hierarchic-heatmap-table-component
Version:
A visualisation tool for displaying rows in a hiearchic manner with heatmap capabilities
994 lines (909 loc) • 96.2 kB
JavaScript
/**
* A neXtProt js client
*/
(function (root) {
//
'use strict';
if (root.Nextprot === undefined) {
root.Nextprot = {};
}
(function () {
//Utility methods
var _getURLParameter = function (name) {
name = name.replace(/[\[]/, "\\[").replace(/[\]]/, "\\]");
var regex = new RegExp("[\\?&]" + name + "=([^&#]*)"),
results = regex.exec(location.search);
return results === null ? "" : decodeURIComponent(results[1].replace(/\+/g, " "));
};
function _changeParamOrAddParamByName(href, paramName, newVal) {
var tmpRegex = new RegExp("(" + paramName + "=)[a-zA-Z0-9_]+", 'ig');
if (href.match(tmpRegex) !== null) {
return href.replace(tmpRegex, '$1' + newVal);
}
return href += (((href.indexOf("?") !== -1) ? "&" : "?") + paramName + "=" + newVal);
}
var _convertToTupleMap = function (data) {
var publiMap = {};
var xrefMap = {};
if (data.entry.publications){
data.entry.publications.forEach(function (p) {
publiMap[p.md5] = p;
});
}
data.entry.xrefs.forEach(function (p) {
xrefMap[p.dbXrefId] = p;
});
//return data.entry.annotations;
return {
annot: data.entry.annotations,
publi: publiMap,
xrefs: xrefMap
};
};
var normalizeEntry = function (entry) {
if (entry.substring(0, 3) !== "NX_") {
entry = "NX_" + entry;
}
return entry;
};
var environment = _getURLParameter("env") || 'pro'; //By default returns the production
var apiBaseUrl = "https://api.nextprot.org";
if (environment !== 'pro') {
apiBaseUrl = "http://" + environment + "-api.nextprot.org";
}
var sparqlEndpoint = apiBaseUrl + "/sparql";
var sparqlFormat = "?output=json";
var applicationName = null;
var clientInfo = null;
function _getJSON(url) {
var finalURL = url;
finalURL = _changeParamOrAddParamByName(finalURL, "clientInfo", clientInfo);
finalURL = _changeParamOrAddParamByName(finalURL, "applicationName", applicationName);
return Promise.resolve($.getJSON(finalURL));
//return get(url).then(JSON.parse);
}
var _getEntry = function (entry, context) {
var entryName = normalizeEntry(entry || (_getURLParameter("nxentry") || 'NX_P01308'));
var url = apiBaseUrl + "/entry/" + entryName;
if (context) {
url += "/" + context;
}
return _getJSON(url);
};
var _callPepX = function (seq, mode) {
var url = apiBaseUrl + "/entries/search/peptide?peptide=" + seq + "&modeIL=" + mode;
return _getJSON(url);
};
var _callTerminology = function (terminologyName) {
var url = apiBaseUrl + "/terminology/" + terminologyName;
return _getJSON(url);
};
var NextprotClient = function (appName, clientInformation) {
applicationName = appName;
clientInfo = clientInformation;
if (!appName) {
throw "Please provide some application name ex: new Nextprot.Client('demo application for visualizing peptides', clientInformation);";
}
if (!clientInformation) {
throw "Please provide some client information ex: new Nextprot.Client(applicationName, 'Calipho SIB at Geneva');";
}
};
//////////////// BEGIN Setters ////////////////////////////////////////////////////////////////////////
/** By default it is set to https://api.nextprot.org */
NextprotClient.prototype.setApiBaseUrl = function (_apiBaseUrl) {
apiBaseUrl = _apiBaseUrl;
sparqlEndpoint = apiBaseUrl + "/sparql";
};
/** By default it is set to https://api.nextprot.org/sparql */
NextprotClient.prototype.setSparqlEndpoint = function (_sparqlEndpoint) {
sparqlEndpoint = _sparqlEndpoint;
};
//////////////// END Setters ////////////////////////////////////////////////////////////////////////
//Gets the entry set in the parameter
NextprotClient.prototype.getEnvironment = function () {
return _getURLParameter("env") || 'pro'; //By default returns the insulin
};
NextprotClient.prototype.getApiBaseUrl = function () {
return apiBaseUrl;
};
//Gets the entry set in the parameter
NextprotClient.prototype.getEntryName = function () {
return normalizeEntry(_getURLParameter("nxentry") || 'NX_P01308'); //By default returns the insulin
};
NextprotClient.prototype.getInputOption = function () {
return _getURLParameter("inputOption") || ''; //By default returns the insulin
};
NextprotClient.prototype.changeEntry = function (elem) {
var new_url = _changeParamOrAddParamByName(window.location.href, "nxentry", elem.value);
window.location.href = new_url;
};
NextprotClient.prototype.getEntryforPeptide = function (seq) {
return _callPepX(seq, "true").then(function (data) {
return data;
});
};
var _transformPrefixesFunction = function (result) {
var sparqlPrefixes = "";
result.map(function (p) {
sparqlPrefixes += (p + "\n");
});
return sparqlPrefixes;
};
// Keeps SPARQL prefixes in cache
var sparqlPrefixPromise;
NextprotClient.prototype.getSparqlPrefixes = function () {
sparqlPrefixPromise = sparqlPrefixPromise || _getJSON(apiBaseUrl + "/sparql-prefixes").then(_transformPrefixesFunction);
return sparqlPrefixPromise;
};
NextprotClient.prototype.executeSparql = function (sparql, includePrefixes) {
return this.getSparqlPrefixes().then(function (sparqlPrefixes) {
var incPrefs = (includePrefixes === undefined) ? true : includePrefixes;
var sparqlQuery = incPrefs ? sparqlPrefixes + sparql : sparql; //add SPARQL prefixes if flag not set to false
var url = sparqlEndpoint + sparqlFormat + "&query=" + encodeURIComponent(sparqlQuery);
return _getJSON(url);
});
};
NextprotClient.prototype.getEntryProperties = function (entry) {
return _getEntry(entry, "accession").then(function (data) {
return data.entry.properties;
});
};
NextprotClient.prototype.getProteinOverview = function (entry) {
return _getEntry(entry, "overview").then(function (data) {
return data.entry.overview;
});
};
NextprotClient.prototype.getProteinSequence = function (entry) {
return _getEntry(entry, "isoform").then(function (data) {
return data.entry.isoforms;
});
};
NextprotClient.prototype.getXrefs = function (entry) {
return _getEntry(entry, "xref").then(function (data) {
return data.entry.xrefs;
});
};
/** USE THIS INSTEAD OF THE OTHERS for example getEntryPart(NX_1038042, "ptm") */
NextprotClient.prototype.getAnnotationsByCategory = function (entry, category) {
return _getEntry(entry, category).then(function (data) {
return _convertToTupleMap(data);
});
};
NextprotClient.prototype.getFullAnnotationsByCategory = function (entry, category) {
return _getEntry(entry, category).then(function (data) {
return data.entry;
});
};
NextprotClient.prototype.getEntry = function (entry, category) {
return _getEntry(entry, category).then(function (data) {
return data.entry;
});
};
NextprotClient.prototype.getEntryProperties = function (entry) {
return _getEntry(entry, "accession").then(function (data) {
return data.entry.properties;
});
};
/* Special method to retrieve isoforms mapping on the master sequence (should not be used by public) */
NextprotClient.prototype.getIsoformMapping = function (entry) {
return _getEntry(entry, "isoform/mapping").then(function (data) {
return data;
});
};
NextprotClient.prototype.getGenomicMappings = function (entry) {
return _getEntry(entry, "genomic-mapping").then(function (data) {
return data.entry.genomicMappings;
});
};
// BEGIN Special cases to be deprecated //////////////////////////////////////////////////////////////////////////////
NextprotClient.prototype.getPeptide = function (entry) {
console.warn("getPeptide is deprecated. use getAnnotationsByCategory(entry, 'peptide-mapping') instead ");
return _getEntry(entry, "peptide-mapping").then(function (data) {
return data.entry.peptideMappings;
});
};
NextprotClient.prototype.getSrmPeptide = function (entry) {
console.warn("getSrmPeptide is deprecated. use getAnnotationsByCategory(entry, 'srm-peptide-mapping') instead ");
return _getEntry(entry, "srm-peptide-mapping").then(function (data) {
return data.entry.srmPeptideMappings;
});
};
NextprotClient.prototype.getAntibody = function (entry) {
//this is not deprecated yet
return _getEntry(entry, "antibody").then(function (data) {
return data.entry.antibodyMappings;
});
};
// END Special cases to be deprecated //////////////////////////////////////////////////////////////////////////////
NextprotClient.prototype.getTerminologyByName = function (terminologyName) {
return _callTerminology(terminologyName).then(function (data) {
return data;
});
};
//node.js compatibility
if (typeof exports !== 'undefined') {
exports.Client = NextprotClient;
}
root.Nextprot.Client = NextprotClient;
}());
}(this));
;
//Utility methods
var NXUtils = {
checkIsoformMatch: function (isoname, isonumber) {
return isoname.endsWith("-" + isonumber)
},
getIsoforms: function(isoforms){
if (isoforms && isoforms.length > 1 ) {
isoforms.sort(NXUtils.sortIsoformNames);
isoforms.forEach(function(iso){
if (iso.synonyms && iso.synonyms.length > 1) iso.synonyms.sort(NXUtils.sortByAlphabet);
})
return isoforms;
}
else return null;
},
getORFNames: function (geneName) {
var names = [];
if (geneName.category === "ORF") {
names.push({name: geneName.name})
}
if (geneName.synonyms) {
geneName.synonyms.forEach(function (gns) {
if (gns.category === "ORF") {
names.push({name: gns.name})
}
})
}
if (names.length) names.sort(NXUtils.sortByAlphabet);
return names;
},
getSynonyms: function (syn) {
var synonyms = {};
if (syn) {
syn.forEach(function (s) {
if (synonyms.hasOwnProperty(s.qualifier)) {
synonyms[s.qualifier].push(s.name);
}
else {
synonyms[s.qualifier]=[s.name];
}
});
}
for (var qualifier in synonyms) {
synonyms[qualifier].sort(NXUtils.sortByAlphabet);
}
return synonyms;
},
sortSynonyms: function(a,b){
var a = a;
var b = b;
if (typeof a !== "string") {
var a = a.name;
var b = b.name;
}
if (a.length === b.length) {
return a.toLowerCase() > b.toLowerCase()
}
return b.toLowerCase().length - a.toLowerCase().length;
},
sortIsoformNames: function(a,b){
if (parseInt(a.name.replace("Iso", "").replace(" ", ""))) {
var first = parseInt(a.name.replace("Iso", "").replace(" ", ""));
var second = parseInt(b.name.replace("Iso", "").replace(" ", ""));
if(first > second) return 1;
if(first < second) return -1;
return 0;
}
else return a.name > b.name;
},
sortByAlphabet: function(a,b) {
var a = typeof a === "string" ? a.toLowerCase() : a.name ? a.name.toLowerCase() : null;
var b = typeof b === "string" ? b.toLowerCase() : b.name ? b.name.toLowerCase() : null;
if (a < b) return -1;
if (a > b) return 1;
return 0;
},
getRecommendedName: function (geneName) {
var name = "";
if (geneName.category === "gene name" && geneName.main === true) {
name = geneName.name;
}
return name;
},
getAlternativeNames: function (altNames) {
var names = [];
if (altNames) {
altNames.forEach(function (an) {
var found = false;
var type = an.type === "name" ? "Alternative name" : an.type === "International Nonproprietary Names" ? "International Nonproprietary Name" : an.type === "allergen" ? "Allergen" : an.type;
for (var elem in names) {
if (names[elem].type === type) {
names[elem].names.push({name: an.name, synonyms: NXUtils.getSynonyms(NXUtils.mergeArraysOfObjects(an.clazz,an.synonyms, an.otherRecommendedEntityNames))});
found = true;
}
}
if (!found) {
names.push({type: type, names: [{name: an.name, synonyms: NXUtils.getSynonyms(NXUtils.mergeArraysOfObjects(an.clazz,an.synonyms, an.otherRecommendedEntityNames))}]})
}
});
}
names.map(function(n){n.names.sort(NXUtils.sortByAlphabet)});
// names.forEach(function(n) {if (n.type === "Alternative name" && n.names.length > 1) {n.type = "Alternative names"}});
return names;
},
mergeArraysOfObjects: function(type,arr1,arr2){
if (!(arr2 && arr2.length> 0)) return arr1;
else if (!(arr1 && arr1.length> 0)) return arr2;
var arr3 = [];
for(var i in arr1){
var shared = false;
for (var j in arr2)
if (arr2[j].name == arr1[i].name) {
shared = true;
break;
}
if(!shared) arr3.push(arr1[i])
}
arr3 = arr3.concat(arr2);
return arr3;
},
getMainSynonym: function (sy) {
var mainName;
var syProtNames= sy.filter(function(a) {return a.qualifier === "full"});
if (syProtNames.length) {
var name = syProtNames.sort(function (a, b) {
return b.name.length - a.name.length;
})[0];
mainName = {
name: name.name,
synonym: name.synonyms && name.synonyms.length > 0 ? name.synonyms.sort(NXUtils.sortByAlphabet)[0].name : null
}
}
return mainName;
},
getMainShort: function (sh) {
var name;
name = sh[sh.length-1].charAt(0) === "h" ? sh[sh.length-2] ? sh[sh.length-2] : sh[sh.length-1] : sh[sh.length-1];
return name;
},
getFamily: function (f,family) {
f.level === "Superfamily" ? family["superfamily"]= {name:f.name, accession:f.accession} : "";
f.level === "Family" ? family["family"]= {name:f.name, accession:f.accession} : "";
f.level === "Subfamily" ? family["subfamily"]= {name:f.name, accession:f.accession} : "";
if (f.parent) {
NXUtils.getFamily(f.parent,family);
}
return family;
},
getProteinExistence: function(term){
var existence = term.split('_').join(' ').toLowerCase();
mainSentence = "Entry whose protein(s) existence is ";
based = "based on ";
switch(existence) {
case "uncertain":
return mainSentence + existence;
break;
case "inferred from homology":
return mainSentence + existence;
break;
default:
return mainSentence + based + existence;
break;
}
},
getSequenceForIsoform: function (isoSequences, isoformName) {
var result = null;
//TODO allow users to specify isoform name without NX_
//TODO the API should return the results in a sorted array
if (typeof isoformName === "number") {
isoSequences.forEach(function (d) {
if (d.uniqueName.endsWith("-" + isoformName)) {
result = d.sequence;
}
});
} else {
isoSequences.forEach(function (d) {
if (d.uniqueName === isoformName)
return d.sequence;
})
}
return result;
},
getLinkForFeature: function (accession, description, type) {
if (type === "Peptide" || type === "SRM Peptide") {
if (description) {
var url = "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptide?searchWithinThis=Peptide+Name&searchForThis=" + description + ";organism_name=Human";
return "<a href='" + url + "'>" + description + "</a>";
}
} else if (type === "antibody") {
var url = accession;
return "<a href='" + url + "'>" + description + "</a>";
} else if (accession) {
var url = "http://www.nextprot.org/db/term/" + accession;
return "<a href='" + url + "'>" + description + "</a>";
} else if (type === "publication") {
var url = "http://www.nextprot.org/db/publication/" + accession;
return "<a href='" + url + "'>" + description + "</a>";
} else if (description) return description;
else return "";
},
getDescription: function (elem, category) {
if (category === "Peptide" || category === "SRM Peptide") {
for (var ev in elem.evidences) {
if (elem.evidences[ev].resourceDb === "PeptideAtlas" || elem.evidences[ev].resourceDb === "SRMAtlas") {
return elem.evidences[ev].resourceAccession;
}
}
return "";
}
else return elem.description;
},
getEvidenceCodeName: function (elem, category) {
if (category === "Peptide") {
return "EXP";
}
else return elem.evidenceCodeName;
},
getAssignedBy: function (elem) {
if (elem === "Uniprot") {
return "UniprotKB";
}
if (elem.startsWith("MD") || elem.startsWith("PM")) {
return "neXtProt";
}
else return elem;
},
getProteotypicity: function (elem) {
if (elem) {
var proteo = true;
elem.forEach(function(p) {
if (p.name === "is proteotypic" && p.value === "N") proteo=false;
});
return proteo;
}
else return true;
},
convertMappingsToIsoformMap: function (featMappings, category, group) {
var mappings = jQuery.extend([], featMappings);
var publiActive = false;
if (featMappings.hasOwnProperty("annot")) {
publiActive = true;
mappings = jQuery.extend([], featMappings.annot);
}
var result = {};
mappings.forEach(function (mapping) {
if (mapping.hasOwnProperty("targetingIsoformsMap")) {
for (var name in mapping.targetingIsoformsMap) {
if (mapping.targetingIsoformsMap.hasOwnProperty(name)) {
var start = mapping.targetingIsoformsMap[name].firstPosition,
end = mapping.targetingIsoformsMap[name].lastPosition,
description = NXUtils.getDescription(mapping,category),
link = NXUtils.getLinkForFeature(mapping.cvTermAccessionCode, description, category),
quality = mapping.qualityQualifier !== "GOLD" ? mapping.qualityQualifier.toLowerCase() : "",
proteotypic = NXUtils.getProteotypicity(mapping.properties),
source = mapping.evidences.map(function (d) {
var pub = null;
var xref = null;
if (publiActive) {
if (featMappings.publi[d.publicationMD5]) {
pub = d.publicationMD5;
}
if (featMappings.xrefs[d.resourceId]) {
xref = featMappings.xrefs[d.resourceId];
}
return {
evidenceCodeName: NXUtils.getEvidenceCodeName(d,category),
assignedBy: NXUtils.getAssignedBy(d.assignedBy),
resourceDb: d.resourceDb,
externalDb: d.resourceDb !== "UniProt",
publicationMD5: d.publicationMD5,
title: pub ? NXUtils.getLinkForFeature(featMappings.publi[pub].publicationId, featMappings.publi[pub].title, "publication") : "",
authors: pub ? featMappings.publi[pub].authors.map(function (d) {
return {
lastName: d.lastName,
initials: d.initials
}
}) : [],
journal: pub ? featMappings.publi[pub].cvJournal ? featMappings.publi[pub].cvJournal.name : "" : "",
volume: pub ? featMappings.publi[pub].volume : "",
year: pub ? featMappings.publi[pub].publicationYear : "",
firstPage: pub ? featMappings.publi[pub].firstPage : "",
lastPage: pub ? (featMappings.publi[pub].lastPage === "" ? featMappings.publi[pub].firstPage : featMappings.publi[pub].lastPage) : "",
pubId: pub ? featMappings.publi[pub].publicationId : "",
abstract: pub ? featMappings.publi[pub].abstractText : "",
dbXrefs: pub ? featMappings.publi[pub].dbXrefs.map(function (o) {
return {
name: o.databaseName === "DOI" ? "Full Text" : o.databaseName,
url: o.resolvedUrl,
accession: o.accession
}
}) : [],
crossRef: xref ? {
dbName: xref.databaseName,
name: xref.accession,
url: xref.resolvedUrl
} : null
}
} else return {
evidenceCodeName: NXUtils.getEvidenceCodeName(d,category),
assignedBy: NXUtils.getAssignedBy(d.assignedBy),
publicationMD5: d.publicationMD5,
title: "",
authors: [],
journal: "",
volume: "",
abstract: ""
}
}),
variant = false;
if (mapping.hasOwnProperty("variant") && !jQuery.isEmptyObject(mapping.variant)) {
link = "<span style='color:#00C500'>" + mapping.variant.original + " → " + mapping.variant.variant + "</span>";
description = "<span style=\"color:#00C500\">" + mapping.variant.original + " → " + mapping.variant.variant + "</span> ";
variant = true;
if (mapping.description) {
var reg = /\[(.*?)\]/g;
var match = reg.exec(mapping.description);
var desc = mapping.description;
if (match) {
var parseMatch = match[1].split(":");
var desc = mapping.description.replace(/(\[.*?\])/g, NXUtils.getLinkForFeature(parseMatch[2], parseMatch[0]));
}
link += " ; " + desc;
}
}
if (!result[name]) result[name] = [];
result[name].push({
start: start,
end: end,
length: end - start + 1,
id: category.replace(/\s/g, '') + "_" + start.toString() + "_" + end.toString(),
description: description,
quality: quality,
proteotypicity: proteotypic,
category: category,
group: group,
link: link,
evidenceLength: source.length,
source: source,
variant: variant
});
}
}
}
//TODO This is the old format, the API should evolve
else if (mapping.hasOwnProperty("isoformSpecificity")) {
for (var name in mapping.isoformSpecificity) {
if (mapping.isoformSpecificity.hasOwnProperty(name)) {
for (var i = 0; i < mapping.isoformSpecificity[name].positions.length; i++) {
var start = mapping.isoformSpecificity[name].positions[i].first,
end = mapping.isoformSpecificity[name].positions[i].second,
description = "",
link = "",
source = [];
if (mapping.hasOwnProperty("evidences")) {
source = mapping.evidences.map(function (d) {
return {
evidenceCodeName: d.evidenceCodeName,
assignedBy: d.assignedBy,
publicationMD5: d.publicationMD5
}
});
}
if (mapping.hasOwnProperty("xrefs")) {
description = mapping.xrefs[0].accession;
link = NXUtils.getLinkForFeature(mapping.xrefs[0].resolvedUrl, description, "antibody")
} else {
description = mapping.evidences[0].accession;
for (ev in mapping.evidences)
if (mapping.evidences[ev].databaseName === "PeptideAtlas" || mapping.evidences[ev].databaseName === "SRMAtlas") {
description = mapping.evidences[ev].accession;
link = NXUtils.getLinkForFeature(description, description, "peptide");
break;
}
}
if (!result[name]) result[name] = [];
result[name].push({
start: start,
end: end,
length: end - start,
id: category.replace(/\s/g, '') + "_" + start.toString() + "_" + end.toString(),
description: description,
category: category,
group: group,
link: link,
evidenceLength: source.length,
source: source
});
}
}
}
}
});
for (var iso in result) {
result[iso].sort(function (a, b) {
if (a.start === b.start) {
if (a.length === b.length) return b.id > a.id;
else return b.length - a.length;
}
if (a.end === null) return 1;
return a.start - b.start;
})
}
return result;
},
convertPublications: function (publi, HashMD5) {
for (var pub in publi) {
HashMD5[publi[pub].md5] = {
title: publi[pub].title,
author: publi[pub].authors.map(function (d) {
return {
lastName: d.lastName,
initials: d.initials
}
}),
journal: publi[pub].cvJournal.name,
volume: publi[pub].volume,
abstract: publi[pub].abstractText
}
}
},
convertExonsMappingsToIsoformMap: function (mappings) {
return mappings.map(function (d) {
return {
uniqueName: d.uniqueName,
isoMainName: d.isoMainName,
mapping: d.positionsOfIsoformOnReferencedGene.map(function (o) {
return {
start: o.key,
end: o.value
};
})
}
})
}
};
var NXViewerUtils = {
convertNXAnnotations: function (annotations, metadata) {
if (!annotations) return "Cannot load this";
var result = {};
for (name in annotations) {
var meta = jQuery.extend({}, metadata);
meta.data = annotations[name].map(function (annotation) {
return {
x: annotation.start,
y: annotation.end,
id: annotation.id,
category: annotation.category,
description: annotation.description
}
});
result[name] = meta;
}
return result;
}
};
if ( typeof module === "object" && typeof module.exports === "object" ) {
module.exports = {
NXUtils: NXUtils,
NXViewerUtils : NXViewerUtils
}
};
$(function () {
var loadOverview = function (overview, nxEntryName) {
if ($("#nx-overview").length > 0) {
Handlebars.registerHelper('link_to', function (type, options) {
switch (type) {
case "term":
var url = "http://www.nextprot.org/db/term/" + this.accession;
return "<a target='_blank' href='" + url + "'>" + this.name + "</a>";
case "EC" :
var url = "http://www.nextprot.org/db/term/" + this;
return "<a target='_blank' href='" + url + "'> EC " + this + " </a>";
case "history":
var url = "http://www.uniprot.org/uniprot/" + this.slice(3) + "?version=*";
return "<a target='_blank' href='" + url + "'>Complete UniProtKB history</a>";
}
});
Handlebars.registerHelper('plural', function (array, options) {
return array.length > 1 ? "s" : "";
});
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);
}
var recommendedProteinSynonyms = NXUtils.getSynonyms(overview.recommendedProteinName.synonyms);
var isonames = overview.isoformNames;
var 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,{})}),
"proteineEvidence": NXUtils.getProteinExistence(overview.proteinExistence),
"proteineEvidenceCaution": overview.proteinExistenceInfo,
"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": overview.history.lastSequenceUpdate,
"accessionNumber": nxEntryName
};
var template = HBtemplates['templates/overviewProtein.tmpl'];
var result = template(data);
$("#nx-overview").append(result);
$("#extender").click(function (event) {
event.stopPropagation();
//var isScrollbarActiveAtFirst= $(window).hasVerticalScrollBar();
$("#INFOS-FULL").toggle("slow");
$("#INFOS-LESS").toggle("slow");
//var isScrollbarActiveAtEnd= $(window).hasVerticalScrollBar();
//if ((isScrollbarActiveAtFirst) && isScrollbarActiveAtFirst !== isScrollbarActiveAtEnd) {
// $(body).removeClass("ignoreShift");
//}
//else if ((isScrollbarActiveAtFirst === false) && isScrollbarActiveAtFirst !== isScrollbarActiveAtEnd) {
// $(body).addClass("ignoreShift");
//}
$(this).text(function (i, text) {
return text === "Extend overview" ? "Collapse overview" : "Extend overview";
});
});
}
};
if ($("#nx-overview").length > 0) { // load the overview if it exists
var Nextprot = window.Nextprot;
var nx = new Nextprot.Client("neXtprot overview loader", "Calipho Group");
var nxEntryName = nx.getEntryName();
nx.getProteinOverview().then(function (data) {
loadOverview(data, nxEntryName);
var nxInputOption = nx.getInputOption();
function addEntrySelection() {
$("body").prepend("<div id=\"inputOptionDiv\" class=\"col-md-2 col-md-offset-5 centered\" style=\"position:absolute;padding:10px;padding-top:0px;z-index:12\">" +
"<div class=\"panel panel-default\"><div class=\"panel-body\">" +
"<input id=\"entrySelector\" type=\"text\" class=\"form-control\" placeholder=\"neXtProt or UniProt accession...\"></div>" +
"</div></div>");
$('#entrySelector').keyup(function (e) {
if (e.keyCode == 13) nx.changeEntry(this);
})
}
if (nxInputOption === "true") {
addEntrySelection();
nx.getEntryProperties().then(function (data) {
$(function () {
$("#inputOptionDiv").append("<div class=\"alert alert-success entry-alert\" role=\"alert\" style=\"display:none\">You successfully load the entry !</div>");
$(".entry-alert").fadeIn("slow");
$(".entry-alert").delay(2000).fadeOut("slow");
});
}, function (error) {
$(function () {
$("#inputOptionDiv").append("<div class=\"alert alert-danger entry-alert\" role=\"alert\">This accession is not available !</div>");
});
console.error("Failed!", error);
});
}
});
if(nx.getEnvironment() !== 'pro'){
$("body").append("<span style='position: absolute; top: 0; left: 0; border: 0; color: darkred; margin: 20px; font-weight: bold'>" + nx.getEnvironment().toUpperCase() + " API</span>");
}
}
});
;
this["HBtemplates"] = this["HBtemplates"] || {};
this["HBtemplates"]["templates/overviewProtein.tmpl"] = Handlebars.template({"1":function(container,depth0,helpers,partials,data) {
var stack1;
return " "
+ ((stack1 = helpers["if"].call(depth0 != null ? depth0 : {},((stack1 = ((stack1 = (depth0 != null ? depth0.geneName : depth0)) != null ? stack1["0"] : stack1)) != null ? stack1.name : stack1),{"name":"if","hash":{},"fn":container.program(2, data, 0),"inverse":container.noop,"data":data})) != null ? stack1 : "");
},"2":function(container,depth0,helpers,partials,data) {
var stack1;
return container.escapeExpression(container.lambda(((stack1 = ((stack1 = (depth0 != null ? depth0.geneName : depth0)) != null ? stack1["0"] : stack1)) != null ? stack1.name : stack1), depth0))
+ " → ";
},"4":function(container,depth0,helpers,partials,data) {
var stack1, alias1=depth0 != null ? depth0 : {};
return ((stack1 = helpers["if"].call(alias1,(depth0 != null ? depth0.EC : depth0),{"name":"if","hash":{},"fn":container.program(5, data, 0),"inverse":container.noop,"data":data})) != null ? stack1 : "")
+ ((stack1 = helpers["if"].call(alias1,(depth0 != null ? depth0.mainShortName : depth0),{"name":"if","hash":{},"fn":container.program(9, data, 0),"inverse":container.noop,"data":data})) != null ? stack1 : "");
},"5":function(container,depth0,helpers,partials,data) {
var stack1, helper, options, buffer =
"[";
stack1 = ((helper = (helper = helpers.EC || (depth0 != null ? depth0.EC : depth0)) != null ? helper : helpers.helperMissing),(options={"name":"EC","hash":{},"fn":container.program(6, data, 0),"inverse":container.noop,"data":data}),(typeof helper === "function" ? helper.call(depth0 != null ? depth0 : {},options) : helper));
if (!helpers.EC) { stack1 = helpers.blockHelperMissing.call(depth0,stack1,options)}
if (stack1 != null) { buffer += stack1; }
return buffer + " ] ";
},"6":function(container,depth0,helpers,partials,data) {
var stack1, alias1=depth0 != null ? depth0 : {};
return " "
+ ((stack1 = (helpers.link_to || (depth0 && depth0.link_to) || helpers.helperMissing).call(alias1,"EC",{"name":"link_to","hash":{},"data":data})) != null ? stack1 : "")
+ " "
+ ((stack1 = helpers.unless.call(alias1,(data && data.last),{"name":"unless","hash":{},"fn":container.program(7, data, 0),"inverse":container.noop,"data":data})) != null ? stack1 : "")
+ " ";
},"7":function(container,depth0,helpers,partials,data) {
return ",";
},"9":function(container,depth0,helpers,partials,data) {
var helper;
return "( "
+ container.escapeExpression(((helper = (helper = helpers.mainShortName || (depth0 != null ? depth0.mainShortName : depth0)) != null ? helper : helpers.helperMissing),(typeof helper === "function" ? helper.call(depth0 != null ? depth0 : {},{"name":"mainShortName","hash":{},"data":data}) : helper)))
+ " ) ";
},"11":function(container,depth0,helpers,partials,data) {
var stack1, helper, options, buffer =
" <div id=\"synonym-less\" class=\"row\">\r\n <div class=\"col-md-3 col-xs-3\" style=\"color: grey;text-align:right\">Protein also known as :</div>\r\n <div class=\"col-md-9 col-xs-9\">";
stack1 = ((helper = (helper = helpers.recommendedProteinName || (depth0 != null ? depth0.recommendedProteinName : depth0)) != null ? helper : helpers.helperMissing),(options={"name":"recommendedProteinName","hash":{},"fn":container.program(12, data, 0),"inverse":container.noop,"data":data}),(typeof helper === "function" ? helper.call(depth0 != null ? depth0 : {},options) : helper));
if (!helpers.recommendedProteinName) { stack1 = helpers.blockHelperMissing.call(depth0,stack1,options)}
if (stack1 != null) { buffer += stack1; }
return buffer + "</div>\r\n </div>\r\n";
},"12":function(container,depth0,helpers,partials,data) {
var stack1, helper, options, alias1=depth0 != null ? depth0 : {}, alias2=helpers.helperMissing, alias3="function", alias4=helpers.blockHelperMissing, buffer = "";
stack1 = ((helper = (helper = helpers.mainSynonymName || (depth0 != null ? depth0.mainSynonymName : depth0)) != null ? helper : alias2),(options={"name":"mainSynonymName","hash":{},"fn":container.program(13, data, 0),"inverse":container.noop,"data":data}),(typeof helper === alias3 ? helper.call(alias1,options) : helper));
if (!helpers.mainSynonymName) { stack1 = alias4.call(depth0,stack1,options)}
if (stack1 != null) { buffer += stack1; }
buffer += " "
+ ((stack1 = helpers["if"].call(alias1,(depth0 != null ? depth0.others : depth0),{"name":"if","hash":{},"fn":container.program(16, data, 0),"inverse":container.noop,"data":data})) != null ? stack1 : "");
stack1 = ((helper = (helper = helpers.others || (depth0 != null ? depth0.others : depth0)) != null ? helper : alias2),(options={"name":"others","hash":{},"fn":container.program(18, data, 0),"inverse":container.noop,"data":data}),(typeof helper === alias3 ? helper.call(alias1,options) : helper));
if (!helpers.others) { stack1 = alias4.call(depth0,stack1,options)}
if (stack1 != null) { buffer += stack1; }
return buffer;
},"13":function(container,depth0,helpers,partials,data) {
var stack1, helper, alias1=depth0 != null ? depth0 : {};
return container.escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helpers.helperMissing),(typeof helper === "function" ? helper.call(alias1,{"name":"name","hash":{},"data":data}) : helper)))
+ ((stack1 = helpers["if"].call(alias1,(depth0 != null ? depth0.synonym : depth0),{"name":"if","hash":{},"fn":container.program(14, data, 0),"inverse":container.noop,"data":data})) != null ? stack1 : "");
},"14":function(container,depth0,helpers,partials,data) {
var helper;
return " ("
+ container.escapeExpression(((helper = (helper = helpers.synonym || (depth0 != null ? depth0.synonym : depth0)) != null ? helper : helpers.helperMissing),(typeof helper === "function" ? helper.call(depth0 != null ? depth0 : {},{"name":"synonym","hash":{},"data":data}) : helper)))
+ ") ";
},"16":function(container,depth0,helpers,partials,data) {
return " ; ";
},"18":function(container,depth0,helpers,partials,data) {
var stack1, helper, options, alias1=depth0 != null ? depth0 : {}, alias2=helpers.helperMissing, alias3="function", alias4=container.escapeExpression, buffer =
alias4(((helper = (helper = helpers.type || (depth0 != null ? depth0.type : depth0)) != null ? helper : alias2),(typeof helper === alias3 ? helper.call(alias1,{"name":"type","hash":{},"data":data}) : helper)))
+ alias4((helpers.plural || (depth0 && depth0.plural) || alias2).call(alias1,(depth0 != null ? depth0.names : depth0),{"name":"plural","hash":{},"data":data}))
+ ":";
stack1 = ((helper = (helper = helpers.names || (depth0 != null ? depth0.names : depth0)) != null ? helper : alias2),(options={"name":"names","hash":{},"fn":container.program(19, data, 0),"inverse":container.noop,"data":data}),(typeof helper === alias3 ? helper.call(alias1,options) : helper));
if (!helpers.names) { stack1 = helpers.blockHelperMissing.call(depth0,stack1,options)}
if (stack1 != null) { buffer += stack1; }
return buffer + ((stack1 = helpers.unless.call(alias1,(data && data.last),{"name":"unless","hash":{},"fn":container.program(21, data, 0),"inverse":container.noop,"data":data})) != null ? stack1 : "");
},"19":function(container,depth0,helpers,partials,data) {
var stack1, helper, alias1=depth0 != null ? depth0 : {};
return " "
+ container.escapeExpression(((helper = (helper = helpers.name || (depth0 != null ? depth0.name : depth0)) != null ? helper : helpers.helperMissing),(typeof helper === "function" ? helper.call(alias1,{"name":"name","hash":{},"data":data}) : helper)))
+ ((stack1 = helpers.unless.call(alias1,(data && data.last),{"name":"unless","hash":{},"fn":container.program(7, data, 0),"inverse":container.noop,"data":data})) != null ? stack1 : "");
},"21":function(container,depth0,helpers,partials,data) {
return "; ";
},"23":function(container,depth0,helpers,partials,data) {
var stack1;
return ((stack1 = helpers["if"].call(depth0 != null ? depth0 : {},((stack1 = (depth0 != null ? depth0.recommendedProteinName : depth0)) != null ? stack1.others : stack1),{"name":"if","hash":{},"fn":container.program(24, data, 0),"inverse":container.noop,"data":data})) != null ? stack1 : "");
},"24":function(container,depth0,helpers,partials,data) {
var stack1, helper, options, buffer =
" <div id=\"synonym-other-less\" class=\"row\">\r\n <div class=\"col-md-3 col-xs-3\" style=\"color: grey;text-align:right\">Protein also known as :</div>\r\n <div class=\"col-md-9 col-xs-9\">";
stack1 = ((helper = (helper = helpers.recommendedProteinName || (depth0 != null ? depth0.recommendedProteinName : depth0)) != null ? helper : helpers.helperMissing),(options={"name":"recommendedProteinName","hash":{},"fn":container.program(25, data, 0),"inverse":c