@jbrowse/plugin-sequence 2.3.3 → 2.4.0

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 (13) hide show
  1. package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js +1 -1
  2. package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js.map +1 -1
  3. package/dist/LinearReferenceSequenceDisplay/model.d.ts +63 -7
  4. package/dist/LinearReferenceSequenceDisplay/model.js +13 -5
  5. package/dist/LinearReferenceSequenceDisplay/model.js.map +1 -1
  6. package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js +1 -1
  7. package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js.map +1 -1
  8. package/esm/LinearReferenceSequenceDisplay/model.d.ts +63 -7
  9. package/esm/LinearReferenceSequenceDisplay/model.js +13 -5
  10. package/esm/LinearReferenceSequenceDisplay/model.js.map +1 -1
  11. package/package.json +2 -2
  12. package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts +1 -1
  13. package/src/LinearReferenceSequenceDisplay/model.ts +12 -5
package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js CHANGED
@@ -48,7 +48,7 @@ class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
48
48
  const loc = this.getConf('metadataLocation');
49
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  return loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml'
50
50
  ? null
51
- : (0, io_1.openLocation)(loc).readFile('utf8');
51
+ : (0, io_1.openLocation)(loc, this.pluginManager).readFile('utf8');
52
52
  }
53
53
  async setup() {
54
54
  if (!this.setupP) {
package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"IndexedFastaAdapter.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/IndexedFastaAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qDAAiD;AACjD,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,6CAA2D;AAC3D,sFAA2D;AAC3D,2EAAkD;AAIlD,eAAqB,SAAQ,iCAAmB;IAAhD;;QAGU,aAAQ,GAAG,IAAI,iCAAqB,CAAwB;YAClE,KAAK,EAAE,IAAI,kBAAQ,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC;YACrC,IAAI,EAAE,KAAK,EAAE,IAAO,EAAE,MAAoB,EAAE,EAAE;gBAC5C,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,IAAI,CAAA;gBAC3C,OAAO,KAAK,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;YACpE,CAAC;SACF,CAAC,CAAA;IAyFJ,CAAC;IAvFQ,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,OAAO,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAEM,KAAK,CAAC,UAAU,CAAC,IAAkB;QACxC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;QACnD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAEM,KAAK,CAAC,QAAQ;QACnB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QACnE,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAiB,CAAA;QAE/D,OAAO;YACL,KAAK,EAAE,IAAI,2BAAY,CAAC;gBACtB,KAAK,EAAE,IAAA,iBAAY,EAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;gBACtD,GAAG,EAAE,IAAA,iBAAY,EAAC,WAAW,EAAE,IAAI,CAAC,aAAa,CAAC;aACnD,CAAC;SACH,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,kBAAkB,CAAC,CAAA;QAC5C,OAAO,GAAG,CAAC,GAAG,KAAK,EAAE,IAAI,GAAG,CAAC,GAAG,KAAK,2BAA2B;YAC9D,CAAC,CAAC,IAAI;YACN,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IACxC,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACtC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,WAAW,CAAC,MAAwB,EAAE,IAAkB;QAC7D,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACpC,MAAM,IAAI,GAAG,MAAM,KAAK,CAAC,eAAe,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,MAAM,GAAG,EAAE,CAAA;YACjB,MAAM,SAAS,GAAG,MAAM,CAAA;YAExB,MAAM,CAAC,GAAG,KAAK,GAAG,CAAC,KAAK,GAAG,SAAS,CAAC,CAAA;YACrC,MAAM,CAAC,GAAG,GAAG,GAAG,CAAC,SAAS,GAAG,CAAC,GAAG,GAAG,SAAS,CAAC,CAAC,CAAA;YAC/C,KAAK,IAAI,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,IAAI,SAAS,EAAE;gBAChE,MAAM,CAAC,GAAG;oBACR,OAAO;oBACP,KAAK,EAAE,UAAU;oBACjB,GAAG,EAAE,UAAU,GAAG,SAAS;iBAC5B,CAAA;gBACD,MAAM,CAAC,IAAI,CACT,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,EAAE,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,MAAM,CAAC,CACpE,CAAA;aACF;YACD,MAAM,GAAG,GAAG,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;iBACpC,IAAI,CAAC,EAAE,CAAC;iBACR,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC;iBAChB,KAAK,CAAC,CAAC,EAAE,GAAG,GAAG,KAAK,CAAC,CAAA;YACxB,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AAlGD,4BAkGC"}
1
+ {"version":3,"file":"IndexedFastaAdapter.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/IndexedFastaAdapter.ts"],"names":[],"mappings":";;;;;AAAA,qDAAiD;AACjD,yEAGgD;AAEhD,8CAAoD;AACpD,kDAA0D;AAC1D,6CAA2D;AAC3D,sFAA2D;AAC3D,2EAAkD;AAIlD,eAAqB,SAAQ,iCAAmB;IAAhD;;QAGU,aAAQ,GAAG,IAAI,iCAAqB,CAAwB;YAClE,KAAK,EAAE,IAAI,kBAAQ,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC;YACrC,IAAI,EAAE,KAAK,EAAE,IAAO,EAAE,MAAoB,EAAE,EAAE;gBAC5C,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,IAAI,CAAA;gBAC3C,OAAO,KAAK,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;YACpE,CAAC;SACF,CAAC,CAAA;IAyFJ,CAAC;IAvFQ,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,OAAO,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAEM,KAAK,CAAC,UAAU,CAAC,IAAkB;QACxC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;QACnD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAEM,KAAK,CAAC,QAAQ;QACnB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QACnE,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAiB,CAAA;QAE/D,OAAO;YACL,KAAK,EAAE,IAAI,2BAAY,CAAC;gBACtB,KAAK,EAAE,IAAA,iBAAY,EAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;gBACtD,GAAG,EAAE,IAAA,iBAAY,EAAC,WAAW,EAAE,IAAI,CAAC,aAAa,CAAC;aACnD,CAAC;SACH,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,kBAAkB,CAAC,CAAA;QAC5C,OAAO,GAAG,CAAC,GAAG,KAAK,EAAE,IAAI,GAAG,CAAC,GAAG,KAAK,2BAA2B;YAC9D,CAAC,CAAC,IAAI;YACN,CAAC,CAAC,IAAA,iBAAY,EAAC,GAAG,EAAE,IAAI,CAAC,aAAa,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IAC5D,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACtC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,WAAW,CAAC,MAAwB,EAAE,IAAkB;QAC7D,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,OAAO,IAAA,uBAAgB,EAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACpC,MAAM,IAAI,GAAG,MAAM,KAAK,CAAC,eAAe,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,MAAM,GAAG,EAAE,CAAA;YACjB,MAAM,SAAS,GAAG,MAAM,CAAA;YAExB,MAAM,CAAC,GAAG,KAAK,GAAG,CAAC,KAAK,GAAG,SAAS,CAAC,CAAA;YACrC,MAAM,CAAC,GAAG,GAAG,GAAG,CAAC,SAAS,GAAG,CAAC,GAAG,GAAG,SAAS,CAAC,CAAC,CAAA;YAC/C,KAAK,IAAI,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,IAAI,SAAS,EAAE;gBAChE,MAAM,CAAC,GAAG;oBACR,OAAO;oBACP,KAAK,EAAE,UAAU;oBACjB,GAAG,EAAE,UAAU,GAAG,SAAS;iBAC5B,CAAA;gBACD,MAAM,CAAC,IAAI,CACT,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,EAAE,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,MAAM,CAAC,CACpE,CAAA;aACF;YACD,MAAM,GAAG,GAAG,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;iBACpC,IAAI,CAAC,EAAE,CAAC;iBACR,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC;iBAChB,KAAK,CAAC,CAAC,EAAE,GAAG,GAAG,KAAK,CAAC,CAAA;YACxB,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,oBAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD;AAlGD,4BAkGC"}
package/dist/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -9,7 +9,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
9
9
  type: import("mobx-state-tree").ISimpleType<string>;
10
10
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
11
11
  } & {
12
- height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
12
+ heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
13
13
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
14
14
  key: import("mobx-state-tree").ISimpleType<string>;
15
15
  region: import("mobx-state-tree").IModelType<{
@@ -108,9 +108,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
109
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  }, {
110
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  rendererTypeName: string;
111
- error: unknown; /**
112
- * #method
113
- */
111
+ error: unknown;
114
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  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
115
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  }> | null;
116
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  readonly adapterConfig: any;
@@ -134,6 +132,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
135
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  estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
136
134
  } & {
135
+ readonly height: any;
137
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  readonly blockType: "dynamicBlocks" | "staticBlocks";
138
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  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
139
138
  } & {
@@ -163,7 +162,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
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  setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
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  clearRegionStats(): void;
166
- setHeight(displayHeight: number): number;
165
+ setHeight(displayHeight: number): any;
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  resizeHeight(distance: number): number;
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  setScrollTop(scrollTop: number): void;
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  updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
@@ -196,6 +195,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  } & {
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  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
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  overrideHeight: number;
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+ theme: import("@mui/material").ThemeOptions;
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  }): Promise<JSX.Element>;
200
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  } & {
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  /**
@@ -235,11 +235,67 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
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  checked: boolean;
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  onClick: () => void;
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  }[];
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- }, import("mobx-state-tree")._NotCustomized, {
238
+ }, {
239
+ type: string;
240
+ } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
241
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
242
+ type: import("mobx-state-tree").ISimpleType<string>;
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+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
244
+ } & {
245
+ heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
246
+ blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
247
+ key: import("mobx-state-tree").ISimpleType<string>;
248
+ region: import("mobx-state-tree").IModelType<{
249
+ refName: import("mobx-state-tree").ISimpleType<string>;
250
+ start: import("mobx-state-tree").ISimpleType<number>;
251
+ end: import("mobx-state-tree").ISimpleType<number>;
252
+ reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
253
+ } & {
254
+ assemblyName: import("mobx-state-tree").ISimpleType<string>;
255
+ }, {
256
+ setRefName(newRefName: string): void;
257
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
258
+ reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
259
+ isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
260
+ isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
261
+ }, {
262
+ renderInProgress: AbortController | undefined;
263
+ filled: boolean;
264
+ reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
265
+ features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
266
+ layout: any;
267
+ status: string;
268
+ error: unknown;
269
+ message: string | undefined;
270
+ maxHeightReached: boolean;
271
+ ReactComponent: ({ model, }: {
272
+ model: any;
273
+ }) => any;
274
+ renderProps: any;
275
+ } & {
276
+ doReload(): void;
277
+ afterAttach(): void;
278
+ setStatus(message: string): void;
279
+ setLoading(abortController: AbortController): void;
280
+ setMessage(messageText: string): void;
281
+ setRendered(props: {
282
+ reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
283
+ features: Map<string, import("@jbrowse/core/util").Feature>;
284
+ layout: any;
285
+ maxHeightReached: boolean;
286
+ renderProps: any;
287
+ } | undefined): void;
288
+ setError(error: unknown): void;
289
+ reload(): void;
290
+ beforeDestroy(): void;
291
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
292
+ userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
293
+ userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
294
+ }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
239
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  type: string;
240
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  id: string;
241
- height: number;
242
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  rpcDriverName: string | undefined;
298
+ heightPreConfig: number | undefined;
243
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  userBpPerPxLimit: number | undefined;
244
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  userByteSizeLimit: number | undefined;
245
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  } & import("mobx-state-tree")._NotCustomized>;
package/dist/LinearReferenceSequenceDisplay/model.js CHANGED
@@ -88,12 +88,20 @@ function modelFactory(configSchema) {
88
88
  self.showTranslation = !self.showTranslation;
89
89
  },
90
90
  afterAttach() {
91
- // auto-adjust height depending on settings
92
91
  (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
93
- const t = self.showTranslation ? 100 : 0;
94
- const r = self.showReverse ? 20 : 0;
95
- const s = self.showForward ? 20 : 0;
96
- self.setHeight(t + r + s);
92
+ const view = (0, util_1.getContainingView)(self);
93
+ if ((view === null || view === void 0 ? void 0 : view.bpPerPx) >= 1) {
94
+ self.setHeight(50);
95
+ }
96
+ else {
97
+ const { showTranslation, showReverse, showForward } = self;
98
+ const r1 = showReverse && showTranslation ? 60 : 0;
99
+ const r2 = showForward && showTranslation ? 60 : 0;
100
+ const t = r1 + r2;
101
+ const r = showReverse ? 20 : 0;
102
+ const s = showForward ? 20 : 0;
103
+ self.setHeight(t + r + s);
104
+ }
97
105
  }));
98
106
  },
99
107
  }))
package/dist/LinearReferenceSequenceDisplay/model.js.map CHANGED
@@ -1 +1 @@
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package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js CHANGED
@@ -43,7 +43,7 @@ export default class extends BaseSequenceAdapter {
43
43
  const loc = this.getConf('metadataLocation');
44
44
  return loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml'
45
45
  ? null
46
- : openLocation(loc).readFile('utf8');
46
+ : openLocation(loc, this.pluginManager).readFile('utf8');
47
47
  }
48
48
  async setup() {
49
49
  if (!this.setupP) {
package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"IndexedFastaAdapter.js","sourceRoot":"","sources":["../../src/IndexedFastaAdapter/IndexedFastaAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAA;AACjD,OAAO,EACL,mBAAmB,GAEpB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,aAAa,EAAW,MAAM,oBAAoB,CAAA;AAC3D,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,QAAQ,MAAM,6BAA6B,CAAA;AAIlD,MAAM,CAAC,OAAO,MAAO,SAAQ,mBAAmB;IAAhD;;QAGU,aAAQ,GAAG,IAAI,qBAAqB,CAAwB;YAClE,KAAK,EAAE,IAAI,QAAQ,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,CAAC;YACrC,IAAI,EAAE,KAAK,EAAE,IAAO,EAAE,MAAoB,EAAE,EAAE;gBAC5C,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,IAAI,CAAA;gBAC3C,OAAO,KAAK,CAAC,WAAW,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;YACpE,CAAC;SACF,CAAC,CAAA;IAyFJ,CAAC;IAvFQ,KAAK,CAAC,WAAW,CAAC,IAAkB;QACzC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,OAAO,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAEM,KAAK,CAAC,UAAU,CAAC,IAAkB;QACxC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;QACnD,OAAO,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC;YAC3C,OAAO;YACP,KAAK,EAAE,CAAC;YACR,GAAG,EAAE,QAAQ,CAAC,OAAO,CAAC;SACvB,CAAC,CAAC,CAAA;IACL,CAAC;IAEM,KAAK,CAAC,QAAQ;QACnB,MAAM,aAAa,GAAG,IAAI,CAAC,OAAO,CAAC,eAAe,CAAiB,CAAA;QACnE,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAiB,CAAA;QAE/D,OAAO;YACL,KAAK,EAAE,IAAI,YAAY,CAAC;gBACtB,KAAK,EAAE,YAAY,CAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;gBACtD,GAAG,EAAE,YAAY,CAAC,WAAW,EAAE,IAAI,CAAC,aAAa,CAAC;aACnD,CAAC;SACH,CAAA;IACH,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,kBAAkB,CAAC,CAAA;QAC5C,OAAO,GAAG,CAAC,GAAG,KAAK,EAAE,IAAI,GAAG,CAAC,GAAG,KAAK,2BAA2B;YAC9D,CAAC,CAAC,IAAI;YACN,CAAC,CAAC,YAAY,CAAC,GAAG,EAAE,IAAI,CAAC,aAAa,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;IAC5D,CAAC;IAEM,KAAK,CAAC,KAAK;QAChB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACtC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAEM,WAAW,CAAC,MAAwB,EAAE,IAAkB;QAC7D,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,MAAM,CAAA;QACtC,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACpC,MAAM,IAAI,GAAG,MAAM,KAAK,CAAC,eAAe,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;YACvD,MAAM,SAAS,GAAG,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;YAChE,MAAM,MAAM,GAAG,EAAE,CAAA;YACjB,MAAM,SAAS,GAAG,MAAM,CAAA;YAExB,MAAM,CAAC,GAAG,KAAK,GAAG,CAAC,KAAK,GAAG,SAAS,CAAC,CAAA;YACrC,MAAM,CAAC,GAAG,GAAG,GAAG,CAAC,SAAS,GAAG,CAAC,GAAG,GAAG,SAAS,CAAC,CAAC,CAAA;YAC/C,KAAK,IAAI,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,IAAI,SAAS,EAAE;gBAChE,MAAM,CAAC,GAAG;oBACR,OAAO;oBACP,KAAK,EAAE,UAAU;oBACjB,GAAG,EAAE,UAAU,GAAG,SAAS;iBAC5B,CAAA;gBACD,MAAM,CAAC,IAAI,CACT,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,EAAE,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,MAAM,CAAC,CACpE,CAAA;aACF;YACD,MAAM,GAAG,GAAG,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;iBACpC,IAAI,CAAC,EAAE,CAAC;iBACR,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC;iBAChB,KAAK,CAAC,CAAC,EAAE,GAAG,GAAG,KAAK,CAAC,CAAA;YACxB,IAAI,GAAG,EAAE;gBACP,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,OAAO,IAAI,KAAK,IAAI,SAAS,EAAE;oBACtC,IAAI,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,EAAE;iBAC9C,CAAC,CACH,CAAA;aACF;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACI,aAAa,EAAC,gBAAgB,IAAS,CAAC;CAChD"}
package/esm/LinearReferenceSequenceDisplay/model.d.ts CHANGED
@@ -9,7 +9,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
9
9
  type: import("mobx-state-tree").ISimpleType<string>;
10
10
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
11
11
  } & {
12
- height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
12
+ heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
13
13
  blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
14
14
  key: import("mobx-state-tree").ISimpleType<string>;
15
15
  region: import("mobx-state-tree").IModelType<{
@@ -108,9 +108,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
108
108
  rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
109
109
  }, {
110
110
  rendererTypeName: string;
111
- error: unknown; /**
112
- * #method
113
- */
111
+ error: unknown;
114
112
  }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
115
113
  }> | null;
116
114
  readonly adapterConfig: any;
@@ -134,6 +132,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
134
132
  estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
135
133
  estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
136
134
  } & {
135
+ readonly height: any;
137
136
  readonly blockType: "dynamicBlocks" | "staticBlocks";
138
137
  readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
139
138
  } & {
@@ -163,7 +162,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
163
162
  setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
164
163
  setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
165
164
  clearRegionStats(): void;
166
- setHeight(displayHeight: number): number;
165
+ setHeight(displayHeight: number): any;
167
166
  resizeHeight(distance: number): number;
168
167
  setScrollTop(scrollTop: number): void;
169
168
  updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
@@ -196,6 +195,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
196
195
  } & {
197
196
  renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
198
197
  overrideHeight: number;
198
+ theme: import("@mui/material").ThemeOptions;
199
199
  }): Promise<JSX.Element>;
200
200
  } & {
201
201
  /**
@@ -235,11 +235,67 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
235
235
  checked: boolean;
236
236
  onClick: () => void;
237
237
  }[];
238
- }, import("mobx-state-tree")._NotCustomized, {
238
+ }, {
239
+ type: string;
240
+ } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
241
+ id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
242
+ type: import("mobx-state-tree").ISimpleType<string>;
243
+ rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
244
+ } & {
245
+ heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
246
+ blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
247
+ key: import("mobx-state-tree").ISimpleType<string>;
248
+ region: import("mobx-state-tree").IModelType<{
249
+ refName: import("mobx-state-tree").ISimpleType<string>;
250
+ start: import("mobx-state-tree").ISimpleType<number>;
251
+ end: import("mobx-state-tree").ISimpleType<number>;
252
+ reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
253
+ } & {
254
+ assemblyName: import("mobx-state-tree").ISimpleType<string>;
255
+ }, {
256
+ setRefName(newRefName: string): void;
257
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
258
+ reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
259
+ isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
260
+ isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
261
+ }, {
262
+ renderInProgress: AbortController | undefined;
263
+ filled: boolean;
264
+ reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
265
+ features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
266
+ layout: any;
267
+ status: string;
268
+ error: unknown;
269
+ message: string | undefined;
270
+ maxHeightReached: boolean;
271
+ ReactComponent: ({ model, }: {
272
+ model: any;
273
+ }) => any;
274
+ renderProps: any;
275
+ } & {
276
+ doReload(): void;
277
+ afterAttach(): void;
278
+ setStatus(message: string): void;
279
+ setLoading(abortController: AbortController): void;
280
+ setMessage(messageText: string): void;
281
+ setRendered(props: {
282
+ reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
283
+ features: Map<string, import("@jbrowse/core/util").Feature>;
284
+ layout: any;
285
+ maxHeightReached: boolean;
286
+ renderProps: any;
287
+ } | undefined): void;
288
+ setError(error: unknown): void;
289
+ reload(): void;
290
+ beforeDestroy(): void;
291
+ }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
292
+ userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
293
+ userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
294
+ }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
239
295
  type: string;
240
296
  id: string;
241
- height: number;
242
297
  rpcDriverName: string | undefined;
298
+ heightPreConfig: number | undefined;
243
299
  userBpPerPxLimit: number | undefined;
244
300
  userByteSizeLimit: number | undefined;
245
301
  } & import("mobx-state-tree")._NotCustomized>;
package/esm/LinearReferenceSequenceDisplay/model.js CHANGED
@@ -85,12 +85,20 @@ export function modelFactory(configSchema) {
85
85
  self.showTranslation = !self.showTranslation;
86
86
  },
87
87
  afterAttach() {
88
- // auto-adjust height depending on settings
89
88
  addDisposer(self, autorun(() => {
90
- const t = self.showTranslation ? 100 : 0;
91
- const r = self.showReverse ? 20 : 0;
92
- const s = self.showForward ? 20 : 0;
93
- self.setHeight(t + r + s);
89
+ const view = getContainingView(self);
90
+ if ((view === null || view === void 0 ? void 0 : view.bpPerPx) >= 1) {
91
+ self.setHeight(50);
92
+ }
93
+ else {
94
+ const { showTranslation, showReverse, showForward } = self;
95
+ const r1 = showReverse && showTranslation ? 60 : 0;
96
+ const r2 = showForward && showTranslation ? 60 : 0;
97
+ const t = r1 + r2;
98
+ const r = showReverse ? 20 : 0;
99
+ const s = showForward ? 20 : 0;
100
+ self.setHeight(t + r + s);
101
+ }
94
102
  }));
95
103
  },
96
104
  }))
package/esm/LinearReferenceSequenceDisplay/model.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACpD,OAAO,EACL,iBAAiB,GAElB,MAAM,oCAAoC,CAAA;AAC3C,OAAO,EAEL,sBAAsB,GACvB,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9B;;;GAGG;AACH,MAAM,UAAU,YAAY,CAAC,YAAwC;IACnE,OAAO,KAAK;SACT,OAAO,CACN,gCAAgC,EAChC,iBAAiB,EACjB,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,gCAAgC,CAAC;QACrD;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD;;WAEG;QACH,WAAW,EAAE,IAAI;QACjB;;WAEG;QACH,WAAW,EAAE,IAAI;QACjB;;WAEG;QACH,eAAe,EAAE,IAAI;KACtB,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EAAE,WAAW,EAAE,gBAAgB,EAAE,GAAG,IAAI,CAAA;QAC9C,OAAO;YACL;;eAEG;YACH,WAAW;gBACT,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,eAAe,EAAE,GAAG,IAAI,CAAA;gBAC1D,OAAO;oBACL,GAAG,gBAAgB,EAAE;oBACrB,aAAa,EAAE,IAAI,CAAC,aAAa;oBACjC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;oBACnC,WAAW;oBACX,WAAW;oBACX,eAAe;iBAChB,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,sBAAsB,EAAC,YAAY;YACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;YAC7D,OAAO,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,KAAI,CAAC,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,SAAS,CAAA;QACnE,CAAC;QACD;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,iBAAiB;YACf,IAAI,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,WAAW,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,iBAAiB;YACf,IAAI,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,WAAW,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,qBAAqB;YACnB,IAAI,CAAC,eAAe,GAAG,CAAC,IAAI,CAAC,eAAe,CAAA;QAC9C,CAAC;QACD,WAAW;YACT,2CAA2C;YAC3C,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,MAAM,CAAC,GAAG,IAAI,CAAC,eAAe,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;gBACxC,MAAM,CAAC,GAAG,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;gBACnC,MAAM,CAAC,GAAG,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;gBACnC,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;YAC3B,CAAC,CAAC,CACH,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,cAAc;YACZ,OAAO;gBACL;oBACE,KAAK,EAAE,cAAc;oBACrB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,WAAW;oBACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,EAAE;iBACxC;gBACD;oBACE,KAAK,EAAE,cAAc;oBACrB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,WAAW;oBACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,EAAE;iBACxC;gBACD;oBACE,KAAK,EAAE,kBAAkB;oBACzB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,eAAe;oBAC7B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,qBAAqB,EAAE;iBAC5C;aACF,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
1
+ {"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReferenceSequenceDisplay/model.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AACpD,OAAO,EACL,iBAAiB,GAElB,MAAM,oCAAoC,CAAA;AAC3C,OAAO,EAEL,sBAAsB,GACvB,MAAM,6BAA6B,CAAA;AACpC,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAA;AACtD,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9B;;;GAGG;AACH,MAAM,UAAU,YAAY,CAAC,YAAwC;IACnE,OAAO,KAAK;SACT,OAAO,CACN,gCAAgC,EAChC,iBAAiB,EACjB,KAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,KAAK,CAAC,OAAO,CAAC,gCAAgC,CAAC;QACrD;;WAEG;QACH,aAAa,EAAE,sBAAsB,CAAC,YAAY,CAAC;QACnD;;WAEG;QACH,WAAW,EAAE,IAAI;QACjB;;WAEG;QACH,WAAW,EAAE,IAAI;QACjB;;WAEG;QACH,eAAe,EAAE,IAAI;KACtB,CAAC,CACH;SACA,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EAAE,WAAW,EAAE,gBAAgB,EAAE,GAAG,IAAI,CAAA;QAC9C,OAAO;YACL;;eAEG;YACH,WAAW;gBACT,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,eAAe,EAAE,GAAG,IAAI,CAAA;gBAC1D,OAAO;oBACL,GAAG,gBAAgB,EAAE;oBACrB,aAAa,EAAE,IAAI,CAAC,aAAa;oBACjC,MAAM,EAAE,IAAI,CAAC,aAAa,CAAC,QAAQ;oBACnC,WAAW;oBACX,WAAW;oBACX,eAAe;iBAChB,CAAA;YACH,CAAC;SACF,CAAA;IACH,CAAC,CAAC;SACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,sBAAsB,EAAC,YAAY;YACjC,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;YAC7D,OAAO,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,KAAI,CAAC,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,SAAS,CAAA;QACnE,CAAC;QACD;;WAEG;QACH,IAAI,gBAAgB;YAClB,OAAO,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAA;QACzC,CAAC;KACF,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;WAEG;QACH,iBAAiB;YACf,IAAI,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,WAAW,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,iBAAiB;YACf,IAAI,CAAC,WAAW,GAAG,CAAC,IAAI,CAAC,WAAW,CAAA;QACtC,CAAC;QACD;;WAEG;QACH,qBAAqB;YACnB,IAAI,CAAC,eAAe,GAAG,CAAC,IAAI,CAAC,eAAe,CAAA;QAC9C,CAAC;QACD,WAAW;YACT,WAAW,CACT,IAAI,EACJ,OAAO,CAAC,GAAG,EAAE;gBACX,MAAM,IAAI,GAAG,iBAAiB,CAAC,IAAI,CAA0B,CAAA;gBAC7D,IAAI,CAAA,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,KAAI,CAAC,EAAE;oBACtB,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,CAAA;iBACnB;qBAAM;oBACL,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;oBAC1D,MAAM,EAAE,GAAG,WAAW,IAAI,eAAe,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAClD,MAAM,EAAE,GAAG,WAAW,IAAI,eAAe,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAClD,MAAM,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;oBACjB,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC9B,MAAM,CAAC,GAAG,WAAW,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC9B,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAA;iBAC1B;YACH,CAAC,CAAC,CACH,CAAA;QACH,CAAC;KACF,CAAC,CAAC;SACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACd;;WAEG;QACH,cAAc;YACZ,OAAO;gBACL;oBACE,KAAK,EAAE,cAAc;oBACrB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,WAAW;oBACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,EAAE;iBACxC;gBACD;oBACE,KAAK,EAAE,cAAc;oBACrB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,WAAW;oBACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,iBAAiB,EAAE;iBACxC;gBACD;oBACE,KAAK,EAAE,kBAAkB;oBACzB,IAAI,EAAE,UAAU;oBAChB,OAAO,EAAE,IAAI,CAAC,eAAe;oBAC7B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,qBAAqB,EAAE;iBAC5C;aACF,CAAA;QACH,CAAC;KACF,CAAC,CAAC,CAAA;AACP,CAAC"}
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/plugin-sequence",
3
- "version": "2.3.3",
3
+ "version": "2.4.0",
4
4
  "description": "JBrowse 2 sequence adapters, tracks, etc.",
5
5
  "keywords": [
6
6
  "jbrowse",
@@ -58,5 +58,5 @@
58
58
  "distModule": "esm/index.js",
59
59
  "srcModule": "src/index.ts",
60
60
  "module": "esm/index.js",
61
- "gitHead": "283e0387ccd5acc9f092cf00804d1fcac212e68d"
61
+ "gitHead": "78707a2bc3ba8489f26a590ef83f62ede945d048"
62
62
  }
package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts CHANGED
@@ -54,7 +54,7 @@ export default class extends BaseSequenceAdapter {
54
54
  const loc = this.getConf('metadataLocation')
55
55
  return loc.uri === '' || loc.uri === '/path/to/fa.metadata.yaml'
56
56
  ? null
57
- : openLocation(loc).readFile('utf8')
57
+ : openLocation(loc, this.pluginManager).readFile('utf8')
58
58
  }
59
59
 
60
60
  public async setup() {
package/src/LinearReferenceSequenceDisplay/model.ts CHANGED
@@ -96,14 +96,21 @@ export function modelFactory(configSchema: AnyConfigurationSchemaType) {
96
96
  self.showTranslation = !self.showTranslation
97
97
  },
98
98
  afterAttach() {
99
- // auto-adjust height depending on settings
100
99
  addDisposer(
101
100
  self,
102
101
  autorun(() => {
103
- const t = self.showTranslation ? 100 : 0
104
- const r = self.showReverse ? 20 : 0
105
- const s = self.showForward ? 20 : 0
106
- self.setHeight(t + r + s)
102
+ const view = getContainingView(self) as LinearGenomeViewModel
103
+ if (view?.bpPerPx >= 1) {
104
+ self.setHeight(50)
105
+ } else {
106
+ const { showTranslation, showReverse, showForward } = self
107
+ const r1 = showReverse && showTranslation ? 60 : 0
108
+ const r2 = showForward && showTranslation ? 60 : 0
109
+ const t = r1 + r2
110
+ const r = showReverse ? 20 : 0
111
+ const s = showForward ? 20 : 0
112
+ self.setHeight(t + r + s)
113
+ }
107
114
  }),
108
115
  )
109
116
  },