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exons-mapping-table.html
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<link rel="import" href="exon-item.html">
<link rel="import" href="external-scripts.html">
<link rel="import" href="nextprot-elements-shared-styles.html">
<!--
`exons-mapping-table`
exons mapping table demo
@demo demo/exons-mapping-table-demo.html
-->
<dom-module id="exons-mapping-table">
<template>
<style include="nextprot-elements-shared-styles">
:host {
padding-bottom: 20px;
}
#exonTable {
width: auto;
white-space: nowrap;
}
#exonTable thead {
border-left: 1px solid #ddd;
border-right: 1px solid #ddd;
}
#exonTable th {
text-align: center;
vertical-align: top;
border-right: 1px solid #ddd;
border-left: 1px solid #ddd;
border-bottom: 1px solid #ddd;
padding: 5px;
}
#exonTable td {
text-align: left;
padding: 1px 5px;
border-bottom: 0;
border-top: 0;
border-left: 1px solid #ddd;
border-right: 1px solid #ddd;
}
#exonTable .aligned-right {
text-align: right;
}
#exonTable ul {
padding-left: 0;
}
ul {
list-style-type: none;
}
.iso-canonical {
color: #C50064;
font-size: 12px;
font-weight: 500;
letter-spacing: 0.1px;
vertical-align: text-top;
}
th > div {
position: absolute;
top: 0;
border-left: 1px solid lightgray;
padding: 5px 3px;
min-height: 80px;
}
th:first-of-type > div {
border-left: 0;
}
#tableCont {
position: relative;
overflow-x: auto;
display: inline-block;
border: 1px solid lightgray;
max-width: 100%;
background-color: #f8f8f8;
max-height: calc(100% - 70px);
overflow-y: hidden;
}
#tableDiv{
overflow-y: auto;
overflow-x: hidden;
max-height:500px;
display:inline-block;
border-top:1px solid lightgray;
background-color: white;
}
#tableDiv th {
height: 0;
padding: 0;
border: 0;
white-space: nowrap;
}
#tableDiv td {
min-width: 70px;
border-right: 0;
}
#exonTable td:first-of-type {
border-left: 0;
}
#exonTable {
margin: 0;
border-right: 0;
border-left: 0;
}
</style>
<paper-spinner-lite id="spinner" active></paper-spinner-lite>
<template is="dom-if" if="[[_hasData(data)]]">
<div class="category-header">
<h4 class="category-title">Exons</h4>
</div>
<div id="tableCont">
<div id="tableDiv">
<table id="exonTable" class="table table-hover">
<thead>
<tr>
<th class="thead-column">
<div>Identifier</div>
</th>
<th class="thead-column">
<div>Position<br>on gene</div>
</th>
<th class="thead-column">
<div>Length</div>
</th>
<template is="dom-repeat" items="[[_getMappedIsoformInfos(data)]]" as="iso">
<th style="text-align:center;" class="thead-column">
<div>Coding for <br>
[[iso.name]]
<template is="dom-if" if="[[_displayTranscriptMappingInfos(iso)]]">
<template is="dom-if" if="[[iso.canonical]]">
<span class="iso-canonical">(canonical)</span>
</template>
<div>
<a class="ext-link"
href="http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=[[iso.main-transcript]]"
target='_blank'>[[iso.main-transcript]]</a>
</div>
<template is="dom-if" if="[[iso.other-transcripts]]">
<span on-tap="_toggle">
<span id="transcripts_[[index]]" class="fa fa-chevron-right"
style="display: inline-block;width:14px;"></span>
<span id="showHide_[[index]]" style="display: inline-block;width:36px;"> show</span> <span>transcripts ([[iso.other-transcripts.length]])</span>
</span>
<iron-collapse id="collapse_[[index]]" no-animation>
<ul>
<template is="dom-repeat" items="[[iso.other-transcripts]]"
as="other">
<li><a class="ext-link"
href="http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=[[other]]"
target='_blank'>[[other]]</a></li>
</template>
</ul>
</iron-collapse>
</template>
</template>
</div>
</th>
</template>
</tr>
</thead>
<tbody>
<template is="dom-repeat" items="[[_rows]]" as="row">
<tr>
<template is="dom-repeat" items="[[row]]" as="cell">
<template is="dom-if" if="[[!_exonCell(index)]]">
<td class$="[[_getCellClass(index)]]">[[cell]]</td>
</template>
<template is="dom-if" if="[[_exonCell(index)]]">
<td>
<exon-item data="[[cell]]"></exon-item>
</td>
</template>
</template>
</tr>
</template>
</tbody>
</table>
</div>
</div>
</template>
</template>
<script>
Polymer({
is: 'exons-mapping-table',
properties: {
data: {
type: Object,
observer: "_prepareData"
},
_rows: {
type: Array,
value: []
},
_dataLoaded: {
type: Boolean,
observer: '_updateSpinnerStatus'
}
},
_prepareData: function () {
var i;
this._rows = [];
for (i = 0; i < this.data.sortedExonKeys.length; i++) {
this._rows.push(this._newRow(this.data.sortedExonKeys[i]));
}
var self = this;
Polymer.RenderStatus.afterNextRender(self, function () {
self._dataLoaded = true;
self._updateHeaderWidth();
self._updateHeaderHeight();
});
},
_newRow: function (pos) {
var exonByIsoform = this.data.exons[pos];
var row = [this._findENSE(exonByIsoform), this._formatPos(pos), this._calcLength(pos)];
var i;
for (i = 0; i < this.data.sortedMappedIsoformInfoKeys.length; i++) {
var isoformAccession = this.data.sortedMappedIsoformInfoKeys[i];
if (isoformAccession in exonByIsoform) {
var exon = exonByIsoform[isoformAccession];
exon.drawCodingPartOnly = this.data.mappedIsoformInfos[isoformAccession].quality === "BRONZE" && this.data.lowQualityMappings;
row.push(exon);
}
else {
row.push(null);
}
}
return row;
},
_formatPos: function (pos) {
var fromAndTo = pos.split("-");
return fromAndTo[0] + " - " + fromAndTo[1];
},
_calcLength: function (pos) {
var fromAndTo = pos.split("-");
return fromAndTo[1] - fromAndTo[0] + 1;
},
_exonCell: function (index) {
return index > 2;
},
_findENSE: function (exonByIsoform) {
var i;
var accessions = [];
for (i = 0; i < this.data.sortedMappedIsoformInfoKeys.length; i++) {
if (this.data.sortedMappedIsoformInfoKeys[i] in exonByIsoform) {
if (exonByIsoform[this.data.sortedMappedIsoformInfoKeys[i]].accession) {
accessions.push(exonByIsoform[this.data.sortedMappedIsoformInfoKeys[i]].accession);
}
}
}
if (accessions.length > 0) {
return accessions[0];
}
return null;
},
_getMappedIsoformInfos: function (data) {
var i;
var infos = [];
for (i = 0; i < data.sortedMappedIsoformInfoKeys.length; i++) {
infos.push(data.mappedIsoformInfos[data.sortedMappedIsoformInfoKeys[i]]);
}
return infos;
},
_getCellClass: function (index) {
if (index === 1 || index === 2) {
return "aligned-right"
}
else return ""
},
_updateHeaderWidth: function () {
var headerColumns = this.$$("#exonTable").querySelectorAll(".thead-column");
for (var h = 0; h < headerColumns.length; h++) {
headerColumns[h].getElementsByTagName("div")[0].style.width =
window.getComputedStyle(headerColumns[h]).getPropertyValue('width');
}
},
_updateHeaderHeight: function () {
var headerColumns = this.$$("#exonTable").querySelectorAll(".thead-column");
var heightMax = 0;
for (var h = 0; h < headerColumns.length; h++) {
headerColumns[h].getElementsByTagName("div")[0].style.height = "auto";
var colheight = headerColumns[h].getElementsByTagName("div")[0].clientHeight;
if (heightMax < colheight) heightMax = colheight;
}
for (var h = 0; h < headerColumns.length; h++) {
headerColumns[h].getElementsByTagName("div")[0].style.height = heightMax + "px";
}
this.$$("#tableCont").style.paddingTop = heightMax + "px";
},
_toggle: function (event) {
var index = event.model.index;
this.$$("#collapse_" + index).toggle();
var opened = this.$$("#collapse_" + index).opened;
this.$$("#transcripts_" + index).classList.toggle("fa-chevron-down");
this.$$("#showHide_" + index).innerText = opened ? "Hide" : "Show";
this._updateHeaderHeight();
},
_hasData: function (data) {
return data && data.sortedExonKeys.length > 0;
},
_displayTranscriptMappingInfos: function (infos) {
return infos.quality && infos.quality === "GOLD";
},
_updateSpinnerStatus: function (dataLoaded) {
if (dataLoaded) {
this.$.spinner.active = false;
this.$.spinner.hidden = true;
}
}
});
</script>
</dom-module>