react-msaview 5.10.0 → 6.1.0

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 (226) hide show
  1. package/bundle/index.js +99 -99
  2. package/bundle/index.js.map +4 -4
  3. package/dist/clustalX.js +22 -22
  4. package/dist/clustalX.js.map +1 -1
  5. package/dist/columnCounts.d.ts +7 -0
  6. package/dist/columnCounts.js +18 -0
  7. package/dist/columnCounts.js.map +1 -1
  8. package/dist/components/CopyButton.d.ts +9 -0
  9. package/dist/components/CopyButton.js +23 -0
  10. package/dist/components/CopyButton.js.map +1 -0
  11. package/dist/components/DragHandle.d.ts +25 -0
  12. package/dist/components/DragHandle.js +49 -0
  13. package/dist/components/DragHandle.js.map +1 -0
  14. package/dist/components/Loading.js +2 -2
  15. package/dist/components/Loading.js.map +1 -1
  16. package/dist/components/MSAView.js +2 -2
  17. package/dist/components/MSAView.js.map +1 -1
  18. package/dist/components/ResizeHandles.d.ts +4 -2
  19. package/dist/components/ResizeHandles.js +35 -54
  20. package/dist/components/ResizeHandles.js.map +1 -1
  21. package/dist/components/SequenceTextArea.js +3 -10
  22. package/dist/components/SequenceTextArea.js.map +1 -1
  23. package/dist/components/VerticalScrollbar.js +11 -25
  24. package/dist/components/VerticalScrollbar.js.map +1 -1
  25. package/dist/components/dialogs/FeatureDialog.js +3 -3
  26. package/dist/components/dialogs/FeatureDialog.js.map +1 -1
  27. package/dist/components/dialogs/InterProScanDialog.js +52 -129
  28. package/dist/components/dialogs/InterProScanDialog.js.map +1 -1
  29. package/dist/components/dialogs/{UserProvidedDomainsDialog.d.ts → InterProScanFileDialog.d.ts} +2 -2
  30. package/dist/components/dialogs/{UserProvidedDomainsDialog.js → InterProScanFileDialog.js} +6 -10
  31. package/dist/components/dialogs/InterProScanFileDialog.js.map +1 -0
  32. package/dist/components/dialogs/TrackInfoDialog.d.ts +2 -4
  33. package/dist/components/dialogs/TrackInfoDialog.js +8 -14
  34. package/dist/components/dialogs/TrackInfoDialog.js.map +1 -1
  35. package/dist/components/header/FileMenu.js +3 -3
  36. package/dist/components/header/FileMenu.js.map +1 -1
  37. package/dist/components/header/GappynessSlider.js +1 -1
  38. package/dist/components/header/GappynessSlider.js.map +1 -1
  39. package/dist/components/header/{getDomainsMenu.d.ts → getAnnotationsMenu.d.ts} +1 -1
  40. package/dist/components/header/{getDomainsMenu.js → getAnnotationsMenu.js} +10 -9
  41. package/dist/components/header/getAnnotationsMenu.js.map +1 -0
  42. package/dist/components/header/settingsMenuItems.js +15 -0
  43. package/dist/components/header/settingsMenuItems.js.map +1 -1
  44. package/dist/components/import/ImportForm.js +1 -1
  45. package/dist/components/import/ImportForm.js.map +1 -1
  46. package/dist/components/import/ImportFormExamples.js +66 -57
  47. package/dist/components/import/ImportFormExamples.js.map +1 -1
  48. package/dist/components/minimap/Minimap.js +40 -23
  49. package/dist/components/minimap/Minimap.js.map +1 -1
  50. package/dist/components/minimap/MinimapSVG.d.ts +2 -1
  51. package/dist/components/minimap/MinimapSVG.js +3 -4
  52. package/dist/components/minimap/MinimapSVG.js.map +1 -1
  53. package/dist/components/minimap/minimapLayout.d.ts +10 -1
  54. package/dist/components/minimap/minimapLayout.js +15 -10
  55. package/dist/components/minimap/minimapLayout.js.map +1 -1
  56. package/dist/components/msa/{DomainLegend.d.ts → AnnotationLegend.d.ts} +2 -2
  57. package/dist/components/msa/{DomainLegend.js → AnnotationLegend.js} +4 -4
  58. package/dist/components/msa/AnnotationLegend.js.map +1 -0
  59. package/dist/components/msa/MSACanvas.js +9 -3
  60. package/dist/components/msa/MSACanvas.js.map +1 -1
  61. package/dist/components/msa/MSACanvasBlock.js +12 -3
  62. package/dist/components/msa/MSACanvasBlock.js.map +1 -1
  63. package/dist/components/msa/MSAMouseoverCanvas.js +1 -2
  64. package/dist/components/msa/MSAMouseoverCanvas.js.map +1 -1
  65. package/dist/components/msa/MSAPanel.js +2 -2
  66. package/dist/components/msa/MSAPanel.js.map +1 -1
  67. package/dist/components/msa/domainBandCursor.d.ts +17 -0
  68. package/dist/components/msa/domainBandCursor.js +39 -0
  69. package/dist/components/msa/domainBandCursor.js.map +1 -0
  70. package/dist/components/msa/msaRaster.d.ts +63 -0
  71. package/dist/components/msa/msaRaster.js +252 -0
  72. package/dist/components/msa/msaRaster.js.map +1 -0
  73. package/dist/components/msa/renderMSABlock.d.ts +2 -1
  74. package/dist/components/msa/renderMSABlock.js +27 -41
  75. package/dist/components/msa/renderMSABlock.js.map +1 -1
  76. package/dist/components/msa/renderMSAMouseover.js +1 -2
  77. package/dist/components/msa/renderMSAMouseover.js.map +1 -1
  78. package/dist/components/msa/tileColor.d.ts +6 -0
  79. package/dist/components/msa/tileColor.js +35 -0
  80. package/dist/components/msa/tileColor.js.map +1 -0
  81. package/dist/components/renderCtx.d.ts +1 -1
  82. package/dist/components/tracks/TrackBlocks.d.ts +14 -0
  83. package/dist/components/tracks/TrackBlocks.js +65 -0
  84. package/dist/components/tracks/TrackBlocks.js.map +1 -0
  85. package/dist/components/tracks/{renderTracksSvg.d.ts → drawTracks.d.ts} +22 -10
  86. package/dist/components/tracks/drawTracks.js +193 -0
  87. package/dist/components/tracks/drawTracks.js.map +1 -0
  88. package/dist/components/tree/TreeCanvas.js +8 -2
  89. package/dist/components/tree/TreeCanvas.js.map +1 -1
  90. package/dist/components/tree/TreeCanvasBlock.js +7 -4
  91. package/dist/components/tree/TreeCanvasBlock.js.map +1 -1
  92. package/dist/components/tree/TreeRuler.js +5 -2
  93. package/dist/components/tree/TreeRuler.js.map +1 -1
  94. package/dist/components/tree/renderTreeCanvas.js +5 -2
  95. package/dist/components/tree/renderTreeCanvas.js.map +1 -1
  96. package/dist/constants.d.ts +3 -0
  97. package/dist/constants.js +8 -0
  98. package/dist/constants.js.map +1 -1
  99. package/dist/ggplotPalettes.d.ts +0 -1
  100. package/dist/ggplotPalettes.js +0 -3
  101. package/dist/ggplotPalettes.js.map +1 -1
  102. package/dist/hierarchy.d.ts +2 -6
  103. package/dist/hierarchy.js +4 -6
  104. package/dist/hierarchy.js.map +1 -1
  105. package/dist/index.d.ts +2 -2
  106. package/dist/launchInterProScan.d.ts +0 -23
  107. package/dist/launchInterProScan.js +2 -5
  108. package/dist/launchInterProScan.js.map +1 -1
  109. package/dist/measureTextCanvas.js +21 -6
  110. package/dist/measureTextCanvas.js.map +1 -1
  111. package/dist/model/DataModel.d.ts +1 -4
  112. package/dist/model/DataModel.js +8 -10
  113. package/dist/model/DataModel.js.map +1 -1
  114. package/dist/model.d.ts +86 -107
  115. package/dist/model.js +238 -162
  116. package/dist/model.js.map +1 -1
  117. package/dist/neighborJoining.js +34 -18
  118. package/dist/neighborJoining.js.map +1 -1
  119. package/dist/renderTestEnv.d.ts +43 -0
  120. package/dist/renderTestEnv.js +88 -0
  121. package/dist/renderTestEnv.js.map +1 -0
  122. package/dist/renderToSvg.js +3 -3
  123. package/dist/renderToSvg.js.map +1 -1
  124. package/dist/rowCoordinateCalculations.d.ts +13 -17
  125. package/dist/rowCoordinateCalculations.js +45 -39
  126. package/dist/rowCoordinateCalculations.js.map +1 -1
  127. package/dist/sequenceLogo.d.ts +28 -0
  128. package/dist/sequenceLogo.js +47 -0
  129. package/dist/sequenceLogo.js.map +1 -0
  130. package/dist/types.d.ts +6 -11
  131. package/dist/version.d.ts +1 -1
  132. package/dist/version.js +1 -1
  133. package/dist/version.js.map +1 -1
  134. package/package.json +5 -5
  135. package/src/clustalX.ts +22 -22
  136. package/src/colSpace.test.ts +27 -0
  137. package/src/columnCounts.test.ts +15 -0
  138. package/src/columnCounts.ts +19 -0
  139. package/src/components/CopyButton.tsx +44 -0
  140. package/src/components/DragHandle.tsx +81 -0
  141. package/src/components/Loading.tsx +10 -1
  142. package/src/components/MSAView.tsx +2 -3
  143. package/src/components/ResizeHandles.tsx +70 -87
  144. package/src/components/SequenceTextArea.tsx +3 -16
  145. package/src/components/VerticalScrollbar.tsx +20 -33
  146. package/src/components/dialogs/FeatureDialog.tsx +3 -4
  147. package/src/components/dialogs/InterProScanDialog.tsx +54 -131
  148. package/src/components/dialogs/{UserProvidedDomainsDialog.tsx → InterProScanFileDialog.tsx} +6 -14
  149. package/src/components/dialogs/TrackInfoDialog.tsx +18 -20
  150. package/src/components/header/FileMenu.tsx +3 -3
  151. package/src/components/header/GappynessSlider.tsx +4 -1
  152. package/src/components/header/{getDomainsMenu.ts → getAnnotationsMenu.ts} +10 -9
  153. package/src/components/header/settingsMenuItems.ts +18 -0
  154. package/src/components/import/ImportForm.tsx +1 -1
  155. package/src/components/import/ImportFormExamples.tsx +82 -133
  156. package/src/components/minimap/Minimap.tsx +67 -32
  157. package/src/components/minimap/MinimapSVG.tsx +32 -31
  158. package/src/components/minimap/minimapLayout.test.ts +60 -0
  159. package/src/components/minimap/minimapLayout.ts +15 -10
  160. package/src/components/msa/{DomainLegend.tsx → AnnotationLegend.tsx} +7 -3
  161. package/src/components/msa/MSACanvas.tsx +24 -11
  162. package/src/components/msa/MSACanvasBlock.tsx +13 -3
  163. package/src/components/msa/MSAMouseoverCanvas.tsx +1 -3
  164. package/src/components/msa/MSAPanel.tsx +2 -2
  165. package/src/components/msa/domainBandCursor.ts +41 -0
  166. package/src/components/msa/msaRaster.test.ts +145 -0
  167. package/src/components/msa/msaRaster.ts +350 -0
  168. package/src/components/msa/renderMSABlock.ts +34 -43
  169. package/src/components/msa/renderMSAMouseover.ts +1 -3
  170. package/src/components/msa/tileColor.ts +37 -0
  171. package/src/components/renderCtx.ts +2 -0
  172. package/src/components/tracks/TrackBlocks.tsx +111 -0
  173. package/src/components/tracks/drawTracks.ts +323 -0
  174. package/src/components/tree/TreeCanvas.tsx +16 -4
  175. package/src/components/tree/TreeCanvasBlock.tsx +18 -11
  176. package/src/components/tree/TreeRuler.tsx +7 -2
  177. package/src/components/tree/renderTreeCanvas.test.ts +15 -7
  178. package/src/components/tree/renderTreeCanvas.ts +5 -1
  179. package/src/constants.ts +10 -0
  180. package/src/domainBands.test.ts +24 -0
  181. package/src/domainLetterColor.test.ts +80 -0
  182. package/src/ggplotPalettes.ts +0 -4
  183. package/src/hierarchy.test.ts +7 -7
  184. package/src/hierarchy.ts +6 -9
  185. package/src/impgRender.test.tsx +2 -57
  186. package/src/index.ts +4 -1
  187. package/src/largeTree.test.ts +39 -4
  188. package/src/launchInterProScan.ts +3 -30
  189. package/src/loadErrorDisplay.test.tsx +102 -0
  190. package/src/measureTextCanvas.ts +22 -6
  191. package/src/model/DataModel.ts +11 -11
  192. package/src/model.ts +262 -172
  193. package/src/neighborJoining.ts +36 -18
  194. package/src/renderDomainsSvg.test.tsx +2 -57
  195. package/src/renderMinimapSvg.test.tsx +55 -0
  196. package/src/renderSequenceLogoSvg.test.tsx +176 -0
  197. package/src/renderTestEnv.ts +96 -0
  198. package/src/renderToSvg.tsx +3 -3
  199. package/src/rowCoordinateCalculations.ts +48 -44
  200. package/src/sequenceLogo.test.ts +88 -0
  201. package/src/sequenceLogo.ts +63 -0
  202. package/src/types.ts +17 -16
  203. package/src/version.ts +1 -1
  204. package/src/viewChrome.test.tsx +134 -0
  205. package/dist/components/ConservationTrack.d.ts +0 -8
  206. package/dist/components/ConservationTrack.js +0 -49
  207. package/dist/components/ConservationTrack.js.map +0 -1
  208. package/dist/components/TextTrack.d.ts +0 -8
  209. package/dist/components/TextTrack.js +0 -58
  210. package/dist/components/TextTrack.js.map +0 -1
  211. package/dist/components/dialogs/DomainDialog.d.ts +0 -6
  212. package/dist/components/dialogs/DomainDialog.js +0 -19
  213. package/dist/components/dialogs/DomainDialog.js.map +0 -1
  214. package/dist/components/dialogs/UserProvidedDomainsDialog.js.map +0 -1
  215. package/dist/components/header/SettingsMenu.d.ts +0 -6
  216. package/dist/components/header/SettingsMenu.js +0 -40
  217. package/dist/components/header/SettingsMenu.js.map +0 -1
  218. package/dist/components/header/getDomainsMenu.js.map +0 -1
  219. package/dist/components/msa/DomainLegend.js.map +0 -1
  220. package/dist/components/tracks/renderTracksSvg.js +0 -126
  221. package/dist/components/tracks/renderTracksSvg.js.map +0 -1
  222. package/src/components/ConservationTrack.tsx +0 -99
  223. package/src/components/TextTrack.tsx +0 -103
  224. package/src/components/dialogs/DomainDialog.tsx +0 -45
  225. package/src/components/header/SettingsMenu.tsx +0 -57
  226. package/src/components/tracks/renderTracksSvg.ts +0 -247
package/dist/model.js.map CHANGED
@@ -1 +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
+ {"version":3,"file":"renderTestEnv.js","sourceRoot":"","sources":["../src/renderTestEnv.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AACH,MAAM,OAAO,aAAa;IACxB,CAAC,CAAQ;IACT,CAAC,CAAQ;IACT,CAAC,CAAQ;IACT,CAAC,CAAQ;IACT,CAAC,CAAQ;IACT,CAAC,CAAQ;IAET,YAAY,IAAe;QACzB,MAAM,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,IAAI,EAAE,CAAA;QAC7D,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;QACV,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;QACV,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;QACV,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;QACV,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;QACV,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;IACZ,CAAC;IAED,QAAQ,CAAC,CAAgB;QACvB,OAAO,IAAI,aAAa,CAAC;YACvB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;YAC3B,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;YAC3B,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;YAC3B,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC;YAC3B,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;YACpC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;SACrC,CAAC,CAAA;IACJ,CAAC;IAED,SAAS,CAAC,CAAS,EAAE,CAAC,GAAG,CAAC;QACxB,OAAO,IAAI,CAAC,QAAQ,CAAC,IAAI,aAAa,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7D,CAAC;IAED,KAAK,CAAC,CAAS,EAAE,CAAC,GAAG,CAAC;QACpB,OAAO,IAAI,CAAC,QAAQ,CAAC,IAAI,aAAa,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;IAC7D,CAAC;CACF;AAED,MAAM,OAAO,YAAY;IAEd,CAAC;IACD,CAAC;IAFV,YACS,CAAC,GAAG,CAAC,EACL,CAAC,GAAG,CAAC;iBADL,CAAC;iBACD,CAAC;IACP,CAAC;IAEJ,eAAe,CAAC,CAAgB;QAC9B,OAAO,IAAI,YAAY,CACrB,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EACjC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAClC,CAAA;IACH,CAAC;CACF;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,oBAAoB;IAClC,MAAM,CAAC,GAAG,UAAqC,CAAA;IAC/C,CAAC,CAAC,SAAS,GAAG,aAAa,CAAA;IAC3B,CAAC,CAAC,QAAQ,GAAG,YAAY,CAAA;IACzB,iBAAiB,CAAC,SAAS,CAAC,UAAU,GAAG;QACvC,IAAI,IAAI,GAAG,iBAAiB,CAAA;QAC5B,OAAO;YACL,IAAI,IAAI;gBACN,OAAO,IAAI,CAAA;YACb,CAAC;YACD,IAAI,IAAI,CAAC,CAAS;gBAChB,IAAI,GAAG,CAAC,CAAA;YACV,CAAC;YACD,WAAW,EAAE,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC;gBAC3B,KAAK,EAAE,CAAC,CAAC,MAAM,GAAG,CAAC,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,GAAG,GAAG;aACxD,CAAC;SACoC,CAAA;IAC1C,CAA6D,CAAA;AAC/D,CAAC;AAED,iEAAiE;AACjE,MAAM,CAAC,MAAM,qBAAqB,GAAG,GAAG,CAAA"}
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
@@ -72,13 +72,13 @@ function MsaSvg({ model, theme, Context, layout, }) {
72
72
  React.createElement("rect", { width: "100%", height: "100%", fill: "white" }),
73
73
  includeMinimap ? (React.createElement(React.Fragment, null,
74
74
  React.createElement("g", { transform: `translate(${treeAreaWidth} 0)` },
75
- React.createElement(MinimapSVG, { model: model })),
75
+ React.createElement(MinimapSVG, { model: model, width: width - treeAreaWidth })),
76
76
  React.createElement("g", { transform: `translate(0 ${minimapHeight})` }, body))) : (body),
77
77
  legendWidth > 0 ? (React.createElement("g", { transform: `translate(${width} ${legendTop})` },
78
78
  React.createElement(LegendSVG, { model: model, width: legendWidth }))) : null));
79
79
  }
80
80
  // the domain color key drawn as a reserved column to the right of the
81
- // alignment, mirroring the on-screen DomainLegend overlay
81
+ // alignment, mirroring the on-screen AnnotationLegend overlay
82
82
  function LegendSVG({ model, width }) {
83
83
  const { visibleDomainTypes, fillPalette, strokePalette } = model;
84
84
  const boxHeight = LEGEND_PAD * 2 + visibleDomainTypes.length * LEGEND_ROW_H;
package/dist/renderToSvg.js.map CHANGED
@@ -1 +1 @@
1
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1
+ 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package/dist/rowCoordinateCalculations.d.ts CHANGED
@@ -1,20 +1,3 @@
1
- /**
2
- * MSA Coordinate Systems:
3
- *
4
- * 1. **Global Column (globalCol)**: The column index in the full, unfiltered MSA.
5
- * Range: 0 to (MSA width - 1)
6
- * This is the "true" column position before any gap-hiding is applied.
7
- *
8
- * 2. **Visible Column (visibleCol)**: The column index after hiding gappy columns.
9
- * Range: 0 to (numColumns - 1) where numColumns = MSA width - blanks.length
10
- * This is what the user sees on screen when "Hide columns w/ N% gaps" is enabled.
11
- * When gap hiding is disabled, visibleCol === globalCol.
12
- *
13
- * 3. **Sequence Position (seqPos)**: The position within a specific row's ungapped sequence.
14
- * Range: 0 to (ungapped sequence length - 1)
15
- * This counts only non-gap characters ('-' and '.' are gaps).
16
- * Each row can have different seqPos values for the same globalCol due to gaps.
17
- */
18
1
  /**
19
2
  * Convert a visible column index to a global column index.
20
3
  * This is used when translating mouse/screen coordinates to MSA coordinates.
@@ -33,6 +16,19 @@ export declare function visibleColToGlobalCol(blanks: number[], visibleCol: numb
33
16
  * @returns The visible column index, or undefined if the column is hidden
34
17
  */
35
18
  export declare function globalColToVisibleCol(blanks: number[], globalCol: number): number | undefined;
19
+ /**
20
+ * How many visible columns come before a global column. For a visible column
21
+ * that is its own visible index; for a hidden one it is the index of the next
22
+ * visible column, i.e. where the hidden column collapses to.
23
+ *
24
+ * That total answer is what spans want: resolving both ends of a span through
25
+ * globalColToVisibleCol instead loses the whole span whenever either end lands
26
+ * in a hidden column.
27
+ *
28
+ * @param blanks - Sorted array of global column indices that are hidden
29
+ * @param globalCol - The global column index in the full MSA
30
+ */
31
+ export declare function visibleColsBefore(blanks: number[], globalCol: number): number;
36
32
  /**
37
33
  * Convert a visible column to a row-specific sequence position.
38
34
  * Returns undefined if the position is a gap in the sequence.