Difference between revisions of "Template:Heidelberg/safetynet/JS"

Revision as of 16:26, 1 November 2017

function safetyblast_create_table(name, organism, organism_safety,

                                 functionality, functionality_safety, id,
                                 identity, e_value, onkogenes) {

 var table_head = [
   'Name', 'Organism', 'Group', 'Functionality', 'ID', 'Identity', 'E-Value',
   'Onkogenicity'
 ];

 var div = document.getElementById('safety_table');
 var table = document.createElement('table');
 var thead = document.createElement('thead');
 var tbody = document.createElement('tbody');

 var tr_head = document.createElement('tr');
 for (var i = 0; i < 8; i++) {
   var td_head = document.createElement('th');
   td_head.append(document.createTextNode(table_head[i]));
   tr_head.appendChild(td_head);
 }
 thead.appendChild(tr_head);

 for (var j = 0; j < organism.length; j++) {
   var table_body = [];

   table_body[0] = name[j];
   table_body[1] = organism[j];
   table_body[2] = "S" + organism_safety[j].toString();
   table_body[3] = functionality[j];

   table_body[4] = id[j];
   table_body[5] = identity[j];
   table_body[6] = e_value[j];
   table_body[7] = onkogenes[j];

   var tr_body = document.createElement('tr');
   for (var k = 0; k < 8; k++) {
     var td_body = document.createElement('td');

     if (k == 3) {

       var inner_func = table_body[k].split(',');
       for (var w = 0; w < functionality[j].split(',').length; w++) {
         var tr_inner = document.createElement('tr');
         var td_inner = document.createElement('td');
         td_inner.append(document.createTextNode(inner_func[w]));
         tr_inner.appendChild(td_inner);
         td_body.appendChild(tr_inner);
       }

     } else {
       td_body.append(document.createTextNode(table_body[k]));
       if (organism_safety[j] > 1 && k == 2) {
         td_body.style.backgroundColor = 'red';
       } else if (organism_safety[j] <= 1 && k == 2) {
         td_body.style.backgroundColor = 'green';
       } else {
         // Nothing
       }
     }

     if (functionality_safety[j] && k == 3) {
       td_body.style.backgroundColor = 'red';
     } else if (!functionality_safety[j] && k == 3) {
       td_body.style.backgroundColor = 'green';
     } else {
       // Nothing
     }
     tr_body.appendChild(td_body);
   }
   tbody.appendChild(tr_body);
 }

 table.appendChild(thead);
 table.appendChild(tbody);
 table.className = "table table-bordered mdl-shadow--4dp";
 div.appendChild(table);

}

function safetynet_create_table(goterms) {

 return getDatabase().then(function(db) {
   safetynet_create_table_impl(goterms, db);
 });

}

function safetynet_create_table_impl(goterms, database) {

 var gored = "#9d1c20";
 var gogreen = "#009e73";
 $("#deeprotein_results") = document.createElement("div");
 $("#deeprotein_results").id = "deeprotein_results";
 var card_section = document.createElement("section");
 card_section.className = "teaser content equal_height";
 card_section.style = "padding-top: 100px";
 var evilgos = Object.keys(database.functions);
 for (let idx = 0; idx < goterms.length; ++idx) {
   var isEvil = false;
   for (let idy = 0; idy < evilgos.length; ++idy) {
     if (goterms[idx].go === evilgos[idy]) {
       isEvil = true;
       break;
     }
   }
   let gocolor = isEvil ? gored : gogreen;
   let goevil = isEvil ? "Potentially Dangerous" : "Safe";
   let gotitle = document.createElement("h4");
   gotitle.class = "card-title";
   gotitle.text = goevil;
   let gocontent = document.createElement("p");
   gocontent.class = "card-content";
   gocontent.text = goterms[idx].name;
   let gobody = document.createElement("div");
   gobody.class = "card-body";
   gobody.appendChild(gotitle);
   gobody.appendChild(gocontent);
   let gocard = document.createElement("div");
   gocard.className = "card";
   gocard.style = "border-left: 10px solid; border-color: " + gocolor;
   gocard.appendChild(gobody);
   let gocol = document.createElement("div");
   gocol.className = "col-lg-4 col-md-4 col-xs-12";
   gocol.appendChild(gocard);
 }
 card_section.appendChild(gocol);
 $("#deeprotein_results").appendChild(gocol);

}

function safetyblast_register_handlers() {

 $("#fastablast").on("change", function() {
   let file = $("#fastablast")[0].files[0];
   var reader = new FileReader();
   reader.onload = function() {
     var res = this.result.replace(/ /g, "");
     res = res.replace(/\t/g, "");
     if (res.indexOf(">") != -1 || res.indexOf("\n") != -1) {
       var ressplit = res.split("\n");
       res = "";
       for (let idx = 1; idx < ressplit.length; ++idx) {
         res += ressplit[idx];
       }
     }
     console.log(res);
     $("#blast_sequence").val(res);
   };
   reader.readAsText(file);
 });
 $("#blastit").one("click", function() {
   sequence = $("#blast_sequence")[0].value;
   $("#blast_status").text("Starting...");
   $("#blast_status").css("cssText", "background-color: black !important");
   doSafetyQuery(sequence).then(function(result) {
     let nhits = result.hits.length;
     var name = [];
     var organism = [];
     var organism_safety = [];
     var functionality = [];
     var functionality_safety = [];
     var id = [];
     var identity = [];
     var e_value = [];
     var onkogenes = [];
     for (idx = 0; idx < nhits; ++idx) {
       name.push(result.hits[idx].name);
       organism.push(result.matches[idx]);
       organism_safety.push(result.organisms[idx][1]);
       functionality.push(result.functions[idx]);
       functionality_safety.push(result.functionality_safety[idx]);
       id.push(result.hits[idx].id);
       identity.push(result.hits[idx].identity);
       e_value.push(result.hits[idx].evalue);
       onkogenes.push(result.onkogenes[idx]);
     }
     safetyblast_create_table(name, organism, organism_safety, functionality,
                              functionality_safety, id, identity, e_value,
                              onkogenes);
     $("#blast_status").text("Done!");
     $("#blast_status").css("cssText", "background-color: green !important");
   });
 });
 $("#hyperreference2").one("click", function() {
   rid = $("#get_sequence")[0].value;
   doSafetyQueryWithRID(rid).then(function(result) {
     let nhits = result.hits.length;
     var name = [];
     var organism = [];
     var organism_safety = [];
     var functionality = [];
     var functionality_safety = [];
     var id = [];
     var identity = [];
     var e_value = [];
     var onkogenes = [];
     for (idx = 0; idx < nhits; ++idx) {
       name.push(result.hits[idx].name);
       organism.push(result.matches[idx]);
       organism_safety.push(result.organisms[idx][1]);
       functionality.push(result.functions[idx]);
       functionality_safety.push(result.functionality_safety[idx]);
       id.push(result.hits[idx].id);
       identity.push(result.hits[idx].identity);
       e_value.push(result.hits[idx].evalue);
       onkogenes.push(result.onkogenes[idx]);
     }
     safetyblast_create_table(name, organism, organism_safety, functionality,
                              functionality_safety, id, identity, e_value,
                              onkogenes);
   });
 });

}

function safetynet_register_handlers() {

 window.ctx = newDeeProteinContext();
 $("#download").on("click", function() {
   top.location.href =
       "https://static.igem.org/mediawiki/2017/0/0f/DeeProteinWeights.zip";
 });
 $("#deepweights").on("change", function() {
   status.text("Loading Weights ...");
   var file = $("#deepweights")[0].files[0];
   ctx.loadWeightsFromFile(file);
 });
 $("#fastadeep").on("change", function() {
   let file = $("#fastadeep")[0].files[0];
   var reader = new FileReader();
   reader.onload = function() {
     var res = this.result.replace(/ /g, "");
     res = res.replace(/\t/g, "");
     if (res.indexOf(">") != -1 || res.indexOf("\n") != -1) {
       var ressplit = res.split("\n");
       res = "";
       for (let idx = 1; idx < ressplit.length; ++idx) {
         res += ressplit[idx];
       }
     }
     console.log(res);
     $("#deep_sequence").val(res);
   };
   reader.readAsText(file);
 });
 $("#deepit").one("click", function() {
   let string = $("#deep_sequence")[0].value;
   ctx.infer(string);
 });
 ctx.onready = function() {
   var status = $("#deeprotein_status");
   status.css("cssText", "background-color: black !important");
   status.text("Initialized ...");
 };
 ctx.onloadfile = function() {
   var status = $("#deep_status");
   status.css("cssText", "background-color blue !important");
   status.text("Weights loaded ...")
 };
 ctx.oninfer = function(result) {
   safetynet_create_table(result);
   status.css("cssText", "background-color green !important");
   status.text("Inferred!");
 };

}

$(document).ready(function() {

 safetyblast_register_handlers();
 safetynet_register_handlers();

});