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Build # 2118

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eweitz

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Consolidate Gene Hints into Gene Leads

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/src/js/ideogram.js

/**
 * @fileoverview Core module of Ideogram.js, links all other modules
 * This file defines the Ideogram class, its constructor method, and its
 * static methods.  All instance methods are defined in other modules.
 *
 */

import version from './version';

import {
  configure, initDrawChromosomes, handleRotateOnClick, onLoad,
  init, finishInit, writeContainer
} from './init/init';

import {
  onLoadAnnots, onDrawAnnots, processAnnotData, restoreDefaultTracks,
  updateDisplayedTracks, initAnnotSettings, fetchAnnots, drawAnnots,
  getHistogramBars, drawHeatmaps, deserializeAnnotsForHeatmap, fillAnnots,
  drawProcessedAnnots, drawSynteny, startHideAnnotTooltipTimeout,
  showAnnotTooltip, onWillShowAnnotTooltip, onDidShowAnnotTooltip,
  setOriginalTrackIndexes,
  afterRawAnnots, onClickAnnot, downloadAnnotations, addAnnotLabel,
  removeAnnotLabel, fillAnnotLabels, clearAnnotLabels, flattenAnnots
  // fadeOutAnnotLabels
} from './annotations/annotations';

import {highlight, unhighlight} from './annotations/highlight';

import {
  esearch, esummary, elink,
  getOrganismFromEutils, getTaxids,
  getAssemblyAndChromosomesFromEutils
} from './services/services';

import {
  drawBandLabels, getBandColorGradients, processBandData,
  setBandsToShow, hideUnshownBandLabels, drawBandLabelText, drawBandLabelStalk
} from './bands/bands';

import {onBrushMove, onBrushEnd, createBrush} from './brush';
import {onCursorMove, createClickCursor} from './cursor';
import {drawSexChromosomes, setSexChromosomes} from './sex-chromosomes';
import {convertBpToPx, convertPxToBp} from './coordinate-converters';
import {
  unpackAnnots, packAnnots, initCrossFilter, filterAnnots
} from './filter';

import {
  assemblyIsAccession, getDataDir, round, onDidRotate, getSvg, d3,
  getTaxid, getCommonName, getScientificName, fetch as _fetch,
  isRoman, parseRoman
} from './lib';

import {
  getChromosomeModel, getChromosomePixels
} from './views/chromosome-model';

import {
  appendHomolog, drawChromosome, rotateAndToggleDisplay, setOverflowScroll
} from './views/draw-chromosomes';

import {
  drawChromosomeLabels, rotateChromosomeLabels
} from './views/chromosome-labels.js';

import {
  _initGeneLeads, _initRelatedGenes,
  plotRelatedGenes, getRelatedGenesByType
} from './kit/related-genes';

export default class Ideogram {
  constructor(config) {

    // Functions from init.js
    this.configure = configure;
    this.initDrawChromosomes = initDrawChromosomes;
    this.onLoad = onLoad;
    this.handleRotateOnClick = handleRotateOnClick;
    this.init = init;
    this.finishInit = finishInit;
    this.writeContainer = writeContainer;

    // Functions from annotations.js
    this.onLoadAnnots = onLoadAnnots;
    this.onDrawAnnots = onDrawAnnots;
    this.processAnnotData = processAnnotData;
    this.restoreDefaultTracks = restoreDefaultTracks;
    this.updateDisplayedTracks = updateDisplayedTracks;
    this.initAnnotSettings = initAnnotSettings;
    this.fetchAnnots = fetchAnnots;
    this.drawAnnots = drawAnnots;
    this.getHistogramBars = getHistogramBars;
    this.drawHeatmaps = drawHeatmaps;
    this.deserializeAnnotsForHeatmap = deserializeAnnotsForHeatmap;
    this.fillAnnots = fillAnnots;
    this.drawProcessedAnnots = drawProcessedAnnots;
    this.drawSynteny = drawSynteny;
    this.startHideAnnotTooltipTimeout = startHideAnnotTooltipTimeout;
    this.showAnnotTooltip = showAnnotTooltip;
    this.onWillShowAnnotTooltip = onWillShowAnnotTooltip;
    this.onDidShowAnnotTooltip = onDidShowAnnotTooltip;
    this.onClickAnnot = onClickAnnot;
    this.setOriginalTrackIndexes = setOriginalTrackIndexes;
    this.afterRawAnnots = afterRawAnnots;
    this.downloadAnnotations = downloadAnnotations;
    this.addAnnotLabel = addAnnotLabel;
    this.removeAnnotLabel = removeAnnotLabel;
    // this.fadeOutAnnotLabels = fadeOutAnnotLabels;
    this.fillAnnotLabels = fillAnnotLabels;
    this.clearAnnotLabels = clearAnnotLabels;
    this.flattenAnnots = flattenAnnots;

    this.highlight = highlight;
    this.unhighlight = unhighlight;

    // Variables and functions from services.js
    this.esearch = esearch;
    this.esummary = esummary;
    this.elink = elink;
    this.getOrganismFromEutils = getOrganismFromEutils;
    this.getTaxids = getTaxids;
    this.getAssemblyAndChromosomesFromEutils =
      getAssemblyAndChromosomesFromEutils;

    // Functions from bands.js
    this.drawBandLabels = drawBandLabels;
    this.getBandColorGradients = getBandColorGradients;
    this.processBandData = processBandData;
    this.setBandsToShow = setBandsToShow;
    this.hideUnshownBandLabels = hideUnshownBandLabels;
    this.drawBandLabelText = drawBandLabelText;
    this.drawBandLabelStalk = drawBandLabelStalk;

    // Functions from brush.js
    this.onBrushMove = onBrushMove;
    this.onBrushEnd = onBrushEnd;
    this.createBrush = createBrush;

    // Functions from cursor.js
    this.createClickCursor = createClickCursor;
    this.onCursorMove = onCursorMove;

    // Functions from sex-chromosomes.js
    this.drawSexChromosomes = drawSexChromosomes;
    this.setSexChromosomes = setSexChromosomes;

    // Functions from coordinate-converters.js
    this.convertBpToPx = convertBpToPx;
    this.convertPxToBp = convertPxToBp;

    // Functions from filter.js
    this.unpackAnnots = unpackAnnots;
    this.packAnnots = packAnnots;
    this.initCrossFilter = initCrossFilter;
    this.filterAnnots = filterAnnots;

    // Functions from lib
    this.assemblyIsAccession = assemblyIsAccession;
    this.getDataDir = getDataDir;
    this.round = round;
    this.onDidRotate = onDidRotate;
    this.getSvg = getSvg;
    this.fetch = _fetch;
    this.getTaxid = getTaxid;
    this.getCommonName = getCommonName;
    this.getScientificName = getScientificName;

    // Functions from views/chromosome-model.js
    this.getChromosomeModel = getChromosomeModel;
    this.getChromosomePixels = getChromosomePixels;

    // Functions from views/chromosome-labels.js
    this.drawChromosomeLabels = drawChromosomeLabels;
    this.rotateChromosomeLabels = rotateChromosomeLabels;

    // Functions from views/draw-chromosomes.js
    this.appendHomolog = appendHomolog;
    this.drawChromosome = drawChromosome;
    this.rotateAndToggleDisplay = rotateAndToggleDisplay;
    this.setOverflowScroll = setOverflowScroll;

    this.plotRelatedGenes = plotRelatedGenes;
    this.getRelatedGenesByType = getRelatedGenesByType;

    this.configure(config);
  }

  /**
   * Get the current version of Ideogram.js
   */
  static get version() {
    return version;
  }

  /**
  * Enable use of D3 in client apps, via "d3 = Ideogram.d3"
  */
  static get d3() {
    return d3;
  }

  /**
   * Request data from Ensembl REST API
   * Docs: https://rest.ensembl.org/
   *
   * @param {String} path URL path
   * @param {Object} body POST body
   * @param {String} method HTTP method; 'GET' (default) or 'POST'
   */
  static async fetchEnsembl(path, body = null, method = 'GET') {
    const init = {
      method: method
    };
    if (body !== null) init.body = JSON.stringify(body);
    if (method === 'GET') {
      // Use HTTP parameter, not header, to avoid needless OPTIONS request
      const delimiter = path.includes('&') ? '&' : '?';
      path += delimiter + 'content-type=application/json';
    } else {
      // Method is POST, so content-type must be defined in header
      init.headers = {'Content-Type': 'application/json'};
    }

    // const random = Math.random();
    // console.log(random)
    // if (random < 0.5) {
    const response = await fetch(`https://rest.ensembl.org${path}`, init);
    const json = await response.json();
    return json;
    // } else {
    //   // Mock error
    //   init.headers = {'Content-Type': 'application/json'};
    //   const response = await fetch('https://httpstat.us/500/cors', init);
    //   const json = await response.json();
    //   return json;
    // }
  }

  /**
   * Helper for sortChromosomes().
   * Gets names and biological types for diverse chromosome variables
   */
  static getChrSortNamesAndTypes(a, b) {
    var chrAName, chrBName,
      aIsCP, bIsCP, aIsMT, bIsMT, aIsAP, bIsAP, aIsNuclear, bIsNuclear;

    if (typeof a === 'string' || 'chr' in a && 'annots' in a) {
      // Chromosome data is from either:
      //    - Ideogram static file cache (e.g. homo-sapiens.json)
      //    - Ideogram raw annotations
      chrAName = (typeof a === 'string') ? a : a.chr;
      chrBName = (typeof b === 'string') ? b : b.chr;

      aIsCP = chrAName === 'CP';
      bIsCP = chrBName === 'CP';
      aIsMT = chrAName === 'MT';
      bIsMT = chrBName === 'MT';
      aIsAP = chrAName === 'AP';
      bIsAP = chrBName === 'AP';
      aIsNuclear = (!aIsCP && !aIsMT && !aIsAP);
      bIsNuclear = (!bIsCP && !bIsMT && !bIsAP);
    } else {
      // Chromosome data is from NCBI E-Utils web API
      chrAName = a.name;
      chrBName = b.name;

      aIsCP = a.type === 'chloroplast';
      bIsCP = b.type === 'chloroplast';
      aIsMT = a.type === 'mitochondrion';
      bIsMT = b.type === 'mitochondrion';
      aIsAP = a.type === 'apicoplast';
      bIsAP = b.type === 'apicoplast';
      aIsNuclear = a.type === 'nuclear';
      bIsNuclear = b.type === 'nuclear';
    }

    const chrTypes = {
      aIsNuclear, bIsNuclear, aIsCP, bIsCP, aIsMT, bIsMT, aIsAP, bIsAP
    };

    return [chrAName, chrBName, chrTypes];
  }

  /**
   * Sorts two chromosome objects by type and name
   * - Nuclear chromosomes come before non-nuclear chromosomes.
   * - Among nuclear chromosomes, use "natural sorting", e.g.
   *   numbers come before letters
   * - Among non-nuclear chromosomes, i.e. "MT" (mitochondrial DNA) and
   *   "CP" (chromoplast DNA), MT comes first
   *
   * @param a Chromosome string or object "A"
   * @param b Chromosome string or object "B"
   * @returns {Number} JavaScript sort order indicator
   */
  static sortChromosomes(a, b) {

    let [chrAName, chrBName, chrTypes] =
      Ideogram.getChrSortNamesAndTypes(a, b);

    const {
      aIsNuclear, bIsNuclear, aIsCP, bIsCP, aIsMT, bIsMT, aIsAP, bIsAP
    } = chrTypes;

    if (aIsNuclear && bIsNuclear) {

      if (isRoman(chrAName) && isRoman(chrBName)) {
        // As in yeast genome
        chrAName = parseRoman(chrAName).toString();
        chrBName = parseRoman(chrBName).toString();
      }

      return chrAName.localeCompare(chrBName, 'en', {numeric: true});
    } else if (!aIsNuclear && bIsNuclear) {
      return 1;
    } else if (aIsMT && bIsCP) {
      return 1;
    } else if (aIsCP && bIsMT) {
      return -1;
    } else if (!aIsAP && !aIsMT && !aIsCP && (bIsMT || bIsCP || bIsAP)) {
      return -1;
    }
  }

  /**
   * Wrapper for Ideogram constructor, with generic "Related genes" options
   *
   * @param {Object} config Ideogram configuration object
   */
  static initRelatedGenes(config, annotsInList='all') {
    return _initRelatedGenes(config, annotsInList);
  }


  /**
   * Wrapper for Ideogram constructor, with generic "Gene leads" options
   *
   * @param {Object} config Ideogram configuration object
  */
  static initGeneLeads(config, annotsInList='all') {
    return _initGeneLeads(config, annotsInList);
  }
}

1	/**
2	* @fileoverview Core module of Ideogram.js, links all other modules
3	* This file defines the Ideogram class, its constructor method, and its
4	* static methods. All instance methods are defined in other modules.
5	*
6	*/
7
8	import version from './version';
9
10	import {
11	configure, initDrawChromosomes, handleRotateOnClick, onLoad,
12	init, finishInit, writeContainer
13	} from './init/init';
14
15	import {
16	onLoadAnnots, onDrawAnnots, processAnnotData, restoreDefaultTracks,
17	updateDisplayedTracks, initAnnotSettings, fetchAnnots, drawAnnots,
18	getHistogramBars, drawHeatmaps, deserializeAnnotsForHeatmap, fillAnnots,
19	drawProcessedAnnots, drawSynteny, startHideAnnotTooltipTimeout,
20	showAnnotTooltip, onWillShowAnnotTooltip, onDidShowAnnotTooltip,
21	setOriginalTrackIndexes,
22	afterRawAnnots, onClickAnnot, downloadAnnotations, addAnnotLabel,
23	removeAnnotLabel, fillAnnotLabels, clearAnnotLabels, flattenAnnots
24	// fadeOutAnnotLabels
25	} from './annotations/annotations';
26
27	import {highlight, unhighlight} from './annotations/highlight';
28
29	import {
30	esearch, esummary, elink,
31	getOrganismFromEutils, getTaxids,
32	getAssemblyAndChromosomesFromEutils
33	} from './services/services';
34
35	import {
36	drawBandLabels, getBandColorGradients, processBandData,
37	setBandsToShow, hideUnshownBandLabels, drawBandLabelText, drawBandLabelStalk
38	} from './bands/bands';
39
40	import {onBrushMove, onBrushEnd, createBrush} from './brush';
41	import {onCursorMove, createClickCursor} from './cursor';
42	import {drawSexChromosomes, setSexChromosomes} from './sex-chromosomes';
43	import {convertBpToPx, convertPxToBp} from './coordinate-converters';
44	import {
45	unpackAnnots, packAnnots, initCrossFilter, filterAnnots
46	} from './filter';
47
48	import {
49	assemblyIsAccession, getDataDir, round, onDidRotate, getSvg, d3,
50	getTaxid, getCommonName, getScientificName, fetch as _fetch,
51	isRoman, parseRoman
52	} from './lib';
53
54	import {
55	getChromosomeModel, getChromosomePixels
56	} from './views/chromosome-model';
57
58	import {
59	appendHomolog, drawChromosome, rotateAndToggleDisplay, setOverflowScroll
60	} from './views/draw-chromosomes';
61
62	import {
63	drawChromosomeLabels, rotateChromosomeLabels
64	} from './views/chromosome-labels.js';
65
66	import {
67	_initGeneLeads, _initRelatedGenes,
68	plotRelatedGenes, getRelatedGenesByType
69	} from './kit/related-genes';
70
71	export default class Ideogram {
72	constructor(config) {
73
74	// Functions from init.js
75	this.configure = configure;	84✔
76	this.initDrawChromosomes = initDrawChromosomes;	84✔
77	this.onLoad = onLoad;	84✔
78	this.handleRotateOnClick = handleRotateOnClick;	84✔
79	this.init = init;	84✔
80	this.finishInit = finishInit;	84✔
81	this.writeContainer = writeContainer;	84✔
82
83	// Functions from annotations.js
84	this.onLoadAnnots = onLoadAnnots;	84✔
85	this.onDrawAnnots = onDrawAnnots;	84✔
86	this.processAnnotData = processAnnotData;	84✔
87	this.restoreDefaultTracks = restoreDefaultTracks;	84✔
88	this.updateDisplayedTracks = updateDisplayedTracks;	84✔
89	this.initAnnotSettings = initAnnotSettings;	84✔
90	this.fetchAnnots = fetchAnnots;	84✔
91	this.drawAnnots = drawAnnots;	84✔
92	this.getHistogramBars = getHistogramBars;	84✔
93	this.drawHeatmaps = drawHeatmaps;	84✔
94	this.deserializeAnnotsForHeatmap = deserializeAnnotsForHeatmap;	84✔
95	this.fillAnnots = fillAnnots;	84✔
96	this.drawProcessedAnnots = drawProcessedAnnots;	84✔
97	this.drawSynteny = drawSynteny;	84✔
98	this.startHideAnnotTooltipTimeout = startHideAnnotTooltipTimeout;	84✔
99	this.showAnnotTooltip = showAnnotTooltip;	84✔
100	this.onWillShowAnnotTooltip = onWillShowAnnotTooltip;	84✔
101	this.onDidShowAnnotTooltip = onDidShowAnnotTooltip;	84✔
102	this.onClickAnnot = onClickAnnot;	84✔
103	this.setOriginalTrackIndexes = setOriginalTrackIndexes;	84✔
104	this.afterRawAnnots = afterRawAnnots;	84✔
105	this.downloadAnnotations = downloadAnnotations;	84✔
106	this.addAnnotLabel = addAnnotLabel;	84✔
107	this.removeAnnotLabel = removeAnnotLabel;	84✔
108	// this.fadeOutAnnotLabels = fadeOutAnnotLabels;
109	this.fillAnnotLabels = fillAnnotLabels;	84✔
110	this.clearAnnotLabels = clearAnnotLabels;	84✔
111	this.flattenAnnots = flattenAnnots;	84✔
112
113	this.highlight = highlight;	84✔
114	this.unhighlight = unhighlight;	84✔
115
116	// Variables and functions from services.js
117	this.esearch = esearch;	84✔
118	this.esummary = esummary;	84✔
119	this.elink = elink;	84✔
120	this.getOrganismFromEutils = getOrganismFromEutils;	84✔
121	this.getTaxids = getTaxids;	84✔
122	this.getAssemblyAndChromosomesFromEutils =	84✔
123	getAssemblyAndChromosomesFromEutils;
124
125	// Functions from bands.js
126	this.drawBandLabels = drawBandLabels;	84✔
127	this.getBandColorGradients = getBandColorGradients;	84✔
128	this.processBandData = processBandData;	84✔
129	this.setBandsToShow = setBandsToShow;	84✔
130	this.hideUnshownBandLabels = hideUnshownBandLabels;	84✔
131	this.drawBandLabelText = drawBandLabelText;	84✔
132	this.drawBandLabelStalk = drawBandLabelStalk;	84✔
133
134	// Functions from brush.js
135	this.onBrushMove = onBrushMove;	84✔
136	this.onBrushEnd = onBrushEnd;	84✔
137	this.createBrush = createBrush;	84✔
138
139	// Functions from cursor.js
140	this.createClickCursor = createClickCursor;	84✔
141	this.onCursorMove = onCursorMove;	84✔
142
143	// Functions from sex-chromosomes.js
144	this.drawSexChromosomes = drawSexChromosomes;	84✔
145	this.setSexChromosomes = setSexChromosomes;	84✔
146
147	// Functions from coordinate-converters.js
148	this.convertBpToPx = convertBpToPx;	84✔
149	this.convertPxToBp = convertPxToBp;	84✔
150
151	// Functions from filter.js
152	this.unpackAnnots = unpackAnnots;	84✔
153	this.packAnnots = packAnnots;	84✔
154	this.initCrossFilter = initCrossFilter;	84✔
155	this.filterAnnots = filterAnnots;	84✔
156
157	// Functions from lib
158	this.assemblyIsAccession = assemblyIsAccession;	84✔
159	this.getDataDir = getDataDir;	84✔
160	this.round = round;	84✔
161	this.onDidRotate = onDidRotate;	84✔
162	this.getSvg = getSvg;	84✔
163	this.fetch = _fetch;	84✔
164	this.getTaxid = getTaxid;	84✔
165	this.getCommonName = getCommonName;	84✔
166	this.getScientificName = getScientificName;	84✔
167
168	// Functions from views/chromosome-model.js
169	this.getChromosomeModel = getChromosomeModel;	84✔
170	this.getChromosomePixels = getChromosomePixels;	84✔
171
172	// Functions from views/chromosome-labels.js
173	this.drawChromosomeLabels = drawChromosomeLabels;	84✔
174	this.rotateChromosomeLabels = rotateChromosomeLabels;	84✔
175
176	// Functions from views/draw-chromosomes.js
177	this.appendHomolog = appendHomolog;	84✔
178	this.drawChromosome = drawChromosome;	84✔
179	this.rotateAndToggleDisplay = rotateAndToggleDisplay;	84✔
180	this.setOverflowScroll = setOverflowScroll;	84✔
181
182	this.plotRelatedGenes = plotRelatedGenes;	84✔
183	this.getRelatedGenesByType = getRelatedGenesByType;	84✔
184
185	this.configure(config);	84✔
186	}
187
188	/**
189	* Get the current version of Ideogram.js
190	*/
191	static get version() {
192	return version;	15✔
193	}
194
195	/**
196	* Enable use of D3 in client apps, via "d3 = Ideogram.d3"
197	*/
198	static get d3() {
199	return d3;	17✔
200	}
201
202	/**
203	* Request data from Ensembl REST API
204	* Docs: https://rest.ensembl.org/
205	*
206	* @param {String} path URL path
207	* @param {Object} body POST body
208	* @param {String} method HTTP method; 'GET' (default) or 'POST'
209	*/
210	static async fetchEnsembl(path, body = null, method = 'GET') {	×
211	const init = {	×
212	method: method
213	};
214	if (body !== null) init.body = JSON.stringify(body);	×
215	if (method === 'GET') {	×
216	// Use HTTP parameter, not header, to avoid needless OPTIONS request
217	const delimiter = path.includes('&') ? '&' : '?';	×
218	path += delimiter + 'content-type=application/json';	×
219	} else {
220	// Method is POST, so content-type must be defined in header
221	init.headers = {'Content-Type': 'application/json'};	×
222	}
223
224	// const random = Math.random();
225	// console.log(random)
226	// if (random < 0.5) {
227	const response = await fetch(`https://rest.ensembl.org${path}`, init);	×
228	const json = await response.json();	×
229	return json;	×
230	// } else {
231	// // Mock error
232	// init.headers = {'Content-Type': 'application/json'};
233	// const response = await fetch('https://httpstat.us/500/cors', init);
234	// const json = await response.json();
235	// return json;
236	// }
237	}
238
239	/**
240	* Helper for sortChromosomes().
241	* Gets names and biological types for diverse chromosome variables
242	*/
243	static getChrSortNamesAndTypes(a, b) {
244	var chrAName, chrBName,
245	aIsCP, bIsCP, aIsMT, bIsMT, aIsAP, bIsAP, aIsNuclear, bIsNuclear;
246
247	if (typeof a === 'string' \|\| 'chr' in a && 'annots' in a) {	4,235✔
248	// Chromosome data is from either:
249	// - Ideogram static file cache (e.g. homo-sapiens.json)
250	// - Ideogram raw annotations
251	chrAName = (typeof a === 'string') ? a : a.chr;	4,066✔
252	chrBName = (typeof b === 'string') ? b : b.chr;	4,066✔
253
254	aIsCP = chrAName === 'CP';	4,066✔
255	bIsCP = chrBName === 'CP';	4,066✔
256	aIsMT = chrAName === 'MT';	4,066✔
257	bIsMT = chrBName === 'MT';	4,066✔
258	aIsAP = chrAName === 'AP';	4,066✔
259	bIsAP = chrBName === 'AP';	4,066✔
260	aIsNuclear = (!aIsCP && !aIsMT && !aIsAP);	4,066✔
261	bIsNuclear = (!bIsCP && !bIsMT && !bIsAP);	4,066✔
262	} else {
263	// Chromosome data is from NCBI E-Utils web API
264	chrAName = a.name;	169✔
265	chrBName = b.name;	169✔
266
267	aIsCP = a.type === 'chloroplast';	169✔
268	bIsCP = b.type === 'chloroplast';	169✔
269	aIsMT = a.type === 'mitochondrion';	169✔
270	bIsMT = b.type === 'mitochondrion';	169✔
271	aIsAP = a.type === 'apicoplast';	169✔
272	bIsAP = b.type === 'apicoplast';	169✔
273	aIsNuclear = a.type === 'nuclear';	169✔
274	bIsNuclear = b.type === 'nuclear';	169✔
275	}
276
277	const chrTypes = {	4,235✔
278	aIsNuclear, bIsNuclear, aIsCP, bIsCP, aIsMT, bIsMT, aIsAP, bIsAP
279	};
280
281	return [chrAName, chrBName, chrTypes];	4,235✔
282	}
283
284	/**
285	* Sorts two chromosome objects by type and name
286	* - Nuclear chromosomes come before non-nuclear chromosomes.
287	* - Among nuclear chromosomes, use "natural sorting", e.g.
288	* numbers come before letters
289	* - Among non-nuclear chromosomes, i.e. "MT" (mitochondrial DNA) and
290	* "CP" (chromoplast DNA), MT comes first
291	*
292	* @param a Chromosome string or object "A"
293	* @param b Chromosome string or object "B"
294	* @returns {Number} JavaScript sort order indicator
295	*/
296	static sortChromosomes(a, b) {
297
298	let [chrAName, chrBName, chrTypes] =
299	Ideogram.getChrSortNamesAndTypes(a, b);	4,235✔
300
301	const {
302	aIsNuclear, bIsNuclear, aIsCP, bIsCP, aIsMT, bIsMT, aIsAP, bIsAP
303	} = chrTypes;	4,235✔
304
305	if (aIsNuclear && bIsNuclear) {	4,235✔
306
307	if (isRoman(chrAName) && isRoman(chrBName)) {	4,178✔
308	// As in yeast genome
309	chrAName = parseRoman(chrAName).toString();	92✔
310	chrBName = parseRoman(chrBName).toString();	92✔
311	}
312
313	return chrAName.localeCompare(chrBName, 'en', {numeric: true});	4,178✔
314	} else if (!aIsNuclear && bIsNuclear) {	57✔
315	return 1;	7✔
316	} else if (aIsMT && bIsCP) {	50!
317	return 1;	×
318	} else if (aIsCP && bIsMT) {	50!
319	return -1;	×
320	} else if (!aIsAP && !aIsMT && !aIsCP && (bIsMT \|\| bIsCP \|\| bIsAP)) {	50✔
321	return -1;	49✔
322	}
323	}
324
325	/**
326	* Wrapper for Ideogram constructor, with generic "Related genes" options
327	*
328	* @param {Object} config Ideogram configuration object
329	*/
330	static initRelatedGenes(config, annotsInList='all') {	11✔
331	return _initRelatedGenes(config, annotsInList);	11✔
332	}
333
334
335	/**
336	* Wrapper for Ideogram constructor, with generic "Gene leads" options
337	*
338	* @param {Object} config Ideogram configuration object
339	*/
340	static initGeneLeads(config, annotsInList='all') {	×
341	return _initGeneLeads(config, annotsInList);	×
342	}
343	}

eweitz / ideogram / 2118

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