12131714885

Committed 03 Dec 2024 02:21AM UTC coverage: 82.273% (-1.1%) from 83.356%

Build # 12131714885

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #375 from eweitz/smooth-repeat-hover

Avoid hiding tooltip on first hover of previous clicked annotation

Run Details

2359 of 3225 branches covered (73.15%)

Branch coverage included in aggregate %.

10 of 15 new or added lines in 3 files covered. (66.67%)

455 existing lines in 18 files now uncovered.

5410 of 6218 relevant lines covered (87.01%)

27653.67 hits per line

Source File
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89.63

/src/js/annotations/process.js

import {add2dAnnotsForChr} from './heatmap-2d';
import {setAnnotRanks} from './annotations';

// Default colors for tracks of annotations
var colorMap = [
  ['F00'], // If there is 1 track, then color it red.
  ['F00', '88F'], // If 2 tracks, color one red and one light blue.
  ['F00', 'CCC', '88F'], // If 3, color one red, one grey, one light blue.
  ['F00', 'FA0', '0AF', '88F'], // And so on.
  ['F00', 'FA0', 'CCC', '0AF', '88F'],
  ['F00', 'FA0', '875', '578', '0AF', '88F'],
  ['F00', 'FA0', '875', 'CCC', '578', '0AF', '88F'],
  ['F00', 'FA0', '7A0', '875', '0A7', '578', '0AF', '88F'],
  ['F00', 'FA0', '7A0', '875', 'CCC', '0A7', '578', '0AF', '88F'],
  ['F00', 'FA0', '7A0', '875', '552', '255', '0A7', '578', '0AF', '88F']
];

/**
 * Ensure annotation containers are ordered by chromosome.
 */
function orderAnnotContainers(annots, ideo) {
  var unorderedAnnots, i, j, annot, chr, chrs;

  unorderedAnnots = annots;
  annots = [];
  chrs = ideo.chromosomesArray;
  for (i = 0; i < chrs.length; i++) {
    chr = chrs[i].name;
    for (j = 0; j < unorderedAnnots.length; j++) {
      annot = unorderedAnnots[j];
      if (annot.chr === chr) {
        annots.push(annot);
      }
    }
  }

  return annots;
}

/**
 * Add client annotations, as in annotations-tracks.html
 */
function addClientAnnot(annots, annot, ra, m, ideo) {
  var annotTrack;

  annot.trackIndex = ra[3];
  annotTrack = ideo.config.annotationTracks[annot.trackIndex];
  if (annotTrack.color) {
    annot.color = annotTrack.color;
  }
  if (annotTrack.shape) {
    annot.shape = annotTrack.shape;
  }

  annots[m].annots.push(annot);

  return annots;
}

/**
 * Add sparse server annotations, as in annotations-track-filters.html
 */
function addSparseServerAnnot(annot, ra, omittedAnnots, annots, m, ideo) {
  var colors = colorMap[ideo.numAvailTracks - 1];

  annot.trackIndex = ra[3];
  annot.trackIndexOriginal = ra[4];
  annot.color = '#' + colors[annot.trackIndexOriginal];

  // Catch annots that will be omitted from display
  if (annot.trackIndex > ideo.config.numTracks - 1) {
    if (annot.trackIndex in omittedAnnots) {
      omittedAnnots[annot.trackIndex].push(annot);
    } else {
      omittedAnnots[annot.trackIndex] = [annot];
    }
    return [annots, omittedAnnots];
  }
  annots[m].annots.push(annot);

  return [annots, omittedAnnots];
}

/**
 * Basic client annotations, as in annotations-basic.html
 * and annotations-external.html
 */
function addBasicClientAnnot(annots, annot, m, ideo) {
  annot.trackIndex = 0;
  if (!annot.color) {
    annot.color = ideo.config.annotationsColor;
  }
  if (!annot.shape) {
    annot.shape = 'triangle';
  }
  annots[m].annots.push(annot);

  return annots;
}

function addAnnot(annot, keys, ra, omittedAnnots, annots, m, ideo) {

  if (ideo.config.annotationTracks) {
    annots = addClientAnnot(annots, annot, ra, m, ideo);
  } else if (keys[3] === 'trackIndex' && ideo.numAvailTracks !== 1) {
    [annots, omittedAnnots] =
      addSparseServerAnnot(annot, ra, omittedAnnots, annots, m, ideo);
  // } else if (
  //   keys.length > 3 &&
  //   keys[3] in {trackIndex: 1, color: 1, shape: 1} === false &&
  //   keys[4] === 'trackIndexOriginal'
  // ) {
  //   annots = addDenseServerAnnot(keys, annots, annot, m);
  } else {
    annots = addBasicClientAnnot(annots, annot, m, ideo);
  }

  return [annots, omittedAnnots];
}

function getAnnotDomId(chrIndex, annotIndex) {
  return '_c' + chrIndex + '_a' + annotIndex;
}

function addAnnotsForChr(annots, omittedAnnots, annotsByChr, chrModel,
  m, keys, ideo) {
  var j, k, annot, ra;

  // Assign DOM ID if annots are rendered as individual DOM elements
  const shouldAssignDomId = (
    !ideo.config.annotationsLayout ||
    ideo.config.annotationsLayout === 'tracks'
  );

  for (j = 0; j < annotsByChr.annots.length; j++) {
    ra = annotsByChr.annots[j];
    annot = {};

    for (k = 0; k < keys.length; k++) {
      annot[keys[k]] = ra[k];
    }

    annot.stop = annot.start + annot.length;

    annot.chr = annotsByChr.chr;
    annot.chrIndex = m;
    annot.startPx = ideo.convertBpToPx(chrModel, annot.start);
    annot.stopPx = ideo.convertBpToPx(chrModel, annot.stop);
    annot.px = Math.round((annot.startPx + annot.stopPx) / 2);
    if (shouldAssignDomId) annot.domId = getAnnotDomId(m, j);

    [annots, omittedAnnots] =
      addAnnot(annot, keys, ra, omittedAnnots, annots, m, ideo);
  }

  if (shouldAssignDomId) {
    if (ideo.annotSortFunction) {
      annots[m].annots = setAnnotRanks(annots[m].annots, ideo);
      annots[m].annots.sort((a, b) => {
        // Reverse-sort, so first annots are drawn last, and thus at top layer
        return -ideo.annotSortFunction(a, b);
      });
    } else {
      // Sort by genomic position, in ascending order
      annots[m].annots.sort((a, b) => a[1] - b[1]);
    }

    for (j = 0; j < annots[m].annots.length; j++) {
      annots[m].annots[j].domId = getAnnotDomId(m, j);
    }
  }

  return [annots, omittedAnnots];
}

function warnOfUndefinedChromosome(annotsByChr) {
  console.warn(
    'Chromosome "' + annotsByChr.chr + '" undefined in ideogram; ' +
    annotsByChr.annots.length + ' annotations not shown'
  );
}

function addAnnots(rawAnnots, keys, ideo) {
  var m, i, annotsByChr, chrModel,
    annots = [],
    omittedAnnots = {};

  m = -1;
  for (i = 0; i < rawAnnots.length; i++) {
    annotsByChr = rawAnnots[i];
    chrModel = ideo.chromosomes[ideo.config.taxid][annotsByChr.chr];

    if (typeof chrModel === 'undefined') {
      warnOfUndefinedChromosome(annotsByChr);
      continue;
    }

    m++;
    annots.push({chr: annotsByChr.chr, annots: []});

    if (ideo.config.annotationsLayout !== 'heatmap-2d') {
      [annots, omittedAnnots] =
        addAnnotsForChr(annots, omittedAnnots, annotsByChr, chrModel, m,
          keys, ideo);
    } else {
      [annots, omittedAnnots] =
        add2dAnnotsForChr(annots, omittedAnnots, annotsByChr, chrModel, m,
          keys, ideo);
    }
  }
  return [annots, omittedAnnots];
}

function sendTrackAndAnnotWarnings(omittedAnnots, ideo) {
  var numOmittedTracks,
    layout = ideo.config.annotationsLayout,
    numTracks = ideo.config.numAnnotTracks;

  if (!/heatmap/.test(layout) && numTracks > 10) {
    console.error(
      'Ideogram only displays up to 10 tracks at a time.  ' +
      'You specified ' + numTracks + ' tracks.  ' +
      'Perhaps consider a different way to visualize your data.'
    );
  }

  numOmittedTracks = Object.keys(omittedAnnots).length;
  if (numOmittedTracks) {
    console.warn(
      'Ideogram configuration specified ' + numTracks + ' tracks, ' +
      'but loaded annotations contain ' + numOmittedTracks + ' ' +
      'extra tracks.'
    );
  }
}

/**
 * Proccesses genome annotation data.
 *
 * This method converts raw annotation data from server, which is structured as
 * an array of arrays, into a more verbose data structure consisting of an
 * array of objects.  It also adds pixel offset information.
 */
function processAnnotData(rawAnnots) {
  var keys, annots, omittedAnnots,
    ideo = this;

  keys = rawAnnots.keys;
  rawAnnots = rawAnnots.annots;

  [annots, omittedAnnots] = addAnnots(rawAnnots, keys, ideo);
  annots = orderAnnotContainers(annots, ideo);

  sendTrackAndAnnotWarnings(omittedAnnots, ideo);

  return annots;
}

export {processAnnotData, getAnnotDomId};

1	import {add2dAnnotsForChr} from './heatmap-2d';
2	import {setAnnotRanks} from './annotations';
3
4	// Default colors for tracks of annotations
5	var colorMap = [	1✔
6	['F00'], // If there is 1 track, then color it red.
7	['F00', '88F'], // If 2 tracks, color one red and one light blue.
8	['F00', 'CCC', '88F'], // If 3, color one red, one grey, one light blue.
9	['F00', 'FA0', '0AF', '88F'], // And so on.
10	['F00', 'FA0', 'CCC', '0AF', '88F'],
11	['F00', 'FA0', '875', '578', '0AF', '88F'],
12	['F00', 'FA0', '875', 'CCC', '578', '0AF', '88F'],
13	['F00', 'FA0', '7A0', '875', '0A7', '578', '0AF', '88F'],
14	['F00', 'FA0', '7A0', '875', 'CCC', '0A7', '578', '0AF', '88F'],
15	['F00', 'FA0', '7A0', '875', '552', '255', '0A7', '578', '0AF', '88F']
16	];
17
18	/**
19	* Ensure annotation containers are ordered by chromosome.
20	*/
21	function orderAnnotContainers(annots, ideo) {
22	var unorderedAnnots, i, j, annot, chr, chrs;
23
24	unorderedAnnots = annots;	85✔
25	annots = [];	85✔
26	chrs = ideo.chromosomesArray;	85✔
27	for (i = 0; i < chrs.length; i++) {	85✔
28	chr = chrs[i].name;	1,977✔
29	for (j = 0; j < unorderedAnnots.length; j++) {	1,977✔
30	annot = unorderedAnnots[j];	45,670✔
31	if (annot.chr === chr) {	45,670✔
32	annots.push(annot);	1,919✔
33	}
34	}
35	}
36
37	return annots;	85✔
38	}
39
40	/**
41	* Add client annotations, as in annotations-tracks.html
42	*/
43	function addClientAnnot(annots, annot, ra, m, ideo) {
44	var annotTrack;
45
46	annot.trackIndex = ra[3];	163,394✔
47	annotTrack = ideo.config.annotationTracks[annot.trackIndex];	163,394✔
48	if (annotTrack.color) {	163,394✔
49	annot.color = annotTrack.color;	5,002✔
50	}
51	if (annotTrack.shape) {	163,394✔
52	annot.shape = annotTrack.shape;	2,000✔
53	}
54
55	annots[m].annots.push(annot);	163,394✔
56
57	return annots;	163,394✔
58	}
59
60	/**
61	* Add sparse server annotations, as in annotations-track-filters.html
62	*/
63	function addSparseServerAnnot(annot, ra, omittedAnnots, annots, m, ideo) {
64	var colors = colorMap[ideo.numAvailTracks - 1];	5,391✔
65
66	annot.trackIndex = ra[3];	5,391✔
67	annot.trackIndexOriginal = ra[4];	5,391✔
68	annot.color = '#' + colors[annot.trackIndexOriginal];	5,391✔
69
70	// Catch annots that will be omitted from display
71	if (annot.trackIndex > ideo.config.numTracks - 1) {	5,391!
72	if (annot.trackIndex in omittedAnnots) {	×
73	omittedAnnots[annot.trackIndex].push(annot);	×
74	} else {
75	omittedAnnots[annot.trackIndex] = [annot];	×
76	}
77	return [annots, omittedAnnots];	×
78	}
79	annots[m].annots.push(annot);	5,391✔
80
81	return [annots, omittedAnnots];	5,391✔
82	}
83
84	/**
85	* Basic client annotations, as in annotations-basic.html
86	* and annotations-external.html
87	*/
88	function addBasicClientAnnot(annots, annot, m, ideo) {
89	annot.trackIndex = 0;	83,809✔
90	if (!annot.color) {	83,809✔
91	annot.color = ideo.config.annotationsColor;	83,290✔
92	}
93	if (!annot.shape) {	83,809!
94	annot.shape = 'triangle';	83,809✔
95	}
96	annots[m].annots.push(annot);	83,809✔
97
98	return annots;	83,809✔
99	}
100
101	function addAnnot(annot, keys, ra, omittedAnnots, annots, m, ideo) {
102
103	if (ideo.config.annotationTracks) {	252,594✔
104	annots = addClientAnnot(annots, annot, ra, m, ideo);	163,394✔
105	} else if (keys[3] === 'trackIndex' && ideo.numAvailTracks !== 1) {	89,200✔
106	[annots, omittedAnnots] =	5,391✔
107	addSparseServerAnnot(annot, ra, omittedAnnots, annots, m, ideo);
108	// } else if (
109	// keys.length > 3 &&
110	// keys[3] in {trackIndex: 1, color: 1, shape: 1} === false &&
111	// keys[4] === 'trackIndexOriginal'
112	// ) {
113	// annots = addDenseServerAnnot(keys, annots, annot, m);
114	} else {
115	annots = addBasicClientAnnot(annots, annot, m, ideo);	83,809✔
116	}
117
118	return [annots, omittedAnnots];	252,594✔
119	}
120
121	function getAnnotDomId(chrIndex, annotIndex) {
122	return '_c' + chrIndex + '_a' + annotIndex;	16,310✔
123	}
124
125	function addAnnotsForChr(annots, omittedAnnots, annotsByChr, chrModel,
126	m, keys, ideo) {
127	var j, k, annot, ra;
128
129	// Assign DOM ID if annots are rendered as individual DOM elements
130	const shouldAssignDomId = (
131	!ideo.config.annotationsLayout \|\|	1,919✔
132	ideo.config.annotationsLayout === 'tracks'
133	);
134
135	for (j = 0; j < annotsByChr.annots.length; j++) {	1,919✔
136	ra = annotsByChr.annots[j];	252,594✔
137	annot = {};	252,594✔
138
139	for (k = 0; k < keys.length; k++) {	252,594✔
140	annot[keys[k]] = ra[k];	1,822,469✔
141	}
142
143	annot.stop = annot.start + annot.length;	252,594✔
144
145	annot.chr = annotsByChr.chr;	252,594✔
146	annot.chrIndex = m;	252,594✔
147	annot.startPx = ideo.convertBpToPx(chrModel, annot.start);	252,594✔
148	annot.stopPx = ideo.convertBpToPx(chrModel, annot.stop);	252,594✔
149	annot.px = Math.round((annot.startPx + annot.stopPx) / 2);	252,594✔
150	if (shouldAssignDomId) annot.domId = getAnnotDomId(m, j);	252,594✔
151
152	[annots, omittedAnnots] =	252,594✔
153	addAnnot(annot, keys, ra, omittedAnnots, annots, m, ideo);
154	}
155
156	if (shouldAssignDomId) {	1,919✔
157	if (ideo.annotSortFunction) {	1,624✔
158	annots[m].annots = setAnnotRanks(annots[m].annots, ideo);	1,264✔
159	annots[m].annots.sort((a, b) => {	1,264✔
160	// Reverse-sort, so first annots are drawn last, and thus at top layer
161	return -ideo.annotSortFunction(a, b);	208✔
162	});
163	} else {
164	// Sort by genomic position, in ascending order
165	annots[m].annots.sort((a, b) => a[1] - b[1]);	16,364✔
166	}
167
168	for (j = 0; j < annots[m].annots.length; j++) {	1,624✔
169	annots[m].annots[j].domId = getAnnotDomId(m, j);	7,846✔
170	}
171	}
172
173	return [annots, omittedAnnots];	1,919✔
174	}
175
176	function warnOfUndefinedChromosome(annotsByChr) {
177	console.warn(	2✔
178	'Chromosome "' + annotsByChr.chr + '" undefined in ideogram; ' +
179	annotsByChr.annots.length + ' annotations not shown'
180	);
181	}
182
183	function addAnnots(rawAnnots, keys, ideo) {
184	var m, i, annotsByChr, chrModel,
185	annots = [],	85✔
186	omittedAnnots = {};	85✔
187
188	m = -1;	85✔
189	for (i = 0; i < rawAnnots.length; i++) {	85✔
190	annotsByChr = rawAnnots[i];	1,921✔
191	chrModel = ideo.chromosomes[ideo.config.taxid][annotsByChr.chr];	1,921✔
192
193	if (typeof chrModel === 'undefined') {	1,921✔
194	warnOfUndefinedChromosome(annotsByChr);	2✔
195	continue;	2✔
196	}
197
198	m++;	1,919✔
199	annots.push({chr: annotsByChr.chr, annots: []});	1,919✔
200
201	if (ideo.config.annotationsLayout !== 'heatmap-2d') {	1,919!
202	[annots, omittedAnnots] =	1,919✔
203	addAnnotsForChr(annots, omittedAnnots, annotsByChr, chrModel, m,
204	keys, ideo);
205	} else {
UNCOV 206	[annots, omittedAnnots] =	×
207	add2dAnnotsForChr(annots, omittedAnnots, annotsByChr, chrModel, m,
208	keys, ideo);
209	}
210	}
211	return [annots, omittedAnnots];	85✔
212	}
213
214	function sendTrackAndAnnotWarnings(omittedAnnots, ideo) {
215	var numOmittedTracks,
216	layout = ideo.config.annotationsLayout,	85✔
217	numTracks = ideo.config.numAnnotTracks;	85✔
218
219	if (!/heatmap/.test(layout) && numTracks > 10) {	85!
220	console.error(	×
221	'Ideogram only displays up to 10 tracks at a time. ' +
222	'You specified ' + numTracks + ' tracks. ' +
223	'Perhaps consider a different way to visualize your data.'
224	);
225	}
226
227	numOmittedTracks = Object.keys(omittedAnnots).length;	85✔
228	if (numOmittedTracks) {	85!
229	console.warn(	×
230	'Ideogram configuration specified ' + numTracks + ' tracks, ' +
231	'but loaded annotations contain ' + numOmittedTracks + ' ' +
232	'extra tracks.'
233	);
234	}
235	}
236
237	/**
238	* Proccesses genome annotation data.
239	*
240	* This method converts raw annotation data from server, which is structured as
241	* an array of arrays, into a more verbose data structure consisting of an
242	* array of objects. It also adds pixel offset information.
243	*/
244	function processAnnotData(rawAnnots) {
245	var keys, annots, omittedAnnots,
246	ideo = this;	85✔
247
248	keys = rawAnnots.keys;	85✔
249	rawAnnots = rawAnnots.annots;	85✔
250
251	[annots, omittedAnnots] = addAnnots(rawAnnots, keys, ideo);	85✔
252	annots = orderAnnotContainers(annots, ideo);	85✔
253
254	sendTrackAndAnnotWarnings(omittedAnnots, ideo);	85✔
255
256	return annots;	85✔
257	}
258
259	export {processAnnotData, getAnnotDomId};

eweitz / ideogram / 12131714885

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