@figtreejs/core 0.0.1-alpha.0

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Files changed (111) hide show
  1. package/CHANGELOG.md +9 -0
  2. package/eslint.config.js +9 -0
  3. package/package.json +76 -0
  4. package/src/@custom-types/normalize-svg-path.d.ts +13 -0
  5. package/src/@custom-types/parse-svg-path.d.ts +8 -0
  6. package/src/@custom-types/svg-path-types.d.ts +37 -0
  7. package/src/bauble-makers/makers.ts +112 -0
  8. package/src/bauble-makers/set-up-baubles.ts +197 -0
  9. package/src/bauble-makers/utils.ts +61 -0
  10. package/src/components/baubles/bauble.tsx +61 -0
  11. package/src/components/baubles/branches.tsx +13 -0
  12. package/src/components/baubles/clades/cartoon.tsx +68 -0
  13. package/src/components/baubles/clades/highlight.tsx +96 -0
  14. package/src/components/baubles/clades/index.ts +1 -0
  15. package/src/components/baubles/clades.tsx +45 -0
  16. package/src/components/baubles/helpers.tsx +62 -0
  17. package/src/components/baubles/index.ts +16 -0
  18. package/src/components/baubles/labels.tsx +38 -0
  19. package/src/components/baubles/nodes.tsx +51 -0
  20. package/src/components/baubles/shapes/branch.tsx +53 -0
  21. package/src/components/baubles/shapes/circle.tsx +64 -0
  22. package/src/components/baubles/shapes/index.ts +9 -0
  23. package/src/components/baubles/shapes/label.tsx +104 -0
  24. package/src/components/baubles/shapes/rectangle.tsx +83 -0
  25. package/src/components/baubles/types.ts +99 -0
  26. package/src/components/decorations/axis/axis-types.ts +123 -0
  27. package/src/components/decorations/axis/axis.tsx +21 -0
  28. package/src/components/decorations/axis/index.ts +2 -0
  29. package/src/components/decorations/axis/polar-axis-bars.tsx +102 -0
  30. package/src/components/decorations/axis/polar-axis.tsx +175 -0
  31. package/src/components/decorations/axis/rectangular-axis-bars.tsx +53 -0
  32. package/src/components/decorations/axis/rectangular-axis.tsx +151 -0
  33. package/src/components/decorations/index.ts +2 -0
  34. package/src/components/decorations/legend/discrete-legend.tsx +93 -0
  35. package/src/components/decorations/legend/index.ts +1 -0
  36. package/src/components/decorations/legend/legend.tsx +1 -0
  37. package/src/components/figtree/figtree-types.ts +69 -0
  38. package/src/components/figtree/figtree.tsx +136 -0
  39. package/src/components/figtree/index.ts +3 -0
  40. package/src/components/hoc/index.ts +7 -0
  41. package/src/components/hoc/with-branch.tsx +148 -0
  42. package/src/components/hoc/with-branches.tsx +54 -0
  43. package/src/components/hoc/with-clades.tsx +47 -0
  44. package/src/components/hoc/with-node.tsx +183 -0
  45. package/src/components/hoc/with-nodes.tsx +45 -0
  46. package/src/components/index.ts +4 -0
  47. package/src/context/aminated-context.ts +3 -0
  48. package/src/context/dimension-context.ts +22 -0
  49. package/src/context/layout-context.ts +20 -0
  50. package/src/context/scale-context.ts +12 -0
  51. package/src/evo/index.ts +1 -0
  52. package/src/evo/tree/index.ts +5 -0
  53. package/src/evo/tree/mcc-tree.ts +0 -0
  54. package/src/evo/tree/normalized-tree/immutable-tree-helpers.ts +136 -0
  55. package/src/evo/tree/normalized-tree/immutable-tree.test.ts +158 -0
  56. package/src/evo/tree/normalized-tree/immutable-tree.ts +1365 -0
  57. package/src/evo/tree/normalized-tree/index.ts +3 -0
  58. package/src/evo/tree/parsers/annotation-parser.ts +276 -0
  59. package/src/evo/tree/parsers/index.ts +3 -0
  60. package/src/evo/tree/parsers/newick-character-parser.ts +246 -0
  61. package/src/evo/tree/parsers/newick-parsing.ts +22 -0
  62. package/src/evo/tree/parsers/nexus-parser.ts +12 -0
  63. package/src/evo/tree/parsers/nexus-parsing.ts +68 -0
  64. package/src/evo/tree/parsers/parsing.test.ts +289 -0
  65. package/src/evo/tree/parsers/stream-reader/index.ts +1 -0
  66. package/src/evo/tree/parsers/stream-reader/newick-importer.txt +395 -0
  67. package/src/evo/tree/parsers/stream-reader/nexus-importer.test.ts +99 -0
  68. package/src/evo/tree/parsers/stream-reader/nexus-importer.ts +293 -0
  69. package/src/evo/tree/parsers/stream-reader/nexus-tokenizer.ts +77 -0
  70. package/src/evo/tree/parsers/stream-reader/nexus-transform-stream.txt +109 -0
  71. package/src/evo/tree/taxa/helper-functions.ts +46 -0
  72. package/src/evo/tree/taxa/index.ts +1 -0
  73. package/src/evo/tree/taxa/taxon.ts +116 -0
  74. package/src/evo/tree/traversals/index.ts +1 -0
  75. package/src/evo/tree/traversals/preorder-traversal.ts +89 -0
  76. package/src/evo/tree/traversals/traversal-types.ts +6 -0
  77. package/src/evo/tree/tree-types.ts +197 -0
  78. package/src/evo/tree/utilities.ts +44 -0
  79. package/src/index.ts +6 -0
  80. package/src/layouts/functional/index.ts +2 -0
  81. package/src/layouts/functional/radial-layout.ts +150 -0
  82. package/src/layouts/functional/rectangular-layout.ts +71 -0
  83. package/src/layouts/index.ts +3 -0
  84. package/src/layouts/layout-interface.ts +90 -0
  85. package/src/layouts/types.ts +32 -0
  86. package/src/path.helpers.ts +81 -0
  87. package/src/store/polar-scale.ts +145 -0
  88. package/src/store/store.ts +144 -0
  89. package/src/tests/baubles/__snapshots__/branch-labels.test.tsx.snap +901 -0
  90. package/src/tests/baubles/__snapshots__/node-labels.test.tsx.snap +1516 -0
  91. package/src/tests/baubles/branch-labels.test.tsx +103 -0
  92. package/src/tests/baubles/label.svg +131 -0
  93. package/src/tests/baubles/node-labels.test.tsx +126 -0
  94. package/src/tests/clades/__snapshots__/cartoon.test.tsx.snap +327 -0
  95. package/src/tests/clades/__snapshots__/highlight.test.tsx.snap +337 -0
  96. package/src/tests/clades/cartoon.test.tsx +65 -0
  97. package/src/tests/clades/highlight.test.tsx +66 -0
  98. package/src/tests/figtree/__snapshots__/figtree.test.tsx.snap +761 -0
  99. package/src/tests/figtree/figtree.test.tsx +123 -0
  100. package/src/tests/figtree/simple.svg +47 -0
  101. package/src/tests/layouts/radiallayout.test.ts +23 -0
  102. package/src/tests/layouts/rectangularlayout.test.ts +65 -0
  103. package/src/tests/shapes/branch.test.tsx +40 -0
  104. package/src/tests/shapes/circle.test.tsx +47 -0
  105. package/src/tests/shapes/label.test.tsx +101 -0
  106. package/src/tests/shapes/rectangle.test.tsx +67 -0
  107. package/src/tests/shapes/types.ts +1 -0
  108. package/src/utils.ts +57 -0
  109. package/tsconfig.json +12 -0
  110. package/vite.config.ts +34 -0
  111. package/vitetest.config.ts +11 -0
package/src/tests/clades/__snapshots__/highlight.test.tsx.snap ADDED
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+ </g>
228
+ </g>
229
+ </svg>
230
+ </div>
231
+ </body>,
232
+ "container": <div>
233
+ <svg
234
+ data-testid="figure"
235
+ height="400px"
236
+ width="400px"
237
+ xmlns="http://www.w3.org/2000/svg"
238
+ >
239
+ <g>
240
+ <g
241
+ transform="translate(10,10)"
242
+ >
243
+ <g
244
+ class="branch-layer"
245
+ >
246
+ <path
247
+ d="M 191.0442564366689 190 C191.0442564366689,190 186.399298787742,253.16276972672102 184.07681996327852,284.7441545900815 C184.07681996327852,284.7441545900815 182.9155805510468,300.5348470217618 182.33496084493095,308.4301932376019 C182.33496084493095,308.4301932376019 182.04465099187303,312.37786634552197 181.89949606534407,314.351702899482 C181.89949606534407,314.351702899482 181.82691860207956,315.338621176462 181.79062987044733,315.832080314952 C181.79062987044733,315.832080314952 181.77248550463122,316.078809884197 181.76341332172314,316.20217466881957 C181.76341332172314,316.20217466881957 181.75434113881508,316.32553945344205 181.75434113881508,316.32553945344205 "
248
+ fill="none"
249
+ stroke="black"
250
+ stroke-width="2"
251
+ />
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+ <path
253
+ d="M 181.75434113881508 316.32553945344205 C247.8501082366655,321.1861882228226 306.51906010557065,274.27508823362695 316.31858118777706,208.729335348547 C316.31858118777706,208.729335348547 347.6371623755541,213.41166918568376 363.2964529694426,215.75283610425214 C363.2964529694426,215.75283610425214 371.12609826638686,216.92341956353633 375.040920914859,217.5087112931784 C375.040920914859,217.5087112931784 376.998332239095,217.80135715799946 377.97703790121307,217.94768009041 C377.97703790121307,217.94768009041 378.4663907322721,218.02084155661527 378.7110671478016,218.0574222897179 C378.7110671478016,218.0574222897179 378.9557435633311,218.09400302282052 378.9557435633311,218.09400302282052 "
254
+ fill="none"
255
+ stroke="black"
256
+ stroke-width="2"
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+ />
258
+ <path
259
+ d="M 181.75434113881508 316.32553945344205 C115.65857404096461,311.4648906840615 64.4833022968594,256.4759029000588 64.37775041784722,190.20173603608833 C64.37775041784722,190.20173603608833 32.7111239131418,190.2521700451104 16.877810660789084,190.27738704962144 C16.877810660789084,190.27738704962144 8.961154034612727,190.28999555187698 5.002825721524549,190.29629980300473 C5.002825721524549,190.29629980300473 3.02366156498046,190.2994519285686 2.034079486708415,190.30102799135057 C2.034079486708415,190.30102799135057 1.539288447572393,190.30181602274155 1.2918929280043818,190.302210038437 C1.2918929280043818,190.302210038437 1.0444974084363707,190.3026040541325 1.0444974084363707,190.3026040541325 "
260
+ fill="none"
261
+ stroke="black"
262
+ stroke-width="2"
263
+ />
264
+ <path
265
+ d="M 191.0442564366689 190 C191.0442564366689,190 222.3477640962031,185.21793078393245 237.9995179259702,182.82689617589867 C237.9995179259702,182.82689617589867 245.82539484085373,181.6313788718818 249.73833329829552,181.03362021987334 C249.73833329829552,181.03362021987334 251.6948025270164,180.73474089386912 252.67303714137685,180.585301230867 C252.67303714137685,180.585301230867 253.1621544485571,180.51058139936595 253.4067131021472,180.47322148361542 C253.4067131021472,180.47322148361542 253.52899242894225,180.45454152574015 253.5901320923398,180.44520154680254 C253.5901320923398,180.44520154680254 253.6512717557373,180.4358615678649 253.6512717557373,180.4358615678649 "
266
+ fill="none"
267
+ stroke="black"
268
+ stroke-width="2"
269
+ />
270
+ </g>
271
+ <g
272
+ class="node-layer"
273
+ >
274
+ <path
275
+ d="M-195,0.311A195,195,0,0,0,192.857,28.833L125.274,18.729A126.667,126.667,0,0,1,-126.667,0.202Z"
276
+ fill="red"
277
+ opacity="0.5"
278
+ transform="translate(191.0442564366689,190)"
279
+ />
280
+ </g>
281
+ </g>
282
+ </g>
283
+ </svg>
284
+ </div>,
285
+ "debug": [Function],
286
+ "findAllByAltText": [Function],
287
+ "findAllByDisplayValue": [Function],
288
+ "findAllByLabelText": [Function],
289
+ "findAllByPlaceholderText": [Function],
290
+ "findAllByRole": [Function],
291
+ "findAllByTestId": [Function],
292
+ "findAllByText": [Function],
293
+ "findAllByTitle": [Function],
294
+ "findByAltText": [Function],
295
+ "findByDisplayValue": [Function],
296
+ "findByLabelText": [Function],
297
+ "findByPlaceholderText": [Function],
298
+ "findByRole": [Function],
299
+ "findByTestId": [Function],
300
+ "findByText": [Function],
301
+ "findByTitle": [Function],
302
+ "getAllByAltText": [Function],
303
+ "getAllByDisplayValue": [Function],
304
+ "getAllByLabelText": [Function],
305
+ "getAllByPlaceholderText": [Function],
306
+ "getAllByRole": [Function],
307
+ "getAllByTestId": [Function],
308
+ "getAllByText": [Function],
309
+ "getAllByTitle": [Function],
310
+ "getByAltText": [Function],
311
+ "getByDisplayValue": [Function],
312
+ "getByLabelText": [Function],
313
+ "getByPlaceholderText": [Function],
314
+ "getByRole": [Function],
315
+ "getByTestId": [Function],
316
+ "getByText": [Function],
317
+ "getByTitle": [Function],
318
+ "queryAllByAltText": [Function],
319
+ "queryAllByDisplayValue": [Function],
320
+ "queryAllByLabelText": [Function],
321
+ "queryAllByPlaceholderText": [Function],
322
+ "queryAllByRole": [Function],
323
+ "queryAllByTestId": [Function],
324
+ "queryAllByText": [Function],
325
+ "queryAllByTitle": [Function],
326
+ "queryByAltText": [Function],
327
+ "queryByDisplayValue": [Function],
328
+ "queryByLabelText": [Function],
329
+ "queryByPlaceholderText": [Function],
330
+ "queryByRole": [Function],
331
+ "queryByTestId": [Function],
332
+ "queryByText": [Function],
333
+ "queryByTitle": [Function],
334
+ "rerender": [Function],
335
+ "unmount": [Function],
336
+ }
337
+ `;
package/src/tests/clades/cartoon.test.tsx ADDED
@@ -0,0 +1,65 @@
1
+ import { render } from "@testing-library/react";
2
+ import { ImmutableTree } from "../../evo";
3
+ import { FigTree } from "../../components";
4
+ import { polarLayout, rectangularLayout } from "../../layouts";
5
+ import { u } from "../../utils";
6
+ import { Branches, CartoonClades } from "../../bauble-makers/makers";
7
+
8
+ const tree = ImmutableTree.fromNewick("((A:1,B:1):2,C:1);");
9
+
10
+ describe("Figures", () => {
11
+ test("renders a single highlight", () => {
12
+ const fig = render(
13
+ <svg
14
+ width="400px"
15
+ height="400px"
16
+ data-testid="figure"
17
+ xmlns="http://www.w3.org/2000/svg"
18
+ >
19
+ <FigTree
20
+ width={400}
21
+ height={400}
22
+ tree={tree}
23
+ layout={rectangularLayout}
24
+ baubles={[
25
+ Branches({ attrs: { strokeWidth: 2, stroke: "black" } }),
26
+ CartoonClades({
27
+ attrs: { fill: "red", opacity: 0.5 },
28
+ nodes: [u(tree.getParent(u(tree.getNode("A"))))],
29
+ }),
30
+ ]}
31
+ />
32
+ </svg>,
33
+ );
34
+
35
+ //fig.debug();
36
+ expect(fig).toMatchSnapshot();
37
+ });
38
+ test("renders a single polar highlight", () => {
39
+ const fig = render(
40
+ <svg
41
+ width="400px"
42
+ height="400px"
43
+ data-testid="figure"
44
+ xmlns="http://www.w3.org/2000/svg"
45
+ >
46
+ <FigTree
47
+ width={400}
48
+ height={400}
49
+ tree={tree}
50
+ layout={polarLayout}
51
+ baubles={[
52
+ Branches({ attrs: { strokeWidth: 2, stroke: "black" } }),
53
+ CartoonClades({
54
+ attrs: { fill: "red", opacity: 0.5 },
55
+ nodes: [u(tree.getParent(u(tree.getNode("A"))))],
56
+ }),
57
+ ]}
58
+ />
59
+ </svg>,
60
+ );
61
+ //fig.debug();
62
+ expect(fig).toMatchSnapshot();
63
+ // expect(fig).toBeInTheDocument();
64
+ });
65
+ });
package/src/tests/clades/highlight.test.tsx ADDED
@@ -0,0 +1,66 @@
1
+ import { render } from "@testing-library/react";
2
+ import { ImmutableTree } from "../../evo";
3
+ import { FigTree } from "../../components";
4
+ import { polarLayout, rectangularLayout } from "../../layouts";
5
+
6
+ import { u } from "../../utils";
7
+ import { Branches, HighlightClades } from "../../bauble-makers/makers";
8
+
9
+ const tree = ImmutableTree.fromNewick("((A:1,B:1):2,C:1);");
10
+
11
+ describe("Figures", () => {
12
+ test("renders a single highlight", () => {
13
+ const fig = render(
14
+ <svg
15
+ width="400px"
16
+ height="400px"
17
+ data-testid="figure"
18
+ xmlns="http://www.w3.org/2000/svg"
19
+ >
20
+ <FigTree
21
+ width={400}
22
+ height={400}
23
+ tree={tree}
24
+ layout={rectangularLayout}
25
+ baubles={[
26
+ Branches({ attrs: { strokeWidth: 2, stroke: "black" } }),
27
+ HighlightClades({
28
+ attrs: { fill: "red", opacity: 0.5 },
29
+ nodes: [u(tree.getParent(u(tree.getNode("A"))))],
30
+ }),
31
+ ]}
32
+ />
33
+ </svg>,
34
+ );
35
+ //fig.debug();
36
+ expect(fig).toMatchSnapshot();
37
+ // expect(fig).toBeInTheDocument();
38
+ });
39
+ test("renders a single polar highlight", () => {
40
+ const fig = render(
41
+ <svg
42
+ width="400px"
43
+ height="400px"
44
+ data-testid="figure"
45
+ xmlns="http://www.w3.org/2000/svg"
46
+ >
47
+ <FigTree
48
+ width={400}
49
+ height={400}
50
+ tree={tree}
51
+ layout={polarLayout}
52
+ baubles={[
53
+ Branches({ attrs: { strokeWidth: 2, stroke: "black" } }),
54
+ HighlightClades({
55
+ attrs: { fill: "red", opacity: 0.5 },
56
+ nodes: [u(tree.getParent(u(tree.getNode("A"))))],
57
+ }),
58
+ ]}
59
+ />
60
+ </svg>,
61
+ );
62
+ //fig.debug();
63
+ expect(fig).toMatchSnapshot();
64
+ // expect(fig).toBeInTheDocument();
65
+ });
66
+ });