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protein-overview.html
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<link rel="import" href="external-scripts.html">
<link rel="import" href="nextprot-elements-shared-styles.html">
<!--
`protein-overview`
Protein overview
##### Example
<protein-overview nx-config='{"entry": "P52701"}'></protein-overview>
@demo demo/protein-overview-demo.html
-->
<dom-module id="protein-overview">
<template>
<style include="nextprot-elements-shared-styles">
:host {
display: block;
}
iron-collapse {
--iron-collapse-transition-duration: 500ms;
}
h3 {
text-align: left;
}
dd {
margin-left: 15px;
}
.term-link {
display: inline;
}
.paragraph {
margin: 10px;
}
.ec-link {
display: inline;
}
h3.protein-overview {
line-height: normal;
}
#extender {
float: right;
padding: 1px 6px 1px 0px;
margin-top: -5px;
}
</style>
<div id="proteinTitle">
<button id="extender" class="btn btn-default" on-click="toggle">
<template is="dom-if" if="[[extended]]">
<iron-icon icon="arrow-drop-up"></iron-icon>
Collapse overview
</template>
<template is="dom-if" if="[[!extended]]">
<iron-icon icon="arrow-drop-down"></iron-icon>
Extend overview
</template>
</button>
<h3>
<template is="dom-if" if="[[data.geneName]]">
<template is="dom-if" if="[[data.geneName.0.name]]">
[[data.geneName.0.name]] →
</template>
</template>
[[data.entryName]]
<template is="dom-if" if="[[data.recommendedProteinName]]">
<template is="dom-if" if="[[data.recommendedProteinName.EC.0]]">
[
<template is="dom-repeat" items="[[data.recommendedProteinName.EC]]" as="ec">
<div class="ec-link"><a href="[[nxUrl]]/term/[[ec]]">EC [[ec]]</a></div>
<template is="dom-if" if="[[!_checkIfLast(data.recommendedProteinName.EC,index)]]">,
</template>
</template>
]
</template>
<template is="dom-if" if="[[data.recommendedProteinName.mainShortName]]">
([[data.recommendedProteinName.mainShortName]])
</template>
</template>
<paper-spinner-lite id="spinner" active></paper-spinner-lite>
</h3>
</div>
<iron-collapse id="collapseInfosLess" opened="{{!extended}}">
<div id="infos-less">
<template is="dom-if" if="[[data.recommendedProteinName.mainSynonymName]]">
<div id="synonym-less" class="row">
<div class="col-md-3 col-xs-3 grey-x text-align-right">Protein also known as :</div>
<div class="col-md-9 col-xs-9">
[[data.recommendedProteinName.mainSynonymName.name]]
<template is="dom-if" if="[[data.recommendedProteinName.mainSynonymName.synonym]]">
([[data.recommendedProteinName.mainSynonymName.synonym]])
</template>
<template is="dom-if" if="[[data.recommendedProteinName.others.0]]">;</template>
<template is="dom-if" if="[[!data.recommendedProteinName.others.0]]">.</template>
<template is="dom-repeat" items="[[data.recommendedProteinName.others]]" as="others">
[[others.type]][[_pluralize(others.names)]]:
<template is="dom-repeat" items="[[others.names]]" as="nameArray">
[[nameArray.name]]
<template is="dom-if" if="[[!_checkIfLast(others.names,index)]]">,</template>
</template>
<template is="dom-if" if="[[!_checkIfLast(others,index)]]">.</template>
</template>
</div>
</div>
</template>
<template is="dom-if" if="[[!data.recommendedProteinName.mainSynonymName]]">
<template is="dom-if" if="[[data.recommendedProteinName.others.0]]">
<div id="synonym-other-less" class="row">
<div class="col-md-3 col-xs-3 grey-x text-align-right">Protein also known as :</div>
<div class="col-md-9 col-xs-9">
<template is="dom-repeat" items="[[recommendedProteinName.others]]" as="others">
[[others.type]][[_pluralize(others.names)]]:
<template is="dom-repeat" items="[[others.names]]" as="nameArray">
[[nameArray.name]]
<template is="dom-if" if="[[!_checkIfLast(others.names,index)]]">,</template>
</template>
<template is="dom-if" if="[[!_checkIfLast(others,index)]]">.</template>
</template>
</div>
</div>
</template>
</template>
<template is="dom-if" if="[[data.cleavage.0]]">
<div id="cleavage-less" class="row">
<div class="col-md-3 col-xs-3 grey-x text-align-right">Cleaved into :</div>
<div class="col-md-6 col-xs-6">
<template is="dom-repeat" items="[[data.cleavage]]" as="cleavage">
<template is="dom-repeat" items="[[cleavage.names]]" as="nameArray"><span>[[nameArray.name]]<template
is="dom-if" if="[[!_checkIfLast(cleavage.names,index)]]">; </template></span>
</template>
</template>
</div>
</div>
</template>
<div id="gene-less" class="row">
<template is="dom-if" if="[[data.geneName.0]]">
<template is="dom-if" if="[[data.geneName.0.name]]">
<div class="col-md-3 col-xs-3 grey-x text-align-right">Gene name :</div>
<div class="col-md-6 col-xs-6">
<template is="dom-repeat" items="[[data.geneName]]" as="gn">[[gn.name]]<span
hidden$="[[_checkIfLast(data.geneName,index)]]">; </span></template>
</div>
</template>
<template is="dom-if" if="[[!data.geneName.0.name]]">
<div class="col-md-3 col-xs-3 grey-x text-align-right">ORF name :</div>
<div class="col-md-6 col-xs-6">[[data.geneName.0.orf.0.name]]</div>
</template>
</template>
<template is="dom-if" if="[[!data.geneName.0]]">
<div class="col-md-3 col-xs-3 grey-x text-align-right">Gene name :</div>
<div class="col-md-6 col-xs-6">None assigned yet</div>
</template>
</div>
<template is="dom-if" if="[[data.families.0]]">
<div id="family-less" class="row">
<div class="col-md-3 col-xs-3 grey-x text-align-right">Family name :</div>
<div class="col-md-6 col-xs-6">
<template is="dom-repeat" items="[[data.families]]" as="familyroot">
<span>
<template is="dom-if" if="[[familyroot.superfamily]]">
<div id="collapseInfosLess[[familyroot.superfamily.accession]]" class="term-link">
<a href="[[nxUrl]]/term/[[familyroot.superfamily.accession]]">[[familyroot.superfamily.name]]</a>
</div>
</template>
<template is="dom-if" if="[[familyroot.family]]">
<template is="dom-if" if="[[familyroot.superfamily]]"> >> </template>
<div id="collapseInfosLess[[familyroot.family.accession]]" class="term-link">
<a href="[[nxUrl]]/term/[[familyroot.family.accession]]">[[familyroot.family.name]]</a>
</div>
</template>
<template is="dom-if" if="[[familyroot.subfamily]]">
<template is="dom-if" if="[[familyroot.family]]"> >> </template>
<div id="collapseInfosLess[[familyroot.subfamily.accession]]" class="term-link">
<a href="[[nxUrl]]/term/[[familyroot.subfamily.accession]]">[[familyroot.subfamily.name]]</a>
</div>
</template>
</span>
</template>
</div>
</div>
</template>
</div>
</iron-collapse>
<iron-collapse id="collapseInfosFull" opened="{{extended}}">
<div id="infos-full">
<div id="protein-full" class="row">
<div class="col-md-1 col-xs-2 text-uppercase grey-x">Protein</div>
<div class="col-md-9 col-xs-8">
<dl>
<dt>Recommended name</dt>
<template is="dom-if" if="[[data.recommendedProteinName]]">
<dd>[[data.recommendedProteinName.name]]
<template is="dom-if" if="[[data.recommendedProteinName.EC.0]]">[
<template is="dom-repeat" items="[[data.recommendedProteinName.EC]]" as="ec">
<div class="ec-link">
<a href="[[nxUrl]]/term/[[ec]]">EC [[ec]]</a></div>
<template is="dom-if"
if="[[!_checkIfLast(data.recommendedProteinName.EC,index)]]">,
</template>
</template>
]
</template>
<template is="dom-if" if="[[data.recommendedProteinName.synonyms]]">
<template is="dom-if" if="[[data.recommendedProteinName.synonyms.short]]"><span><span
class="grey-x">Short: </span>
<template is="dom-repeat" items="[[data.recommendedProteinName.synonyms.short]]" as="short">
[[short]]<template is="dom-if"
if="[[!_checkIfLast(data.recommendedProteinName.synonyms.short,index)]]">,</template>
</template></span>
</template>
</template>
</dd>
</template>
<template is="dom-if" if="[[data.alternativeProteinNames]]">
<template is="dom-repeat" items="[[data.alternativeProteinNames]]"
as="alternativeProteinNames">
<dt>[[alternativeProteinNames.type]][[_pluralize(alternativeProteinNames.names)]]
</dt>
<template is="dom-repeat" items="[[alternativeProteinNames.names]]" as="nameroot">
<dd> [[nameroot.name]]
<template is="dom-if" if="[[nameroot.synonyms]]">
<template is="dom-if" if="[[nameroot.synonyms.EC]]">[
<template is="dom-repeat" items="[[nameroot.synonyms.EC]]" as="ec">
<div class="ec-link">
<a href="[[nxUrl]]/term/[[ec]]">EC [[ec]]</a></div>
<template is="dom-if"
if="[[!_checkIfLast(nameroot.synonyms.EC,index)]]">,
</template>
</template>
]
</template>
<template is="dom-if" if="[[nameroot.synonyms.short]]"><span><span
class="grey-x">Short: </span>
<template is="dom-repeat" items="[[nameroot.synonyms.short]]" as="short">
[[short]]<template is="dom-if"
if="[[!_checkIfLast(nameroot.synonyms.short,index)]]">,</template>
</template></span>
</template>
</template>
</dd>
</template>
</template>
</template>
<template is="dom-if" if="[[data.functionalRegionNames]]">
<template is="dom-repeat" items="[[data.functionalRegionNames]]"
as="functionalRegionName">
<dt>Include the following [[functionalRegionName.names.length]] functional
region[[_pluralize(functionalRegionName.names)]]
</dt>
<template is="dom-repeat" items="[[functionalRegionName.names]]" as="regionName">
<dd> [[regionName.name]]
<template is="dom-if" if="[[regionName.synonyms.EC]]">[
<template is="dom-repeat" items="[[regionName.synonyms.EC]]" as="ec">
<div class="ec-link">
<a href="[[nxUrl]]/term/[[ec]]">EC [[ec]]</a></div>
<template is="dom-if"
if="[[!_checkIfLast(regionName.synonyms.EC,index)]]">,
</template>
</template>
]
</template>
<template is="dom-if" if="[[regionName.synonyms.full]]">
<span><span class="grey-x">Alternative name[[_pluralize(regionName.synonyms.full)]]:</span>
<template is="dom-repeat" items="[[regionName.synonyms.full]]" as="full">
[[full]]<template is="dom-if"
if="[[!_checkIfLast(regionName.synonyms.full,index)]]">; </template>
</template>
</span>
</template>
</dd>
</template>
</template>
</template>
<template is="dom-if" if="[[data.cleavage]]">
<template is="dom-repeat" items="[[data.cleavage]]" as="cleavage">
<dt>Cleaved into the following [[cleavage.names.length]]
chain[[_pluralize(cleavage.names)]]
</dt>
<template is="dom-repeat" items="[[cleavage.names]]" as="cleavageName">
<dd>[[cleavageName.name]]
<template is="dom-repeat" items="[[cleavage.synonyms]]" as="synonym">
<template is="dom-if" if="[[cleavage.EC]]">[
<template is="dom-repeat" items="[[cleavage.EC]]" as="ec">
<div class="ec-link">
<a href="[[nxUrl]]/term/[[ec]]">EC [[ec]]</a>
</div>
<template is="dom-if" if="[[!_checkIfLast(cleavage.EC,index)]]">
,
</template>
</template>
]
</template>
<template is="dom-if" if="[[cleavage.full.0]]">
<span><span class="grey-x">Alternative name[[_pluralize(cleavage.full)]]:</span>
<template is="dom-repeat" items="[[cleavage.full]]" as="full">[[full]]
<template is="dom-if" if="[[!_checkIfLast(cleavage.full,index)]]">; </template>
</template></span>
</template>
</template>
</dd>
</template>
</template>
</template>
<template is="dom-if" if="[[data.isoforms]]">
<dt>Spliced into the following [[data.isoforms.length]]
isoform[[_pluralize(data.isoforms)]]
</dt>
<template is="dom-repeat" items="[[data.isoforms]]" as="isoform">
<dd>[[isoform.name]]
<template is="dom-if" if="[[isoform.synonyms.0]]">
<span class="grey-x"> Alternative name[[_pluralize(isoform.synonyms)]]: </span>
<template is="dom-repeat" items="[[isoform.synonyms]]" as="synonym">
[[synonym.name]]
<template is="dom-if" if="[[!_checkIfLast(isoform.synonyms,index)]]">;
</template>
</template>
</template>
</dd>
</template>
</template>
</dl>
</div>
</div>
<div id="gene-full" class="row">
<div class="col-md-1 col-xs-2 text-uppercase grey-x">Gene</div>
<div class="col-md-9 col-xs-8">
<dl>
<template is="dom-if" if="[[data.geneName.0]]">
<template is="dom-repeat" items="[[data.geneName]]" as="geneName">
<template is="dom-if" if="[[geneName.name]]">
<dt>Recommended name</dt>
<dd>[[geneName.name]]</dd>
</template>
<template is="dom-if" if="[[geneName.synonyms.0]]">
<dt>Alternative name[[_pluralize(geneName.synonyms)]]</dt>
<template is="dom-repeat" items="[[geneName.synonyms]]" as="synonym">
<dd> [[synonym.name]]</dd>
</template>
</template>
<template is="dom-if" if="[[geneName.orf.0]]">
<dt>ORF name[[_pluralize(geneName.orf)]]</dt>
<template is="dom-repeat" items="[[geneName.orf]]" as="orf">
<dd> [[orf.name]]</dd>
</template>
</template>
<template is="dom-if" if="[[!_checkIfLast(data.geneName,index)]]">
<br>
</template>
</template>
</template>
<template is="dom-if" if="[[!data.geneName.0]]">
<dt>Recommended name</dt>
<dd>None assigned yet</dd>
</template>
</dl>
</div>
</div>
<template is="dom-if" if="[[data.families.0]]">
<div id="family-full" class="row">
<div class="col-md-1 col-xs-2 text-uppercase grey-x">Family</div>
<div class="col-md-9 col-xs-8">
<dl>
<template is="dom-repeat" items="[[data.families]]" as="familyroot">
<template is="dom-if" if="[[familyroot.superfamily]]">
<dt>Superfamily</dt>
<dd>
<div id="collapseInfosFull[[familyroot.superfamily.accession]]">
<a href="[[nxUrl]]/term/[[familyroot.superfamily.accession]]">[[familyroot.superfamily.name]]</a>
</div>
</dd>
</template>
<template is="dom-if" if="[[familyroot.family]]">
<dt>Family</dt>
<dd>
<div id="collapseInfosFull[[familyroot.family.accession]]">
<a href="[[nxUrl]]/term/[[familyroot.family.accession]]">[[familyroot.family.name]]</a>
</div>
</dd>
</template>
<template is="dom-if" if="[[familyroot.subfamily]]">
<dt>Subfamily</dt>
<dd>
<div id="collapseInfosFull[[familyroot.subfamily.accession]]">
<a href="[[nxUrl]]/term/[[familyroot.subfamily.accession]]">[[familyroot.subfamily.name]]</a>
</div>
</dd>
</template>
</template>
</dl>
</div>
</div>
</template>
<div id="History-full" class="row">
<div class="col-md-1 col-xs-2 text-uppercase grey-x">History</div>
<div class="col-md-9 col-xs-8">
<dl>
<dt>neXtProt</dt>
<dd>Integrated [[data.integDate]]</dd>
<dd>Last updated [[data.lastUpdate]]</dd>
<dt>UniProtKB</dt>
<dd>Integrated [[data.UniprotIntegDate]]</dd>
<dd>Last updated [[data.UniprotLastUpdate]]</dd>
<dd>Entry version [[data.version]]</dd>
<template is="dom-if" if="[[data.lastSeqUpdate]]">
<dd>Last sequence update [[data.lastSeqUpdate]]</dd>
</template>
<dd>Sequence version [[data.seqVersion]]</dd>
<dd>
<template is="dom-if" if="[[data.accessionNumber]]">
<div id="[[data.accessionNumber]]">
<a href="[[_linkToHistory(data.accessionNumber)]]" class="ext-link"
target="_blank">Complete UniProtKB history</a></div>
</template>
</dd>
</dl>
</div>
</div>
</div>
</iron-collapse>
<p class="paragraph">
<template is="dom-if" if="[[data.proteinEvidence]]">[[data.proteinEvidence]].
[[data.proteinEvidenceCaution]]
</template>
</p>
</template>
<script>
Polymer({
is: 'protein-overview',
behaviors: [Polymer.NeonAnimationRunnerBehavior],
properties: {
nxConfig: {
type: Object,
value: {}
},
nxEntry: {
notify: true
},
nxEntryData: {
type: String,
value: ""
},
lazyLoading: {
type: Boolean,
value: false,
},
extended: {
type: Boolean,
value: false
},
animationConfig: {
value: function () {
return {
'enterFullInfos': [{
name: "scale-up-animation",
node: this.$.collapseInfosFull,
transformOrigin: '0% 100%',
timing: {
duration: 600
}
}, {
name: "fade-in-animation",
node: this.$.collapseInfosFull,
timing: {
duration: 1000
}
}],
'exitFullInfos': [{
name: "fade-out-animation",
node: this.$.collapseInfosFull,
timing: {
duration: 600
}
}, {
name: "scale-down-animation",
node: this.$.collapseInfosFull,
timing: {
duration: 1000
}
}],
'enterLessInfos': [{
name: "slide-from-left-animation",
node: this.$.collapseInfosLess,
timing: {
duration: 400
}
}, {
name: "fade-in-animation",
node: this.$.collapseInfosLess,
timing: {
duration: 1600
}
}],
'exitLessInfos': [{
name: "fade-out-animation",
node: this.$.collapseInfosLess,
timing: {
duration: 400
}
}, {
name: "slide-left-animation",
node: this.$.collapseInfosLess,
timing: {
duration: 1200
}
}]
}
}
}
},
ready: function () {
this._initApiClient();
var self = this;
// fetch data from overview
if(!this.lazyLoading) {
this._npClient.getProteinOverview(self.nxConfig.entry).then(function (overview) {
// load data
self._loadData(overview);
self.$.spinner.active = false;
}, function (error) {
self._handleError(error);
});
} else {
if(Object.getOwnPropertyNames(JSON.parse(decodeURIComponent(this.nxEntryData))).length == 0) {
self.$.spinner.active = true;
} else {
this._loadData(JSON.parse(decodeURIComponent(this.nxEntryData)).overview.overview);
self.$.spinner.active = false;
}
}
this.nxEntry = this.nxConfig.entry || this._npClient.getEntryName();
},
_initApiClient: function () {
this._npClient = new Nextprot.Client("neXtProt protein overview", "Calipho Group");
if (this.nxConfig.env) {
this._npClient.updateEnvironment(this.nxConfig.env);
}
},
_loadData: function (overview) {
var EC = [];
var short = [];
if (overview.recommendedProteinName.synonyms) {
overview.recommendedProteinName.synonyms.forEach(function (p) {
if (p.qualifier === "short") short.push(p.name);
});
if (short.length) short.sort(NXUtils.sortByAlphabet);
}
if (overview.recommendedProteinName.otherRecommendedEntityNames) {
overview.recommendedProteinName.otherRecommendedEntityNames.forEach(function (p) {
if (p.qualifier === "EC") EC.push(p.name);
});
if (EC.length) EC.sort(NXUtils.sortByAlphabet);
}
let recommendedProteinSynonyms = NXUtils.getSynonyms(overview.recommendedProteinName.synonyms);
let isonames = overview.isoformNames;
// Workaround to convert the timestamp
// TODO: Could have been better to deal with dates with moment.js
let lastSeqUpdateDate = new Date(overview.history.lastSequenceUpdate);
let month = lastSeqUpdateDate.getMonth();
month = (month + 1) <= 10 ? '0'+ (month + 1) : month + 1;
let date = lastSeqUpdateDate.getDate();
date = date < 10 ? '0'+ date : date;
let formattedLastSeqUpdate = lastSeqUpdateDate.getFullYear() + '-' + month + '-' + date;
this.data = {
"entryName": overview.recommendedProteinName.name,
"recommendedProteinName": {
synonyms: recommendedProteinSynonyms,
name: overview.recommendedProteinName.name,
EC: EC,
short: short,
mainSynonymName: overview.proteinNames[0].synonyms ? NXUtils.getMainSynonym(overview.proteinNames[0].synonyms) : null,
mainShortName: recommendedProteinSynonyms.short ? NXUtils.getMainShort(recommendedProteinSynonyms.short) : null,
others: NXUtils.getAlternativeNames(overview.alternativeProteinNames).filter(function (t) {
return t.type !== "EC" && t.type !== "full" && t.type !== "Alternative names" && t.type !== "Alternative name"
})
},
"alternativeProteinNames": NXUtils.getAlternativeNames(overview.alternativeProteinNames),
"geneName": overview.geneNames ? overview.geneNames.map(function (gn) {
return {
name: NXUtils.getRecommendedName(gn) || null,
synonyms: gn.synonyms ? gn.synonyms.filter(function (gns) {
return gns.category === "gene name"
}).sort(NXUtils.sortByAlphabet) : null,
orf: NXUtils.getORFNames(gn) || null
}
}).sort(NXUtils.sortByAlphabet) : null,
"cleavage": NXUtils.getAlternativeNames(overview.cleavedRegionNames),
"isoforms": NXUtils.getIsoforms(isonames),
"functionalRegionNames": NXUtils.getAlternativeNames(overview.functionalRegionNames),
"families": overview.families.map(function (f) {
return NXUtils.getFamily(f, {})
}),
"proteinEvidence": this._updateProteinExistenceText(overview.proteinExistence),
"integDate": overview.history.formattedNextprotIntegrationDate,
"lastUpdate": overview.history.formattedNextprotUpdateDate,
"UniprotIntegDate": overview.history.formattedUniprotIntegrationDate,
"UniprotLastUpdate": overview.history.formattedUniprotUpdateDate,
"version": overview.history.uniprotVersion,
"seqVersion": overview.history.sequenceVersion,
"lastSeqUpdate": formattedLastSeqUpdate,
"accessionNumber": this.nxEntry
};
},
toggle: function () {
if (this.extended) {
this.playAnimation("exitFullInfos");
this.playAnimation("enterLessInfos");
this.$.collapseInfosLess.toggle();
this.$.collapseInfosFull.toggle();
} else {
this.playAnimation("exitLessInfos");
this.playAnimation("enterFullInfos");
this.$.collapseInfosFull.toggle();
this.$.collapseInfosLess.toggle();
}
this.extended = !this.extended;
},
_checkIfLast: function (array, index) {
if (array.length - 1 === index) return true;
return false;
},
_linkToHistory: function (accession) {
return "http://www.uniprot.org/uniprot/" + accession.slice(3) + "?version=*";
},
_pluralize: function (item) {
return item.length > 1 ? "s" : "";
},
_updateProteinExistenceText: function (pe) {
var description = pe.description;
var existence = description.toLowerCase();
var mainSentence = "Entry whose protein(s) existence is ";
switch (existence) {
case "uncertain":
return mainSentence + existence;
case "inferred from homology":
return mainSentence + existence;
default:
return mainSentence + "based on " + existence;
}
},
_handleError: function (error) {
var responseText = JSON.parse(error.responseText);
this.$.proteinTitle.innerHTML = "<h3>" + responseText.message + "</h3>";
this.$.spinner.active = false;
}
});
</script>
</dom-module>