react-msaview 6.0.0 → 6.1.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (122) hide show
  1. package/bundle/index.js +98 -98
  2. package/bundle/index.js.map +4 -4
  3. package/dist/columnCounts.d.ts +7 -0
  4. package/dist/columnCounts.js +18 -0
  5. package/dist/columnCounts.js.map +1 -1
  6. package/dist/components/DragHandle.d.ts +25 -0
  7. package/dist/components/DragHandle.js +49 -0
  8. package/dist/components/DragHandle.js.map +1 -0
  9. package/dist/components/ResizeHandles.d.ts +4 -2
  10. package/dist/components/ResizeHandles.js +29 -32
  11. package/dist/components/ResizeHandles.js.map +1 -1
  12. package/dist/components/VerticalScrollbar.js +2 -2
  13. package/dist/components/VerticalScrollbar.js.map +1 -1
  14. package/dist/components/dialogs/InterProScanDialog.js +52 -129
  15. package/dist/components/dialogs/InterProScanDialog.js.map +1 -1
  16. package/dist/components/header/settingsMenuItems.js +16 -1
  17. package/dist/components/header/settingsMenuItems.js.map +1 -1
  18. package/dist/components/minimap/Minimap.js +32 -4
  19. package/dist/components/minimap/Minimap.js.map +1 -1
  20. package/dist/components/msa/MSACanvas.js +8 -2
  21. package/dist/components/msa/MSACanvas.js.map +1 -1
  22. package/dist/components/msa/MSACanvasBlock.js +12 -3
  23. package/dist/components/msa/MSACanvasBlock.js.map +1 -1
  24. package/dist/components/msa/msaRaster.d.ts +63 -0
  25. package/dist/components/msa/msaRaster.js +252 -0
  26. package/dist/components/msa/msaRaster.js.map +1 -0
  27. package/dist/components/msa/renderMSABlock.d.ts +2 -1
  28. package/dist/components/msa/renderMSABlock.js +13 -21
  29. package/dist/components/msa/renderMSABlock.js.map +1 -1
  30. package/dist/components/msa/tileColor.d.ts +6 -0
  31. package/dist/components/msa/tileColor.js +35 -0
  32. package/dist/components/msa/tileColor.js.map +1 -0
  33. package/dist/components/renderCtx.d.ts +1 -1
  34. package/dist/components/tracks/TrackBlocks.d.ts +14 -0
  35. package/dist/components/tracks/TrackBlocks.js +65 -0
  36. package/dist/components/tracks/TrackBlocks.js.map +1 -0
  37. package/dist/components/tracks/{renderTracksSvg.d.ts → drawTracks.d.ts} +22 -10
  38. package/dist/components/tracks/drawTracks.js +193 -0
  39. package/dist/components/tracks/drawTracks.js.map +1 -0
  40. package/dist/components/tree/TreeCanvas.js +8 -2
  41. package/dist/components/tree/TreeCanvas.js.map +1 -1
  42. package/dist/components/tree/TreeCanvasBlock.js +7 -4
  43. package/dist/components/tree/TreeCanvasBlock.js.map +1 -1
  44. package/dist/components/tree/renderTreeCanvas.js +27 -21
  45. package/dist/components/tree/renderTreeCanvas.js.map +1 -1
  46. package/dist/constants.d.ts +3 -0
  47. package/dist/constants.js +8 -0
  48. package/dist/constants.js.map +1 -1
  49. package/dist/model/DataModel.d.ts +1 -4
  50. package/dist/model/DataModel.js +8 -10
  51. package/dist/model/DataModel.js.map +1 -1
  52. package/dist/model/treeModel.d.ts +1 -1
  53. package/dist/model/treeModel.js +1 -1
  54. package/dist/model.d.ts +36 -7
  55. package/dist/model.js +113 -58
  56. package/dist/model.js.map +1 -1
  57. package/dist/neighborJoining.js +34 -18
  58. package/dist/neighborJoining.js.map +1 -1
  59. package/dist/renderTestEnv.d.ts +43 -0
  60. package/dist/renderTestEnv.js +88 -0
  61. package/dist/renderTestEnv.js.map +1 -0
  62. package/dist/renderToSvg.js +1 -1
  63. package/dist/renderToSvg.js.map +1 -1
  64. package/dist/sequenceLogo.d.ts +28 -0
  65. package/dist/sequenceLogo.js +47 -0
  66. package/dist/sequenceLogo.js.map +1 -0
  67. package/dist/types.d.ts +2 -0
  68. package/dist/version.d.ts +1 -1
  69. package/dist/version.js +1 -1
  70. package/package.json +3 -3
  71. package/src/columnCounts.test.ts +15 -0
  72. package/src/columnCounts.ts +19 -0
  73. package/src/components/DragHandle.tsx +81 -0
  74. package/src/components/ResizeHandles.tsx +46 -54
  75. package/src/components/VerticalScrollbar.tsx +3 -2
  76. package/src/components/dialogs/InterProScanDialog.tsx +54 -131
  77. package/src/components/header/settingsMenuItems.ts +19 -1
  78. package/src/components/minimap/Minimap.tsx +47 -4
  79. package/src/components/msa/MSACanvas.tsx +30 -10
  80. package/src/components/msa/MSACanvasBlock.tsx +13 -3
  81. package/src/components/msa/msaRaster.test.ts +145 -0
  82. package/src/components/msa/msaRaster.ts +350 -0
  83. package/src/components/msa/renderMSABlock.ts +15 -20
  84. package/src/components/msa/tileColor.ts +37 -0
  85. package/src/components/renderCtx.ts +2 -0
  86. package/src/components/tracks/TrackBlocks.tsx +111 -0
  87. package/src/components/tracks/drawTracks.ts +323 -0
  88. package/src/components/tree/TreeCanvas.tsx +16 -4
  89. package/src/components/tree/TreeCanvasBlock.tsx +18 -11
  90. package/src/components/tree/renderTreeCanvas.test.ts +55 -0
  91. package/src/components/tree/renderTreeCanvas.ts +28 -19
  92. package/src/constants.ts +10 -0
  93. package/src/impgRender.test.tsx +2 -57
  94. package/src/largeTree.test.ts +16 -2
  95. package/src/model/DataModel.ts +11 -11
  96. package/src/model/treeModel.ts +1 -1
  97. package/src/model.ts +128 -60
  98. package/src/neighborJoining.ts +36 -18
  99. package/src/renderDomainsSvg.test.tsx +2 -57
  100. package/src/renderMinimapSvg.test.tsx +2 -56
  101. package/src/renderSequenceLogoSvg.test.tsx +176 -0
  102. package/src/renderTestEnv.ts +96 -0
  103. package/src/renderToSvg.tsx +1 -1
  104. package/src/sequenceLogo.test.ts +88 -0
  105. package/src/sequenceLogo.ts +63 -0
  106. package/src/types.ts +7 -1
  107. package/src/version.ts +1 -1
  108. package/dist/components/ConservationTrack.d.ts +0 -8
  109. package/dist/components/ConservationTrack.js +0 -49
  110. package/dist/components/ConservationTrack.js.map +0 -1
  111. package/dist/components/ScrollbarThumb.d.ts +0 -14
  112. package/dist/components/ScrollbarThumb.js +0 -28
  113. package/dist/components/ScrollbarThumb.js.map +0 -1
  114. package/dist/components/TextTrack.d.ts +0 -8
  115. package/dist/components/TextTrack.js +0 -58
  116. package/dist/components/TextTrack.js.map +0 -1
  117. package/dist/components/tracks/renderTracksSvg.js +0 -126
  118. package/dist/components/tracks/renderTracksSvg.js.map +0 -1
  119. package/src/components/ConservationTrack.tsx +0 -99
  120. package/src/components/ScrollbarThumb.tsx +0 -48
  121. package/src/components/TextTrack.tsx +0 -103
  122. package/src/components/tracks/renderTracksSvg.ts +0 -247
package/dist/model.js.map CHANGED
@@ -1 +1 @@
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package/dist/neighborJoining.js CHANGED
@@ -29,23 +29,39 @@ const BLOSUM62_DATA = [
29
29
  [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4],
30
30
  [-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1],
31
31
  ];
32
- const BLOSUM62 = new Map();
33
- for (let i = 0; i < BLOSUM62_KEYS.length; i++) {
34
- const row = new Map();
35
- for (let j = 0; j < BLOSUM62_KEYS.length; j++) {
36
- row.set(BLOSUM62_KEYS[j], BLOSUM62_DATA[i][j]);
37
- }
38
- BLOSUM62.set(BLOSUM62_KEYS[i], row);
39
- }
40
- function getBlosum62Score(a, b) {
41
- return BLOSUM62.get(a.toUpperCase())?.get(b.toUpperCase()) ?? -4;
32
+ const NUM_SYMBOLS = BLOSUM62_KEYS.length;
33
+ const BLOSUM62 = Int8Array.from(BLOSUM62_DATA.flat());
34
+ // charCode -> row/column in BLOSUM62, -1 for anything the matrix does not name.
35
+ // A flat table rather than a Map of Maps keyed by an upper-cased character, for
36
+ // the reason columnCounts.ts gives: the distance matrix is O(rows^2 * columns)
37
+ // lookups, and on a 120x800 alignment the Map form spent nearly all of its time
38
+ // allocating one-character strings in toUpperCase: 2.6s to build a tree, versus
39
+ // 0.34s here for a byte-identical newick.
40
+ const symbolOfCode = new Int8Array(128).fill(-1);
41
+ for (let i = 0; i < NUM_SYMBOLS; i++) {
42
+ const key = BLOSUM62_KEYS[i];
43
+ symbolOfCode[key.charCodeAt(0)] = i;
44
+ symbolOfCode[key.toLowerCase().charCodeAt(0)] = i;
42
45
  }
46
+ // gap, or past the end of a row shorter than the alignment
47
+ const GAP = -2;
43
48
  // stockholm and a3m write gaps as '.', not just '-'. Scoring a '.' as a residue
44
49
  // charges the pair the unknown-symbol penalty on every padded column, so two
45
50
  // sequences that differ only in where an unrelated row forced padding come out
46
51
  // as divergent.
47
- function isGap(c) {
48
- return c === '-' || c === '.';
52
+ function symbolAt(seq, i) {
53
+ if (i >= seq.length) {
54
+ return GAP;
55
+ }
56
+ const code = seq.charCodeAt(i);
57
+ // bit trick: (code - 45) >>> 0 <= 1 checks for '-' (45) or '.' (46)
58
+ if ((code - 45) >>> 0 <= 1) {
59
+ return GAP;
60
+ }
61
+ return code < 128 ? symbolOfCode[code] : -1;
62
+ }
63
+ function blosumScore(a, b) {
64
+ return a < 0 || b < 0 ? -4 : BLOSUM62[a * NUM_SYMBOLS + b];
49
65
  }
50
66
  function computePairwiseDistance(seq1, seq2) {
51
67
  // ragged input is real -- a3m and hand-edited fasta both produce rows shorter
@@ -57,10 +73,10 @@ function computePairwiseDistance(seq1, seq2) {
57
73
  let totalScore = 0;
58
74
  let maxPossibleScore = 0;
59
75
  for (let i = 0; i < len; i++) {
60
- const a = seq1[i] ?? '-';
61
- const b = seq2[i] ?? '-';
62
- const aGap = isGap(a);
63
- const bGap = isGap(b);
76
+ const a = symbolAt(seq1, i);
77
+ const b = symbolAt(seq2, i);
78
+ const aGap = a === GAP;
79
+ const bGap = b === GAP;
64
80
  if (aGap && bGap) {
65
81
  continue;
66
82
  }
@@ -68,8 +84,8 @@ function computePairwiseDistance(seq1, seq2) {
68
84
  if (aGap || bGap) {
69
85
  continue;
70
86
  }
71
- totalScore += getBlosum62Score(a, b);
72
- maxPossibleScore += Math.max(getBlosum62Score(a, a), getBlosum62Score(b, b));
87
+ totalScore += blosumScore(a, b);
88
+ maxPossibleScore += Math.max(blosumScore(a, a), blosumScore(b, b));
73
89
  }
74
90
  if (compared === 0) {
75
91
  return 1;
package/dist/neighborJoining.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/renderTestEnv.d.ts ADDED
@@ -0,0 +1,43 @@
1
+ /**
2
+ * jsdom shims for the SVG-export tests. Test-only -- nothing in the viewer
3
+ * imports this.
4
+ *
5
+ * jsdom implements neither DOMMatrix nor a canvas 2D context, and
6
+ * `@jbrowse/svgcanvas` needs both: it tracks the current transform as a real
7
+ * matrix, and the renderers ask a throwaway canvas to measure text.
8
+ *
9
+ * The matrix stub has to accept the ARRAY constructor. svgcanvas normalizes
10
+ * every transform through `new DOMMatrix([a, b, c, d, e, f])`, so a stub that
11
+ * only takes six positional arguments silently binds the whole array to `a` and
12
+ * leaves the rest undefined -- every emitted transform then carries `NaN` in its
13
+ * x components, which no assertion on a drawn x-position can survive.
14
+ */
15
+ export declare class TestDOMMatrix {
16
+ a: number;
17
+ b: number;
18
+ c: number;
19
+ d: number;
20
+ e: number;
21
+ f: number;
22
+ constructor(init?: number[]);
23
+ multiply(o: TestDOMMatrix): TestDOMMatrix;
24
+ translate(x: number, y?: number): TestDOMMatrix;
25
+ scale(x: number, y?: number): TestDOMMatrix;
26
+ }
27
+ export declare class TestDOMPoint {
28
+ x: number;
29
+ y: number;
30
+ constructor(x?: number, y?: number);
31
+ matrixTransform(m: TestDOMMatrix): TestDOMPoint;
32
+ }
33
+ /**
34
+ * Install the shims. Call from `beforeAll` in any test that exports SVG.
35
+ *
36
+ * `measureText` reports 0.6em per character, close enough to a real sans-serif
37
+ * average for layout assertions and, more usefully, exactly predictable: a test
38
+ * can compute the width a renderer will see rather than hardcoding a number
39
+ * measured from one machine's fonts.
40
+ */
41
+ export declare function installRenderTestEnv(): void;
42
+ /** the per-character width factor `measureText` above reports */
43
+ export declare const TEST_CHAR_WIDTH_RATIO = 0.6;
package/dist/renderTestEnv.js ADDED
@@ -0,0 +1,88 @@
1
+ /**
2
+ * jsdom shims for the SVG-export tests. Test-only -- nothing in the viewer
3
+ * imports this.
4
+ *
5
+ * jsdom implements neither DOMMatrix nor a canvas 2D context, and
6
+ * `@jbrowse/svgcanvas` needs both: it tracks the current transform as a real
7
+ * matrix, and the renderers ask a throwaway canvas to measure text.
8
+ *
9
+ * The matrix stub has to accept the ARRAY constructor. svgcanvas normalizes
10
+ * every transform through `new DOMMatrix([a, b, c, d, e, f])`, so a stub that
11
+ * only takes six positional arguments silently binds the whole array to `a` and
12
+ * leaves the rest undefined -- every emitted transform then carries `NaN` in its
13
+ * x components, which no assertion on a drawn x-position can survive.
14
+ */
15
+ export class TestDOMMatrix {
16
+ a;
17
+ b;
18
+ c;
19
+ d;
20
+ e;
21
+ f;
22
+ constructor(init) {
23
+ const [a = 1, b = 0, c = 0, d = 1, e = 0, f = 0] = init ?? [];
24
+ this.a = a;
25
+ this.b = b;
26
+ this.c = c;
27
+ this.d = d;
28
+ this.e = e;
29
+ this.f = f;
30
+ }
31
+ multiply(o) {
32
+ return new TestDOMMatrix([
33
+ this.a * o.a + this.c * o.b,
34
+ this.b * o.a + this.d * o.b,
35
+ this.a * o.c + this.c * o.d,
36
+ this.b * o.c + this.d * o.d,
37
+ this.a * o.e + this.c * o.f + this.e,
38
+ this.b * o.e + this.d * o.f + this.f,
39
+ ]);
40
+ }
41
+ translate(x, y = 0) {
42
+ return this.multiply(new TestDOMMatrix([1, 0, 0, 1, x, y]));
43
+ }
44
+ scale(x, y = x) {
45
+ return this.multiply(new TestDOMMatrix([x, 0, 0, y, 0, 0]));
46
+ }
47
+ }
48
+ export class TestDOMPoint {
49
+ x;
50
+ y;
51
+ constructor(x = 0, y = 0) {
52
+ this.x = x;
53
+ this.y = y;
54
+ }
55
+ matrixTransform(m) {
56
+ return new TestDOMPoint(m.a * this.x + m.c * this.y + m.e, m.b * this.x + m.d * this.y + m.f);
57
+ }
58
+ }
59
+ /**
60
+ * Install the shims. Call from `beforeAll` in any test that exports SVG.
61
+ *
62
+ * `measureText` reports 0.6em per character, close enough to a real sans-serif
63
+ * average for layout assertions and, more usefully, exactly predictable: a test
64
+ * can compute the width a renderer will see rather than hardcoding a number
65
+ * measured from one machine's fonts.
66
+ */
67
+ export function installRenderTestEnv() {
68
+ const g = globalThis;
69
+ g.DOMMatrix = TestDOMMatrix;
70
+ g.DOMPoint = TestDOMPoint;
71
+ HTMLCanvasElement.prototype.getContext = function () {
72
+ let font = '10px sans-serif';
73
+ return {
74
+ get font() {
75
+ return font;
76
+ },
77
+ set font(v) {
78
+ font = v;
79
+ },
80
+ measureText: (t) => ({
81
+ width: t.length * (Number.parseFloat(font) || 10) * 0.6,
82
+ }),
83
+ };
84
+ };
85
+ }
86
+ /** the per-character width factor `measureText` above reports */
87
+ export const TEST_CHAR_WIDTH_RATIO = 0.6;
88
+ //# sourceMappingURL=renderTestEnv.js.map
package/dist/renderTestEnv.js.map ADDED
@@ -0,0 +1 @@
1
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package/dist/renderToSvg.js CHANGED
@@ -5,7 +5,7 @@ import { when } from 'mobx';
5
5
  import MinimapSVG from './components/minimap/MinimapSVG.js';
6
6
  import { renderBoxFeatureCanvasBlock } from './components/msa/renderBoxFeatureCanvasBlock.js';
7
7
  import { renderMSABlock } from './components/msa/renderMSABlock.js';
8
- import { renderAllTracks } from './components/tracks/renderTracksSvg.js';
8
+ import { renderAllTracks } from './components/tracks/drawTracks.js';
9
9
  import { renderTreeCanvas } from './components/tree/renderTreeCanvas.js';
10
10
  import { colorContrast } from './util.js';
11
11
  // domain-legend geometry, shared by the width calculation and the renderer so
package/dist/renderToSvg.js.map CHANGED
@@ -1 +1 @@
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1
+ 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package/dist/sequenceLogo.d.ts ADDED
@@ -0,0 +1,28 @@
1
+ import type { ColumnCounts } from './columnCounts.ts';
2
+ export interface LogoLetter {
3
+ letter: string;
4
+ /** height of this letter's slice of the stack, in bits */
5
+ bits: number;
6
+ }
7
+ /** the y-axis ceiling of a logo: the information content of a fully conserved
8
+ * column, log2 of the alphabet size */
9
+ export declare function maxBitsFor(sequenceType: 'dna' | 'rna' | 'amino'): number;
10
+ /**
11
+ * One column of a sequence logo, tallest letter last so a caller can draw the
12
+ * stack bottom-up in array order.
13
+ *
14
+ * Heights follow Schneider & Stephens: the column's information content is
15
+ * `log2(alphabet) - H` bits, and each residue takes the share of that its own
16
+ * frequency earns. Frequencies come from the non-gap residues only, so a column
17
+ * of two residues and eight gaps is read as a two-way choice rather than a
18
+ * ten-way one -- otherwise every gappy column would look uninformative for the
19
+ * wrong reason.
20
+ *
21
+ * The whole stack is then scaled by the non-gap fraction, which plain WebLogo
22
+ * does not do. Here it earns its place: the track sits directly under an
23
+ * alignment where the gaps are visible, and a column that is 90% gap drawing a
24
+ * full-height stack off its one remaining pair of residues reads as a conserved
25
+ * site. Scaling makes stack height mean "how much this column tells you about
26
+ * the family", matching what the conservation track above it already plots.
27
+ */
28
+ export declare function columnLogoStack(colStats: ColumnCounts, col: number, maxBits: number): LogoLetter[];