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digestion-overview.html
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<!DOCTYPE html>
<html>
<link rel="import" href="nextprot-elements-shared-styles.html">
<link rel="import" href="external-scripts.html">
<link rel="import" href="evidence-item.html">
<link rel="import" href="quality-label.html">
<link rel="import" href="heatmap-table-row.html">
<link rel="import" href="paper-input-search.html">
<!-- <link rel="import" href="../iron-icon/iron-icon.html"> -->
<!-- <script src="../nextprot/src/nextprot-core.js"></script>
<script src="../nextprot/src/nextprot-utils.js"></script> -->
<!-- <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css"> -->
<!-- This is where the top navigation menu breaks, as datatables includes bootstrap-->
<!-- <link rel="stylesheet" href="https://cdn.datatables.net/v/bs-3.3.7/jszip-2.5.0/dt-1.10.18/b-1.5.6/b-flash-1.5.6/b-html5-1.5.6/b-print-1.5.6/sl-1.3.0/datatables.min.css">
<script type="text/javascript"
src="https://cdn.datatables.net/v/bs-3.3.7/jszip-2.5.0/dt-1.10.18/b-1.5.6/b-flash-1.5.6/b-html5-1.5.6/b-print-1.5.6/sl-1.3.0/datatables.min.js"></script> -->
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/pdfmake.min.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/pdfmake/0.1.36/vfs_fonts.js"></script>
<link rel="stylesheet" href="bio-viz-v2/vendor/datatable_customized.css">
<script type="text/javascript" src="bio-viz-v2/vendor/datatable_customized.js"></script>
<!-- slider lib : -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/noUiSlider/14.0.2/nouislider.min.js"></script>
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/noUiSlider/14.0.2/nouislider.min.css">
<style>
#table.dataTable tbody tr.selected,#table.dataTable tbody tr.selected td {
color: white;
background-color:#00780066;
}
.pagination>.active>a,
.pagination>.active>a:focus,
.pagination>.active>a:hover,
.pagination>.active>span,
.pagination>.active>span:focus,
.pagination>.active>span:hover {
background-color: #3FB8AF;
}
.pagination>li>a {
color: #3FB8AF;
}
.pagination>.active>a, .pagination>.active>a:focus, .pagination>.active>a:hover, .pagination>.active>span, .pagination>.active>span:focus, .pagination>.active>span:hover {
z-index: 3;
color: #fff;
cursor: default;
border-color: #3FB8AF;
}
#table_1 tfoot{
display: table-header-group;
}
#table_2 tfoot{
display: table-header-group;
}
th div.form-group, th div.form-group input.form-control{
width:100%;
}
.noUi-horizontal {
height: 14px;
margin-bottom:5px;
}
.noUi-horizontal .noUi-handle {
width: 22px;
height: 22px;
left: -17px;
top: -5px;
}
.noUi-handle:after, .noUi-handle:before {
height: 10px;
width: 1px;
left: 8px;
top: 5px;
}
.noUi-handle:after {
left: 12px;
}
.noUi-horizontal .noUi-tooltip {
-webkit-transform: translate(-50%,0);
transform: translate(-50%,0);
left: 50%;
bottom: 105%;
}
.noUi-tooltip {
display: block;
position: absolute;
border: none;
border-radius: 3px;
background:transparent;
color: #000;
padding: 0px;
text-align: center;
white-space: nowrap;
font-size: 11px;
font-weight: 500;
}
#table_1.dataTable tbody tr.selected td {
color: white;
background-color: #3FB8AF;
}
#table_1.dataTable tbody tr.selected {
color: white;
background-color: transparent;
}
.noUi-base .noUi-handle {
color: black;
display: table;
text-align: center;
}
.noUi-base .noUi-handle::before {
background: transparent;
content: attr(data-value);
display: table-cell;
font-size: 12px;
font-weight: 100;
position: static;
width: 100%;
vertical-align: middle;
}
.noUi-base .noUi-handle::after {
display: none;
}
/* #table_2.dataTable tbody td:nth-child(8) {
text-align:center;
} */
#table_2.dataTable thead th {
vertical-align:top;
}
#table_2.dataTable tbody td {
text-align:center;
}
#table_2.dataTable tbody td:nth-child(2),#table_2.dataTable tbody td:nth-child(3) {
text-align:right;
}
#table_2.dataTable tbody td:nth-child(1) {
max-width: 220px;
word-break: break-all;
text-align: left;
}
table.dataTable.tabledos tbody td:nth-child(1) {
max-width: 300px;
min-width: 200px;
}
table.dataTable.tableuno tbody td:nth-child(1),table.dataTable.tableuno thead th:nth-child(1) {
width:20px;
}
table.dataTable tfoot th{
vertical-align: bottom;
}
table.dataTable.table-condensed>tfoot>tr>th {
padding-right: 5px;
}
table.dataTable.table-condensed>tfoot>tr>th:nth-child(2),table.dataTable.table-condensed>tfoot>tr>th:nth-child(3) {
padding: 0px 20px 5px 10px;
}
.nxtooltip {
position: relative;
display: inline-block;
}
.nxtooltip .nxtooltiptext {
visibility: hidden;
width: 120px;
background-color: black;
color: #fff;
text-align: center;
border-radius: 6px;
padding: 5px 0;
position: absolute;
z-index: 1;
top: -5px;
right: 110%;
}
.nxtooltip .nxtooltiptext::after {
content: " ";
position: absolute;
top: 50%;
left: 100%; /* To the right of the tooltip */
margin-top: -5px;
border-width: 5px;
border-style: solid;
border-color: transparent transparent transparent black;
}
.nxtooltip:hover .nxtooltiptext {
visibility: visible;
}
table.table{
padding:0px;
}
table.table tbody tr td,table.table thead tr th{
height:auto;
}
</style>
<!--
`digestion-overview`
Digestion overview
@demo demo/digestion-overview-demo.html
-->
<dom-module id="digestion-overview">
<style>
:host {
margin: 10px;
}
#isoform-digestion{
margin:10px;
}
h1 {
font-family: "Helvetica Neue";
font-weight: 500;
font-size: 30px;
text-align: center;
margin-bottom: 30px;
}
h3 {
font-family: 'Lato';
font-size: 16px;
font-weight: 700;
margin: 30px 10px;
text-align:left;
}
paper-button.nextprot {
background-color: #C50063;
color: white;
}
a.nextprot-link{
text-decoration: none;
color: #C50063;
}
paper-button.peptideViewLink {
background-color: white;
color: #C50063;
padding:5px 10px;
margin-left: 10px;
}
paper-button iron-icon {
padding-right:5px;
font-size:12px;
}
paper-button {
padding: 5px;
margin-bottom: 10px;
}
paper-input {
--paper-input-container-focus-color: #C50063;
}
.table paper-input{
--paper-input-container-focus-color: #3FB8AF;
--paper-input-container: {
padding:0px;
}
}
a {
text-decoration: none;
color: palevioletred;
}
.form-container {
display: flex;
flex-direction: row;
align-items: flex-end;
align-content: flex-end;
margin: 0px 10px;
}
.form-container paper-input {
margin: 0px 10px;
flex-grow: 1;
}
.table-container {
margin: 10px;
}
paper-spinner-lite.nextprot{
--paper-spinner-color: #C50063;
}
.description{
padding: 0px 100px;
}
.info-box{
display:flex;
margin:10px;
box-shadow:0 2px 10px rgba(0, 0, 0, 0.2);
align-items: center;
}
.info-red{
/* background-color:#FF5722; */
background-color:#D1270A;
}
.info-green{
/* background-color:#00C400; */
background-color:#03b004;
}
.info-blue{
background-color:#2196F3;
}
.info-box>div{
display: inline-block;
color:white;
}
.info-content{
width:90%;
text-align: left;
padding: 7px 10px;
}
.info-icon{
width:80px;
background-color:rgba(0,0,0,0.1);
text-align:center;
height:100%;
}
.info-icon iron-icon{
/* line-height: 70px; */
/* font-size: 45px; */
color:rgba(250,250,250,0.8);
width:80%;
height:100%;
padding:5px;
}
table{
background-color:white;
}
.documentation{
font-size:15px;
font-weight: 300;
text-align:center;
margin:20px 0px;
display:flex;
flex-direction:row;
}
.documentation a{
color:white;
font-weight:500;
}
.documentation>div{
flex:1;
}
</style>
<template>
<div id="isoform-digestion">
<!-- <h1>Protein digestion tool </h1> -->
<div class="description" style="font-size:18px; display:inline-block; text-align: center; font-style: italic; font-weight: 300">
The protein digestion tool allows scientists to determine which enzymes and experimental conditions would yield peptides that could be used to confidently identify a protein of interest. </div>
<div class="documentation">
<div class="info-box info-green">
<div class="info-icon">
<iron-icon icon="icons:description"></iron-icon>
</div>
<div class="info-content">
<span style="font-weight:300">
<a href="/help/protein-digestion"> The documentation of this tool is available on this link.</a>
</span>
</div>
</div>
<div class="info-box info-blue">
<div class="info-icon">
<iron-icon icon="icons:lightbulb-outline"></iron-icon>
</div>
<div class="info-content">
<span style="font-weight:500">neXtProt welcomes feedback and suggestions!</span> <br>
<span>
Please use Contact to request new features, suggest modifications to existing features or report bugs.
</span>
</div>
</div>
</div>
<hr id="separationLine" class="" style="margin:15px 0px 15px;">
<div id="first-form">
<div class="form-container">
<paper-input id="nxIso" style="flex-grow:7"
label="Enter neXtProt isoform accession number, i.e NX_P50222-1" value={{isoformAC}}
always-float-label required auto-validate="true" pattern=".+-[0-9]+$" error-message="This is not a neXtProt isoform">
</paper-input>
</div>
<div class="form-container">
<paper-input id="maxMisCleav" style="flex-grow:3" label="Max miscleavages" type=number min=0 max=3
error-message="Max value is 3"
value="{{maxmissedcleavages}}" always-float-label error-message="NOOOOOOO" auto-validate="true"></paper-input>
<paper-input id="minPepLen" style="flex-grow:1" label="Min peptide length" type=number min=7
error-message="Min value for length is 7"
value="{{minPeptideSize}}" always-float-label auto-validate="true"></paper-input>
<paper-input id="maxPepLen"
style="flex-grow:2" label="Max peptide length" type=number min={{minPeptideSize}} value="{{maxPeptideSize}}"
always-float-label auto-validate="true" error-message="Should be <100 & more than min length" max="100"></paper-input>
<paper-button raised class="custom nextprot" on-click="_resetForm">Reset</paper-button>
<paper-button raised class="custom nextprot" on-click="_digestIsoform">Digest</paper-button>
</div>
</div>
<template is="dom-if" if="[[error_message.length]]">
<div class="info-box info-red">
<div class="info-icon">
<!-- <span class="fa fa-exclamation-circle"></span> -->
<iron-icon icon="icons:error"></iron-icon>
</div>
<div class="info-content">
<span style="font-weight:300">
<span style="font-size:20px;font-weight:500">Impossible to get the data !</span>
<span>[[error_message]]</span>
</span>
</div>
</div>
</template>
<div style="text-align: center;margin-top:50px;"><paper-spinner-lite class="nextprot" id="spinner"></paper-spinner-lite></div>
<template is="dom-if" if="[[digestsByProtease.length]]">
<h3> DIGESTED PEPTIDES FOR EACH PROTEASE :</h3>
<div class="table-container">
<table id="table_1" class="table table-striped table-bordered table-condensed tableuno" width="100%">
</table>
</div>
<div>
<div class="form-container">
<paper-input label="Select a protease" value="{{proteases_selected}}">
<iron-icon icon="icons:search" slot="prefix"></iron-icon>
</paper-input>
<paper-button raised class="custom nextprot" on-click="_peptidesList">Get peptides</paper-button>
</div>
</div>
</template>
<template is="dom-if" if="[[show_protease_results]]">
<div class="table-container">
<table id="table_2" class="table table-striped table-bordered table-condensed tabledos" width="100%">
</table>
<!-- <a href="https://www.nextprot.org/entry/+ this.isoformAC + '/peptides'">See details in peptide view</a> -->
<a class="nextprot-link pull-right" href="https://www.nextprot.org/entry/{{isoformAC}}/peptides" tabindex="-1" target="_blank">
<paper-button raised class="custom peptideViewLink"><iron-icon icon="icons:line-style" slot="prefix"></iron-icon> See Peptide View</paper-button>
</a>
</div>
</div>
</template>
</div>
</template>
<script>
Polymer({
is: 'digestion-overview',
properties: {
nxConfig: {
type: Object,
value: { "env": "dev" }
},
proteases: {
type: Array,
value: []
},
isoformAC: {
type: String,
value: ""
},
maxmissedcleavages: {
type: Number,
value: '0',
},
minPeptideSize: {
type: Number,
value: '7'
},
maxPeptideSize: {
type: Number,
value: '100'
},
digestsByProtease: {
type: Array,
value: [],
},
proteases_selected: {
type: String,
value: ""
},
show_protease_results: {
type:Boolean,
value:false
},
new_pep_map: {
type: Object,
value: {}
},
isoform_seq: {
type: String,
value: ""
},
peptide_mapping: {
type: Array,
value: []
},
error_message:{
type: String,
value: ""
}
},
ready: function () {
this.nx = new Nextprot.Client("digestion", "Calipho Group");
this._initApiClient();
var self = this;
this._npClient.getJSON("/digestion/available-protease-list.json", "true")
.then(function (proteases) {
self.proteases = proteases;
});
// Assigns the isoform accession if exists
if(this.nxConfig.isoform) {
this.isoformAC = this.nxConfig.isoform;
}
},
_initApiClient: function () {
this._npClient = new Nextprot.Client("neXtProt protein overview", "Calipho Group");
this._npClient.updateEnvironment("dev");
if (this.nxConfig.env) {
this._npClient.updateEnvironment(this.nxConfig.env);
}
},
_buildURL: function (isoformAC, maxmissedcleavages, minPeptideSize, maxPeptideSize, protease) {
var urladdress = "/digestion/" + isoformAC + ".json?protease=" + protease + "&minpeplen=" + minPeptideSize + "&maxpeplen=" + maxPeptideSize + "&maxmissedcleavages=" + maxmissedcleavages + "&digestmaturepartsonly=true";
return urladdress;
},
_resetForm: function(){
this.maxmissedcleavages=0;
this.minPeptideSize=7;
this.maxPeptideSize="";
this.isoformAC = "";
this.error_message = "";
this._resetValues();
},
_resetValues: function(){
this.error_message = "";
this.show_protease_results = false;
this.set('digestsByProtease', []);
this.set('proteases_selected', "");
if ( $.fn.dataTable.isDataTable( '#table_1' ) ) {
var table1 = $('#table_1').DataTable();
table1.destroy();
}
if ( $.fn.dataTable.isDataTable( '#table_2' ) ) {
var table2 = $('#table_2').DataTable();
table2.destroy();
}
$("#table_1").html("");
$("#table_2").html("");
},
_validateInput: function(){
if (this.isoformAC === ""){
alert("Please enter a neXtProt isoform accession number, i.e NX_P50222-1");
return false;
}
// if (this.isoformAC.length !== 11 && this.isoformAC!==9){
// alert("Please enter a neXtProt isoform accession number, i.e NX_P50222-1");
// return false;
// }
// if (this.isoformAC[0] !== "N" & this.isoformAC[1] !== "X" & this.isoformAC[3] !== "P" & this.isoformAC[3] !== "Q" & this.isoformAC[3] !== "O" ){
// alert("The isoform accession number is false");
// return false;
// }
if (!this.isoformAC.startsWith("NX_")){
// if (this.isoformAC[0] !=="N" && this.isoformAC[1] !=="X" && this.isoformAC[2] !=="_"){
this.isoformAC='NX_'+this.isoformAC;
}
return true;
},
_validateForm: function(){
var self = this;
var validator = true;
var inputs = ["maxMisCleav","minPepLen","maxPepLen"];
inputs.forEach(function(inp){
var valid = self.$[inp].validate();
if(!valid) validator = false;
})
return validator;
},
_getEntryforPeptidePOST: function (peptides, callback) {
var start = new Date().getTime();
var apiBaseUrl = this.nxConfig.env === "dev" ? "https://dev-api.nextprot.org" : this.nxConfig.env === "alpha" ? "https://alpha-api.nextprot.org" : "https://api.nextprot.org";
console.log("number of peptides submitted for post : ",peptides.length);
// console.log(JSON.stringify(peptides));
$.ajax({
url: apiBaseUrl + "/entries/search/peptide-post.json?no-variant-match=true",
type:"POST",
data:JSON.stringify(peptides),
contentType:"application/json",
success: function(dd){
var end = new Date().getTime();
var time = end - start;
console.log('Execution time: ' + time);
callback(dd);
}
})
},
_digestIsoform: function () {
this._resetValues();
var validator = this._validateForm();
if(!validator){
console.log("validator is NOT HAPPY!! è_é")
return;
}
if (!this._validateInput()){
console.log("if: "+this.isoformAC);
return;
};
this._updateSpinnerStatus(true);
console.log(this.isoformAC);
var full_peptide_list = [];
var proteases = this.proteases;
var self = this;
var protease_data = []
var protease_api_call = []
var peptide_mapping_calls = []
this.nx.getProteinSequence(this.isoformAC)
.then(function(iso_data){
console.log("iso_data",iso_data);
var isoform_selected = iso_data.filter(function(iso){
return iso.isoformAccession === self.isoformAC
})
if(!isoform_selected.length){
self._updateSpinnerStatus(false);
self.set('error_message', "The isoform "+self.isoformAC+" doesn't exist.");
}
else{
self.isoform_seq = isoform_selected[0].sequence;
}
// peptide_mapping_calls.push(this.nx.getProteinSequence(this.isoformAC));
peptide_mapping_calls.push(self.nx.getAnnotationsByCategory(self.isoformAC, "peptide-mapping"));
peptide_mapping_calls.push(self.nx.getAnnotationsByCategory(self.isoformAC, "srm-peptide-mapping"));
Promise.all(peptide_mapping_calls).then(function (peptide_nextprot) {
console.log("peptide_nextprot", peptide_nextprot);
// self.isoform_seq = peptide_nextprot[0].filter(function (iso) { return iso.isoformAccession === self.isoformAC })[0];
var natural_pep = peptide_nextprot[0].annot;
var synthetic_pep = peptide_nextprot[1].annot;
console.log("peptide_natural", natural_pep)
console.log("peptide_synthetic", synthetic_pep)
var peptide_mapping = [];
for (var i = 0; i < natural_pep.length; i++) {
if (natural_pep[i].targetingIsoformsMap.hasOwnProperty(self.isoformAC)) {
var key = natural_pep[i].targetingIsoformsMap[self.isoformAC].firstPosition + "-" + natural_pep[i].targetingIsoformsMap[self.isoformAC].lastPosition;
if (peptide_mapping.hasOwnProperty(key)) {
peptide_mapping[key].natural = true;
}
else {
peptide_mapping[key] = {
"natural": true,
"synthetic": false
}
}
}
}
for (var i = 0; i < synthetic_pep.length; i++) {
if (synthetic_pep[i].targetingIsoformsMap.hasOwnProperty(self.isoformAC)) {
var key = synthetic_pep[i].targetingIsoformsMap[self.isoformAC].firstPosition + "-" + synthetic_pep[i].targetingIsoformsMap[self.isoformAC].lastPosition;
if (peptide_mapping.hasOwnProperty(key)) {
peptide_mapping[key].synthetic = true;
}
else {
peptide_mapping[key] = {
"natural": false,
"synthetic": true
}
}
}
}
self.set('peptide_mapping', peptide_mapping);
console.log("peptide_mapping", peptide_mapping);
for (var i = 0; i < proteases.length; i++) {
var protease = proteases[i];
var url = self._buildURL(self.isoformAC, self.maxmissedcleavages, self.minPeptideSize, self.maxPeptideSize, protease);
protease_api_call.push(self._npClient.getJSON(url, true));
}
Promise.all(protease_api_call).then(function (results) {
for (var i = 0; i < proteases.length; i++) {
var digests = results[i];
var peptides_result = digests.map(function(d){return d.sequence});
var pepcount = peptides_result.length;
protease_data.push(
{
"name": proteases[i],
"peptide_list": digests,
"peptide_count": pepcount
});
full_peptide_list = full_peptide_list.concat(peptides_result)
}
full_peptide_list = full_peptide_list.filter(function (item, pos, self) {
return self.indexOf(item) == pos;
})
console.log('Peptide list submitted to pepx : ', full_peptide_list.length);
// var peplist_to_str = full_peptide_list.join(",");
// console.log("peplist_to_str",peplist_to_str);
self._getEntryforPeptidePOST(full_peptide_list, function(data){
console.log("Entry for peptide", data);
self.new_pep_map = self._createPeptideMap(data);
console.log('new_pep_map', self.new_pep_map)
for (var i = 0; i < protease_data.length; i++) {
var uniq_count = 0;
protease_data[i].peptide_list.forEach(function (peptide) {
if (self.new_pep_map[peptide.sequence].uniqueness !== "NOT_UNIQUE") uniq_count += 1;
})
protease_data[i]['unique_peptide_count'] = uniq_count;
}
console.log("Proteases with list of peptides and counts: ", protease_data);
self.set('digestsByProtease', protease_data);
Polymer.RenderStatus.afterNextRender(self, function() {
console.log("protease_data", protease_data)
self._updateSpinnerStatus(false);
var d1_table = $('#table_1').DataTable({
destroy:true,
retreive:true,
orderCellsTop: true,
fixedHeader: true,
dom: "<'row firstHeadTable'<'col-md-12'B>>" +
"<'row secondHeadTable'<'col-sm-3 col-md-4'i><'col-sm-6 pull-right'f>>" +
"<'row no_overmargin'<'col-sm-12 table_overflow'tr>>" +
"<'row no_overmargin'<'col-sm-3 col-md-2'l><'col-sm-9 pull-right pageTable'p>>",
buttons: [
'copy', 'csv', 'excel', 'print'
],
deferRender: true,
processing: true,
scrollY: 300,
scrollCollapse: true,
paging: false,
data: protease_data,
columns: [
{ defaultContent: '' },
{ data: 'name', title: 'Protease name', className: "uniqueClassName"},
{ data: 'peptide_count', title: 'Peptide count', className: "uniqueClassName"},
{ data: 'unique_peptide_count', title: 'Unique peptide count',className: "uniqueClassName" }
],
columnDefs: [
{ width: 10, targets: 0 },
{
orderable: false,
className: 'select-checkbox',
targets: 0
}],
select: {
style: 'single'
},
order: [[3, 'desc']]
});
d1_table
.on('select', function (e, dt, type, indexes) {
var selected_rows = d1_table.rows({ selected: true });
self._updateProteaseSelected(selected_rows[0]);
})
.on('deselect', function (e, dt, type, indexes) {
var selected_rows = d1_table.rows({ selected: true });
self._updateProteaseSelected(selected_rows[0]);
});
});
});
})
})
})
.catch(function(err){
// console.log("iso_data ERROR message: ",err.responseJSON.message);
console.log("err",err);
self.set('error_message', err.responseJSON.message);
self._updateSpinnerStatus(false);
})
},
_updateProteaseSelected: function (protease_indexes) {
var self = this;
var proteases_list = protease_indexes.map(function(elem){
return self.digestsByProtease[elem]['name']
})
this.set('proteases_selected',proteases_list);
this._clearPeptideTable();
},
_clearPeptideTable: function(){
if ( $.fn.dataTable.isDataTable( '#table_2' ) ) {
var table2 = $('#table_2').DataTable();
table2.destroy();
}
$('#table_2').html("");
this.show_protease_results = false;
},
_createPeptideMap: function (data) {
var pepMap = {}
data.forEach(function (el) {
el.annotationsByCategory["pepx-virtual-annotation"].forEach(function (pep) {
if (!pepMap.hasOwnProperty(pep.cvTermName)) {
var uniqueness = pep.properties.filter(function (pp) { return pp.name === "peptide unicity" })[0].value;
pepMap[pep.cvTermName] = {
'entries': [el.uniqueName],
'uniqueness': uniqueness
}
}
else {
pepMap[pep.cvTermName].entries.push(el.uniqueName);
}
})
});
return pepMap;
},
_diffArrays: function(a,b){
return a.filter(function(i){return b.indexOf(i) < 0;});
},
_miscleavageComputation: function(data, protease, callback){
var self = this;
var protease_api_call = [];
var temp_data = [];
var new_data = [];
for (var miscleavage = 0; miscleavage < this.maxmissedcleavages; miscleavage++) {
var url = self._buildURL(this.isoformAC, miscleavage, this.minPeptideSize, this.maxPeptideSize, protease);
protease_api_call.push(this._npClient.getJSON(url, true));
}
Promise.all(protease_api_call).then(function (results) {
results.forEach(function(res,index){
var diff_array = self._diffArrays(res, temp_data);
diff_array.forEach(function(pep){
new_data.push({
"sequence":pep,
"missed_cleavages": index
})
})
temp_data = res;
})
var diff_array = self._diffArrays(data, temp_data);
diff_array.forEach(function(pep){
new_data.push({
"sequence":pep,
"missed_cleavages": self.maxmissedcleavages
})
})
callback(new_data);
})
},
_peptidesList: function () {
this._clearPeptideTable();
this.show_protease_results = true;
var self = this;
console.log("Protease name :", this.proteases_selected);
console.log("Entry name :", this.isoformAC);
var results = this.digestsByProtease.filter(
(a) => a.name == this.proteases_selected)[0].peptide_list;
console.log("results", results);
var pep_data = results.map(function(r){return {
"sequence": r.sequence,
"missed_cleavages" : r.producedWithMiscleavageCount
}})
console.log("pep_data",pep_data);
// this._miscleavageComputation(results, this.proteases_selected,function(pep_data){
// var pep_data = this._getPeptidesPosition(results);
for (var i = 0; i < pep_data.length; i++) {
var position_first = self.isoform_seq.indexOf(pep_data[i].sequence) + 1;
var position_last = position_first + pep_data[i].sequence.length - 1;
pep_data[i]["position"]= position_first + "-" + position_last;
// pep_data[i]["link"]= this.peptide_mapping.hasOwnProperty(pep_data[i].position) && this.peptide_mapping[pep_data[i].position].natural ? ('See details in peptide view <img src="../np-x.png">'.link('https://www.nextprot.org/entry/'+ this.isoformAC + '/peptides')) : this.peptide_mapping.hasOwnProperty(pep_data[i].position) && this.peptide_mapping[pep_data[i].position].synthetic ? "See details in peptide view".link('https://www.nextprot.org/entry/'+ this.isoformAC + '/peptides'):"";
// pep_data[i]["link"]= (self.peptide_mapping.hasOwnProperty(pep_data[i].position) && self.peptide_mapping[pep_data[i].position].natural) || (self.peptide_mapping.hasOwnProperty(pep_data[i].position) && self.peptide_mapping[pep_data[i].position].synthetic) ? '<a class="nxtooltip" href="https://www.nextprot.org/entry/'+ self.isoformAC + '/peptides"><img src="../np-x.png" height="20" width="18"><span class="nxtooltiptext">See details in peptide view</span></a>' : "";
pep_data[i]["length"] = pep_data[i].sequence.length;
pep_data[i]["uniqueness"] = self.new_pep_map[pep_data[i].sequence].uniqueness === "UNIQUE" ? "Yes" : self.new_pep_map[pep_data[i].sequence].uniqueness === "PSEUDO_UNIQUE" ? "Yes (pseudo-unique)" : "No";
pep_data[i]["natural"] = self.peptide_mapping.hasOwnProperty(pep_data[i].position) && self.peptide_mapping[pep_data[i].position].natural ? "Yes" : "No";
pep_data[i]["synthetic"] = self.peptide_mapping.hasOwnProperty(pep_data[i].position) && self.peptide_mapping[pep_data[i].position].synthetic ? "Yes" : "No";
}
console.log("result of getpeptidePosition", pep_data);
function sortNumber(a, b) {
return a - b;
}
var lengthArray = pep_data.map(function(p){return parseInt(p["length"])}).sort(sortNumber);
console.log("lengthArray",lengthArray);
var pepMin = lengthArray[0];
var pepMax = lengthArray[lengthArray.length-1];
var missesdCleavageMax = 0;
pep_data.forEach((peptide) => {
if(missesdCleavageMax < peptide.missed_cleavages) {
missesdCleavageMax = peptide.missed_cleavages;
}
})
var length_range = [pepMin,pepMax];
var missCleav_range = [0,3];
var d2_table;
$.fn.dataTable.ext.search.pop();
$.fn.dataTable.ext.search.pop();
$.fn.dataTable.ext.search.push(
function( settings, data, dataIndex ) {
if(settings.nTable.getAttribute('id') === "table_2" ){
var min = parseFloat(length_range[0]);
var max = parseFloat(length_range[1]);
var col = parseFloat( data[1] ) || 0; // data[number] = column number
if ( ( isNaN( min ) && isNaN( max ) ) ||
( isNaN( min ) && col <= max ) ||
( min <= col && isNaN( max ) ) ||
( min <= col && col <= max ) )
{
return true;
}
return false;
}
else {
return true;
}
}
)
$.fn.dataTable.ext.search.push(
function( settings, data, dataIndex ) {
if(settings.nTable.getAttribute('id') === "table_2" ){
var min = parseFloat(missCleav_range[0]);
var max = parseFloat(missCleav_range[1]);
var col = parseFloat( data[2] ) || 0; // data[number] = column number
if ( ( isNaN( min ) && isNaN( max ) ) ||
( isNaN( min ) && col <= max ) ||
( min <= col && isNaN( max ) ) ||
( min <= col && col <= max ) )
{
return true;
}
return false;
}
else {
return true;
}
}
)
Polymer.RenderStatus.afterNextRender(self, function() {
$('#table_2').html(
"<thead></thead><tfoot><tr>"+
"<th></th>"+
"<th></th>"+
"<th></th>"+
"<th></th>"+
"<th></th>"+
"<th></th>"+
"<th></th>"+
// "<th></th>"+
"</tr></tfoot>"
);
$('#table_2 tfoot tr th').each( function (i) {
if(i !== 1 && i!==2 && i!==3){
var title = $(this).text();
$(this).html("");
var dynamicEl = document.createElement("paper-input-search");
dynamicEl.setAttribute("iconinput", "icons:search");
dynamicEl.setAttribute("text_top", "Filter");
Polymer.dom(this).appendChild(dynamicEl);
$( 'input', this ).on( 'keyup change', function () {
if ( d2_table.column(i).search() !== this.value ) {
d2_table
.column(i)
.search( this.value )
.draw();
}
} );
}
else if(i == 1){
if(pepMin !== pepMax){
$(this).html('<div id=container><div id=slider1></div></div>');
var slider = $('#slider1');
noUiSlider.create(slider[0], {
start: [pepMin, pepMax],
range: { min: pepMin, max: pepMax },
tooltips: [true,true],
step: 1,
connect: true,
format: {
from: function(value) {
return parseInt(value);
},
to: function(value) {
return parseInt(value);
}
}