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triple-viewer.html
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triple-viewer.html
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<link rel="import" href="evidence-item.html">
<link rel="import" href="quality-label.html">
<link rel="import" href="nextprot-elements-shared-styles.html">
<link rel="import" href="external-scripts.html">
<link rel="import" href="feature-table.html">
<!--
<script src="../jquery/dist/jquery.js"></script>
<script src="../bootstrap/dist/js/bootstrap.js"></script>
-->
<!--
`triple-viewer`
Complex element joining nextprot feature viewer, feature table and sequence viewer
@demo demo/triple-viewer-demo.html
-->
<dom-module id="triple-viewer">
<template>
<style is="custom-style" include="nextprot-elements-shared-styles">
:host {
display: block;
}
evidence-item {
padding: 8px 0 0 0;
margin: 5px 40px;
}
td[hidden] {
display: none;
}
.filter-block>div{
box-shadow: 0px 2px 3px -1px rgba(0,0,0,0.15);
margin-top:15px;
display: inline-block;
}
.filter-heading{
display:inline-block;
background:#F8F8F8;
padding:0px 15px;
height:100%;
border-color:#F8F8F8;
border:1px #ddd solid;
vertical-align: middle;
border-top-left-radius: 2px;
border-bottom-left-radius: 2px;
}
.filter-heading .fa{
margin-right:3px;
}
.filter-heading h5{
display: inline-block;
color: #777;
padding: 0px;
height: 30px;
margin: 0px;
line-height: 30px;
}
.filter-body{
display:inline-block;
background:#F8F8F8;
padding:0px 15px 0px 0px;
height:32px;
border-color:#F8F8F8;
border:1px #ddd solid;
margin-left:-1px;
vertical-align: middle;
border-top-right-radius: 2px;
border-bottom-right-radius: 2px;
}
#filtering{
margin-right:10px;
font-size:12px;
}
#allFilters{
border:0px;
height:30px;
border-right:1px solid #ddd;
border-radius:0px;
color: #337ab7;
text-decoration: underline;
}
.filter-box{
position: relative;
display: inline-block;
padding-left: 10px;
margin-bottom: 0;
font-weight: 400;
vertical-align: middle;
cursor: pointer;
}
.filter-box input{
margin-right:5px;
}
.header-help:hover{
text-decoration: none;
cursor:pointer;
}
span.label-info {
background: #5bc0de;
}
#featuresTable {
font-size:11px;
background:#fff;
padding:0px;
height:525px;
/* border: 1px solid #cfd9db;*/
border-radius:4px;
margin:10px 0px;
}
#featuresTable .variant-description{
color:#00C500;
}
table#featTable>tbody>tr>th {
padding: 0 8px;
}
table#featTable>tbody>tr:first-of-type + tr {
border-top: none;
}
table#featTable>tbody>tr {
border-top: 1px solid #ddd;
border-bottom: none;
}
table#featTable>tbody>tr>td {
border: none;
}
table#featTable>tbody>tr .table-row-evidence {
padding: 0 16px 0 8px;
}
#seqViewer ::content > .seqHeader {
width: 100%;
}
#seqViewer ::content > .seqHeader > div {
display: inline-block;
vertical-align: top;
text-align: center;
width: 25%;
}
#seqViewer {
background:#fff;
padding:5px 15px;
height:525px;
/*
border: 1px solid #cfd9db;
border-radius:4px;
*/
}
.seqHeader{
margin-bottom:5px;
border-bottom:1px solid #E7EAEC;
height:45px;
}
.seqHeader>div{
display: inline-block;
margin:10px;
}
#seqViewer .seqInfos{
display: inline-block;
vertical-align: middle;
font-size:11px;
text-align: center;
float:right;
margin: 10px 5px 0px;
}
#seqViewer .seqInfos>.seqLabel{
font-weight: 900;
color:#777;
}
#seqViewer .seqInfos>.seqValue{
color:white;
padding:3px 5px;
text-align: center;
border-radius:3px;
float:right;
}
#seqViewer .seqIso>.seqValue{
background-color:#23c6c8;
}
#seqViewer .seqAALength>.seqValue{
background-color:#33C59E;
font-weight:700;
}
#seqViewer .seqMass>.seqValue{
background-color:#f8ac59;
}
#seqViewer .seqpI>.seqValue{
background-color:#92896F;
}
#evidence-row {
display: table-row;
}
.evidenceNumber {
background: #7CBA0F;
padding: 4px 8px;
border-radius: 2px;
color: white;
vertical-align: top;
cursor: pointer;
}
.filter-block {
margin:0px 20px;
float:left;
}
.tableHighlight {
background-color:rgba(197, 0, 99, 0.1) !important;
}
.tableHighlight td{
background-color:rgba(197, 0, 99, 0.1) !important;
}
.right-block {
margin:10px 0px;
padding-right:0px;
}
.sequenceRangeSpan {
line-height: 0.8;
vertical-align:top;
}
.center {
position: absolute;
margin: 45px 40%;
}
paper-spinner-lite {
--paper-spinner-stroke-width: 3px;
}
#featTableSpinner {
height: 45px;
width: 45px;
}
#featViewerSpinner {
position: absolute;
margin-left: 320px;
margin-top: 16px;
height: 32px;
width: 32px;
}
</style>
<div class="row">
<div id="featureViewer">
<template is="dom-if" if="[[_ifActiveFiltering(activeFiltering)]]">
<div class="filter-block row">
<div class="filter-heading">
<span class="fa fa-filter"></span>
<h5>FILTER</h5>
</div>
<div class="filter-body">
<div id="filtering" class="all-filters">
<button class="btn btn-default btn-sm" id="allFilters" on-tap="_filterAll">All/None</button>
<template is="dom-repeat" items="[[_toArray(activeFiltering)]]" as="filter">
<label class="filter-box" on-mouseover="_highlightCategories" on-mouseout="_dimCategories">
<input type="checkbox" id=[[filter.name]] value="option1" on-change="_toggleFiltering" checked>[[filter.value]]
</label>
</template>
</div>
</div>
</div>
</template>
<paper-spinner-lite id="featViewerSpinner" class="size"></paper-spinner-lite>
</div>
</div>
<div class="row">
<div id="featuresTable">
<feature-table id="featTable" all-features="[[featuresForTable]]">
</feature-table>
</div>
<template is="dom-if" if="[[!hideSequenceViewer]]">
<div class="col-md-6 right-block">
<div id="seqViewer"></div>
</div>
</template>
</div>
</template>
<script>
Polymer({
is: 'triple-viewer',
properties: {
nxConfig: {
type: Object,
value: {},
observer: "reload"
},
nxEntryData: {
type: String,
value: ""
},
lazyLoading: {
type: Boolean,
value: false
},
isoName: {
type: String,
notify: true,
observer: "isoformChange"
},
selection: {
type: Object,
notify: true
},
featuresByIsoform: {
type: Array,
value: [],
notify: true
},
featureList: {
type: Array,
value: [
{
"APIRef": "sequence",
"metadata": {"name": "Sequence"}
}]
},
featuresForViewer: {
type: Array,
value: []
},
featuresByGroup:{
type: Object,
value:{}
},
featuresForTable: {
type:Array,
value:[],
notify:true
},
filterOptions: {
type: Array,
value: {
"none": true
}
},
activeFiltering: {
type: Array,
value: {}
},
hideSequenceViewer: {
type: Boolean,
value: false
},
count: {
type: Number,
notify: true
},
featureViewerReady: {
type: Boolean,
reflectToAttribute: true,
notify: true
}
},
attached: function() {
if(this.lazyLoading && Object.getOwnPropertyNames(JSON.parse(decodeURIComponent(this.nxEntryData))).length == 0) {
return;
}
this.nx = new Nextprot.Client("neXtprot triple viewer", "Calipho Group");
this.nxEntry = this.nx.getEntryName(this.nxConfig.entry);
if(!this.isoName) this.isoName = this.nxEntry+"-1";
var self=this;
Promise.all(self._getFeaturesByView())
.then(function (rawData) {
if(self.lazyLoading) {
let entryData = JSON.parse(decodeURIComponent(self.nxEntryData));
rawData.unshift(entryData.isoforms.isoforms);
}
self.rawData = rawData;
self.sequences = rawData[0];
self._getMetadataByView();
self._getFeaturesByIsoform();
var count = 0;
for (var i in self.rawData){
if (self.rawData[i].annot) count += self.rawData[i].annot.length;
}
self.count = count;
if(self.count){
self.reloadSVG();
self._addFiltering();
// self.$.featTableSpinner.active = false;
}
self.featureViewerReady = true;
//self.$.featViewerSpinner.active = false;
if (self.hideSequenceViewer) self.$$("#featuresTable").classList.add("col-md-12");
else self.$$("#featuresTable").classList.add("col-md-6")
});
},
isoformChange: function(){
this.featuresByGroup = {};
this.reloadSVG();
},
reloadSVG: function(){
var self = this;
Polymer.RenderStatus.afterNextRender(this.$.featureViewer, function() {
// self.$.featTableSpinner.active = true;
$("#featureViewer svg").remove();
if(self.featuresByIsoform.length) {
self._fillTable();
self.hidden=false;
self._renderFeatureViewer();
self._addFeatures();
if ($(".zoomUnit").length) $(".zoomUnit").text("1");
d3.selectAll('div.selectedRect').remove();
self.eventTV();
}else{
self.hidden=true;
}
// self.$.featTableSpinner.active = false;
});
},
reload: function(){
if (this.rawData) {
this._getFeaturesByIsoform();
this.reloadSVG();
}
},
_getFeaturesByIsoform: function(){
this.featuresForViewer = [];
// this.featuresByIsoform = [];
var featsByIso = [];
this.isoforms = this.rawData[0];
var isoLengths = {};
this.isoforms.forEach(function(i){
isoLengths[i.uniqueName] = i.sequenceLength;
})
for (var i=1; i<this.rawData.length-1;i++) {
var feat = NXUtils.convertMappingsToIsoformMap(this.rawData[i],this.metaData[i].name.replace('.',''),this.metaData[i].filter, "");
if (this.nxConfig.goldOnly) feat = this._filterGoldForViewer(feat);
featForViewer = NXViewerUtils.convertNXAnnotations(feat,this.metaData[i],isoLengths);
let frequencyFeature = {};
let frequencyMinValues = {};
if(this.rawData[i].annot.length > 0 ) {
if (this.rawData[i].annot[0].apicategory === 'VARIANT') {
// Get target isoform details
this.rawData[i].annot.map(function (variant) {
let variantAnnotation = variant;
// Add isoforms available
Object.keys(variant.targetingIsoformsMap).forEach(function(isoform) {
if(!(isoform in frequencyFeature)) {
frequencyFeature[isoform] = [];
}
let frequencyEvidence = variant.evidences.filter(function (evidence) {
return (evidence.assignedBy === 'gnomAD');
});
if(frequencyEvidence.length > 0 ) {
frequencyEvidence = frequencyEvidence[0];
let frequency = Number(frequencyEvidence.properties["allele frequency"]);
// Check if the variant has isoform specific position
let variantFrequencyDetails = {};
variantFrequencyDetails["x"] = variant.targetingIsoformsMap[isoform]['firstPosition'];
variantFrequencyDetails["y"] = frequency;
variantFrequencyDetails["id"] = "FREQUENCY_Variant_"+ variantFrequencyDetails["x"] + "_" + variantFrequencyDetails["x"] + "_" + variantAnnotation.uniqueName;
variantFrequencyDetails["category"] = 'Frequency';
let variantDescription = variantAnnotation.variant.original + " → " + variantAnnotation.variant.variant ;
variantFrequencyDetails["description"] = "<span>"+ variant.targetingIsoformsMap[isoform]['firstPosition'] + "<br/>" + variantDescription +"<br/>"+ frequency +"</span>";
frequencyFeature[isoform].push(variantFrequencyDetails);
if(isoform in frequencyMinValues) {
if(frequencyMinValues[isoform] > frequency) {
frequencyMinValues[isoform] = frequency;
}
} else {
frequencyMinValues[isoform] = frequency;
}
}
});
});
}
Object.keys(frequencyFeature).forEach(function(isoform) {
frequencyFeature[isoform].forEach(function(variant) {
variant['y'] = (-Math.log10(frequencyMinValues[isoform])) + 0.2 + Math.log10(variant['y'])
})
});
if(Object.keys(frequencyFeature).length !== 0 ){
featsByIso.push(frequencyFeature);
let frequencyFeatureForViewer = {};
Object.keys(frequencyFeature).forEach(function(key) {
let x = {
className: "freq",
color: "#B3B3C2",
name: "Frequency (Log)",
type: "bar",
filter: 'Frequency',
data: frequencyFeature[key]
}
frequencyFeatureForViewer[key] = x;
});
this.featuresForViewer.push(frequencyFeatureForViewer);
}
this.featuresForViewer.push(featForViewer);
}
featsByIso.push(feat);
}
this.notifyPath("featuresByIsoform", featsByIso);
},
_addDiseaseRelatedVariants: function (variants) {
var calls = [];
calls.push(variants)
calls.push(this.nx.getAnnotationsByCategory(this.nxEntry, "disease-related-variant"))
return Promise.all(calls)
.then(function (rawData) {
var variants = rawData[0];
var diseaseRelatedVariants = rawData[1];
$.extend(variants.contexts, diseaseRelatedVariants.contexts);
// Create utils maps
var variantHashToDrvAnnots = {};
var diseasesHashToDiseaseAnnot = {};
for (let annotKey in diseaseRelatedVariants.annot) {
let a = diseaseRelatedVariants.annot[annotKey];
if (a.apicategory === "DISEASE_RELATED_VARIANT") {
var subjects = a.subjectComponents;
for (let subjectKey in subjects) {
var s = subjects[subjectKey];
variantHashToDrvAnnots[s] = variantHashToDrvAnnots[s] || [];
variantHashToDrvAnnots[s].push(a);
}
} else if (a.apicategory === "DISEASE") {
diseasesHashToDiseaseAnnot[a.annotationHash] = a;
}
}
for (let variantsKey in variants.annot) {
let vAnnot = variants.annot[variantsKey];
if (vAnnot.annotationHash && variantHashToDrvAnnots[vAnnot.annotationHash]) {
let drvAnnots = variantHashToDrvAnnots[vAnnot.annotationHash];
let drvEvidenceNames = new Set();
for (let drvAnnotKey in drvAnnots) {
let drvAnnot = drvAnnots[drvAnnotKey];
let diseaseAnnot = diseasesHashToDiseaseAnnot[drvAnnot.bioObject.annotationHash];
let diseaseDesc = "[" + diseaseAnnot.cvTermName + ":" + diseaseAnnot.cvApiName + ":" + diseaseAnnot.cvTermAccessionCode + "]";
var hasNegEv = false;
var hasNotNegEv = false;
// Each evidences in disease-related-variant (drv) annot has unique similar ev. in variant annot
// (same publication and same assignedBy without experimental context).
// But an evidence in variant annot has several similar ev. in drv annot due to several exp. contexts.
// So we put drv evidences in variant annot and remove similar ev later.
// which are in variant annot if it's the same qualityQualifier.
let evidenceToAdd;
for (const vEvidenceKey in vAnnot.evidences) {
let vEvidence = vAnnot.evidences[vEvidenceKey];
for (let drvEvidenceKey in drvAnnot.evidences) {
let drvEvidence = drvAnnot.evidences[drvEvidenceKey];
drvEvidence.diseaseRelatedVariant = {};
if (drvEvidence.negativeEvidence) {
hasNegEv = true;
drvEvidence.diseaseRelatedVariant.isNegative = true;
drvEvidence.diseaseRelatedVariant.relation = "causes";
} else {
hasNotNegEv = true;
drvEvidence.diseaseRelatedVariant.isNegative = false;
drvEvidence.diseaseRelatedVariant.relation = "Causes" ;
}
drvEvidence.diseaseRelatedVariant.name = diseaseAnnot.cvTermName;
drvEvidence.diseaseRelatedVariant.accession = diseaseAnnot.cvTermAccessionCode;
drvEvidence.diseaseRelatedVariant.experimentalContextId = drvEvidence.experimentalContextId;
drvEvidenceNames.add(JSON.stringify({
name: diseaseAnnot.cvTermName,
accession: diseaseAnnot.cvTermAccessionCode
}));
if (vEvidence.resourceId === drvEvidence.resourceId && vEvidence.assignedBy === drvEvidence.assignedBy) {
evidenceToAdd = drvEvidence;
}
}
}
if(evidenceToAdd) {
let evidenceNames = [];
drvEvidenceNames.forEach(function(evidence) {
evidenceNames.push(JSON.parse(evidence));
});
evidenceToAdd.diseaseRelatedVariant.names = evidenceNames;
vAnnot.evidences.push(evidenceToAdd);
}
if (hasNotNegEv) {
let suffix = "Causes " + diseaseDesc;
if (vAnnot.description) {
vAnnot.description = vAnnot.description + "; " + suffix;
} else {
vAnnot.description = suffix;
}
}
if (hasNegEv) {
let suffix = "Not causes " + diseaseDesc;
if (vAnnot.description) {
if (hasNotNegEv) {
vAnnot.description += " ";
}
vAnnot.description += "; " + suffix;
} else {
vAnnot.description = suffix;
}
}
if (hasNegEv && hasNotNegEv) {
vAnnot.conflict = true;
}
}
}
// NEXTPROT-2230 we remove similar evidences: same publication, same assignedBy,
// without experimental context (not "found in"), not disease releated variant
if (vAnnot.evidences.length < 2) {
continue;
}
let vEvidenceIdsToRemove = [];
for (let vEvidenceKey1 in vAnnot.evidences) {
let vEvidence1 = vAnnot.evidences[vEvidenceKey1];
for (let vEvidenceKey2 in vAnnot.evidences) {
let vEvidence2 = vAnnot.evidences[vEvidenceKey2];
if ( vEvidenceKey1 !== vEvidenceKey2
&& vEvidence1.experimentalContextId === null // we don't remove evidences with EC
&& vEvidence1.diseaseRelatedVariant === undefined // we don't remove disease-related-variant evidences
&& vEvidence1.resourceId === vEvidence2.resourceId
&& vEvidence1.assignedBy === vEvidence2.assignedBy
&& vEvidence1.qualityQualifier === vEvidence2.qualityQualifier) {
vEvidenceIdsToRemove.push(vEvidence1.evidenceId);
}
}
}
if (vEvidenceIdsToRemove) {
vAnnot.evidences = vAnnot.evidences.filter(e => !vEvidenceIdsToRemove.includes(e.evidenceId));
}
}
return variants;
});
},
_getFeaturesByView: function() {
var featuresForViewer = [];
for (var feat in this.featureList) {
switch (this.featureList[feat].APIRef) {
case "sequence":
if(!this.lazyLoading){
featuresForViewer.push(this.nx.getProteinSequence(this.nxEntry));
}
break;
case "antibody":
featuresForViewer.push(this.nx.getAntibody(this.nxEntry));
break;
case "isoform-mapping":
featuresForViewer.push(this.nx.getIsoformMapping(this.nxEntry));
break;
case "variant":
featuresForViewer.push(this._addDiseaseRelatedVariants(this.nx.getAnnotationsByCategory(this.nxEntry, this.featureList[feat].APIRef)));
break;
case "variant-medical":
featuresForViewer.push(this._addDiseaseRelatedVariants(this.nx.getAnnotationsWithProperty(this.nxEntry, "variant", "disease-related", true)));
break;
case "miscellaneous-region-interactions":
featuresForViewer.push(this.nx.getAnnotationsWithProperty(this.nxEntry, "miscellaneous-region", "interaction-related", true));
break;
default:
featuresForViewer.push(this.nx.getAnnotationsByCategory(this.nxEntry, this.featureList[feat].APIRef));
break;
}
}
return featuresForViewer;
},
_getMetadataByView: function() {
this.metaData = [];
for (var i = 0; i < this.featureList.length - 1; i++) {
this.metaData.push(this.featureList[i].metadata);
}
},
_addFiltering: function() {
var activeFiltering = {};
for (var i=0;i<this.featuresForViewer.length;i++) {
if (Object.keys(this.featuresForViewer[i]).length !== 0) {
var filter = this.featuresForViewer[i][Object.keys(this.featuresForViewer[i])[0]].filter;
if (filter !== "none" && (!activeFiltering[filter.split(" ").join("_")])) {
var filterMin = filter.split(" ").join("_");
activeFiltering[filterMin]=filter;
this.filterOptions[filterMin]=true;
}
}
}
if (this._toArray(activeFiltering).length>1) this.activeFiltering = activeFiltering;
},
_filterGoldForViewer: function(features){
var categories = Object.keys(features);
var filteredFeatures = {};
for (var i in categories) {
for (var j in features[categories[i]]) {
if(features[categories[i]][j].quality==="gold") {
if(Object.keys(filteredFeatures).indexOf(categories[i])===-1) filteredFeatures[categories[i]] = [];
filteredFeatures[categories[i]].push(features[categories[i]][j]);
}
}
}
return filteredFeatures;
},
_renderFeatureViewer: function(){
var self=this;
// console.log(this.sequences);
// var seqs = $.map(this.sequences.isoforms, function(s){return s})
// seqs.forEach(function (o) {
this.sequences.forEach(function (o) {
if (o.uniqueName === self.isoName) {
self.currentSeq = o.sequence;
self.ft = new FeatureViewer(self.currentSeq, "#featureViewer", {
showAxis: true,
showSequence: true,
brushActive: true,
toolbar:true,
bubbleHelp:true,
buttonDownload:true,
unit:"aa",
zoomMax:10,
toolbarTemplate: 2,
positionWithoutLetter:true,
tooltipColor:"black"
});
$(".header-help").hover(function(){
$(this).css("text-decoration","none");
$(this).css("cursor","pointer");
})
if (!self.hideSequenceViewer) self._renderSequenceViewer(o);
}
});
},
_renderSequenceViewer: function(sequenceObject){
this.seqView = new Sequence(this.currentSeq, this.isoName);
//TODO CHANGE BELOW API URL HARDOCODE
console.warn("CHANGE BELOW API URL WITH ENVIORNMENT");
this.seqView.render('#seqViewer', {
'showLineNumbers': true,
'wrapAminoAcids': true,
'charsPerLine': 50,
'search':true,
'toolbar':true,
'fasta': true,
'apiURL': (this.nx) ? this.nx.getApiBaseUrl():"https://api.nextprot.org",
'digestion': true,
'header':{
'display':false,
'searchInTitle': false,
'showCpl':false,
'badgeWithUnit':true
}
});
//Customize Sequence viewer - raw version
var seqHeader = document.createElement("div");
seqHeader.setAttribute("class", "seqHeader");
this.$$("#seqViewer").insertBefore(seqHeader, this.$$(".sequenceBody"));
var isoformContainer = document.createElement("div");
var seqLenContainer = document.createElement("div");
var massContainer = document.createElement("div");
var isoElectricPointContainer = document.createElement("div");
isoformContainer.innerHTML = "<strong>Isoform :</strong> " + sequenceObject.mainEntityName.name;
seqLenContainer.innerHTML = sequenceObject.sequence.length + " aa";
massContainer.innerHTML = "<strong>Mass :</strong> " + sequenceObject.massAsString + " Da";
isoElectricPointContainer.innerHTML = "<strong>pI :</strong> " + sequenceObject.isoelectricPointAsString;
this.$$(".seqHeader").appendChild(isoformContainer);
this.$$(".seqHeader").appendChild(seqLenContainer);
this.$$(".seqHeader").appendChild(massContainer);
this.$$(".seqHeader").appendChild(isoElectricPointContainer);
document.querySelector("#seqViewer .inputSearchSeq").setAttribute("placeholder","Search in sequence...");
document.querySelector(".inputSearchSeq").setAttribute("data-toggle","tooltip");
document.querySelector("#seqViewer .inputSearchSeq").setAttribute("data-placement","top");
document.querySelector("#seqViewer .inputSearchSeq").setAttribute("title","Regex supported");
$('#seqViewer [data-toggle="tooltip"]').tooltip();
},
_addFeatures: function() {
for (var i=0;i<this.featuresForViewer.length;i++) {
if (Object.keys(this.featuresForViewer[i]).length !== 0 && this.featuresForViewer[i].hasOwnProperty(this.isoName) && this.filterOptions[this.featuresForViewer[i][this.isoName].filter.split(" ").join("_")] === true) {
var feature = jQuery.extend({}, this.featuresForViewer[i][this.isoName]);
// Only for exp. interaction, sort the features by description
if(feature.name === 'Exp. interaction') {
feature.data.sort(function(a,b){
if(a.description > b.description) {
return 1
} else {
return -1
}
return 0
})
}
this.ft.addFeature(feature);
}
}
},
_sortGroup: function(a,b){
if (a["start"] === "?") return true;
return a["start"] - b["start"];
// })
},
_toFlat: function (obj) {
var self = this;
// var newArr = [];
return Object.keys(obj).map(function (key) {
if (!self.filterOptions[key.split(" ").join("_")]){
return [];
}
var newObj = obj[key].sort(self._sortGroup);
newObj[0]["first"]=true;
return newObj;
}).reduce(function (a, b) {
return a.concat(b);
}, []);
},
_fillTable: function() {
// if ($("#featuresTable").length > 0) {
if (!Object.keys(this.featuresByGroup).length){
var number = 0;
var features = {};
var self=this;
for (feat in this.featuresByIsoform) if(this.featuresByIsoform[feat].hasOwnProperty(this.isoName)) {
var group;
if(this.featuresByIsoform[feat][self.isoName] && this.featuresByIsoform[feat][self.isoName].length > 0) {
group = this.featuresByIsoform[feat][self.isoName][0].group;
}
var featureList = this.featuresByIsoform[feat][self.isoName];
for (var i in featureList){
var feature = featureList[i];
if (!feature.start){
feature.start = "?";
}
if (!feature.end){
feature.end = "?";
}
if (!feature.length){
feature.length = "?";
}
if(feature.variant){
var crossRef = {};
for (var j in feature.source){
if(feature.source[j].externalDb) {
if(feature.source[j].crossRef){
if (feature.source[j].crossRef.dbName==="Cosmic") feature.source[j].crossRef.dbName = "COSMIC";
crossRef[feature.source[j].crossRef.name] = feature.source[j].crossRef;
}
}
}
feature.crossRef = this._toArray(crossRef).sort(this._sortCrossRef);
}
if(this._isDisulfideBondFeature(feature.category)){
feature.length = "";
// Does not differentiate the interchain case when displaying the bond
feature.range = feature.start+"╭╮"+feature.end;
}else if(this._isSingleResidueFeature(feature.length)){
feature.range = feature.start;
}else{
feature.range = feature.start+"-"+feature.end;
}
if (this._isCrossLinkFeature(feature.category)){
feature.length = "";
}
}
if(group) {
if(Object.keys(features).indexOf(group)<0) {
features[group] = featureList;
} else {
features[group] = features[group].concat(featureList);
}
}
number += feature.length;
for (var i=0;i<this.featuresByIsoform[feat][this.isoName].length;i++) if(this.featuresByIsoform[feat][this.isoName][i].source) {
this.featuresByIsoform[feat][this.isoName][i].evidenceSources = this._getUniqueListOfEvidenceSources(this.featuresByIsoform[feat][this.isoName][i].source);
}
}
this.featuresByGroup = features;
}
// Sort region features in the table
if(this.featuresByGroup.Region) {
this.featuresByGroup.Region.sort(function(a,b){
if(a.start === b.start && a.end === b.end && a.length === b.length) {
if(a.description > b.description) {
return 1
} else {
return -1
}
return 0
} else {
return -1
}
})
}
this.featuresForTable = this._toFlat(this.featuresByGroup);
// Rename the experimental interactions (This is an exceptional case)
this.featuresForTable.forEach(feature => {
if(feature.category === 'Exp interaction' ) {
feature.category = 'Exp. interaction'
}
})
document.querySelector('iron-list').fire('iron-resize');
},
_reloadFeatureTable: function(){
this._fillTable();
// if(this.$$("#featureTableTemplate")) this.$$("#featureTableTemplate").render();
},
_highlightCategories: function(mouseEvent){
srcElement = mouseEvent.target || mouseEvent.srcElement || mouseEvent.srcElement.childNodes[1];
srcElementId = srcElement.tagName === "LABEL" ? srcElement.firstChild.id : srcElement.id;
this.ft.showFilteredFeature(srcElementId, "#795B42", document.location.href);
},
_dimCategories: function(mouseEvent){
srcElement = mouseEvent.target || mouseEvent.srcElement || mouseEvent.srcElement.childNodes[1];
srcElementId = srcElement.tagName === "LABEL" ? srcElement.firstChild.id : srcElement.id;
this.ft.hideFilteredFeature(srcElementId, "#795B42", document.location.href);
},
_filterAll: function() {
if ($("#filtering").hasClass("all-filters")){
$("#filtering input[type=checkbox]").prop("checked", false);
for(var key in this.filterOptions) {
this.filterOptions[key] = false;
}
$("#filtering").removeClass("all-filters");
} else {
$("#filtering input[type=checkbox]").prop("checked", true);
for(var key in this.filterOptions) {
this.filterOptions[key] = true;
}
$("#filtering").addClass("all-filters");
}
this._applyFiltering();
this.reloadSVG();
},
_filterGold: function(item){
if (this.nxConfig.goldOnly) return item.quality==="gold";
return true;
},
_toggleFiltering: function() {
if (!$("#filtering input:checkbox:not(:checked)").length) {
$("#filtering").addClass("all-filters");
} else {
$("#filtering").removeClass("all-filters");
}
this._applyFiltering();
this.reloadSVG();
},
_applyFiltering: function() {
for (var filter in this.activeFiltering) {
if ($("#"+filter).prop("checked")) {
// $("."+filter).show();
this.filterOptions[filter] = true;
} else {
// $("."+filter).hide();
this.filterOptions[filter] = false;
}
}
},
//Interaction if click on the feature Table
tvSelection: function(event) {
// var highlightedRows = document.getElementsByClassName("tableHighlight");
// if (highlightedRows[0]) highlightedRows[0].classList.remove("tableHighlight");
// var srcElement = event.target || event.srcElement;
// srcElement.parentElement.parentElement.parentElement.classList.add("tableHighlight");
// var currentId = srcElement.parentElement.parentElement.parentElement.id;
var currentId = event;
if (currentId) {
var position = currentId.split("_").slice(1,3).map(Number);
if (position.length === 1) position.push(position[0]);
var svgId = "#" + "f" + currentId;
position[0] -= 1;
if (!position[0]) position[0] = 0;
if (!position[1]) position[1] = this.currentSeq.length;
if (!this.hideSequenceViewer) {
this.seqView.selection(position[0], position[1], "#C50063");
this._scrollAuto(".stringSelected", ".scroller", 200);
}
this.selection = {'start': position[0], 'end': position[1]};
this.ft.addRectSelection(svgId);
}
},
//Listen if click on the feature Table & feature Viewer
eventTV: function() {
var self=this;
this.ft.onFeatureSelected(function(d){
if(d.detail.id.includes('FREQUENCY')) {
d.detail.id = d.detail.id.replace("FREQUENCY_","")
d.detail.end = d.detail.start;
}
self.selection = d.detail;
// update isoform selector
//console.log("feature selected");
//console.log(d);