@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/baubles/__snapshots__/branch-labels.test.tsx.snap ADDED
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+ // Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
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+
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+ exports[`Branch labels > renders a tree branchlabels - polar 1`] = `
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+ {
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+ </body>,
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+ "container": <div>
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+ <svg
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+ data-testid="figure"
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+ xmlns="http://www.w3.org/2000/svg"
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+ "getAllByPlaceholderText": [Function],
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+ "queryByTitle": [Function],
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+ "rerender": [Function],
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+ "unmount": [Function],
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+ }
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+ `;
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+
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+ exports[`Branch labels > renders a tree node labels 1`] = `
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+ {
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+ "asFragment": [Function],
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+ "baseElement": <body>
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+ <div>
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+ <svg
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+ data-testid="figure"
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+ >
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+ Label!
617
+ </text>
618
+ </g>
619
+ </g>
620
+ </g>
621
+ </g>
622
+ </svg>
623
+ </div>,
624
+ "debug": [Function],
625
+ "findAllByAltText": [Function],
626
+ "findAllByDisplayValue": [Function],
627
+ "findAllByLabelText": [Function],
628
+ "findAllByPlaceholderText": [Function],
629
+ "findAllByRole": [Function],
630
+ "findAllByTestId": [Function],
631
+ "findAllByText": [Function],
632
+ "findAllByTitle": [Function],
633
+ "findByAltText": [Function],
634
+ "findByDisplayValue": [Function],
635
+ "findByLabelText": [Function],
636
+ "findByPlaceholderText": [Function],
637
+ "findByRole": [Function],
638
+ "findByTestId": [Function],
639
+ "findByText": [Function],
640
+ "findByTitle": [Function],
641
+ "getAllByAltText": [Function],
642
+ "getAllByDisplayValue": [Function],
643
+ "getAllByLabelText": [Function],
644
+ "getAllByPlaceholderText": [Function],
645
+ "getAllByRole": [Function],
646
+ "getAllByTestId": [Function],
647
+ "getAllByText": [Function],
648
+ "getAllByTitle": [Function],
649
+ "getByAltText": [Function],
650
+ "getByDisplayValue": [Function],
651
+ "getByLabelText": [Function],
652
+ "getByPlaceholderText": [Function],
653
+ "getByRole": [Function],
654
+ "getByTestId": [Function],
655
+ "getByText": [Function],
656
+ "getByTitle": [Function],
657
+ "queryAllByAltText": [Function],
658
+ "queryAllByDisplayValue": [Function],
659
+ "queryAllByLabelText": [Function],
660
+ "queryAllByPlaceholderText": [Function],
661
+ "queryAllByRole": [Function],
662
+ "queryAllByTestId": [Function],
663
+ "queryAllByText": [Function],
664
+ "queryAllByTitle": [Function],
665
+ "queryByAltText": [Function],
666
+ "queryByDisplayValue": [Function],
667
+ "queryByLabelText": [Function],
668
+ "queryByPlaceholderText": [Function],
669
+ "queryByRole": [Function],
670
+ "queryByTestId": [Function],
671
+ "queryByText": [Function],
672
+ "queryByTitle": [Function],
673
+ "rerender": [Function],
674
+ "unmount": [Function],
675
+ }
676
+ `;
677
+
678
+ exports[`Branch labels > renders a tree with aligned Node labels and a function for text 1`] = `
679
+ {
680
+ "asFragment": [Function],
681
+ "baseElement": <body>
682
+ <div>
683
+ <svg
684
+ data-testid="figure"
685
+ height="400px"
686
+ width="400px"
687
+ xmlns="http://www.w3.org/2000/svg"
688
+ >
689
+ <g>
690
+ <g
691
+ transform="translate(10,10)"
692
+ >
693
+ <g
694
+ class="branch-layer"
695
+ >
696
+ <path
697
+ d="M 0.001 237.5 C0.001,237.5 0,95 0,95 C0,95 126.66666666666666,95.0005 190,95.00075000000001 C190,95.00075000000001 221.66666666666666,95.00087500000001 237.5,95.0009375 C237.5,95.0009375 245.41666666666666,95.00096875 249.375,95.000984375 C249.375,95.000984375 251.35416666666666,95.0009921875 252.34375,95.00099609375 C252.34375,95.00099609375 253.33333333333331,95.001 253.33333333333331,95.001 "
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+ fill="none"
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+ stroke="black"
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+ stroke-width="2"
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+ />
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+ <path
703
+ d="M 253.33433333333332 95 C253.33433333333332,95 253.33333333333331,0 253.33333333333331,0 C253.33333333333331,0 316.66666666666663,0.0005 348.3333333333333,0.00075 C348.3333333333333,0.00075 364.16666666666663,0.000875 372.0833333333333,0.0009375 C372.0833333333333,0.0009375 376.04166666666663,0.00096875 378.0208333333333,0.000984375 C378.0208333333333,0.000984375 379.01041666666663,0.0009921875 379.5052083333333,0.00099609375 C379.5052083333333,0.00099609375 380,0.001 380,0.001 "
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+ fill="none"
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+ stroke="black"
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+ stroke-width="2"
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+ />
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+ <path
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+ d="M 253.33433333333332 95 C253.33433333333332,95 253.33333333333331,190 253.33333333333331,190 C253.33333333333331,190 316.66666666666663,190.0005 348.3333333333333,190.00074999999998 C348.3333333333333,190.00074999999998 364.16666666666663,190.000875 372.0833333333333,190.00093750000002 C372.0833333333333,190.00093750000002 376.04166666666663,190.00096875000003 378.0208333333333,190.00098437500003 C378.0208333333333,190.00098437500003 379.01041666666663,190.0009921875 379.5052083333333,190.00099609375002 C379.5052083333333,190.00099609375002 380,190.001 380,190.001 "
710
+ fill="none"
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+ stroke="black"
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+ stroke-width="2"
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+ />
714
+ <path
715
+ d="M 0.001 237.5 C0.001,237.5 0,380 0,380 C0,380 63.33333333333333,380.0005 95,380.00075 C95,380.00075 110.83333333333333,380.00087499999995 118.75,380.00093749999996 C118.75,380.00093749999996 122.70833333333333,380.00096874999997 124.6875,380.000984375 C124.6875,380.000984375 125.67708333333333,380.00099218749995 126.171875,380.00099609374996 C126.171875,380.00099609374996 126.66666666666666,380.001 126.66666666666666,380.001 "
716
+ fill="none"
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+ stroke="black"
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+ stroke-width="2"
719
+ />
720
+ </g>
721
+ <g
722
+ class="branch-layer"
723
+ >
724
+ <g>
725
+ <text
726
+ alignment-baseline="baseline"
727
+ text-anchor="middle"
728
+ transform="translate(126.66666666666666,89) rotate(0)"
729
+ >
730
+ 1
731
+ </text>
732
+ </g>
733
+ <g>
734
+ <text
735
+ alignment-baseline="baseline"
736
+ text-anchor="middle"
737
+ transform="translate(316.66666666666663,-6) rotate(0)"
738
+ >
739
+ 2
740
+ </text>
741
+ </g>
742
+ <g>
743
+ <text
744
+ alignment-baseline="baseline"
745
+ text-anchor="middle"
746
+ transform="translate(316.66666666666663,184) rotate(0)"
747
+ >
748
+ 3
749
+ </text>
750
+ </g>
751
+ <g>
752
+ <text
753
+ alignment-baseline="baseline"
754
+ text-anchor="middle"
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+ transform="translate(63.33333333333333,374) rotate(0)"
756
+ >
757
+ 4
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+ </text>
759
+ </g>
760
+ </g>
761
+ </g>
762
+ </g>
763
+ </svg>
764
+ </div>
765
+ </body>,
766
+ "container": <div>
767
+ <svg
768
+ data-testid="figure"
769
+ height="400px"
770
+ width="400px"
771
+ xmlns="http://www.w3.org/2000/svg"
772
+ >
773
+ <g>
774
+ <g
775
+ transform="translate(10,10)"
776
+ >
777
+ <g
778
+ class="branch-layer"
779
+ >
780
+ <path
781
+ d="M 0.001 237.5 C0.001,237.5 0,95 0,95 C0,95 126.66666666666666,95.0005 190,95.00075000000001 C190,95.00075000000001 221.66666666666666,95.00087500000001 237.5,95.0009375 C237.5,95.0009375 245.41666666666666,95.00096875 249.375,95.000984375 C249.375,95.000984375 251.35416666666666,95.0009921875 252.34375,95.00099609375 C252.34375,95.00099609375 253.33333333333331,95.001 253.33333333333331,95.001 "
782
+ fill="none"
783
+ stroke="black"
784
+ stroke-width="2"
785
+ />
786
+ <path
787
+ d="M 253.33433333333332 95 C253.33433333333332,95 253.33333333333331,0 253.33333333333331,0 C253.33333333333331,0 316.66666666666663,0.0005 348.3333333333333,0.00075 C348.3333333333333,0.00075 364.16666666666663,0.000875 372.0833333333333,0.0009375 C372.0833333333333,0.0009375 376.04166666666663,0.00096875 378.0208333333333,0.000984375 C378.0208333333333,0.000984375 379.01041666666663,0.0009921875 379.5052083333333,0.00099609375 C379.5052083333333,0.00099609375 380,0.001 380,0.001 "
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+ fill="none"
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+ stroke="black"
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+ stroke-width="2"
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+ />
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+ <path
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+ d="M 253.33433333333332 95 C253.33433333333332,95 253.33333333333331,190 253.33333333333331,190 C253.33333333333331,190 316.66666666666663,190.0005 348.3333333333333,190.00074999999998 C348.3333333333333,190.00074999999998 364.16666666666663,190.000875 372.0833333333333,190.00093750000002 C372.0833333333333,190.00093750000002 376.04166666666663,190.00096875000003 378.0208333333333,190.00098437500003 C378.0208333333333,190.00098437500003 379.01041666666663,190.0009921875 379.5052083333333,190.00099609375002 C379.5052083333333,190.00099609375002 380,190.001 380,190.001 "
794
+ fill="none"
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+ stroke="black"
796
+ stroke-width="2"
797
+ />
798
+ <path
799
+ d="M 0.001 237.5 C0.001,237.5 0,380 0,380 C0,380 63.33333333333333,380.0005 95,380.00075 C95,380.00075 110.83333333333333,380.00087499999995 118.75,380.00093749999996 C118.75,380.00093749999996 122.70833333333333,380.00096874999997 124.6875,380.000984375 C124.6875,380.000984375 125.67708333333333,380.00099218749995 126.171875,380.00099609374996 C126.171875,380.00099609374996 126.66666666666666,380.001 126.66666666666666,380.001 "
800
+ fill="none"
801
+ stroke="black"
802
+ stroke-width="2"
803
+ />
804
+ </g>
805
+ <g
806
+ class="branch-layer"
807
+ >
808
+ <g>
809
+ <text
810
+ alignment-baseline="baseline"
811
+ text-anchor="middle"
812
+ transform="translate(126.66666666666666,89) rotate(0)"
813
+ >
814
+ 1
815
+ </text>
816
+ </g>
817
+ <g>
818
+ <text
819
+ alignment-baseline="baseline"
820
+ text-anchor="middle"
821
+ transform="translate(316.66666666666663,-6) rotate(0)"
822
+ >
823
+ 2
824
+ </text>
825
+ </g>
826
+ <g>
827
+ <text
828
+ alignment-baseline="baseline"
829
+ text-anchor="middle"
830
+ transform="translate(316.66666666666663,184) rotate(0)"
831
+ >
832
+ 3
833
+ </text>
834
+ </g>
835
+ <g>
836
+ <text
837
+ alignment-baseline="baseline"
838
+ text-anchor="middle"
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+ transform="translate(63.33333333333333,374) rotate(0)"
840
+ >
841
+ 4
842
+ </text>
843
+ </g>
844
+ </g>
845
+ </g>
846
+ </g>
847
+ </svg>
848
+ </div>,
849
+ "debug": [Function],
850
+ "findAllByAltText": [Function],
851
+ "findAllByDisplayValue": [Function],
852
+ "findAllByLabelText": [Function],
853
+ "findAllByPlaceholderText": [Function],
854
+ "findAllByRole": [Function],
855
+ "findAllByTestId": [Function],
856
+ "findAllByText": [Function],
857
+ "findAllByTitle": [Function],
858
+ "findByAltText": [Function],
859
+ "findByDisplayValue": [Function],
860
+ "findByLabelText": [Function],
861
+ "findByPlaceholderText": [Function],
862
+ "findByRole": [Function],
863
+ "findByTestId": [Function],
864
+ "findByText": [Function],
865
+ "findByTitle": [Function],
866
+ "getAllByAltText": [Function],
867
+ "getAllByDisplayValue": [Function],
868
+ "getAllByLabelText": [Function],
869
+ "getAllByPlaceholderText": [Function],
870
+ "getAllByRole": [Function],
871
+ "getAllByTestId": [Function],
872
+ "getAllByText": [Function],
873
+ "getAllByTitle": [Function],
874
+ "getByAltText": [Function],
875
+ "getByDisplayValue": [Function],
876
+ "getByLabelText": [Function],
877
+ "getByPlaceholderText": [Function],
878
+ "getByRole": [Function],
879
+ "getByTestId": [Function],
880
+ "getByText": [Function],
881
+ "getByTitle": [Function],
882
+ "queryAllByAltText": [Function],
883
+ "queryAllByDisplayValue": [Function],
884
+ "queryAllByLabelText": [Function],
885
+ "queryAllByPlaceholderText": [Function],
886
+ "queryAllByRole": [Function],
887
+ "queryAllByTestId": [Function],
888
+ "queryAllByText": [Function],
889
+ "queryAllByTitle": [Function],
890
+ "queryByAltText": [Function],
891
+ "queryByDisplayValue": [Function],
892
+ "queryByLabelText": [Function],
893
+ "queryByPlaceholderText": [Function],
894
+ "queryByRole": [Function],
895
+ "queryByTestId": [Function],
896
+ "queryByText": [Function],
897
+ "queryByTitle": [Function],
898
+ "rerender": [Function],
899
+ "unmount": [Function],
900
+ }
901
+ `;