@jbrowse/plugin-alignments 2.11.0 → 2.11.1

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -11,6 +11,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
@@ -36,6 +47,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "BaseFeatureWidget";
@@ -45,6 +67,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/dist/BamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function BamAdapterF(pluginManager: PluginManager): void;

package/dist/BamAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function BamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'BamAdapter',
@@ -37,4 +37,5 @@ exports.default = (pluginManager) => {
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./BamAdapter'))).then(r => r.default),
         });
     });
-};
+}
+exports.default = BamAdapterF;

package/dist/CramAdapter/CramTestAdapters.js

@@ -64,6 +64,7 @@ class SequenceAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 .then(ret => {
                 observer.next(new simpleFeature_1.default({
                     uniqueId: `${refName}-${start}-${end}`,
+                    refName,
                     seq: ret,
                     start,
                     end,

package/dist/CramAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function CramAdapterF(pluginManager: PluginManager): void;

package/dist/CramAdapter/index.js

@@ -29,7 +29,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 // locals
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function CramAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'CramAdapter',
@@ -38,4 +38,5 @@ exports.default = (pluginManager) => {
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./CramAdapter'))).then(r => r.default),
         });
     });
-};
+}
+exports.default = CramAdapterF;

package/dist/GuessAlignmentsTypes/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function GuessAlignmentsTypesF(pluginManager: PluginManager): void;

package/dist/GuessAlignmentsTypes/index.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const tracks_1 = require("@jbrowse/core/util/tracks");
-exports.default = (pluginManager) => {
+function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.cram$/i;
@@ -52,4 +52,5 @@ exports.default = (pluginManager) => {
             return trackTypeGuesser(adapterName);
         };
     });
-};
+}
+exports.default = GuessAlignmentsTypesF;

package/dist/HtsgetBamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function HtsgetBamAdapterF(pluginManager: PluginManager): void;

package/dist/HtsgetBamAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const configSchema_1 = __importDefault(require("./configSchema"));
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-exports.default = (pluginManager) => {
+function HtsgetBamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'HtsgetBamAdapter',
@@ -40,4 +40,5 @@ exports.default = (pluginManager) => {
             getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./HtsgetBamAdapter'))).then(r => r.default),
         });
     });
-};
+}
+exports.default = HtsgetBamAdapterF;

package/dist/LinearAlignmentsDisplay/index.d.ts

@@ -1,2 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pluginManager: PluginManager): void;
+export default function LinearAlignmentsDisplayF(pluginManager: PluginManager): void;

package/dist/LinearAlignmentsDisplay/index.js

@@ -8,7 +8,7 @@ const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTyp
 const configSchema_1 = __importDefault(require("./models/configSchema"));
 const model_1 = __importDefault(require("./models/model"));
 const AlignmentsDisplay_1 = __importDefault(require("./components/AlignmentsDisplay"));
-function default_1(pluginManager) {
+function LinearAlignmentsDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
@@ -22,4 +22,4 @@ function default_1(pluginManager) {
         });
     });
 }
-exports.default = default_1;
+exports.default = LinearAlignmentsDisplayF;

package/dist/PileupRPC/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function PileupRPCMethodsF(pm: PluginManager): void;

package/dist/PileupRPC/index.js

@@ -1,8 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 const rpcMethods_1 = require("./rpcMethods");
-exports.default = (pm) => {
+function PileupRPCMethodsF(pm) {
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetGlobalValueForTag(pm));
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetVisibleModifications(pm));
     pm.addRpcMethod(() => new rpcMethods_1.PileupGetReducedFeatures(pm));
-};
+}
+exports.default = PileupRPCMethodsF;

package/dist/SNPCoverageAdapter/index.d.ts

@@ -1,2 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pluginManager: PluginManager): void;
+export default function SNPCoverageAdapterF(pluginManager: PluginManager): void;

package/dist/SNPCoverageAdapter/index.js

@@ -28,7 +28,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-function default_1(pluginManager) {
+function SNPCoverageAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType_1.default({
             name: 'SNPCoverageAdapter',
@@ -41,4 +41,4 @@ function default_1(pluginManager) {
         });
     });
 }
-exports.default = default_1;
+exports.default = SNPCoverageAdapterF;

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -11,6 +11,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
@@ -36,6 +47,17 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+        intronBp: number;
+        upDownBp: number;
+        upperCaseCDS: boolean;
+    } & {
+        setUpDownBp(f: number): void;
+        setIntronBp(f: number): void;
+        setUpperCaseCDS(f: boolean): void;
+    } & {
+        afterAttach(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     id: string;
     type: "BaseFeatureWidget";
@@ -45,6 +67,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: string | undefined;
     maxDepth: number | undefined;
     formattedFields: any;
+    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/esm/BamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function BamAdapterF(pluginManager: PluginManager): void;

package/esm/BamAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function BamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'BamAdapter',
@@ -9,4 +9,4 @@ export default (pluginManager) => {
             getAdapterClass: () => import('./BamAdapter').then(r => r.default),
         });
     });
-};
+}

package/esm/CramAdapter/CramTestAdapters.js

@@ -56,6 +56,7 @@ export class SequenceAdapter extends BaseFeatureDataAdapter {
                 .then(ret => {
                 observer.next(new SimpleFeature({
                     uniqueId: `${refName}-${start}-${end}`,
+                    refName,
                     seq: ret,
                     start,
                     end,

package/esm/CramAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function CramAdapterF(pluginManager: PluginManager): void;

package/esm/CramAdapter/index.js

@@ -1,7 +1,7 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 // locals
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function CramAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'CramAdapter',
@@ -10,4 +10,4 @@ export default (pluginManager) => {
             getAdapterClass: () => import('./CramAdapter').then(r => r.default),
         });
     });
-};
+}

package/esm/GuessAlignmentsTypes/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function GuessAlignmentsTypesF(pluginManager: PluginManager): void;

package/esm/GuessAlignmentsTypes/index.js

@@ -1,5 +1,5 @@
 import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
-export default (pluginManager) => {
+export default function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
             const regexGuess = /\.cram$/i;
@@ -50,4 +50,4 @@ export default (pluginManager) => {
             return trackTypeGuesser(adapterName);
         };
     });
-};
+}

package/esm/HtsgetBamAdapter/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function HtsgetBamAdapterF(pluginManager: PluginManager): void;

package/esm/HtsgetBamAdapter/index.js

@@ -1,6 +1,6 @@
 import configSchema from './configSchema';
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
-export default (pluginManager) => {
+export default function HtsgetBamAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'HtsgetBamAdapter',
@@ -12,4 +12,4 @@ export default (pluginManager) => {
             getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default),
         });
     });
-};
+}

package/esm/LinearAlignmentsDisplay/index.d.ts

@@ -1,2 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pluginManager: PluginManager): void;
+export default function LinearAlignmentsDisplayF(pluginManager: PluginManager): void;

package/esm/LinearAlignmentsDisplay/index.js

@@ -3,7 +3,7 @@ import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType';
 import configSchemaFactory from './models/configSchema';
 import modelFactory from './models/model';
 import ReactComponent from './components/AlignmentsDisplay';
-export default function (pluginManager) {
+export default function LinearAlignmentsDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({

package/esm/PileupRPC/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function PileupRPCMethodsF(pm: PluginManager): void;

package/esm/PileupRPC/index.js

@@ -1,6 +1,6 @@
 import { PileupGetGlobalValueForTag, PileupGetVisibleModifications, PileupGetReducedFeatures, } from './rpcMethods';
-export default (pm) => {
+export default function PileupRPCMethodsF(pm) {
     pm.addRpcMethod(() => new PileupGetGlobalValueForTag(pm));
     pm.addRpcMethod(() => new PileupGetVisibleModifications(pm));
     pm.addRpcMethod(() => new PileupGetReducedFeatures(pm));
-};
+}

package/esm/SNPCoverageAdapter/index.d.ts

@@ -1,2 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-export default function (pluginManager: PluginManager): void;
+export default function SNPCoverageAdapterF(pluginManager: PluginManager): void;

package/esm/SNPCoverageAdapter/index.js

@@ -1,6 +1,6 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-export default function (pluginManager) {
+export default function SNPCoverageAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
             name: 'SNPCoverageAdapter',

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.11.0",
+  "version": "2.11.1",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
+  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
 }