@jbrowse/plugin-alignments 3.0.3 → 3.0.5

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Files changed (17) hide show
  1. package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +3 -4
  2. package/dist/LinearPileupDisplay/doAfterAttach.js +4 -2
  3. package/dist/PileupRenderer/PileupLayoutSession.d.ts +9 -19
  4. package/dist/PileupRenderer/PileupLayoutSession.js +14 -15
  5. package/dist/PileupRenderer/PileupRenderer.d.ts +1 -1
  6. package/dist/PileupRenderer/PileupRenderer.js +1 -1
  7. package/dist/shared/getUniqueModifications.d.ts +1 -1
  8. package/dist/shared/getUniqueModifications.js +4 -1
  9. package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js +3 -4
  10. package/esm/LinearPileupDisplay/doAfterAttach.js +5 -3
  11. package/esm/PileupRenderer/PileupLayoutSession.d.ts +9 -19
  12. package/esm/PileupRenderer/PileupLayoutSession.js +13 -14
  13. package/esm/PileupRenderer/PileupRenderer.d.ts +1 -1
  14. package/esm/PileupRenderer/PileupRenderer.js +1 -1
  15. package/esm/shared/getUniqueModifications.d.ts +1 -1
  16. package/esm/shared/getUniqueModifications.js +4 -1
  17. package/package.json +6 -6
package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js CHANGED
@@ -267,7 +267,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
267
267
  const { feature } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
268
268
  featureId: f,
269
269
  sessionId,
270
- layoutId: (0, util_1.getContainingView)(self).id,
270
+ layoutId: (0, util_1.getContainingTrack)(self).id,
271
271
  rendererType: 'PileupRenderer',
272
272
  }));
273
273
  if ((0, mobx_state_tree_1.isAlive)(self) && feature) {
@@ -296,7 +296,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
296
296
  const { feature } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
297
297
  featureId: f,
298
298
  sessionId,
299
- layoutId: (0, util_1.getContainingView)(self).id,
299
+ layoutId: (0, util_1.getContainingTrack)(self).id,
300
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  rendererType: 'PileupRenderer',
301
301
  }));
302
302
  if (feature) {
@@ -489,11 +489,10 @@ function SharedLinearPileupDisplayMixin(configSchema) {
489
489
  }
490
490
  else {
491
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  const sessionId = (0, tracks_1.getRpcSessionId)(self);
492
- const view = (0, util_1.getContainingView)(self);
493
492
  const { feature } = (await session.rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
494
493
  featureId,
495
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  sessionId,
496
- layoutId: view.id,
495
+ layoutId: (0, util_1.getContainingTrack)(self).id,
497
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  rendererType: 'PileupRenderer',
498
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  }));
499
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  if ((0, mobx_state_tree_1.isAlive)(self) &&
package/dist/LinearPileupDisplay/doAfterAttach.js CHANGED
@@ -37,10 +37,12 @@ function doAfterAttach(model) {
37
37
  adapterConfig,
38
38
  rendererType: rendererType.name,
39
39
  sessionId: (0, tracks_1.getRpcSessionId)(model),
40
- layoutId: view.id,
40
+ layoutId: (0, util_1.getContainingTrack)(model).id,
41
41
  timeout: 1000000,
42
42
  statusCallback: (arg) => {
43
- model.setMessage(arg);
43
+ if ((0, mobx_state_tree_1.isAlive)(model)) {
44
+ model.setMessage(arg);
45
+ }
44
46
  },
45
47
  ...model.renderPropsPre(),
46
48
  });
package/dist/PileupRenderer/PileupLayoutSession.d.ts CHANGED
@@ -1,33 +1,23 @@
1
- import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
1
+ import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession';
2
2
  import type { FilterBy, SortedBy } from '../shared/types';
3
- import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
4
- import type SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
3
+ import type { CachedLayout, LayoutSessionProps } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession';
5
4
  import type GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
6
5
  import type MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
7
- export interface PileupLayoutSessionProps {
8
- config: AnyConfigurationModel;
9
- bpPerPx: number;
10
- filters: SerializableFilterChain;
6
+ export interface PileupLayoutSessionProps extends LayoutSessionProps {
11
7
  filterBy: FilterBy;
12
8
  sortedBy: SortedBy;
13
9
  showSoftClip: boolean;
14
10
  }
15
11
  type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
16
- interface CachedPileupLayout {
17
- layout: MyMultiLayout;
18
- config: AnyConfigurationModel;
19
- filters?: SerializableFilterChain;
20
- filterBy?: FilterBy;
21
- sortedBy?: SortedBy;
22
- showSoftClip: boolean;
12
+ interface CachedPileupLayout extends CachedLayout {
13
+ props: PileupLayoutSessionProps;
23
14
  }
24
15
  export declare class PileupLayoutSession extends LayoutSession {
25
- sortedBy?: SortedBy;
26
- filterBy?: FilterBy;
27
- showSoftClip: boolean;
28
- constructor(args: PileupLayoutSessionProps);
29
- cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
16
+ props: PileupLayoutSessionProps;
30
17
  cachedLayout: CachedPileupLayout | undefined;
18
+ constructor(props: PileupLayoutSessionProps);
19
+ update(props: PileupLayoutSessionProps): this;
20
+ cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
31
21
  get layout(): MyMultiLayout;
32
22
  }
33
23
  export {};
package/dist/PileupRenderer/PileupLayoutSession.js CHANGED
@@ -4,30 +4,29 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
4
4
  };
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  exports.PileupLayoutSession = void 0;
7
- const configuration_1 = require("@jbrowse/core/configuration");
8
- const BoxRendererType_1 = require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType");
7
+ const LayoutSession_1 = require("@jbrowse/core/pluggableElementTypes/renderers/LayoutSession");
9
8
  const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
10
- class PileupLayoutSession extends BoxRendererType_1.LayoutSession {
11
- constructor(args) {
12
- super(args);
13
- this.showSoftClip = false;
14
- this.config = args.config;
9
+ class PileupLayoutSession extends LayoutSession_1.LayoutSession {
10
+ constructor(props) {
11
+ super(props);
12
+ this.props = props;
13
+ }
14
+ update(props) {
15
+ super.update(props);
16
+ this.props = props;
17
+ return this;
15
18
  }
16
19
  cachedLayoutIsValid(cachedLayout) {
17
20
  return (super.cachedLayoutIsValid(cachedLayout) &&
18
- this.showSoftClip === cachedLayout.showSoftClip &&
19
- (0, fast_deep_equal_1.default)(this.sortedBy, cachedLayout.sortedBy) &&
20
- (0, fast_deep_equal_1.default)(this.filterBy, cachedLayout.filterBy));
21
+ this.props.showSoftClip === cachedLayout.props.showSoftClip &&
22
+ (0, fast_deep_equal_1.default)(this.props.sortedBy, cachedLayout.props.sortedBy) &&
23
+ (0, fast_deep_equal_1.default)(this.props.filterBy, cachedLayout.props.filterBy));
21
24
  }
22
25
  get layout() {
23
26
  if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
24
27
  this.cachedLayout = {
25
28
  layout: this.makeLayout(),
26
- config: (0, configuration_1.readConfObject)(this.config),
27
- filters: this.filters,
28
- filterBy: this.filterBy,
29
- sortedBy: this.sortedBy,
30
- showSoftClip: this.showSoftClip,
29
+ props: this.props,
31
30
  };
32
31
  }
33
32
  return this.cachedLayout.layout;
package/dist/PileupRenderer/PileupRenderer.d.ts CHANGED
@@ -43,6 +43,6 @@ export default class PileupRenderer extends BoxRendererType {
43
43
  reactElement?: React.ReactElement;
44
44
  html?: string;
45
45
  }>;
46
- createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
46
+ createLayoutSession(args: PileupLayoutSessionProps): PileupLayoutSession;
47
47
  }
48
48
  export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
package/dist/PileupRenderer/PileupRenderer.js CHANGED
@@ -122,7 +122,7 @@ class PileupRenderer extends BoxRendererType_1.default {
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  containsNoTransferables: true,
123
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  };
124
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  }
125
- createSession(args) {
125
+ createLayoutSession(args) {
126
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  return new PileupLayoutSession_1.PileupLayoutSession(args);
127
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  }
128
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  }
package/dist/shared/getUniqueModifications.d.ts CHANGED
@@ -1,7 +1,7 @@
1
+ import { type IAnyStateTreeNode } from 'mobx-state-tree';
1
2
  import type { ModificationType } from './types';
2
3
  import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
3
4
  import type { BlockSet } from '@jbrowse/core/util/blockTypes';
4
- import type { IAnyStateTreeNode } from 'mobx-state-tree';
5
5
  export interface ModificationOpts {
6
6
  headers?: Record<string, string>;
7
7
  stopToken?: string;
package/dist/shared/getUniqueModifications.js CHANGED
@@ -3,6 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
3
3
  exports.getUniqueModifications = getUniqueModifications;
4
4
  const util_1 = require("@jbrowse/core/util");
5
5
  const tracks_1 = require("@jbrowse/core/util/tracks");
6
+ const mobx_state_tree_1 = require("mobx-state-tree");
6
7
  async function getUniqueModifications({ model, adapterConfig, blocks, opts, }) {
7
8
  const { rpcManager } = (0, util_1.getSession)(model);
8
9
  const sessionId = (0, tracks_1.getRpcSessionId)(model);
@@ -11,7 +12,9 @@ async function getUniqueModifications({ model, adapterConfig, blocks, opts, }) {
11
12
  sessionId,
12
13
  regions: blocks.contentBlocks,
13
14
  statusCallback: (arg) => {
14
- model.setMessage(arg);
15
+ if ((0, mobx_state_tree_1.isAlive)(model)) {
16
+ model.setMessage(arg);
17
+ }
15
18
  },
16
19
  ...opts,
17
20
  });
package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js CHANGED
@@ -228,7 +228,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
228
228
  const { feature } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
229
229
  featureId: f,
230
230
  sessionId,
231
- layoutId: getContainingView(self).id,
231
+ layoutId: getContainingTrack(self).id,
232
232
  rendererType: 'PileupRenderer',
233
233
  }));
234
234
  if (isAlive(self) && feature) {
@@ -257,7 +257,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
257
257
  const { feature } = (await rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
258
258
  featureId: f,
259
259
  sessionId,
260
- layoutId: getContainingView(self).id,
260
+ layoutId: getContainingTrack(self).id,
261
261
  rendererType: 'PileupRenderer',
262
262
  }));
263
263
  if (feature) {
@@ -450,11 +450,10 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
450
450
  }
451
451
  else {
452
452
  const sessionId = getRpcSessionId(self);
453
- const view = getContainingView(self);
454
453
  const { feature } = (await session.rpcManager.call(sessionId, 'CoreGetFeatureDetails', {
455
454
  featureId,
456
455
  sessionId,
457
- layoutId: view.id,
456
+ layoutId: getContainingTrack(self).id,
458
457
  rendererType: 'PileupRenderer',
459
458
  }));
460
459
  if (isAlive(self) &&
package/esm/LinearPileupDisplay/doAfterAttach.js CHANGED
@@ -1,4 +1,4 @@
1
- import { getContainingView, getSession } from '@jbrowse/core/util';
1
+ import { getContainingTrack, getContainingView, getSession, } from '@jbrowse/core/util';
2
2
  import { getRpcSessionId } from '@jbrowse/core/util/tracks';
3
3
  import { isAlive } from 'mobx-state-tree';
4
4
  import { getUniqueModifications } from '../shared/getUniqueModifications';
@@ -34,10 +34,12 @@ export function doAfterAttach(model) {
34
34
  adapterConfig,
35
35
  rendererType: rendererType.name,
36
36
  sessionId: getRpcSessionId(model),
37
- layoutId: view.id,
37
+ layoutId: getContainingTrack(model).id,
38
38
  timeout: 1000000,
39
39
  statusCallback: (arg) => {
40
- model.setMessage(arg);
40
+ if (isAlive(model)) {
41
+ model.setMessage(arg);
42
+ }
41
43
  },
42
44
  ...model.renderPropsPre(),
43
45
  });
package/esm/PileupRenderer/PileupLayoutSession.d.ts CHANGED
@@ -1,33 +1,23 @@
1
- import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
1
+ import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession';
2
2
  import type { FilterBy, SortedBy } from '../shared/types';
3
- import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
4
- import type SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
3
+ import type { CachedLayout, LayoutSessionProps } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession';
5
4
  import type GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
6
5
  import type MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';
7
- export interface PileupLayoutSessionProps {
8
- config: AnyConfigurationModel;
9
- bpPerPx: number;
10
- filters: SerializableFilterChain;
6
+ export interface PileupLayoutSessionProps extends LayoutSessionProps {
11
7
  filterBy: FilterBy;
12
8
  sortedBy: SortedBy;
13
9
  showSoftClip: boolean;
14
10
  }
15
11
  type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>;
16
- interface CachedPileupLayout {
17
- layout: MyMultiLayout;
18
- config: AnyConfigurationModel;
19
- filters?: SerializableFilterChain;
20
- filterBy?: FilterBy;
21
- sortedBy?: SortedBy;
22
- showSoftClip: boolean;
12
+ interface CachedPileupLayout extends CachedLayout {
13
+ props: PileupLayoutSessionProps;
23
14
  }
24
15
  export declare class PileupLayoutSession extends LayoutSession {
25
- sortedBy?: SortedBy;
26
- filterBy?: FilterBy;
27
- showSoftClip: boolean;
28
- constructor(args: PileupLayoutSessionProps);
29
- cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
16
+ props: PileupLayoutSessionProps;
30
17
  cachedLayout: CachedPileupLayout | undefined;
18
+ constructor(props: PileupLayoutSessionProps);
19
+ update(props: PileupLayoutSessionProps): this;
20
+ cachedLayoutIsValid(cachedLayout: CachedPileupLayout): boolean;
31
21
  get layout(): MyMultiLayout;
32
22
  }
33
23
  export {};
package/esm/PileupRenderer/PileupLayoutSession.js CHANGED
@@ -1,27 +1,26 @@
1
- import { readConfObject } from '@jbrowse/core/configuration';
2
- import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
1
+ import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/LayoutSession';
3
2
  import deepEqual from 'fast-deep-equal';
4
3
  export class PileupLayoutSession extends LayoutSession {
5
- constructor(args) {
6
- super(args);
7
- this.showSoftClip = false;
8
- this.config = args.config;
4
+ constructor(props) {
5
+ super(props);
6
+ this.props = props;
7
+ }
8
+ update(props) {
9
+ super.update(props);
10
+ this.props = props;
11
+ return this;
9
12
  }
10
13
  cachedLayoutIsValid(cachedLayout) {
11
14
  return (super.cachedLayoutIsValid(cachedLayout) &&
12
- this.showSoftClip === cachedLayout.showSoftClip &&
13
- deepEqual(this.sortedBy, cachedLayout.sortedBy) &&
14
- deepEqual(this.filterBy, cachedLayout.filterBy));
15
+ this.props.showSoftClip === cachedLayout.props.showSoftClip &&
16
+ deepEqual(this.props.sortedBy, cachedLayout.props.sortedBy) &&
17
+ deepEqual(this.props.filterBy, cachedLayout.props.filterBy));
15
18
  }
16
19
  get layout() {
17
20
  if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
18
21
  this.cachedLayout = {
19
22
  layout: this.makeLayout(),
20
- config: readConfObject(this.config),
21
- filters: this.filters,
22
- filterBy: this.filterBy,
23
- sortedBy: this.sortedBy,
24
- showSoftClip: this.showSoftClip,
23
+ props: this.props,
25
24
  };
26
25
  }
27
26
  return this.cachedLayout.layout;
package/esm/PileupRenderer/PileupRenderer.d.ts CHANGED
@@ -43,6 +43,6 @@ export default class PileupRenderer extends BoxRendererType {
43
43
  reactElement?: React.ReactElement;
44
44
  html?: string;
45
45
  }>;
46
- createSession(args: PileupLayoutSessionProps): PileupLayoutSession;
46
+ createLayoutSession(args: PileupLayoutSessionProps): PileupLayoutSession;
47
47
  }
48
48
  export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
package/esm/PileupRenderer/PileupRenderer.js CHANGED
@@ -84,7 +84,7 @@ export default class PileupRenderer extends BoxRendererType {
84
84
  containsNoTransferables: true,
85
85
  };
86
86
  }
87
- createSession(args) {
87
+ createLayoutSession(args) {
88
88
  return new PileupLayoutSession(args);
89
89
  }
90
90
  }
package/esm/shared/getUniqueModifications.d.ts CHANGED
@@ -1,7 +1,7 @@
1
+ import { type IAnyStateTreeNode } from 'mobx-state-tree';
1
2
  import type { ModificationType } from './types';
2
3
  import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
3
4
  import type { BlockSet } from '@jbrowse/core/util/blockTypes';
4
- import type { IAnyStateTreeNode } from 'mobx-state-tree';
5
5
  export interface ModificationOpts {
6
6
  headers?: Record<string, string>;
7
7
  stopToken?: string;
package/esm/shared/getUniqueModifications.js CHANGED
@@ -1,5 +1,6 @@
1
1
  import { getSession } from '@jbrowse/core/util';
2
2
  import { getRpcSessionId } from '@jbrowse/core/util/tracks';
3
+ import { isAlive } from 'mobx-state-tree';
3
4
  export async function getUniqueModifications({ model, adapterConfig, blocks, opts, }) {
4
5
  const { rpcManager } = getSession(model);
5
6
  const sessionId = getRpcSessionId(model);
@@ -8,7 +9,9 @@ export async function getUniqueModifications({ model, adapterConfig, blocks, opt
8
9
  sessionId,
9
10
  regions: blocks.contentBlocks,
10
11
  statusCallback: (arg) => {
11
- model.setMessage(arg);
12
+ if (isAlive(model)) {
13
+ model.setMessage(arg);
14
+ }
12
15
  },
13
16
  ...opts,
14
17
  });
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-alignments",
3
- "version": "3.0.3",
3
+ "version": "3.0.5",
4
4
  "description": "JBrowse 2 alignments adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -38,10 +38,10 @@
38
38
  "dependencies": {
39
39
  "@gmod/bam": "^5.0.0",
40
40
  "@gmod/cram": "^4.0.1",
41
- "@jbrowse/core": "^3.0.3",
42
- "@jbrowse/plugin-linear-genome-view": "^3.0.3",
43
- "@jbrowse/plugin-wiggle": "^3.0.3",
44
- "@jbrowse/sv-core": "^3.0.3",
41
+ "@jbrowse/core": "^3.0.5",
42
+ "@jbrowse/plugin-linear-genome-view": "^3.0.5",
43
+ "@jbrowse/plugin-wiggle": "^3.0.5",
44
+ "@jbrowse/sv-core": "^3.0.5",
45
45
  "@mui/icons-material": "^6.0.0",
46
46
  "@mui/material": "^6.0.0",
47
47
  "canvas2svg": "^1.0.16",
@@ -63,5 +63,5 @@
63
63
  "distModule": "esm/index.js",
64
64
  "srcModule": "src/index.ts",
65
65
  "module": "esm/index.js",
66
- "gitHead": "f516540428282351d26e46743e69a724651bfb2c"
66
+ "gitHead": "a03749efe19e51609922272b845a331897346789"
67
67
  }