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Template:TestClassification

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    {{ 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>');
    }}

     

     

     

     

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