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isoform-selector.html
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isoform-selector.html
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<link rel="import" href="nextprot-elements-shared-styles.html">
<link rel="import" href="external-scripts.html">
<!--
`isoform-selector`
Widget visualizing isoform sequence coverage, allows switching between isoforms.
@demo demo/isoform-selector-demo.html
-->
<dom-module id="isoform-selector">
<template>
<style is="isoform-selector-style" include="nextprot-elements-shared-styles">
:host {
display: block;
}
iron-dropdown {
background: white;
margin-top: 35px;
padding: 10px 0;
border-radius: 5px;
}
#nxIsoformChoice {
margin-bottom: 5px;
font-size: 16px;
font-weight: 500;
}
#visuContainer {
background:#fff;
padding:0px;
border: 1px solid #cfd9db;
border-radius:4px;
}
</style>
<div id="nxIsoformChoice" class="col-md-12">
<span class="grey-x">Displayed isoform: </span>[[isoformLabel]]
<span id="isoformMap" class="colored-label definition-button" on-tap="_toggleIsoformMap">Change isoform</span>
<template is="dom-if" if="[[!featureViewerReady]]">
<paper-spinner-lite id="featViewerSpinner" class="size" active></paper-spinner-lite>
</template>
</div>
<div class="row">
<div id="visuContainer" class="col-md-12">
<iron-collapse id="isoformMapContainer" opened="[[showIsoformMap]]">
<div id="isoformDisplayed"></div>
</iron-collapse>
</div>
</div>
</template>
<script>
Polymer({
is: 'isoform-selector',
properties: {
nxConfig: {
type: Object,
value: {}
},
nxEntryData: {
type: String,
value: ""
},
lazyLoading: {
type: Boolean,
value: false,
},
isoforms: {
type: Object
},
sequences: {
type: Object
},
isoformMapping: {
type: Object
},
isoName: {
type: String,
notify: true
},
showIsoformMap: {
type: Boolean
},
showAllTab: {
type: Boolean,
value: false
},
featureViewerReady: {
type: Boolean,
}
},
ready: function() {
if(this.lazyLoading) {
if(Object.getOwnPropertyNames(JSON.parse(decodeURIComponent(this.nxEntryData))).length == 0) {
return;
}
}
var nx = new Nextprot.Client("neXtprot isoform selector", "Calipho Group");
if (this.nxConfig.env) nx.updateEnvironment(this.nxConfig.env);
var nxEntry = this.nxConfig.entry || nx.getEntryName();
this.isoName = this.nxConfig.isoform;
var self=this;
nx.getIsoformMapping(nxEntry).then(
function(data){
self.isoforms=data;
if(self.isoName && !self._checkIfIsoformExists()) self.isoName = "";
self.isoformMapping = self._testAlgoObject(data);
if(self.lazyLoading) {
let entryData = JSON.parse(decodeURIComponent(self.nxEntryData));
self.sequences = entryData.isoforms.isoforms;
self._initialize();
} else {
nx.getProteinSequence(nxEntry).then(
function (sequences) {
self.sequences = sequences;
self._initialize();
}
)
}
}
).catch(function (err) {
// catch any error that happened so far
console.log("Argh, broken: " + err.message);
console.log("Error at line : " + err.stack);
});
},
_initialize: function () {
this.isoforms = this.sequences.sort(function (a, b) {
return parseInt(a.uniqueName.split("-")[1]) - parseInt(b.uniqueName.split("-")[1])
});
this.isoformLabels = [];
for(var i in this.isoforms) this.isoformLabels[this.isoforms[i].uniqueName] = this.isoforms[i].mainEntityName.name;
if(!this.isoName) {
this.isoName = this.isoforms[0].uniqueName;
this.isoformLabel = this.isoforms[0].mainEntityName.name;
} else this.isoformLabel = this.isoformLabels[this.isoName];
this._displayIsoform(this.isoName);
},
reload: function (isoIdentifier) {
this.isoName = isoIdentifier;
this._changeIsoform();
},
_checkIfIsoformExists: function(){
for(var i in this.isoforms) {
if (this.isoName === this._objectValues(this.isoforms)[i].isoformAc) return true;
}
return false;
},
_testAlgoObject: function(isoformsMap) {
if (isoformsMap.length<2) this.$.isoformMap.hidden = true;
var isoformsMapping = Object.assign({}, isoformsMap);
var positions=[];
var decalage=[];
// GET All positions x & y into new array positions
for (var iso in isoformsMapping) {
isoformsMapping[iso].positions.forEach(function (o) {
positions.push(o.first, o.second);
})
}
//delete double in list of positions
positions = positions.filter(function(elem, index, self) {
return index == self.indexOf(elem);});
// sort positions
positions.sort(function(a,b) {return a-b});
//for each interval between position, check if there is something in isoforms
//if not, add the empty interval to array decalage
for (var i=0;i<positions.length-1;i++) {
var presence = false;
for (var j in this.isoforms) {
for (var k in isoformsMapping[j].positions) {
if (isoformsMapping[j].positions[k].first > positions[i+1]) break;
else if (isoformsMapping[j].positions[k].first<= positions[i] && isoformsMapping[j].positions[k].second >= positions[i+1]) {
presence=true;
break;
}
}
if (presence === true) break;
}
if (presence === false) decalage.push({x:positions[i],length:positions[i+1]-positions[i]});
}
////For each "hole", apply a shift by adding the length of the hole to the values after the hole
////In the same time, if i[y] == i+1[x] merge those two
for (var i=decalage.length-1;i>=0;i--) {
for (var j in isoformsMapping) {
for (var k=isoformsMapping[j].positions.length-1;k>=0;k--) {
if (isoformsMapping[j].positions[k].first < decalage[i].x) {
if (k !=isoformsMapping[j].positions.length-1 && i===0 && isoformsMapping[j].positions[k+1].first === isoformsMapping[j].positions[k].second) {
isoformsMapping[j].positions[k].second = isoformsMapping[j].positions[k+1].second;
isoformsMapping[j].positions.splice(k+1,1);
}
break;
} else {
isoformsMapping[j].positions[k].first -= decalage[i].length;
isoformsMapping[j].positions[k].second -= decalage[i].length;
}
if (k !=isoformsMapping[j].positions.length-1 && isoformsMapping[j].positions[k+1].first === isoformsMapping[j].positions[k].second) {
isoformsMapping[j].positions[k].second = isoformsMapping[j].positions[k+1].second;
isoformsMapping[j].positions.splice(k+1,1);
}
}
}
}
return isoformsMapping;
},
_changeIsoform: function(){
if(typeof angular !== 'undefined') angular.element(document.getElementById("main")).scope().$apply(angular.element(document.getElementById("main")).injector().get('$location').search('isoform', this.isoName));
else history.pushState(null, null, window.location.pathname+"?isoform="+ this.isoName);
},
_displayIsoform: function(isoIdentifier) {
var isoContainer = this.$$("#isoformDisplayed #isoContainer")
if(isoContainer) isoContainer.innerHTML="";
if (!$('#isoContainer').length > 0) {
$("#isoformDisplayed").append("<div id=\"isoContainer\"></div>");
}
var self = this;
function getMax() {
var max = 0;
for (name in self.isoformMapping) {
for (var pos in self.isoformMapping[name].positions) {
if (self.isoformMapping[name].positions[pos].second > max) max = self.isoformMapping[name].positions[pos].second;
}
}
return max;
}
function getMin() {
var min = 100000000;
for (name in self.isoformMapping) {
for (var pos in self.isoformMapping[name].positions) {
if (self.isoformMapping[name].positions[pos].first < min) min = self.isoformMapping[name].positions[pos].first;
}
}
return min;
}
var max = getMax();
var min = getMin();
var position = 20;
this.containerWidth = document.getElementById("visuContainer").offsetWidth || document.body.offsetWidth-315;
var margin = {top: 5, right: 25, bottom: 0, left: 25},
width = this.containerWidth - margin.left - margin.right,
height = 200 - margin.top - margin.bottom;
var coverageLength = 33000;
var scaling = d3.scale.linear()
.domain([min, max])
.range([0, width]);
var line = d3.svg.line()
.interpolate("curve-linear")
.x(function (d) {
return scaling(d.x);
})
.y(function (d) {
return d.y + 6;
});
var svgIso = d3.select("#isoformDisplayed #isoContainer").append("svg")
.attr("width", width + margin.left + margin.right)
.attr("height", height + margin.top + margin.bottom)
.style("z-index", "2");
var svgIsoform = svgIso
.append("g")
.attr("transform", "translate(" + margin.left + "," + margin.top + ")");
var selectIsoform = function (iso) {
};
function fillSVGIsoform(data) {
var rectHeight = 12;
var rectShift = 20;
var rectsPro = svgIsoform.append("g")
.attr("class", "rectangle")
.attr("transform", "translate(0," + position + ")");
rectsPro.append("path")
.attr("d", line([{x: min, y: 0}, {x: max, y: 0}]))
.attr("class", function () {
return "line"
})
.style("z-index", "0")
.style("stroke", "#C2DEC8")
.style("stroke-width", "1px");
var rectsProGroup = rectsPro.selectAll("." + data.isoformAc + "Group")
.data(data.positions)
.enter()
.append("g")
.attr("class", data.isoformAc + "Group isoGroup")
.attr("transform", function (d) {
return "translate(" + scaling(d.first) + ",0)"
});
rectsProGroup
.append("rect")
.attr("class", "element " + data.isoformAc + "Rect")
.attr("width", function (d) {
return (scaling(d.second) - scaling(d.first))
})
.attr("height", 12)
.style("fill", function () {
return (data.isoformAc === isoIdentifier || isoIdentifier==="all") ? "#74EB78" : "#C2DEC8"
})
.style("z-index", "13")
.style("cursor", "pointer")
.on("click", function () {
svgIsoform.selectAll("rect").style("fill", "#C2DEC8");
d3.selectAll("." + data.isoformAc + "Rect").style("fill", "#74EB78");
self.isoformLabel = data.isoformMainName;
self.reload(data.isoformAc);
});
rectsProGroup
.append("text")
.attr("class", "element " + data.isoformAc + "Text")
.attr("y", 6)
.attr("dy", "0.35em")
.style("font-size", "10px")
.text(function (d) {
return data.isoformMainName
})
.style("fill", "black")
.style("z-index", "15")
.style("visibility", function (d) {
if (data.isoformMainName) {
return (scaling(d.second) - scaling(d.first)) > data.isoformMainName.length * 8 ? "visible" : "hidden";
}
else return "hidden";
});
position += 20;
}
for (var name in self.isoformMapping) {
fillSVGIsoform(self.isoformMapping[name], name);
}
$(window).resize(function () {
updateIsoSVG();
});
function updateIsoSVG() {
width = $("#visuContainer").width() - margin.left - margin.right;
d3.select("#isoformDisplayed svg")
.attr("width", width + margin.left + margin.right);
d3.select("#isoformDisplayed clippath>rect").attr("width", width);
scaling.range([5, width - 5]);
svgIsoform.selectAll(".line").attr("d", line([{x: min, y: 0}, {x: max, y: 0}]));
svgIsoform.selectAll(".isoGroup").attr("transform", function (d) {
return "translate(" + scaling(d.first) + ",0)"
});
svgIsoform.selectAll(".isoGroup rect").attr("width", function (d) {
return (scaling(d.second) - scaling(d.first))
});
svgIsoform.selectAll(".isoGroup text").style("visibility", function (d) {
var textContent = d3.select(this).text();
if (textContent && textContent.length) {
return (scaling(d.second) - scaling(d.first)) > textContent.length * 8 ? "visible" : "hidden";
}
else return "hidden";
});
}
svgIso.attr("height", position + 10 + "px");
},
_toggleIsoformMap: function() {
this.$$("#isoformMapContainer").toggle();
},
_objectValues: function(obj) {
var vals = [];
for( var key in obj ) {
if ( obj.hasOwnProperty(key) ) {
vals.push(obj[key]);
}
}
return vals;
}
});
</script>
</dom-module>