let kegghtml = ''; let stringhtml = ''; let seedhtml = '';
}
else {
var uniprotcontent = '';
var uniprotmap = {'xsi': 'http://uniprot.org/uniprot'};
let uniprotXml = web.xml('http://www.uniprot.org/uniprot/'..args.uniprotId..'.xml');
var accession = xml.text(uniprotXml, '//xsi:accession', uniprotmap);
var name = xml.text(uniprotXml, '//xsi:name', uniprotmap);
if (accession && accession != ''){
var expasyEC = xml.text(uniprotXml, "//xsi:dbReference[@type='EC']//@id", uniprotmap);
let uniprotcontent..=('<b>'..web.link('http://www.uniprot.org/uniprot/'..accession, accession,'','_blank')..'</b>');
if(expasyEC && expasyEC != '') {let uniprotcontent..=('<b> | EC: '..web.link('http://www.expasy.org/enzyme/'..expasyEC, expasyEC, '', '_blank')..'</b>');}
let fullName = xml.text(uniprotXml, '//xsi:recommendedName/xsi:fullName', uniprotmap);
let shortName = xml.text(uniprotXml, '//xsi:recommendedName/xsi:shortName', uniprotmap);
if(fullName && fullName != ''){
let uniprotcontent..=('<br /><b><u>'..fullName..'</u></b>');
if(shortName && shortName != ''){let uniprotcontent..=('<b><u> ('..shortName..') </b></u>');} }
let function = xml.text(uniprotXml, "//xsi:comment[@type='function']/xsi:text", uniprotmap);
let function2 = xml.text(uniprotXml, "//xsi:fullName", uniprotmap);
if(function2 && function2 != '') { let uniprotcontent..=('<table style="font-size:11px; width:300px"><tr><td width="20px"></td><td><i>'..function2..'</i></td></tr></table>'); }
let uniprothtml =('<li class="'..'Uniprot'..topselect..'"><span><b>'..'Uniprot</b>'..dropicon..'</span><ul>'..uniprotcontent..'</ul></li>'); } 

var pfamcontent = '';
if (accession && accession != ''){
let pfamcontent..=('<b>'..web.link('http://pfam.sanger.ac.uk//protein/'..accession, accession,'','_blank')..'</b>');}
if(name && name != '') {let pfamcontent..=('<b> | '..name..'</b>');}
let pfamXml = web.xml('http://pfam.sanger.ac.uk//protein/'..accession..'?output=xml');
let pfammap = {'xsi': 'http://pfam.sanger.ac.uk/'};
let pfamdescription = xml.format(xml.select(pfamXml, '//_:description'), 'plain');
let pfamdescription = string.replace(string.replace(pfamdescription, ']]>',''), '<![CDATA[', '');
let pfamcontent..=('<table style="font-size:11px; width:300px">');
if(pfamdescription && pfamdescription != ''){let pfamcontent..=('<tr><td><b><u>Description</u></b></td></tr><tr><td><i>'..pfamdescription..'</i></td></tr>'); }
let matches = xml.list(pfamXml, '//xsi:match', pfammap, 'true');
if(#matches >0){
let pfamcontent..=('<tr><td><div id="tabsss"><ul style="list-style:none">');
foreach(var match in matches) {
let tempAccession = xml.text(web.xml(match), '//xsi:match//@accession', pfammap);
let pfamcontent..=('<li style="font-size:11px"><a href=#'..tempAccession..' style="text-decoration: none"><span>'..tempAccession..'</span></a></li>');}
let pfamcontent..=('</ul>');
foreach(var match in matches){
var webmatch = web.xml(match); let tempAccession = xml.text(webmatch, '//xsi:match//@accession', pfammap);
let tempId = xml.text(webmatch, '//xsi:match//@id', pfammap);
let start = xml.text(webmatch, '//xsi:match/xsi:location/@start', pfammap);
let end = xml.text(webmatch, '//xsi:match/xsi:location/@end', pfammap);
let tempXml = web.xml('http://pfam.sanger.ac.uk/family/'..tempAccession..'?output=xml');
let tempDescription = xml.format(xml.select(tempXml, '//_:description'), 'plain');
let tempDescription = string.replace(string.replace(tempDescription, '<description xmlns="http://pfam.sanger.ac.uk/">',''), '</description>', '');
let tempDescription = string.replace(string.replace(tempDescription, ']]>',''), '<![CDATA[', '');
let tempComment = xml.format(xml.select(tempXml, '//_:comment'), 'plain');
let tempComment = string.replace(string.replace(tempComment, '<comment xmlns="http://pfam.sanger.ac.uk/">',''), '</comment>', '');
let tempComment = string.replace(string.replace(tempComment, ']]>',''), '<![CDATA[', '');
if(string.Length(tempComment) > 400) { let tempComment = string.remove(tempComment, 400)..'[...]'; }
let pfamcontent..=('<div id='..tempAccession..'><table cellpadding="4" style="font-size:11px; border: 1px solid black"><tr><td>'..'<b>[ID: </b>'..web.link('http://pfam.sanger.ac.uk/family?id='..tempId,tempId,'','_blank')..' <b>|</b> '..start..'<b>-</b>'..end..'<b>]</b></td></tr>');
let pfamcontent..=('<tr></tr><tr><td><b><u>'..tempDescription..'</u></b><br /><i>'..tempComment..'</i></td></tr></table></div>');
}}
let pfamcontent..=('</div></td></tr></table>');
let pfamhtml =('<li class="'..'PFAM'..topselect..'"><span><b>'..'PFAM</b>'..dropicon..'</span><ul>'..pfamcontent..'</ul></li>');

var xmlDoc; var stringcontent;
let xmlDoc = web.xml(uri.appendquery("http://172.16.245.154/httptest.php", { id: uniprot }));
var names = xml.list(xmlDoc, '//name');
if (#names != 0){
var functions = xml.list(xmlDoc,'//function');
var scores = xml.list(xmlDoc,'//score');
var links = xml.list(xmlDoc,'//link');
let stringcontent =('<table border="0" cellpadding="4" style="font-size:11px"><tr><td width="330px" valign="top"><b>'..'Input:</b> <br />'..web.link(links[0], names[0], 'STRING page for '..names[0], '_blank')..' => '..functions[0]..'<hr /><table style="font-size:11px"><tr><td valign="top" width="auto"><b>Interactors</b><table style="font-size:11px"><tr><td>ID</td><td>Score</td></tr>');
var listLoop = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10];
var listId = ['',"one","two","three","four","five","six","seven","eight","nine","ten"];
var listId2 = ['',"a","b","c","d","e","f","g","h","i","j"];
foreach (var num in listLoop){if (num < #names){let stringcontent..=('<tr><td><a id=\"'..listId[num]..'\">'..names[num]..'</a>&nbsp;</td><td>&nbsp;'..scores[num]..'&nbsp;<input type="hidden" value=\"'..names[num]..'|'..functions[num]..'|'..links[num]..'\" id=\"'..listId2[num]..'\"/></td></tr>');}}
let stringcontent..=('</table></td><td valign="top"><b>Description</b><div id="toBeChanged" class="scroll">');
if (#names > 1 ){ let stringcontent..=('<i>Place cursor over interactors to view function information</i>'); }
else { let stringcontent..=('<i>No predicted functional associations at medium confidence (&gt;.400)</i>');}
let stringcontent..=('</div></td></tr></table>');
let stringcontent..=('</td><td width="360px">'..'<ul><img width="100%" src='..scores[0]..'></ul><ul style="font-size:9px">This is a STRING generated image, click '..web.link(links[0]..'&use_java=yes', 'here', 'STRING', '_blank')..' to view the interactive version.</ul>'..'</td></tr></table>');
let stringhtml =('<li class="'..'STRING'..topselect..'"><span><b>'..'STRING</b>'..dropicon..'</span><ul>'..' '..stringcontent..'</ul></li>');}

var xmlDoc; var keggcontent;
let xmlDoc = web.xml(uri.appendquery("http://172.16.245.154/keggpath.php", { id: args.uniprotId }));
var description = xml.list(xmlDoc, '//description');
if (#description != 0){
var picture = xml.list(xmlDoc, '//picture');
var keggcontent = ('<table id="keggstyle" border="0" cellpadding="2"><b>'..args.uniprotId..'</b>');
foreach (var temp in description) {
let link = web.link(picture[list.indexof(description, temp)], temp, temp, '_blank');
let link = string.replace(link, 'www.', 'http://www.');
let keggcontent..=('<tr><td>'..link..'</td></tr>');}
let keggcontent..=('</table>');
let kegghtml = ('<li class="'..'KEGG'..topselect..'"><span><b>'..'KEGG</b>'..dropicon..'</span><ul>'..' '..keggcontent..'</ul></li>');}

var xmlDoc; var seedcontent;
let xmlDoc = web.xml("http://172.16.245.154/cgi-bin/seedresults.pl?id="..args.uniprotId);
var subsystems = xml.list(xmlDoc, '//subsystem');
var fid = xml.list(xmlDoc, '//fid');
var peg = xml.list(xmlDoc, '//peg');
if( fid[0] != '' || peg[0] != '' || subsystems[0] != ''){
let seedcontent = ('<table border="0" cellpadding="2" style="font-size:12px" width="350px">');
if( fid[0] && fid[0] != ''){ let seedcontent..= ('<td style="font-size:12px"><b>[SEED ID: </b>'..web.link("http://theseed.uchicago.edu/FIG/seedviewer.cgi?page=Annotation&feature="..fid[0], fid[0], 'SEED page for '..fid[0], '_blank'));
if(peg[0] && peg[0] != ''){ let seedcontent..=('<b> | FIGfam: </b>'..web.link('http://theseed.uchicago.edu/FIG/seedviewer.cgi?page=FigFamViewer&figfam='..peg[0], peg[0], "FIG Family for "..peg[0], '_blank')); } let seedcontent..= ('<b>]</b></td><tr><td><b><u>Subsystem Information</u></b></td></tr>');}
if( subsystems[0] && subsystems[0] != ''){ foreach (var temp in subsystems) {
var input = "//function[@id='"..temp.."']";
var functions = xml.list(xmlDoc,input);
let seedcontent..=('<tr><td><b>'..temp..'</b>');
foreach (var temp2 in functions) { if (#functions > 1) {let seedcontent..=('<ul>'..temp2..'</ul>');} else { let seedcontent..=('<b>: </b>'..temp2);} } let seedcontent..=('</td></tr>');}}
else{ let seedcontent..=('<tr><td><ul>No function or subsystem information found.</ul></td></tr>');} 
let seedcontent..=('</table>');
let seedhtml =('<li class="'..'SEED'..topselect..'"><span><b>'..'SEED</b>'..dropicon..'</span><ul>'..' '..seedcontent..'</ul></li>');}
} }

if (args.pdbId && args.pdbId != '') { 
var pdb = '\''..args.pdbId..'\'';
var cathresult = myproteins.recordlist('SELECT domainID, class, arch, topol, homol, cathID FROM cath_info WHERE pdbID = '..pdb);
if (#cathresult != 0){
var cathcontent = ('<div id="tabs"><ul style="list-style:none">');
foreach (var temp in cathresult){
let cathcontent..=('<li style="font-size:11px"><a href=#'..temp['domainID']..' style="text-decoration: none"><span>'..temp['domainID']..'</span></a></li>');}
let cathcontent..=('</ul>');
foreach (var temp in cathresult){
let cathcontent..=('<div id ='..temp['domainID']..'>'..'<table border="0" cellpadding="2" style="font-size:11px><tr><td>'..web.image('http://data.cathdb.info/v3_2_0/molscript/'..temp['domainID']..'.850.jpg', 135, 135, "Domain Picture")..'</td><td><b>'..temp['domainID']..': ['..web.link('http://www.cathdb.info/cathnode/'..temp['cathID'], temp['cathID'], temp['cathID'], '_blank')..']'..'</b><hr /><ul>'..'<b>C:</b> '..temp['class']..'</ul>'..'<ul>'..'<b>A:</b> '..temp['arch']..'</ul>'..'<ul>'..'<b>T:</b> '..temp['topol']..'</ul>'..'<ul>'..'<b>H:</b> '..temp['homol']..'</ul><hr /></td></tr></table></div>');}
let cathcontent..=('</div>');
let cathhtml = ('<li class="'..'CATH'..topselect..'"><span><b>'..'CATH</b>'..dropicon..'</span><ul>'..' '..cathcontent..'</ul></li>');}

var scopcontent = ('<div id="tabss"><ul style="list-style:none">');
var result = myproteins.recordlist('SELECT scop_id, level, parent, name FROM scop_info WHERE pdb_id = '..pdb);
if (#result != 0){
foreach (var temp in result) {let scopcontent..=('<li style="font-size:11px"><a href=#'..temp['scop_id']..' style="text-decoration: none"><span>'..temp['name']..'</span></a></li>');}
let scopcontent..=('</ul>');
foreach (var temp in result){
var scop = temp['scop_id'];
let tempList = {0:[(temp['level']), (temp['name']), (temp['scop_id'])]};
var listLoop = [ 1, 2, 3, 4, 5, 6];
foreach (var num in listLoop) {
var parent = '\''..temp['parent']..'\'';
let temp = myproteins.record('SELECT scop_id, level, parent, name FROM scop_info WHERE scop_id = '..parent);
let tempList..= {(num):[(temp['level']), (temp['name']), (temp['scop_id'])]};
}
let scopcontent..=('<div id ='..scop..'><table border="0" cellpadding="2" style="font-size:11px"><tr><td><hr />');
var listLoop = [6, 5, 4, 3, 2, 1];
var hierarchy = [ 'holder', 'Species', 'Domain', 'Family', 'Superfamily', 'Fold', 'Class']; 
foreach (var i in listLoop) {let scopcontent..=('<ul style="font-size=12px"><b>'..hierarchy[i]..': </b>'..tempList[i][1]..' ['..tempList[i][2]..']'..'</ul>');}
let scopcontent..=('<hr /><b>'..tempList[0][1]..' ['..tempList[0][2]..']'..'</b></td></tr></table></div>');}
let scopcontent..=('</div>');
let scophtml =('<li class="'..'SCOP'..topselect..'"><span><b>'..'SCOP</b>'..dropicon..'</span><ul>'..scopcontent..'</ul></li>');
}
} if (args.uniprotId && args.uniprotId != '') { let navhtml..=stringhtml..uniprothtml..pfamhtml..seedhtml..kegghtml; }
if (args.pdbId && args.pdbId != '') { let navhtml..=cathhtml..scophtml; } 
web.html('<ul id="DWdynnav">'..navhtml..'</ul>');
}}