@jbrowse/plugin-sequence 2.3.4 → 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.
- package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js +1 -1
- package/dist/IndexedFastaAdapter/IndexedFastaAdapter.js.map +1 -1
- package/dist/LinearReferenceSequenceDisplay/model.d.ts +62 -4
- package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js +1 -1
- package/esm/IndexedFastaAdapter/IndexedFastaAdapter.js.map +1 -1
- package/esm/LinearReferenceSequenceDisplay/model.d.ts +62 -4
- package/package.json +2 -2
- package/src/IndexedFastaAdapter/IndexedFastaAdapter.ts +1 -1
|
@@ -48,7 +48,7 @@ class default_1 extends BaseAdapter_1.BaseSequenceAdapter {
|
|
|
48
48
|
const loc = this.getConf('metadataLocation');
|
|
49
49
|
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) {
|
|
@@ -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;
|
|
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"}
|
|
@@ -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
|
-
|
|
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<{
|
|
@@ -132,6 +132,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
|
|
132
132
|
estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
|
|
133
133
|
estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
|
|
134
134
|
} & {
|
|
135
|
+
readonly height: any;
|
|
135
136
|
readonly blockType: "dynamicBlocks" | "staticBlocks";
|
|
136
137
|
readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
137
138
|
} & {
|
|
@@ -161,7 +162,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
|
|
161
162
|
setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
|
|
162
163
|
setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
|
|
163
164
|
clearRegionStats(): void;
|
|
164
|
-
setHeight(displayHeight: number):
|
|
165
|
+
setHeight(displayHeight: number): any;
|
|
165
166
|
resizeHeight(distance: number): number;
|
|
166
167
|
setScrollTop(scrollTop: number): void;
|
|
167
168
|
updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
|
|
@@ -194,6 +195,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
|
|
194
195
|
} & {
|
|
195
196
|
renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
|
|
196
197
|
overrideHeight: number;
|
|
198
|
+
theme: import("@mui/material").ThemeOptions;
|
|
197
199
|
}): Promise<JSX.Element>;
|
|
198
200
|
} & {
|
|
199
201
|
/**
|
|
@@ -233,11 +235,67 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
|
|
233
235
|
checked: boolean;
|
|
234
236
|
onClick: () => void;
|
|
235
237
|
}[];
|
|
236
|
-
},
|
|
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, {
|
|
237
295
|
type: string;
|
|
238
296
|
id: string;
|
|
239
|
-
height: number;
|
|
240
297
|
rpcDriverName: string | undefined;
|
|
298
|
+
heightPreConfig: number | undefined;
|
|
241
299
|
userBpPerPxLimit: number | undefined;
|
|
242
300
|
userByteSizeLimit: number | undefined;
|
|
243
301
|
} & import("mobx-state-tree")._NotCustomized>;
|
|
@@ -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) {
|
|
@@ -1 +1 @@
|
|
|
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,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;
|
|
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"}
|
|
@@ -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
|
-
|
|
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<{
|
|
@@ -132,6 +132,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
|
|
132
132
|
estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
|
|
133
133
|
estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
|
|
134
134
|
} & {
|
|
135
|
+
readonly height: any;
|
|
135
136
|
readonly blockType: "dynamicBlocks" | "staticBlocks";
|
|
136
137
|
readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
|
|
137
138
|
} & {
|
|
@@ -161,7 +162,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
|
|
161
162
|
setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
|
|
162
163
|
setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
|
|
163
164
|
clearRegionStats(): void;
|
|
164
|
-
setHeight(displayHeight: number):
|
|
165
|
+
setHeight(displayHeight: number): any;
|
|
165
166
|
resizeHeight(distance: number): number;
|
|
166
167
|
setScrollTop(scrollTop: number): void;
|
|
167
168
|
updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
|
|
@@ -194,6 +195,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
|
|
194
195
|
} & {
|
|
195
196
|
renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
|
|
196
197
|
overrideHeight: number;
|
|
198
|
+
theme: import("@mui/material").ThemeOptions;
|
|
197
199
|
}): Promise<JSX.Element>;
|
|
198
200
|
} & {
|
|
199
201
|
/**
|
|
@@ -233,11 +235,67 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
|
|
|
233
235
|
checked: boolean;
|
|
234
236
|
onClick: () => void;
|
|
235
237
|
}[];
|
|
236
|
-
},
|
|
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, {
|
|
237
295
|
type: string;
|
|
238
296
|
id: string;
|
|
239
|
-
height: number;
|
|
240
297
|
rpcDriverName: string | undefined;
|
|
298
|
+
heightPreConfig: number | undefined;
|
|
241
299
|
userBpPerPxLimit: number | undefined;
|
|
242
300
|
userByteSizeLimit: number | undefined;
|
|
243
301
|
} & import("mobx-state-tree")._NotCustomized>;
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-sequence",
|
|
3
|
-
"version": "2.
|
|
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": "
|
|
61
|
+
"gitHead": "78707a2bc3ba8489f26a590ef83f62ede945d048"
|
|
62
62
|
}
|
|
@@ -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() {
|