Template:Heidelberg/safetynet/JS
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');
$(div).empty();
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";
var goredimg =
"
";
var gogreenimg =
"
";
$("#deeprotein_results").empty();
$("#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;
}
}
var gocolor = isEvil ? gored : gogreen;
var goevil = isEvil ? "Potentially Dangerous" : "Safe";
var goimage = document.createElement("img");
goimage.src = isEvil ? goredimg : gogreenimg;
goimage.class = "card-image";
goimage.style = "width: 100%";
var gotitle = document.createElement("h4");
gotitle.class = "card-title";
$(gotitle).text(goevil);
var gocontent = document.createElement("p");
gocontent.class = "card-content";
$(gocontent).text(goterms[idx].name);
var gobody = document.createElement("div");
gobody.class = "card-body";
gobody.appendChild(gotitle);
gobody.appendChild(gocontent);
var gocard = document.createElement("div");
gocard.className = "card";
gocard.style = "border-left: 10px solid; border-color: " + gocolor;
gocard.appendChild(goimage);
gocard.appendChild(gobody);
var gocol = document.createElement("div");
gocol.className = "col-lg-4 col-md-4 col-xs-12";
gocol.appendChild(gocard);
card_section.appendChild(gocol);
}
$("#deep_results").append(card_section);
}
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").on("click", function() {
sequence =
$("#blast_sequence")[0].value.replace(/ /g, "").replace(/\t/g, "");
$("#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();
ctx.ready();
$("#download").on("click", function() {
top.location.href =
"https://static.igem.org/mediawiki/2017/f/fd/T--Heidelberg--2017_DeeProteinWeights.zip";
});
$("#deepweights").on("change", function() {
var status = $("#deep_status");
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").on("click", function() {
var status = $("#deeprotein_status");
status.text("Inferring ...");
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) {
var status = $("#deep_status");
safetynet_create_table(result);
console.log(result);
status.css("cssText", "background-color: green !important");
status.text("Inferred!");
};
}
$(document).ready(function() {
safetyblast_register_handlers(); safetynet_register_handlers();
});
