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Build # 1397

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push

travis-ci

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web-flow

Commit Message

Merge pull request #160 from plotly/add-transition-dep

Add d3-transition to the list of dependencies

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638 of 988 branches covered (64.57%)

Branch coverage included in aggregate %.

1934 of 2507 relevant lines covered (77.14%)

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80.77

/src/js/bands/bands.js

/**
 * @fileoverview Methods for processing chromosome length and banding data.
 *
 * Ideogram.js depicts chromosomes using data on their length, name, and
 * (if dealing with a very well-studied organism) cytogenetic banding data.
 * This file processes cytoband data that comes from biological research
 * institutions.
 *
 * For background on cytogenetic bands and how they are used in genomics, see:
 * https://ghr.nlm.nih.gov/primer/howgeneswork/genelocation
 *
 */

import naturalSort from 'es6-natural-sort';

import {
  drawBandLabels, getBandColorGradients, hideUnshownBandLabels, setBandsToShow,
  drawBandLabelText, drawBandLabelStalk
} from './draw';
import {parseBands} from './parse';

/**
 * TODO: Should this be in services/organism.js?
 */
function setTaxids(ideo) {
  var i, taxid, taxids;

  if (ideo.config.multiorganism === true) {
    ideo.coordinateSystem = 'bp';
    taxids = ideo.config.taxids;
    for (i = 0; i < taxids.length; i++) {
      taxid = taxids[i];
    }
  } else {
    if (typeof ideo.config.taxid === 'undefined') {
      ideo.config.taxid = ideo.config.taxids[0];
    }
    taxid = ideo.config.taxid;
    taxids = [taxid];
    ideo.config.taxids = taxids;
  }

  return [taxid, taxids];
}

/**
 * Updates bands array, sets ideo.maxLength
 */
function updateBandsArray(chromosome, bandsByChr, bandsArray, ideo) {
  var bands, chrLength;

  bands = bandsByChr[chromosome];
  bandsArray.push(bands);

  chrLength = {
    iscn: bands[bands.length - 1].iscn.stop,
    bp: bands[bands.length - 1].bp.stop
  };

  if (chrLength.iscn > ideo.maxLength.iscn) {
    ideo.maxLength.iscn = chrLength.iscn;
  }

  if (chrLength.bp > ideo.maxLength.bp) {
    ideo.maxLength.bp = chrLength.bp;
  }

  return bandsArray;
}

/**
 * Updates bandsArray, sets ideo.config.chromosomes and ideo.numChromosomes
 */
function setChrsByTaxidsWithBands(taxid, chrs, bandsArray, ideo) {
  var bandData, bandsByChr, chromosome, k;

  bandData = ideo.bandData[taxid];

  bandsByChr = ideo.parseBands(bandData, taxid, chrs);

  chrs = Object.keys(bandsByChr).sort(function(a, b) {
    return naturalSort(a, b);
  });

  ideo.config.chromosomes[taxid] = chrs.slice();
  ideo.numChromosomes += ideo.config.chromosomes[taxid].length;

  for (k = 0; k < chrs.length; k++) {
    chromosome = chrs[k];
    bandsArray = updateBandsArray(chromosome, bandsByChr, bandsArray, ideo);
  }

  return bandsArray;
}

function setChromosomesByTaxid(taxid, chrs, bandsArray, ideo) {
  var chr, k;

  if (ideo.coordinateSystem === 'iscn' || ideo.config.multiorganism) {
    bandsArray = setChrsByTaxidsWithBands(taxid, chrs, bandsArray, ideo);
  } else if (ideo.coordinateSystem === 'bp') {
    // If lacking band-level data
    ideo.config.chromosomes[taxid] = chrs.slice();
    ideo.numChromosomes += ideo.config.chromosomes[taxid].length;

    for (k = 0; k < chrs.length; k++) {
      chr = chrs[k];
      if (chr.length > ideo.maxLength.bp) ideo.maxLength.bp = chr.length;
    }
  }

  return bandsArray;
}

function reportPerformance(t0, ideo) {
  var t1 = new Date().getTime();
  if (ideo.config.debug) {
    console.log('Time in processBandData: ' + (t1 - t0) + ' ms');
  }
}

/**
 * Completes default ideogram initialization by calling downstream functions
 * to process raw band data into full JSON objects, render chromosome and
 * cytoband figures and labels, apply initial graphical transformations,
 * hide overlapping band labels, and execute callbacks defined by client code
 */
function processBandData() {
  var bandsArray, j, taxid, taxids, chrs, chrsByTaxid,
    t0 = new Date().getTime(),
    ideo = this;

  bandsArray = [];

  [taxid, taxids] = setTaxids(ideo);

  if ('chromosomes' in ideo.config) chrs = ideo.config.chromosomes;
  if (ideo.config.multiorganism) chrsByTaxid = chrs;
  ideo.config.chromosomes = {};

  for (j = 0; j < taxids.length; j++) {
    taxid = taxids[j];
    if (ideo.config.multiorganism) chrs = chrsByTaxid[taxid];
    bandsArray = setChromosomesByTaxid(taxid, chrs, bandsArray, ideo);
  }

  reportPerformance(t0, ideo);
  return bandsArray;
}

export {
  parseBands, drawBandLabels, getBandColorGradients, processBandData,
  setBandsToShow, hideUnshownBandLabels, drawBandLabelText, drawBandLabelStalk
}

1	/**
2	* @fileoverview Methods for processing chromosome length and banding data.
3	*
4	* Ideogram.js depicts chromosomes using data on their length, name, and
5	* (if dealing with a very well-studied organism) cytogenetic banding data.
6	* This file processes cytoband data that comes from biological research
7	* institutions.
8	*
9	* For background on cytogenetic bands and how they are used in genomics, see:
10	* https://ghr.nlm.nih.gov/primer/howgeneswork/genelocation
11	*
12	*/
13
14	import naturalSort from 'es6-natural-sort';
15
16	import {
17	drawBandLabels, getBandColorGradients, hideUnshownBandLabels, setBandsToShow,
18	drawBandLabelText, drawBandLabelStalk
19	} from './draw';
20	import {parseBands} from './parse';
21
22	/**
23	* TODO: Should this be in services/organism.js?
24	*/
25	function setTaxids(ideo) {
26	var i, taxid, taxids;
27
28	if (ideo.config.multiorganism === true) {	38✔
29	ideo.coordinateSystem = 'bp';	1✔
30	taxids = ideo.config.taxids;	1✔
31	for (i = 0; i < taxids.length; i++) {	1✔
32	taxid = taxids[i];	2✔
33	}
34	} else {
35	if (typeof ideo.config.taxid === 'undefined') {	37!
36	ideo.config.taxid = ideo.config.taxids[0];	×
37	}
38	taxid = ideo.config.taxid;	37✔
39	taxids = [taxid];	37✔
40	ideo.config.taxids = taxids;	37✔
41	}
42
43	return [taxid, taxids];	38✔
44	}
45
46	/**
47	* Updates bands array, sets ideo.maxLength
48	*/
49	function updateBandsArray(chromosome, bandsByChr, bandsArray, ideo) {
50	var bands, chrLength;
51
52	bands = bandsByChr[chromosome];	795✔
53	bandsArray.push(bands);	795✔
54
55	chrLength = {	795✔
56	iscn: bands[bands.length - 1].iscn.stop,
57	bp: bands[bands.length - 1].bp.stop
58	};
59
60	if (chrLength.iscn > ideo.maxLength.iscn) {	795✔
61	ideo.maxLength.iscn = chrLength.iscn;	38✔
62	}
63
64	if (chrLength.bp > ideo.maxLength.bp) {	795✔
65	ideo.maxLength.bp = chrLength.bp;	38✔
66	}
67
68	return bandsArray;	795✔
69	}
70
71	/**
72	* Updates bandsArray, sets ideo.config.chromosomes and ideo.numChromosomes
73	*/
74	function setChrsByTaxidsWithBands(taxid, chrs, bandsArray, ideo) {
75	var bandData, bandsByChr, chromosome, k;
76
77	bandData = ideo.bandData[taxid];	39✔
78
79	bandsByChr = ideo.parseBands(bandData, taxid, chrs);	39✔
80
81	chrs = Object.keys(bandsByChr).sort(function(a, b) {	39✔
82	return naturalSort(a, b);	784✔
83	});
84
85	ideo.config.chromosomes[taxid] = chrs.slice();	39✔
86	ideo.numChromosomes += ideo.config.chromosomes[taxid].length;	39✔
87
88	for (k = 0; k < chrs.length; k++) {	39✔
89	chromosome = chrs[k];	795✔
90	bandsArray = updateBandsArray(chromosome, bandsByChr, bandsArray, ideo);	795✔
91	}
92
93	return bandsArray;	39✔
94	}
95
96	function setChromosomesByTaxid(taxid, chrs, bandsArray, ideo) {
97	var chr, k;
98
99	if (ideo.coordinateSystem === 'iscn' \|\| ideo.config.multiorganism) {	39!
100	bandsArray = setChrsByTaxidsWithBands(taxid, chrs, bandsArray, ideo);	39✔
101	} else if (ideo.coordinateSystem === 'bp') {	×
102	// If lacking band-level data
103	ideo.config.chromosomes[taxid] = chrs.slice();	×
104	ideo.numChromosomes += ideo.config.chromosomes[taxid].length;	×
105
106	for (k = 0; k < chrs.length; k++) {	×
107	chr = chrs[k];	×
108	if (chr.length > ideo.maxLength.bp) ideo.maxLength.bp = chr.length;	×
109	}
110	}
111
112	return bandsArray;	39✔
113	}
114
115	function reportPerformance(t0, ideo) {
116	var t1 = new Date().getTime();	38✔
117	if (ideo.config.debug) {	38!
118	console.log('Time in processBandData: ' + (t1 - t0) + ' ms');	×
119	}
120	}
121
122	/**
123	* Completes default ideogram initialization by calling downstream functions
124	* to process raw band data into full JSON objects, render chromosome and
125	* cytoband figures and labels, apply initial graphical transformations,
126	* hide overlapping band labels, and execute callbacks defined by client code
127	*/
128	function processBandData() {
129	var bandsArray, j, taxid, taxids, chrs, chrsByTaxid,
130	t0 = new Date().getTime(),	38✔
131	ideo = this;	38✔
132
133	bandsArray = [];	38✔
134
135	[taxid, taxids] = setTaxids(ideo);	38✔
136
137	if ('chromosomes' in ideo.config) chrs = ideo.config.chromosomes;	38✔
138	if (ideo.config.multiorganism) chrsByTaxid = chrs;	38✔
139	ideo.config.chromosomes = {};	38✔
140
141	for (j = 0; j < taxids.length; j++) {	38✔
142	taxid = taxids[j];	39✔
143	if (ideo.config.multiorganism) chrs = chrsByTaxid[taxid];	39✔
144	bandsArray = setChromosomesByTaxid(taxid, chrs, bandsArray, ideo);	39✔
145	}
146
147	reportPerformance(t0, ideo);	38✔
148	return bandsArray;	38✔
149	}
150
151	export {
152	parseBands, drawBandLabels, getBandColorGradients, processBandData,
153	setBandsToShow, hideUnshownBandLabels, drawBandLabelText, drawBandLabelStalk
154	}

eweitz / ideogram / 1397

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