@jbrowse/plugin-spreadsheet-view 3.6.5 → 4.0.0

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 (84) hide show
  1. package/esm/LaunchSpreadsheetView/index.js +6 -13
  2. package/esm/SpreadsheetView/ImportWizard.d.ts +11 -15
  3. package/esm/SpreadsheetView/ImportWizard.js +45 -47
  4. package/esm/SpreadsheetView/SpreadsheetModel.d.ts +13 -16
  5. package/esm/SpreadsheetView/SpreadsheetModel.js +14 -22
  6. package/esm/SpreadsheetView/SpreadsheetViewModel.d.ts +68 -171
  7. package/esm/SpreadsheetView/SpreadsheetViewModel.js +54 -16
  8. package/esm/SpreadsheetView/components/BreakpointSplitViewChoiceDialog.d.ts +1 -0
  9. package/esm/SpreadsheetView/components/BreakpointSplitViewChoiceDialog.js +1 -0
  10. package/esm/SpreadsheetView/components/FeatureMenu.js +6 -29
  11. package/esm/SpreadsheetView/components/ImportWizard.d.ts +1 -1
  12. package/esm/SpreadsheetView/components/ImportWizard.js +5 -6
  13. package/esm/SpreadsheetView/components/LocationCell.js +3 -3
  14. package/esm/SpreadsheetView/components/NumberEditor.d.ts +1 -1
  15. package/esm/SpreadsheetView/components/NumberEditor.js +2 -2
  16. package/esm/SpreadsheetView/components/SpreadsheetDataGrid.d.ts +1 -1
  17. package/esm/SpreadsheetView/components/SpreadsheetDataGrid.js +4 -3
  18. package/esm/SpreadsheetView/components/SpreadsheetView.d.ts +1 -1
  19. package/esm/SpreadsheetView/components/SpreadsheetView.js +4 -5
  20. package/esm/SpreadsheetView/components/SpreadsheetViewActual.d.ts +1 -1
  21. package/esm/SpreadsheetView/components/SpreadsheetViewActual.js +3 -3
  22. package/esm/SpreadsheetView/components/TrackSelector.d.ts +1 -1
  23. package/esm/SpreadsheetView/components/TrackSelector.js +4 -5
  24. package/esm/SpreadsheetView/importAdapters/BedImport.js +4 -5
  25. package/esm/SpreadsheetView/importAdapters/BedpeImport.js +3 -4
  26. package/esm/SpreadsheetView/importAdapters/STARFusionImport.js +2 -2
  27. package/esm/SpreadsheetView/importAdapters/VcfImport.js +6 -4
  28. package/esm/SpreadsheetView/index.d.ts +1 -1
  29. package/esm/SpreadsheetView/index.js +2 -2
  30. package/esm/index.d.ts +1 -1
  31. package/esm/index.js +4 -6
  32. package/package.json +29 -36
  33. package/dist/LaunchSpreadsheetView/index.d.ts +0 -2
  34. package/dist/LaunchSpreadsheetView/index.js +0 -21
  35. package/dist/SpreadsheetView/ImportWizard.d.ts +0 -51
  36. package/dist/SpreadsheetView/ImportWizard.js +0 -250
  37. package/dist/SpreadsheetView/SpreadsheetModel.d.ts +0 -78
  38. package/dist/SpreadsheetView/SpreadsheetModel.js +0 -119
  39. package/dist/SpreadsheetView/SpreadsheetViewModel.d.ts +0 -299
  40. package/dist/SpreadsheetView/SpreadsheetViewModel.js +0 -101
  41. package/dist/SpreadsheetView/components/BreakendMultiLevelOptionDialog.d.ts +0 -1
  42. package/dist/SpreadsheetView/components/BreakendMultiLevelOptionDialog.js +0 -5
  43. package/dist/SpreadsheetView/components/BreakendSingleLevelOptionDialog.d.ts +0 -1
  44. package/dist/SpreadsheetView/components/BreakendSingleLevelOptionDialog.js +0 -5
  45. package/dist/SpreadsheetView/components/FeatureMenu.d.ts +0 -7
  46. package/dist/SpreadsheetView/components/FeatureMenu.js +0 -105
  47. package/dist/SpreadsheetView/components/ImportWizard.d.ts +0 -5
  48. package/dist/SpreadsheetView/components/ImportWizard.js +0 -47
  49. package/dist/SpreadsheetView/components/LocationCell.d.ts +0 -7
  50. package/dist/SpreadsheetView/components/LocationCell.js +0 -29
  51. package/dist/SpreadsheetView/components/NumberEditor.d.ts +0 -8
  52. package/dist/SpreadsheetView/components/NumberEditor.js +0 -32
  53. package/dist/SpreadsheetView/components/SpreadsheetDataGrid.d.ts +0 -5
  54. package/dist/SpreadsheetView/components/SpreadsheetDataGrid.js +0 -23
  55. package/dist/SpreadsheetView/components/SpreadsheetView.d.ts +0 -5
  56. package/dist/SpreadsheetView/components/SpreadsheetView.js +0 -48
  57. package/dist/SpreadsheetView/components/SpreadsheetViewActual.d.ts +0 -5
  58. package/dist/SpreadsheetView/components/SpreadsheetViewActual.js +0 -34
  59. package/dist/SpreadsheetView/components/TrackSelector.d.ts +0 -6
  60. package/dist/SpreadsheetView/components/TrackSelector.js +0 -27
  61. package/dist/SpreadsheetView/components/util.d.ts +0 -1
  62. package/dist/SpreadsheetView/components/util.js +0 -17
  63. package/dist/SpreadsheetView/importAdapters/BedImport.d.ts +0 -26
  64. package/dist/SpreadsheetView/importAdapters/BedImport.js +0 -58
  65. package/dist/SpreadsheetView/importAdapters/BedpeImport.d.ts +0 -36
  66. package/dist/SpreadsheetView/importAdapters/BedpeImport.js +0 -79
  67. package/dist/SpreadsheetView/importAdapters/STARFusionImport.d.ts +0 -25
  68. package/dist/SpreadsheetView/importAdapters/STARFusionImport.js +0 -35
  69. package/dist/SpreadsheetView/importAdapters/VcfImport.d.ts +0 -20
  70. package/dist/SpreadsheetView/importAdapters/VcfImport.js +0 -66
  71. package/dist/SpreadsheetView/importAdapters/isNumber.d.ts +0 -1
  72. package/dist/SpreadsheetView/importAdapters/isNumber.js +0 -14
  73. package/dist/SpreadsheetView/importAdapters/util.d.ts +0 -2
  74. package/dist/SpreadsheetView/importAdapters/util.js +0 -22
  75. package/dist/SpreadsheetView/index.d.ts +0 -3
  76. package/dist/SpreadsheetView/index.js +0 -52
  77. package/dist/SpreadsheetView/util.d.ts +0 -7
  78. package/dist/SpreadsheetView/util.js +0 -13
  79. package/dist/index.d.ts +0 -8
  80. package/dist/index.js +0 -33
  81. package/esm/SpreadsheetView/components/BreakendMultiLevelOptionDialog.d.ts +0 -1
  82. package/esm/SpreadsheetView/components/BreakendMultiLevelOptionDialog.js +0 -1
  83. package/esm/SpreadsheetView/components/BreakendSingleLevelOptionDialog.d.ts +0 -1
  84. package/esm/SpreadsheetView/components/BreakendSingleLevelOptionDialog.js +0 -1
@@ -1,78 +0,0 @@
1
- import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
2
- import type { Instance } from 'mobx-state-tree';
3
- export interface Row {
4
- feature?: SimpleFeatureSerialized;
5
- cellData?: Record<string, unknown>;
6
- cells?: {
7
- text: unknown;
8
- }[];
9
- }
10
- export interface RowSet {
11
- rows: Row[];
12
- }
13
- export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
14
- rowSet: import("mobx-state-tree").IType<RowSet | undefined, RowSet | undefined, RowSet | undefined>;
15
- columns: import("mobx-state-tree").IType<{
16
- name: string;
17
- }[], {
18
- name: string;
19
- }[], {
20
- name: string;
21
- }[]>;
22
- assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
23
- visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
24
- }, {
25
- visibleRowFlags: Record<number, boolean> | undefined;
26
- } & {
27
- readonly rows: {
28
- id: number;
29
- feature: SimpleFeatureSerialized | undefined;
30
- }[] | undefined;
31
- readonly initialized: boolean | undefined;
32
- } & {
33
- readonly dataGridColumns: ({
34
- field: string;
35
- width: number;
36
- type: "number" | undefined;
37
- } | {
38
- field: string;
39
- width: number;
40
- renderCell: ({ row }: import("@mui/x-data-grid").GridRenderCellParams<{
41
- id: number;
42
- feature: SimpleFeatureSerialized | undefined;
43
- }, any, any, import("@mui/x-data-grid").GridTreeNodeWithRender>) => import("react/jsx-runtime").JSX.Element | "N/A";
44
- type?: undefined;
45
- valueGetter?: undefined;
46
- valueFormatter?: undefined;
47
- } | {
48
- field: string;
49
- type: "number";
50
- width: number;
51
- valueGetter: (_val: unknown, row: {
52
- feature?: SimpleFeatureSerialized;
53
- }) => number | undefined;
54
- valueFormatter: (arg: never) => string;
55
- renderCell?: undefined;
56
- })[] | undefined;
57
- } & {
58
- readonly visibleRows: {
59
- id: number;
60
- feature: SimpleFeatureSerialized | undefined;
61
- }[] | undefined;
62
- } & {
63
- setVisibleRows(arg?: Record<number, boolean>): void;
64
- setVisibleColumns(arg: Record<string, boolean>): void;
65
- }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
66
- rowSet: import("mobx-state-tree").IType<RowSet | undefined, RowSet | undefined, RowSet | undefined>;
67
- columns: import("mobx-state-tree").IType<{
68
- name: string;
69
- }[], {
70
- name: string;
71
- }[], {
72
- name: string;
73
- }[]>;
74
- assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
75
- visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
76
- }>>, import("mobx-state-tree")._NotCustomized>;
77
- export type SpreadsheetStateModel = ReturnType<typeof stateModelFactory>;
78
- export type SpreadsheetModel = Instance<SpreadsheetStateModel>;
@@ -1,119 +0,0 @@
1
- "use strict";
2
- var __importDefault = (this && this.__importDefault) || function (mod) {
3
- return (mod && mod.__esModule) ? mod : { "default": mod };
4
- };
5
- Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.default = stateModelFactory;
7
- const jsx_runtime_1 = require("react/jsx-runtime");
8
- const util_1 = require("@jbrowse/core/util");
9
- const mobx_state_tree_1 = require("mobx-state-tree");
10
- const LocationCell_1 = __importDefault(require("./components/LocationCell"));
11
- function stateModelFactory() {
12
- return mobx_state_tree_1.types
13
- .model('Spreadsheet', {
14
- rowSet: mobx_state_tree_1.types.frozen(),
15
- columns: mobx_state_tree_1.types.frozen(),
16
- assemblyName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
17
- visibleColumns: mobx_state_tree_1.types.frozen(),
18
- })
19
- .volatile(() => ({
20
- visibleRowFlags: undefined,
21
- }))
22
- .views(self => ({
23
- get rows() {
24
- var _a;
25
- return (_a = self.rowSet) === null || _a === void 0 ? void 0 : _a.rows.map((row, i) => ({
26
- id: i,
27
- feature: row.feature,
28
- ...Object.fromEntries(self.columns.map((c, idx) => {
29
- var _a, _b, _c, _d;
30
- return [
31
- c.name,
32
- (_b = (_a = row.cellData) === null || _a === void 0 ? void 0 : _a[c.name]) !== null && _b !== void 0 ? _b : (_d = (_c = row.cells) === null || _c === void 0 ? void 0 : _c[idx]) === null || _d === void 0 ? void 0 : _d.text,
33
- ];
34
- })),
35
- }));
36
- },
37
- get initialized() {
38
- var _a;
39
- const session = (0, util_1.getSession)(self);
40
- const name = self.assemblyName;
41
- return (self.rowSet &&
42
- (name ? (_a = session.assemblyManager.get(name)) === null || _a === void 0 ? void 0 : _a.initialized : false));
43
- },
44
- }))
45
- .views(self => ({
46
- get dataGridColumns() {
47
- const { rows } = self;
48
- return rows
49
- ? [
50
- {
51
- field: 'Location',
52
- width: (0, util_1.measureGridWidth)(rows.map(row => row.feature ? (0, util_1.assembleLocStringFast)(row.feature) : 0)) + 40,
53
- renderCell: ({ row }) => {
54
- const { feature } = row;
55
- return feature ? ((0, jsx_runtime_1.jsx)(LocationCell_1.default, { model: self, feature: feature })) : ('N/A');
56
- },
57
- },
58
- {
59
- field: 'Length',
60
- type: 'number',
61
- width: (0, util_1.measureGridWidth)(rows.map(row => {
62
- const { feature } = row;
63
- return feature ? feature.end - feature.start : 0;
64
- })),
65
- valueGetter: (_val, row) => {
66
- const { feature } = row;
67
- return feature ? feature.end - feature.start : undefined;
68
- },
69
- valueFormatter: arg => (0, util_1.toLocale)(arg),
70
- },
71
- ...self.columns.map(f => ({
72
- field: f.name,
73
- width: (0, util_1.measureGridWidth)([...rows.map(r => r[f.name]), f.name], { minWidth: 20 }),
74
- type: typeof rows[0][f.name] === 'number'
75
- ? 'number'
76
- : undefined,
77
- })),
78
- ]
79
- : undefined;
80
- },
81
- }))
82
- .views(self => ({
83
- get visibleRows() {
84
- var _a;
85
- const { visibleRowFlags } = self;
86
- return visibleRowFlags
87
- ? (_a = self.rows) === null || _a === void 0 ? void 0 : _a.filter((_f, idx) => !!visibleRowFlags[idx])
88
- : self.rows;
89
- },
90
- }))
91
- .actions(self => ({
92
- setVisibleRows(arg) {
93
- self.visibleRowFlags = arg;
94
- },
95
- setVisibleColumns(arg) {
96
- self.visibleColumns = arg;
97
- },
98
- }))
99
- .preProcessSnapshot(snap => {
100
- return snap
101
- ? {
102
- ...snap,
103
- columns: snap.columns.filter(f => !f.isDerived),
104
- rowSet: snap.rowSet
105
- ? {
106
- ...snap.rowSet,
107
- rows: snap.rowSet.rows.map(r => {
108
- var _a, _b;
109
- return ({
110
- ...r,
111
- feature: (_a = r.feature) !== null && _a !== void 0 ? _a : (_b = r.extendedData) === null || _b === void 0 ? void 0 : _b.vcfFeature,
112
- });
113
- }),
114
- }
115
- : undefined,
116
- }
117
- : snap;
118
- });
119
- }
@@ -1,299 +0,0 @@
1
- import type { SpreadsheetModel } from './SpreadsheetModel';
2
- import type { MenuItem } from '@jbrowse/core/ui';
3
- import type { Instance } from 'mobx-state-tree';
4
- export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
5
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
6
- displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
7
- minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
8
- } & {
9
- type: import("mobx-state-tree").ISimpleType<"SpreadsheetView">;
10
- offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
11
- height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
12
- hideVerticalResizeHandle: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
13
- hideFilterControls: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
14
- importWizard: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
15
- fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
16
- hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
17
- columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
18
- selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
19
- cachedFileLocation: import("mobx-state-tree").IType<import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined>;
20
- }, {
21
- fileTypes: string[];
22
- fileSource: any;
23
- error: unknown;
24
- loading: boolean;
25
- } & {
26
- readonly isReadyToOpen: any;
27
- readonly fileName: any;
28
- readonly requiresUnzip: any;
29
- isValidRefName(refName: string, assemblyName?: string): boolean;
30
- tracksForAssembly(selectedAssembly: string): {
31
- track: {
32
- [x: string]: any;
33
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
34
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
35
- [x: string]: any;
36
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
37
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
38
- [x: string]: any;
39
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
40
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
41
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
42
- label: string;
43
- assemblyNames: any;
44
- type: string;
45
- loc: import("@jbrowse/core/util").FileLocation;
46
- }[];
47
- } & {
48
- setSelectedAssemblyName(s: string): void;
49
- setFileSource(newSource: unknown): void;
50
- setColumnNameLineNumber(newnumber: number): void;
51
- setFileType(typeName: string): void;
52
- setError(error: unknown): void;
53
- setLoading(arg: boolean): void;
54
- cancelButton(): void;
55
- setCachedFileHandle(arg: import("@jbrowse/core/util").FileLocation): void;
56
- } & {
57
- import(assemblyName: string): Promise<void>;
58
- } & {
59
- afterAttach(): void;
60
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
61
- spreadsheet: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
62
- rowSet: import("mobx-state-tree").IType<import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined>;
63
- columns: import("mobx-state-tree").IType<{
64
- name: string;
65
- }[], {
66
- name: string;
67
- }[], {
68
- name: string;
69
- }[]>;
70
- assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
71
- visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
72
- }, {
73
- visibleRowFlags: Record<number, boolean> | undefined;
74
- } & {
75
- readonly rows: {
76
- id: number;
77
- feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
78
- }[] | undefined;
79
- readonly initialized: boolean | undefined;
80
- } & {
81
- readonly dataGridColumns: ({
82
- field: string;
83
- width: number;
84
- type: "number" | undefined;
85
- } | {
86
- field: string;
87
- width: number;
88
- renderCell: ({ row }: import("@mui/x-data-grid").GridRenderCellParams<{
89
- id: number;
90
- feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
91
- }, any, any, import("@mui/x-data-grid").GridTreeNodeWithRender>) => import("react/jsx-runtime").JSX.Element | "N/A";
92
- type?: undefined;
93
- valueGetter?: undefined;
94
- valueFormatter?: undefined;
95
- } | {
96
- field: string;
97
- type: "number";
98
- width: number;
99
- valueGetter: (_val: unknown, row: {
100
- feature?: import("@jbrowse/core/util").SimpleFeatureSerialized;
101
- }) => number | undefined;
102
- valueFormatter: (arg: never) => string;
103
- renderCell?: undefined;
104
- })[] | undefined;
105
- } & {
106
- readonly visibleRows: {
107
- id: number;
108
- feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
109
- }[] | undefined;
110
- } & {
111
- setVisibleRows(arg?: Record<number, boolean>): void;
112
- setVisibleColumns(arg: Record<string, boolean>): void;
113
- }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
114
- rowSet: import("mobx-state-tree").IType<import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined>;
115
- columns: import("mobx-state-tree").IType<{
116
- name: string;
117
- }[], {
118
- name: string;
119
- }[], {
120
- name: string;
121
- }[]>;
122
- assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
123
- visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
124
- }>>, import("mobx-state-tree")._NotCustomized>>;
125
- }, {
126
- width: number;
127
- } & {
128
- menuItems(): MenuItem[];
129
- } & {
130
- setDisplayName(name: string): void;
131
- setWidth(newWidth: number): void;
132
- setMinimized(flag: boolean): void;
133
- } & {
134
- width: number;
135
- rowMenuItems: MenuItem[];
136
- } & {
137
- readonly assembly: any;
138
- } & {
139
- setRowMenuItems(newItems: MenuItem[]): void;
140
- setWidth(newWidth: number): number;
141
- setHeight(newHeight: number): number;
142
- resizeHeight(distance: number): number;
143
- resizeWidth(distance: number): number;
144
- displaySpreadsheet(spreadsheet?: SpreadsheetModel): void;
145
- } & {
146
- menuItems(): {
147
- label: string;
148
- icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
149
- muiName: string;
150
- };
151
- onClick: () => void;
152
- }[];
153
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree").ModelSnapshotType<{
154
- id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
155
- displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
156
- minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
157
- } & {
158
- type: import("mobx-state-tree").ISimpleType<"SpreadsheetView">;
159
- offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
160
- height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
161
- hideVerticalResizeHandle: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
162
- hideFilterControls: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
163
- importWizard: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
164
- fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
165
- hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
166
- columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
167
- selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
168
- cachedFileLocation: import("mobx-state-tree").IType<import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined>;
169
- }, {
170
- fileTypes: string[];
171
- fileSource: any;
172
- error: unknown;
173
- loading: boolean;
174
- } & {
175
- readonly isReadyToOpen: any;
176
- readonly fileName: any;
177
- readonly requiresUnzip: any;
178
- isValidRefName(refName: string, assemblyName?: string): boolean;
179
- tracksForAssembly(selectedAssembly: string): {
180
- track: {
181
- [x: string]: any;
182
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
183
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
184
- [x: string]: any;
185
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
186
- setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
187
- [x: string]: any;
188
- } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
189
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
190
- } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
191
- label: string;
192
- assemblyNames: any;
193
- type: string;
194
- loc: import("@jbrowse/core/util").FileLocation;
195
- }[];
196
- } & {
197
- setSelectedAssemblyName(s: string): void;
198
- setFileSource(newSource: unknown): void;
199
- setColumnNameLineNumber(newnumber: number): void;
200
- setFileType(typeName: string): void;
201
- setError(error: unknown): void;
202
- setLoading(arg: boolean): void;
203
- cancelButton(): void;
204
- setCachedFileHandle(arg: import("@jbrowse/core/util").FileLocation): void;
205
- } & {
206
- import(assemblyName: string): Promise<void>;
207
- } & {
208
- afterAttach(): void;
209
- }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
210
- spreadsheet: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
211
- rowSet: import("mobx-state-tree").IType<import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined>;
212
- columns: import("mobx-state-tree").IType<{
213
- name: string;
214
- }[], {
215
- name: string;
216
- }[], {
217
- name: string;
218
- }[]>;
219
- assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
220
- visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
221
- }, {
222
- visibleRowFlags: Record<number, boolean> | undefined;
223
- } & {
224
- readonly rows: {
225
- id: number;
226
- feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
227
- }[] | undefined;
228
- readonly initialized: boolean | undefined;
229
- } & {
230
- readonly dataGridColumns: ({
231
- field: string;
232
- width: number;
233
- type: "number" | undefined;
234
- } | {
235
- field: string;
236
- width: number;
237
- renderCell: ({ row }: import("@mui/x-data-grid").GridRenderCellParams<{
238
- id: number;
239
- feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
240
- }, any, any, import("@mui/x-data-grid").GridTreeNodeWithRender>) => import("react/jsx-runtime").JSX.Element | "N/A";
241
- type?: undefined;
242
- valueGetter?: undefined;
243
- valueFormatter?: undefined;
244
- } | {
245
- field: string;
246
- type: "number";
247
- width: number;
248
- valueGetter: (_val: unknown, row: {
249
- feature?: import("@jbrowse/core/util").SimpleFeatureSerialized;
250
- }) => number | undefined;
251
- valueFormatter: (arg: never) => string;
252
- renderCell?: undefined;
253
- })[] | undefined;
254
- } & {
255
- readonly visibleRows: {
256
- id: number;
257
- feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
258
- }[] | undefined;
259
- } & {
260
- setVisibleRows(arg?: Record<number, boolean>): void;
261
- setVisibleColumns(arg: Record<string, boolean>): void;
262
- }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
263
- rowSet: import("mobx-state-tree").IType<import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined, import("./SpreadsheetModel").RowSet | undefined>;
264
- columns: import("mobx-state-tree").IType<{
265
- name: string;
266
- }[], {
267
- name: string;
268
- }[], {
269
- name: string;
270
- }[]>;
271
- assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
272
- visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
273
- }>>, import("mobx-state-tree")._NotCustomized>>;
274
- }> | {
275
- spreadsheet: {
276
- columns: {
277
- name: string;
278
- }[];
279
- assemblyName: string | undefined;
280
- visibleColumns: Record<string, boolean>;
281
- };
282
- id: string;
283
- type: "SpreadsheetView";
284
- height: number;
285
- displayName: string | undefined;
286
- minimized: boolean;
287
- hideVerticalResizeHandle: boolean;
288
- offsetPx: number;
289
- hideFilterControls: boolean;
290
- importWizard: import("mobx-state-tree").ModelSnapshotType<{
291
- fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
292
- hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
293
- columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
294
- selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
295
- cachedFileLocation: import("mobx-state-tree").IType<import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined, import("@jbrowse/core/util").FileLocation | undefined>;
296
- }>;
297
- }>;
298
- export type SpreadsheetViewStateModel = ReturnType<typeof stateModelFactory>;
299
- export type SpreadsheetViewModel = Instance<SpreadsheetViewStateModel>;
@@ -1,101 +0,0 @@
1
- "use strict";
2
- var __importDefault = (this && this.__importDefault) || function (mod) {
3
- return (mod && mod.__esModule) ? mod : { "default": mod };
4
- };
5
- Object.defineProperty(exports, "__esModule", { value: true });
6
- exports.default = stateModelFactory;
7
- const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
8
- const util_1 = require("@jbrowse/core/util");
9
- const FolderOpen_1 = __importDefault(require("@mui/icons-material/FolderOpen"));
10
- const mobx_state_tree_1 = require("mobx-state-tree");
11
- const ImportWizard_1 = __importDefault(require("./ImportWizard"));
12
- const SpreadsheetModel_1 = __importDefault(require("./SpreadsheetModel"));
13
- const minHeight = 40;
14
- const defaultHeight = 440;
15
- function x() { }
16
- function stateModelFactory() {
17
- const ImportWizardModel = (0, ImportWizard_1.default)();
18
- return mobx_state_tree_1.types
19
- .compose(models_1.BaseViewModel, mobx_state_tree_1.types
20
- .model('SpreadsheetView', {
21
- type: mobx_state_tree_1.types.literal('SpreadsheetView'),
22
- offsetPx: 0,
23
- height: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, defaultHeight),
24
- hideVerticalResizeHandle: false,
25
- hideFilterControls: false,
26
- importWizard: mobx_state_tree_1.types.optional(ImportWizardModel, () => ImportWizardModel.create()),
27
- spreadsheet: mobx_state_tree_1.types.maybe((0, SpreadsheetModel_1.default)()),
28
- })
29
- .volatile(() => ({
30
- width: 400,
31
- rowMenuItems: [],
32
- }))
33
- .views(self => ({
34
- get assembly() {
35
- var _a, _b;
36
- const name = (_a = self.spreadsheet) === null || _a === void 0 ? void 0 : _a.assemblyName;
37
- return name
38
- ? (_b = (0, util_1.getSession)(self).assemblyManager.get(name)) === null || _b === void 0 ? void 0 : _b.configuration
39
- : undefined;
40
- },
41
- }))
42
- .actions(self => ({
43
- setRowMenuItems(newItems) {
44
- self.rowMenuItems = newItems;
45
- },
46
- setWidth(newWidth) {
47
- self.width = newWidth;
48
- return self.width;
49
- },
50
- setHeight(newHeight) {
51
- self.height = Math.max(newHeight, minHeight);
52
- return self.height;
53
- },
54
- resizeHeight(distance) {
55
- const oldHeight = self.height;
56
- const newHeight = this.setHeight(self.height + distance);
57
- return newHeight - oldHeight;
58
- },
59
- resizeWidth(distance) {
60
- const oldWidth = self.width;
61
- const newWidth = this.setWidth(self.width + distance);
62
- return newWidth - oldWidth;
63
- },
64
- displaySpreadsheet(spreadsheet) {
65
- self.spreadsheet = (0, mobx_state_tree_1.cast)(spreadsheet);
66
- },
67
- }))
68
- .views(self => ({
69
- menuItems() {
70
- return [
71
- {
72
- label: 'Return to import form',
73
- icon: FolderOpen_1.default,
74
- onClick: () => {
75
- self.displaySpreadsheet(undefined);
76
- },
77
- },
78
- ];
79
- },
80
- })))
81
- .postProcessSnapshot(snap => {
82
- const { importWizard, spreadsheet } = snap;
83
- if (importWizard.cachedFileLocation && spreadsheet) {
84
- const { rowSet, ...rest } = spreadsheet;
85
- return {
86
- ...snap,
87
- spreadsheet: rest,
88
- };
89
- }
90
- else if (spreadsheet) {
91
- const { rowSet, ...rest } = spreadsheet;
92
- return rowSet && JSON.stringify(rowSet).length > 1000000
93
- ? {
94
- ...snap,
95
- spreadsheet: rest,
96
- }
97
- : snap;
98
- }
99
- return snap;
100
- });
101
- }
@@ -1 +0,0 @@
1
- export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';
@@ -1,5 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.default = void 0;
4
- var sv_core_1 = require("@jbrowse/sv-core");
5
- Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendMultiLevelOptionDialog; } });
@@ -1 +0,0 @@
1
- export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';
@@ -1,5 +0,0 @@
1
- "use strict";
2
- Object.defineProperty(exports, "__esModule", { value: true });
3
- exports.default = void 0;
4
- var sv_core_1 = require("@jbrowse/sv-core");
5
- Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendSingleLevelOptionDialog; } });
@@ -1,7 +0,0 @@
1
- import type { AbstractSessionModel, SimpleFeatureSerialized } from '@jbrowse/core/util';
2
- export default function FeatureMenu({ assemblyName, session, spreadsheetViewId, feature, }: {
3
- spreadsheetViewId: string;
4
- assemblyName: string;
5
- session: AbstractSessionModel;
6
- feature: SimpleFeatureSerialized;
7
- }): import("react/jsx-runtime").JSX.Element;