@jbrowse/plugin-alignments 2.1.5 → 2.1.7

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Files changed (30) hide show
  1. package/dist/AlignmentsFeatureDetail/index.d.ts +7 -0
  2. package/dist/CramAdapter/CramTestAdapters.js +1 -1
  3. package/dist/CramAdapter/CramTestAdapters.js.map +1 -1
  4. package/dist/LinearAlignmentsDisplay/models/model.d.ts +1 -1
  5. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +2 -2
  6. package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -1
  7. package/dist/LinearPileupDisplay/model.d.ts +6 -2
  8. package/dist/LinearPileupDisplay/model.js +7 -8
  9. package/dist/LinearPileupDisplay/model.js.map +1 -1
  10. package/dist/LinearSNPCoverageDisplay/models/model.d.ts +11 -3
  11. package/dist/LinearSNPCoverageDisplay/models/model.js +10 -16
  12. package/dist/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  13. package/esm/AlignmentsFeatureDetail/index.d.ts +7 -0
  14. package/esm/CramAdapter/CramTestAdapters.js +1 -1
  15. package/esm/CramAdapter/CramTestAdapters.js.map +1 -1
  16. package/esm/LinearAlignmentsDisplay/models/model.d.ts +1 -1
  17. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js +1 -1
  18. package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map +1 -1
  19. package/esm/LinearPileupDisplay/model.d.ts +6 -2
  20. package/esm/LinearPileupDisplay/model.js +8 -9
  21. package/esm/LinearPileupDisplay/model.js.map +1 -1
  22. package/esm/LinearSNPCoverageDisplay/models/model.d.ts +11 -3
  23. package/esm/LinearSNPCoverageDisplay/models/model.js +10 -16
  24. package/esm/LinearSNPCoverageDisplay/models/model.js.map +1 -1
  25. package/package.json +2 -2
  26. package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap +39 -0
  27. package/src/CramAdapter/CramTestAdapters.ts +1 -1
  28. package/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx +1 -1
  29. package/src/LinearPileupDisplay/model.ts +11 -12
  30. package/src/LinearSNPCoverageDisplay/models/model.ts +18 -20
package/dist/AlignmentsFeatureDetail/index.d.ts CHANGED
@@ -8,12 +8,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
8
8
  unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
9
9
  view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
10
10
  track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
11
+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
12
+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
11
13
  } & {
12
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  type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
13
15
  }, {
14
16
  setFeatureData(featureData: Record<string, unknown>): void;
15
17
  clearFeatureData(): void;
16
18
  setFormattedData(feat: Record<string, unknown>): void;
19
+ setExtra(type?: string | undefined, trackId?: string | undefined): void;
17
20
  } & {
18
21
  afterCreate(): void;
19
22
  }, {
@@ -26,11 +29,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
26
29
  unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
27
30
  view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
28
31
  track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
32
+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
33
+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
29
34
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
30
35
  id: string;
31
36
  type: "BaseFeatureWidget";
32
37
  track: import("mobx-state-tree").ReferenceIdentifier | undefined;
33
38
  view: import("mobx-state-tree").ReferenceIdentifier | undefined;
39
+ trackId: string | undefined;
40
+ trackType: string | undefined;
34
41
  formattedFields: any;
35
42
  finalizedFeatureData: any;
36
43
  } & import("mobx-state-tree")._NotCustomized>;
package/dist/CramAdapter/CramTestAdapters.js CHANGED
@@ -14,7 +14,7 @@ function parseSmallFasta(text) {
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14
  .split('>')
15
15
  .filter(t => /\S/.test(t))
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  .map(entryText => {
17
- const [defLine, ...seqLines] = entryText.split('\n');
17
+ const [defLine, ...seqLines] = entryText.split(/\n|\r\n|\r/);
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18
  const [id, ...descriptionLines] = defLine.split(' ');
19
19
  const description = descriptionLines.join(' ');
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  const sequence = seqLines.join('').replace(/\s/g, '');
package/dist/CramAdapter/CramTestAdapters.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"CramTestAdapters.js","sourceRoot":"","sources":["../../src/CramAdapter/CramTestAdapters.ts"],"names":[],"mappings":";;;;;;AACA,+BAAiC;AACjC,qFAA4D;AAC5D,yEAAgF;AAChF,yFAAqF;AAErF,iCAAiC;AACjC,SAAgB,eAAe,CAAC,IAAY;IAC1C,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACpD,MAAM,CAAC,EAAE,EAAE,GAAG,gBAAgB,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QACpD,MAAM,WAAW,GAAG,gBAAgB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC9C,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QACrD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAA;IACtC,CAAC,CAAC,CAAA;AACN,CAAC;AAXD,0CAWC;AAID,MAAa,mBAAmB;IAG9B,YAAY,UAAsB;QAChC,IAAI,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE;YAC9C,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACpC,OAAO,eAAe,CAAC,IAAI,CAAC,CAAA;QAC9B,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,EAAU,EAAE,KAAa,EAAE,GAAW;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,MAAM,KAAK,GAAG,IAAI,CAAC,EAAE,CAAC,CAAA;QACtB,MAAM,MAAM,GAAG,GAAG,GAAG,KAAK,GAAG,CAAC,CAAA;QAC9B,IAAI,CAAC,KAAK,EAAE;YACV,MAAM,IAAI,KAAK,CAAC,uBAAuB,EAAE,SAAS,CAAC,CAAA;SACpD;QACD,OAAO,KAAK,CAAC,QAAQ,CAAC,MAAM,CAAC,KAAK,GAAG,CAAC,EAAE,MAAM,CAAC,CAAA;IACjD,CAAC;IAED,KAAK,CAAC,eAAe;QACnB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,OAAO,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;IACpC,CAAC;CACF;AAxBD,kDAwBC;AAED,MAAa,eAAgB,SAAQ,oCAAsB;IAKzD,YAAY,UAAsB;QAChC,KAAK,CAAC,IAAA,yCAAmB,EAAC,OAAO,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAA;QAHlD,aAAQ,GAAa,EAAE,CAAA;QAIrB,IAAI,CAAC,KAAK,GAAG,IAAI,mBAAmB,CAAC,UAAU,CAAC,CAAA;IAClD,CAAC;IAED,KAAK,CAAC,WAAW;QACf,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED,WAAW,CAAC,EACV,OAAO,EACP,KAAK,EACL,GAAG,GAKJ;QACC,OAAO,IAAI,iBAAU,CAAC,QAAQ,CAAC,EAAE;YAC/B,IAAI,CAAC,KAAK;iBACP,eAAe,EAAE;iBACjB,IAAI,CAAC,QAAQ,CAAC,EAAE;gBACf,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;YAC1B,CAAC,CAAC;iBACD,IAAI,CAAC,GAAG,EAAE,CACT,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,KAAK,EAAE,GAAG,CAAC,CAC7D;iBACA,IAAI,CAAC,GAAG,CAAC,EAAE;gBACV,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,QAAQ,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,GAAG,EAAE;oBACtC,GAAG,EAAE,GAAG;oBACR,KAAK;oBACL,GAAG;iBACJ,CAAC,CACH,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;YACrB,CAAC,CAAC,CAAA;YACJ,OAAO,EAAE,WAAW,EAAE,GAAG,EAAE,GAAE,CAAC,EAAE,CAAA;QAClC,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAhDD,0CAgDC"}
1
+ {"version":3,"file":"CramTestAdapters.js","sourceRoot":"","sources":["../../src/CramAdapter/CramTestAdapters.ts"],"names":[],"mappings":";;;;;;AACA,+BAAiC;AACjC,qFAA4D;AAC5D,yEAAgF;AAChF,yFAAqF;AAErF,iCAAiC;AACjC,SAAgB,eAAe,CAAC,IAAY;IAC1C,OAAO,IAAI;SACR,KAAK,CAAC,GAAG,CAAC;SACV,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;SACzB,GAAG,CAAC,SAAS,CAAC,EAAE;QACf,MAAM,CAAC,OAAO,EAAE,GAAG,QAAQ,CAAC,GAAG,SAAS,CAAC,KAAK,CAAC,YAAY,CAAC,CAAA;QAC5D,MAAM,CAAC,EAAE,EAAE,GAAG,gBAAgB,CAAC,GAAG,OAAO,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;QACpD,MAAM,WAAW,GAAG,gBAAgB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;QAC9C,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;QACrD,OAAO,EAAE,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAA;IACtC,CAAC,CAAC,CAAA;AACN,CAAC;AAXD,0CAWC;AAID,MAAa,mBAAmB;IAG9B,YAAY,UAAsB;QAChC,IAAI,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE;YAC9C,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;YACpC,OAAO,eAAe,CAAC,IAAI,CAAC,CAAA;QAC9B,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,EAAU,EAAE,KAAa,EAAE,GAAW;QAChD,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,MAAM,KAAK,GAAG,IAAI,CAAC,EAAE,CAAC,CAAA;QACtB,MAAM,MAAM,GAAG,GAAG,GAAG,KAAK,GAAG,CAAC,CAAA;QAC9B,IAAI,CAAC,KAAK,EAAE;YACV,MAAM,IAAI,KAAK,CAAC,uBAAuB,EAAE,SAAS,CAAC,CAAA;SACpD;QACD,OAAO,KAAK,CAAC,QAAQ,CAAC,MAAM,CAAC,KAAK,GAAG,CAAC,EAAE,MAAM,CAAC,CAAA;IACjD,CAAC;IAED,KAAK,CAAC,eAAe;QACnB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,IAAI,CAAA;QAC5B,OAAO,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;IACpC,CAAC;CACF;AAxBD,kDAwBC;AAED,MAAa,eAAgB,SAAQ,oCAAsB;IAKzD,YAAY,UAAsB;QAChC,KAAK,CAAC,IAAA,yCAAmB,EAAC,OAAO,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAA;QAHlD,aAAQ,GAAa,EAAE,CAAA;QAIrB,IAAI,CAAC,KAAK,GAAG,IAAI,mBAAmB,CAAC,UAAU,CAAC,CAAA;IAClD,CAAC;IAED,KAAK,CAAC,WAAW;QACf,OAAO,IAAI,CAAC,QAAQ,CAAA;IACtB,CAAC;IAED,WAAW,CAAC,EACV,OAAO,EACP,KAAK,EACL,GAAG,GAKJ;QACC,OAAO,IAAI,iBAAU,CAAC,QAAQ,CAAC,EAAE;YAC/B,IAAI,CAAC,KAAK;iBACP,eAAe,EAAE;iBACjB,IAAI,CAAC,QAAQ,CAAC,EAAE;gBACf,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;YAC1B,CAAC,CAAC;iBACD,IAAI,CAAC,GAAG,EAAE,CACT,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,KAAK,EAAE,GAAG,CAAC,CAC7D;iBACA,IAAI,CAAC,GAAG,CAAC,EAAE;gBACV,QAAQ,CAAC,IAAI,CACX,IAAI,uBAAa,CAAC;oBAChB,QAAQ,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,GAAG,EAAE;oBACtC,GAAG,EAAE,GAAG;oBACR,KAAK;oBACL,GAAG;iBACJ,CAAC,CACH,CAAA;gBACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;YACrB,CAAC,CAAC,CAAA;YACJ,OAAO,EAAE,WAAW,EAAE,GAAG,EAAE,GAAE,CAAC,EAAE,CAAA;QAClC,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAhDD,0CAgDC"}
package/dist/LinearAlignmentsDisplay/models/model.d.ts CHANGED
@@ -61,7 +61,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
61
61
  readonly adapterConfig: any;
62
62
  readonly parentTrack: any;
63
63
  renderProps(): any;
64
- readonly rendererType: any;
64
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
65
65
  readonly DisplayMessageComponent: React.FC<any> | undefined;
66
66
  trackMenuItems(): MenuItem[];
67
67
  readonly viewMenuActions: MenuItem[];
package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js CHANGED
@@ -5,12 +5,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
5
5
  Object.defineProperty(exports, "__esModule", { value: true });
6
6
  const react_1 = __importDefault(require("react"));
7
7
  const mobx_react_1 = require("mobx-react");
8
- const Typography_1 = __importDefault(require("@mui/material/Typography"));
8
+ const material_1 = require("@mui/material");
9
9
  function LinearPileupDisplayBlurb(props) {
10
10
  const { model } = props;
11
11
  const { sortedBy } = model;
12
12
  return sortedBy ? (react_1.default.createElement("div", { "data-testid": `blurb-${model.sortedBy}`, style: { backgroundColor: 'white' } },
13
- react_1.default.createElement(Typography_1.default, { color: "secondary", variant: "caption" }, model.sortedBy
13
+ react_1.default.createElement(material_1.Typography, { color: "secondary", variant: "caption" }, model.sortedBy
14
14
  ? `Sorted by ${sortedBy.type.toLowerCase()} at ${sortedBy.refName}:${sortedBy.pos}`
15
15
  : null))) : null;
16
16
  }
package/dist/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"LinearPileupDisplayBlurb.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,0EAAiD;AAYjD,SAAS,wBAAwB,CAAC,KAAoC;IACpE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,sDACe,SAAS,KAAK,CAAC,QAAQ,EAAE,EACtC,KAAK,EAAE,EAAE,eAAe,EAAE,OAAO,EAAE;QAEnC,8BAAC,oBAAU,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAC,SAAS,IAC5C,KAAK,CAAC,QAAQ;YACb,CAAC,CAAC,aAAa,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,QAAQ,CAAC,OAAO,IAC7D,QAAQ,CAAC,GACX,EAAE;YACJ,CAAC,CAAC,IAAI,CACG,CACT,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,wBAAwB,CAAC,CAAA"}
1
+ {"version":3,"file":"LinearPileupDisplayBlurb.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AACrC,4CAA0C;AAY1C,SAAS,wBAAwB,CAAC,KAAoC;IACpE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,sDACe,SAAS,KAAK,CAAC,QAAQ,EAAE,EACtC,KAAK,EAAE,EAAE,eAAe,EAAE,OAAO,EAAE;QAEnC,8BAAC,qBAAU,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAC,SAAS,IAC5C,KAAK,CAAC,QAAQ;YACb,CAAC,CAAC,aAAa,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,QAAQ,CAAC,OAAO,IAC7D,QAAQ,CAAC,GACX,EAAE;YACJ,CAAC,CAAC,IAAI,CACG,CACT,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AACD,kBAAe,IAAA,qBAAQ,EAAC,wBAAwB,CAAC,CAAA"}
package/dist/LinearPileupDisplay/model.d.ts CHANGED
@@ -131,7 +131,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
131
131
  readonly adapterConfig: any;
132
132
  readonly parentTrack: any;
133
133
  renderProps(): any;
134
- readonly rendererType: any;
134
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
135
135
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
136
136
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
137
137
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -251,7 +251,11 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
251
251
  reload(): void;
252
252
  } & {
253
253
  readonly maxHeight: any;
254
- readonly rendererConfig: any;
254
+ readonly rendererConfig: {
255
+ [x: string]: any;
256
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
257
+ setSubschema(slotName: string, data: unknown): any;
258
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
255
259
  readonly featureHeightSetting: any;
256
260
  readonly mismatchAlphaSetting: any;
257
261
  readonly featureUnderMouse: Feature | undefined;
package/dist/LinearPileupDisplay/model.js CHANGED
@@ -153,18 +153,16 @@ const stateModelFactory = (configSchema) => mobx_state_tree_1.types
153
153
  const { rpcManager } = (0, util_1.getSession)(self);
154
154
  const view = (0, util_1.getContainingView)(self);
155
155
  const { sortedBy, colorBy, parentTrack, adapterConfig, rendererType, } = self;
156
- const { staticBlocks, bpPerPx } = view;
157
- if (!self.estimatedStatsReady) {
158
- return;
159
- }
160
- if (self.regionTooLarge) {
156
+ if (!view.initialized ||
157
+ !self.estimatedStatsReady ||
158
+ self.regionTooLarge) {
161
159
  return;
162
160
  }
161
+ const { staticBlocks, bpPerPx } = view;
163
162
  // continually generate the vc pairing, set and rerender if any
164
163
  // new values seen
165
164
  if (colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) {
166
- const uniqueTagSet = await (0, shared_1.getUniqueTagValues)(self, colorBy, staticBlocks);
167
- self.updateColorTagMap(uniqueTagSet);
165
+ self.updateColorTagMap(await (0, shared_1.getUniqueTagValues)(self, colorBy, staticBlocks));
168
166
  }
169
167
  if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
170
168
  const adapter = (0, configuration_1.getConf)(parentTrack, ['adapter']);
@@ -173,6 +171,7 @@ const stateModelFactory = (configSchema) => mobx_state_tree_1.types
173
171
  if (sortedBy) {
174
172
  const { pos, refName, assemblyName } = sortedBy;
175
173
  // render just the sorted region first
174
+ // @ts-ignore
176
175
  await self.rendererType.renderInClient(rpcManager, {
177
176
  assemblyName,
178
177
  regions: [
@@ -314,7 +313,7 @@ const stateModelFactory = (configSchema) => mobx_state_tree_1.types
314
313
  noSpacing: self.noSpacing,
315
314
  maxHeight: this.maxHeight,
316
315
  mismatchAlpha: self.mismatchAlpha,
317
- }, (0, mobx_state_tree_1.getEnv)(self));
316
+ }, (0, util_1.getEnv)(self));
318
317
  },
319
318
  get featureHeightSetting() {
320
319
  return (self.featureHeight || (0, configuration_1.readConfObject)(this.rendererConfig, 'height'));
package/dist/LinearPileupDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/dist/LinearSNPCoverageDisplay/models/model.d.ts CHANGED
@@ -135,7 +135,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
135
135
  readonly adapterConfig: any;
136
136
  readonly parentTrack: any;
137
137
  renderProps(): any;
138
- readonly rendererType: any;
138
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
139
139
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
140
140
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
141
141
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -255,7 +255,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
255
255
  readonly maxScore: any;
256
256
  readonly minScore: any;
257
257
  } & {
258
- readonly rendererConfig: any;
258
+ readonly rendererConfig: {
259
+ [x: string]: any;
260
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
261
+ setSubschema(slotName: string, data: unknown): any;
262
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
259
263
  } & {
260
264
  readonly filled: any;
261
265
  readonly summaryScoreModeSetting: any;
@@ -331,7 +335,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
331
335
  }): void;
332
336
  updateModificationColorMap(uniqueModifications: string[]): void;
333
337
  } & {
334
- readonly rendererConfig: any;
338
+ readonly rendererConfig: {
339
+ [x: string]: any;
340
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
341
+ setSubschema(slotName: string, data: unknown): any;
342
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
335
343
  readonly drawArcsSetting: any;
336
344
  readonly drawInterbaseCountsSetting: any;
337
345
  readonly drawIndicatorsSetting: any;
package/dist/LinearSNPCoverageDisplay/models/model.js CHANGED
@@ -115,16 +115,16 @@ const stateModelFactory = (pluginManager, configSchema) => mobx_state_tree_1.typ
115
115
  (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
116
116
  try {
117
117
  const { colorBy } = self;
118
- const { staticBlocks } = (0, util_1.getContainingView)(self);
119
- if (!self.estimatedStatsReady) {
120
- return;
121
- }
122
- if (self.regionTooLarge) {
118
+ const view = (0, util_1.getContainingView)(self);
119
+ if (!view.initialized ||
120
+ !self.estimatedStatsReady ||
121
+ self.regionTooLarge) {
123
122
  return;
124
123
  }
124
+ const { staticBlocks } = view;
125
125
  if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
126
- const vals = await (0, shared_1.getUniqueModificationValues)(self, (0, configuration_1.getConf)(self.parentTrack, 'adapter'), colorBy, staticBlocks);
127
- self.updateModificationColorMap(vals);
126
+ const adapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
127
+ self.updateModificationColorMap(await (0, shared_1.getUniqueModificationValues)(self, adapter, colorBy, staticBlocks));
128
128
  }
129
129
  }
130
130
  catch (error) {
@@ -163,25 +163,19 @@ const stateModelFactory = (pluginManager, configSchema) => mobx_state_tree_1.typ
163
163
  label: 'Draw insertion/clipping indicators',
164
164
  type: 'checkbox',
165
165
  checked: self.drawIndicatorsSetting,
166
- onClick: () => {
167
- self.toggleDrawIndicators();
168
- },
166
+ onClick: () => self.toggleDrawIndicators(),
169
167
  },
170
168
  {
171
169
  label: 'Draw insertion/clipping counts',
172
170
  type: 'checkbox',
173
171
  checked: self.drawInterbaseCountsSetting,
174
- onClick: () => {
175
- self.toggleDrawInterbaseCounts();
176
- },
172
+ onClick: () => self.toggleDrawInterbaseCounts(),
177
173
  },
178
174
  {
179
175
  label: 'Draw arcs',
180
176
  type: 'checkbox',
181
177
  checked: self.drawArcsSetting,
182
- onClick: () => {
183
- self.toggleDrawArcs();
184
- },
178
+ onClick: () => self.toggleDrawArcs(),
185
179
  },
186
180
  ];
187
181
  },
package/dist/LinearSNPCoverageDisplay/models/model.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/AlignmentsFeatureDetail/index.d.ts CHANGED
@@ -8,12 +8,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
8
8
  unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
9
9
  view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
10
10
  track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
11
+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
12
+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
11
13
  } & {
12
14
  type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
13
15
  }, {
14
16
  setFeatureData(featureData: Record<string, unknown>): void;
15
17
  clearFeatureData(): void;
16
18
  setFormattedData(feat: Record<string, unknown>): void;
19
+ setExtra(type?: string | undefined, trackId?: string | undefined): void;
17
20
  } & {
18
21
  afterCreate(): void;
19
22
  }, {
@@ -26,11 +29,15 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
26
29
  unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
27
30
  view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
28
31
  track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
32
+ trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
33
+ trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
29
34
  }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
30
35
  id: string;
31
36
  type: "BaseFeatureWidget";
32
37
  track: import("mobx-state-tree").ReferenceIdentifier | undefined;
33
38
  view: import("mobx-state-tree").ReferenceIdentifier | undefined;
39
+ trackId: string | undefined;
40
+ trackType: string | undefined;
34
41
  formattedFields: any;
35
42
  finalizedFeatureData: any;
36
43
  } & import("mobx-state-tree")._NotCustomized>;
package/esm/CramAdapter/CramTestAdapters.js CHANGED
@@ -8,7 +8,7 @@ export function parseSmallFasta(text) {
8
8
  .split('>')
9
9
  .filter(t => /\S/.test(t))
10
10
  .map(entryText => {
11
- const [defLine, ...seqLines] = entryText.split('\n');
11
+ const [defLine, ...seqLines] = entryText.split(/\n|\r\n|\r/);
12
12
  const [id, ...descriptionLines] = defLine.split(' ');
13
13
  const description = descriptionLines.join(' ');
14
14
  const sequence = seqLines.join('').replace(/\s/g, '');
package/esm/CramAdapter/CramTestAdapters.js.map CHANGED
@@ -1 +1 @@
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package/esm/LinearAlignmentsDisplay/models/model.d.ts CHANGED
@@ -61,7 +61,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: Al
61
61
  readonly adapterConfig: any;
62
62
  readonly parentTrack: any;
63
63
  renderProps(): any;
64
- readonly rendererType: any;
64
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
65
65
  readonly DisplayMessageComponent: React.FC<any> | undefined;
66
66
  trackMenuItems(): MenuItem[];
67
67
  readonly viewMenuActions: MenuItem[];
package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js CHANGED
@@ -1,6 +1,6 @@
1
1
  import React from 'react';
2
2
  import { observer } from 'mobx-react';
3
- import Typography from '@mui/material/Typography';
3
+ import { Typography } from '@mui/material';
4
4
  function LinearPileupDisplayBlurb(props) {
5
5
  const { model } = props;
6
6
  const { sortedBy } = model;
package/esm/LinearPileupDisplay/components/LinearPileupDisplayBlurb.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"LinearPileupDisplayBlurb.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,UAAU,MAAM,0BAA0B,CAAA;AAYjD,SAAS,wBAAwB,CAAC,KAAoC;IACpE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,4CACe,SAAS,KAAK,CAAC,QAAQ,EAAE,EACtC,KAAK,EAAE,EAAE,eAAe,EAAE,OAAO,EAAE;QAEnC,oBAAC,UAAU,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAC,SAAS,IAC5C,KAAK,CAAC,QAAQ;YACb,CAAC,CAAC,aAAa,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,QAAQ,CAAC,OAAO,IAC7D,QAAQ,CAAC,GACX,EAAE;YACJ,CAAC,CAAC,IAAI,CACG,CACT,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AACD,eAAe,QAAQ,CAAC,wBAAwB,CAAC,CAAA"}
1
+ {"version":3,"file":"LinearPileupDisplayBlurb.js","sourceRoot":"","sources":["../../../src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,EAAE,UAAU,EAAE,MAAM,eAAe,CAAA;AAY1C,SAAS,wBAAwB,CAAC,KAAoC;IACpE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,QAAQ,EAAE,GAAG,KAAK,CAAA;IAC1B,OAAO,QAAQ,CAAC,CAAC,CAAC,CAChB,4CACe,SAAS,KAAK,CAAC,QAAQ,EAAE,EACtC,KAAK,EAAE,EAAE,eAAe,EAAE,OAAO,EAAE;QAEnC,oBAAC,UAAU,IAAC,KAAK,EAAC,WAAW,EAAC,OAAO,EAAC,SAAS,IAC5C,KAAK,CAAC,QAAQ;YACb,CAAC,CAAC,aAAa,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,QAAQ,CAAC,OAAO,IAC7D,QAAQ,CAAC,GACX,EAAE;YACJ,CAAC,CAAC,IAAI,CACG,CACT,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AACD,eAAe,QAAQ,CAAC,wBAAwB,CAAC,CAAA"}
package/esm/LinearPileupDisplay/model.d.ts CHANGED
@@ -131,7 +131,7 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
131
131
  readonly adapterConfig: any;
132
132
  readonly parentTrack: any;
133
133
  renderProps(): any;
134
- readonly rendererType: any;
134
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
135
135
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
136
136
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
137
137
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -251,7 +251,11 @@ declare const stateModelFactory: (configSchema: LinearPileupDisplayConfigModel)
251
251
  reload(): void;
252
252
  } & {
253
253
  readonly maxHeight: any;
254
- readonly rendererConfig: any;
254
+ readonly rendererConfig: {
255
+ [x: string]: any;
256
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
257
+ setSubschema(slotName: string, data: unknown): any;
258
+ } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
255
259
  readonly featureHeightSetting: any;
256
260
  readonly mismatchAlphaSetting: any;
257
261
  readonly featureUnderMouse: Feature | undefined;
package/esm/LinearPileupDisplay/model.js CHANGED
@@ -1,10 +1,10 @@
1
1
  import { lazy } from 'react';
2
2
  import { autorun, observable } from 'mobx';
3
- import { cast, types, addDisposer, getEnv } from 'mobx-state-tree';
3
+ import { cast, types, addDisposer } from 'mobx-state-tree';
4
4
  import copy from 'copy-to-clipboard';
5
5
  import { ConfigurationReference, readConfObject, getConf, } from '@jbrowse/core/configuration';
6
6
  import { getRpcSessionId } from '@jbrowse/core/util/tracks';
7
- import { getSession, isSessionModelWithWidgets, getContainingView, SimpleFeature, } from '@jbrowse/core/util';
7
+ import { getEnv, getSession, isSessionModelWithWidgets, getContainingView, SimpleFeature, } from '@jbrowse/core/util';
8
8
  import { BaseLinearDisplay, } from '@jbrowse/plugin-linear-genome-view';
9
9
  // icons
10
10
  import VisibilityIcon from '@mui/icons-material/Visibility';
@@ -125,18 +125,16 @@ const stateModelFactory = (configSchema) => types
125
125
  const { rpcManager } = getSession(self);
126
126
  const view = getContainingView(self);
127
127
  const { sortedBy, colorBy, parentTrack, adapterConfig, rendererType, } = self;
128
- const { staticBlocks, bpPerPx } = view;
129
- if (!self.estimatedStatsReady) {
130
- return;
131
- }
132
- if (self.regionTooLarge) {
128
+ if (!view.initialized ||
129
+ !self.estimatedStatsReady ||
130
+ self.regionTooLarge) {
133
131
  return;
134
132
  }
133
+ const { staticBlocks, bpPerPx } = view;
135
134
  // continually generate the vc pairing, set and rerender if any
136
135
  // new values seen
137
136
  if (colorBy === null || colorBy === void 0 ? void 0 : colorBy.tag) {
138
- const uniqueTagSet = await getUniqueTagValues(self, colorBy, staticBlocks);
139
- self.updateColorTagMap(uniqueTagSet);
137
+ self.updateColorTagMap(await getUniqueTagValues(self, colorBy, staticBlocks));
140
138
  }
141
139
  if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
142
140
  const adapter = getConf(parentTrack, ['adapter']);
@@ -145,6 +143,7 @@ const stateModelFactory = (configSchema) => types
145
143
  if (sortedBy) {
146
144
  const { pos, refName, assemblyName } = sortedBy;
147
145
  // render just the sorted region first
146
+ // @ts-ignore
148
147
  await self.rendererType.renderInClient(rpcManager, {
149
148
  assemblyName,
150
149
  regions: [
package/esm/LinearPileupDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
- 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1
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package/esm/LinearSNPCoverageDisplay/models/model.d.ts CHANGED
@@ -135,7 +135,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
135
135
  readonly adapterConfig: any;
136
136
  readonly parentTrack: any;
137
137
  renderProps(): any;
138
- readonly rendererType: any;
138
+ readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
139
139
  readonly DisplayMessageComponent: import("react").FC<any> | undefined;
140
140
  trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
141
141
  readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
@@ -255,7 +255,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
255
255
  readonly maxScore: any;
256
256
  readonly minScore: any;
257
257
  } & {
258
- readonly rendererConfig: any;
258
+ readonly rendererConfig: {
259
+ [x: string]: any;
260
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
261
+ setSubschema(slotName: string, data: unknown): any;
262
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
259
263
  } & {
260
264
  readonly filled: any;
261
265
  readonly summaryScoreModeSetting: any;
@@ -331,7 +335,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
331
335
  }): void;
332
336
  updateModificationColorMap(uniqueModifications: string[]): void;
333
337
  } & {
334
- readonly rendererConfig: any;
338
+ readonly rendererConfig: {
339
+ [x: string]: any;
340
+ } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
341
+ setSubschema(slotName: string, data: unknown): any;
342
+ } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
335
343
  readonly drawArcsSetting: any;
336
344
  readonly drawInterbaseCountsSetting: any;
337
345
  readonly drawIndicatorsSetting: any;
package/esm/LinearSNPCoverageDisplay/models/model.js CHANGED
@@ -110,16 +110,16 @@ const stateModelFactory = (pluginManager, configSchema) => types
110
110
  addDisposer(self, autorun(async () => {
111
111
  try {
112
112
  const { colorBy } = self;
113
- const { staticBlocks } = getContainingView(self);
114
- if (!self.estimatedStatsReady) {
115
- return;
116
- }
117
- if (self.regionTooLarge) {
113
+ const view = getContainingView(self);
114
+ if (!view.initialized ||
115
+ !self.estimatedStatsReady ||
116
+ self.regionTooLarge) {
118
117
  return;
119
118
  }
119
+ const { staticBlocks } = view;
120
120
  if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
121
- const vals = await getUniqueModificationValues(self, getConf(self.parentTrack, 'adapter'), colorBy, staticBlocks);
122
- self.updateModificationColorMap(vals);
121
+ const adapter = getConf(self.parentTrack, 'adapter');
122
+ self.updateModificationColorMap(await getUniqueModificationValues(self, adapter, colorBy, staticBlocks));
123
123
  }
124
124
  }
125
125
  catch (error) {
@@ -158,25 +158,19 @@ const stateModelFactory = (pluginManager, configSchema) => types
158
158
  label: 'Draw insertion/clipping indicators',
159
159
  type: 'checkbox',
160
160
  checked: self.drawIndicatorsSetting,
161
- onClick: () => {
162
- self.toggleDrawIndicators();
163
- },
161
+ onClick: () => self.toggleDrawIndicators(),
164
162
  },
165
163
  {
166
164
  label: 'Draw insertion/clipping counts',
167
165
  type: 'checkbox',
168
166
  checked: self.drawInterbaseCountsSetting,
169
- onClick: () => {
170
- self.toggleDrawInterbaseCounts();
171
- },
167
+ onClick: () => self.toggleDrawInterbaseCounts(),
172
168
  },
173
169
  {
174
170
  label: 'Draw arcs',
175
171
  type: 'checkbox',
176
172
  checked: self.drawArcsSetting,
177
- onClick: () => {
178
- self.toggleDrawArcs();
179
- },
173
+ onClick: () => self.toggleDrawArcs(),
180
174
  },
181
175
  ];
182
176
  },
package/esm/LinearSNPCoverageDisplay/models/model.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-alignments",
3
- "version": "2.1.5",
3
+ "version": "2.1.7",
4
4
  "description": "JBrowse 2 alignments adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -64,5 +64,5 @@
64
64
  "distModule": "esm/index.js",
65
65
  "srcModule": "src/index.ts",
66
66
  "module": "esm/index.js",
67
- "gitHead": "bc5253ecdddeceeb999fffebf6dc6cf5f444e1c9"
67
+ "gitHead": "a1344081f61e22e0f597517efa7386023eef9f33"
68
68
  }
package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap CHANGED
@@ -280,6 +280,45 @@ exports[`open up a widget 1`] = `
280
280
  </div>
281
281
  </div>
282
282
  </div>
283
+ <div
284
+ class="tss-1upvn7b-container2"
285
+ >
286
+ <button
287
+ class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium css-sghohy-MuiButtonBase-root-MuiButton-root"
288
+ tabindex="0"
289
+ type="button"
290
+ >
291
+ Show feature sequence
292
+ <span
293
+ class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
294
+ />
295
+ </button>
296
+ <div
297
+ class="MuiFormControl-root tss-1x17dzq-formControl css-1nrlq1o-MuiFormControl-root"
298
+ >
299
+ <button
300
+ class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-78trlr-MuiButtonBase-root-MuiIconButton-root"
301
+ tabindex="0"
302
+ type="button"
303
+ >
304
+ <svg
305
+ aria-hidden="true"
306
+ class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-i4bv87-MuiSvgIcon-root"
307
+ data-testid="HelpIcon"
308
+ focusable="false"
309
+ viewBox="0 0 24 24"
310
+ >
311
+ <path
312
+ d="M12 2C6.48 2 2 6.48 2 12s4.48 10 10 10 10-4.48 10-10S17.52 2 12 2zm1 17h-2v-2h2v2zm2.07-7.75-.9.92C13.45 12.9 13 13.5 13 15h-2v-.5c0-1.1.45-2.1 1.17-2.83l1.24-1.26c.37-.36.59-.86.59-1.41 0-1.1-.9-2-2-2s-2 .9-2 2H8c0-2.21 1.79-4 4-4s4 1.79 4 4c0 .88-.36 1.68-.93 2.25z"
313
+ />
314
+ </svg>
315
+ <span
316
+ class="MuiTouchRipple-root css-8je8zh-MuiTouchRipple-root"
317
+ />
318
+ </button>
319
+ </div>
320
+ <br />
321
+ </div>
283
322
  </div>
284
323
  </div>
285
324
  </div>
package/src/CramAdapter/CramTestAdapters.ts CHANGED
@@ -10,7 +10,7 @@ export function parseSmallFasta(text: string) {
10
10
  .split('>')
11
11
  .filter(t => /\S/.test(t))
12
12
  .map(entryText => {
13
- const [defLine, ...seqLines] = entryText.split('\n')
13
+ const [defLine, ...seqLines] = entryText.split(/\n|\r\n|\r/)
14
14
  const [id, ...descriptionLines] = defLine.split(' ')
15
15
  const description = descriptionLines.join(' ')
16
16
  const sequence = seqLines.join('').replace(/\s/g, '')
package/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb.tsx CHANGED
@@ -1,6 +1,6 @@
1
1
  import React from 'react'
2
2
  import { observer } from 'mobx-react'
3
- import Typography from '@mui/material/Typography'
3
+ import { Typography } from '@mui/material'
4
4
 
5
5
  export interface LinearPileupDisplayBlurbProps {
6
6
  model: {
package/src/LinearPileupDisplay/model.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  import { lazy } from 'react'
2
2
  import { autorun, observable } from 'mobx'
3
- import { cast, types, addDisposer, getEnv, Instance } from 'mobx-state-tree'
3
+ import { cast, types, addDisposer, Instance } from 'mobx-state-tree'
4
4
  import copy from 'copy-to-clipboard'
5
5
  import {
6
6
  AnyConfigurationModel,
@@ -10,6 +10,7 @@ import {
10
10
  } from '@jbrowse/core/configuration'
11
11
  import { getRpcSessionId } from '@jbrowse/core/util/tracks'
12
12
  import {
13
+ getEnv,
13
14
  getSession,
14
15
  isSessionModelWithWidgets,
15
16
  getContainingView,
@@ -177,24 +178,22 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
177
178
  adapterConfig,
178
179
  rendererType,
179
180
  } = self
180
- const { staticBlocks, bpPerPx } = view
181
181
 
182
- if (!self.estimatedStatsReady) {
183
- return
184
- }
185
- if (self.regionTooLarge) {
182
+ if (
183
+ !view.initialized ||
184
+ !self.estimatedStatsReady ||
185
+ self.regionTooLarge
186
+ ) {
186
187
  return
187
188
  }
188
189
 
190
+ const { staticBlocks, bpPerPx } = view
189
191
  // continually generate the vc pairing, set and rerender if any
190
192
  // new values seen
191
193
  if (colorBy?.tag) {
192
- const uniqueTagSet = await getUniqueTagValues(
193
- self,
194
- colorBy,
195
- staticBlocks,
194
+ self.updateColorTagMap(
195
+ await getUniqueTagValues(self, colorBy, staticBlocks),
196
196
  )
197
- self.updateColorTagMap(uniqueTagSet)
198
197
  }
199
198
 
200
199
  if (colorBy?.type === 'modifications') {
@@ -211,8 +210,8 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
211
210
 
212
211
  if (sortedBy) {
213
212
  const { pos, refName, assemblyName } = sortedBy
214
-
215
213
  // render just the sorted region first
214
+ // @ts-ignore
216
215
  await self.rendererType.renderInClient(rpcManager, {
217
216
  assemblyName,
218
217
  regions: [
package/src/LinearSNPCoverageDisplay/models/model.ts CHANGED
@@ -160,22 +160,26 @@ const stateModelFactory = (
160
160
  async () => {
161
161
  try {
162
162
  const { colorBy } = self
163
- const { staticBlocks } = getContainingView(self) as LGV
163
+ const view = getContainingView(self) as LGV
164
164
 
165
- if (!self.estimatedStatsReady) {
166
- return
167
- }
168
- if (self.regionTooLarge) {
165
+ if (
166
+ !view.initialized ||
167
+ !self.estimatedStatsReady ||
168
+ self.regionTooLarge
169
+ ) {
169
170
  return
170
171
  }
172
+ const { staticBlocks } = view
171
173
  if (colorBy?.type === 'modifications') {
172
- const vals = await getUniqueModificationValues(
173
- self,
174
- getConf(self.parentTrack, 'adapter'),
175
- colorBy,
176
- staticBlocks,
174
+ const adapter = getConf(self.parentTrack, 'adapter')
175
+ self.updateModificationColorMap(
176
+ await getUniqueModificationValues(
177
+ self,
178
+ adapter,
179
+ colorBy,
180
+ staticBlocks,
181
+ ),
177
182
  )
178
- self.updateModificationColorMap(vals)
179
183
  }
180
184
  } catch (error) {
181
185
  console.error(error)
@@ -222,25 +226,19 @@ const stateModelFactory = (
222
226
  label: 'Draw insertion/clipping indicators',
223
227
  type: 'checkbox',
224
228
  checked: self.drawIndicatorsSetting,
225
- onClick: () => {
226
- self.toggleDrawIndicators()
227
- },
229
+ onClick: () => self.toggleDrawIndicators(),
228
230
  },
229
231
  {
230
232
  label: 'Draw insertion/clipping counts',
231
233
  type: 'checkbox',
232
234
  checked: self.drawInterbaseCountsSetting,
233
- onClick: () => {
234
- self.toggleDrawInterbaseCounts()
235
- },
235
+ onClick: () => self.toggleDrawInterbaseCounts(),
236
236
  },
237
237
  {
238
238
  label: 'Draw arcs',
239
239
  type: 'checkbox',
240
240
  checked: self.drawArcsSetting,
241
- onClick: () => {
242
- self.toggleDrawArcs()
243
- },
241
+ onClick: () => self.toggleDrawArcs(),
244
242
  },
245
243
  ]
246
244
  },