@apollo-annotation/shared 0.3.10 → 0.3.12

package/dist/Changes/UndoSplitExonChange.d.ts

@@ -1,6 +1,6 @@
 import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { SplitExonChange } from './SplitExonChange';
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { SplitExonChange } from './SplitExonChange.js';
 interface SerializedUndoSplitExonChangeBase extends SerializedFeatureChange {
     typeName: 'UndoSplitExonChange';
 }
@@ -30,3 +30,4 @@ export declare class UndoSplitExonChange extends FeatureChange {
     getInverse(): SplitExonChange;
 }
 export {};
+//# sourceMappingURL=UndoSplitExonChange.d.ts.map

package/dist/Changes/UndoSplitExonChange.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"UndoSplitExonChange.d.ts","sourceRoot":"","sources":["../../src/Changes/UndoSplitExonChange.ts"],"names":[],"mappings":"AAEA,OAAO,EACL,KAAK,aAAa,EAClB,KAAK,eAAe,EACpB,aAAa,EACb,KAAK,kBAAkB,EACvB,KAAK,uBAAuB,EAC5B,KAAK,eAAe,EACrB,MAAM,2BAA2B,CAAA;AAClC,OAAO,KAAK,EAAE,yBAAyB,EAAE,MAAM,wBAAwB,CAAA;AAGvE,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AAEtD,UAAU,iCAAkC,SAAQ,uBAAuB;IACzE,QAAQ,EAAE,qBAAqB,CAAA;CAChC;AAED,MAAM,WAAW,0BAA0B;IACzC,aAAa,EAAE,yBAAyB,CAAA;IACxC,eAAe,EAAE,MAAM,CAAA;IACvB,WAAW,EAAE,MAAM,EAAE,CAAA;IACrB,WAAW,EAAE,MAAM,CAAA;IACnB,aAAa,EAAE,MAAM,CAAA;IACrB,UAAU,EAAE,MAAM,CAAA;IAClB,WAAW,EAAE,MAAM,CAAA;CACpB;AAED,UAAU,mCACR,SAAQ,iCAAiC,EACvC,0BAA0B;CAAG;AAEjC,UAAU,qCACR,SAAQ,iCAAiC;IACzC,OAAO,EAAE,0BAA0B,EAAE,CAAA;CACtC;AAED,MAAM,MAAM,6BAA6B,GACrC,mCAAmC,GACnC,qCAAqC,CAAA;AACzC,qBAAa,mBAAoB,SAAQ,aAAa;IACpD,QAAQ,wBAAiC;IACzC,OAAO,EAAE,0BAA0B,EAAE,CAAA;gBAEzB,IAAI,EAAE,6BAA6B,EAAE,OAAO,CAAC,EAAE,aAAa;IAKxE,MAAM,IAAI,6BAA6B;IA+BjC,eAAe,CAAC,OAAO,EAAE,eAAe;IAsCxC,kBAAkB,CAAC,QAAQ,EAAE,kBAAkB;IAI/C,eAAe,CAAC,SAAS,EAAE,eAAe;IA0BhD,UAAU;CAwBX"}

package/dist/Changes/UndoSplitExonChange.js

@@ -1,11 +1,8 @@
-"use strict";
 /* eslint-disable @typescript-eslint/require-await */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.UndoSplitExonChange = void 0;
-const common_1 = require("@apollo-annotation/common");
-const DeleteFeatureChange_1 = require("./DeleteFeatureChange");
-const SplitExonChange_1 = require("./SplitExonChange");
-class UndoSplitExonChange extends common_1.FeatureChange {
+import { FeatureChange, } from '@apollo-annotation/common';
+import { findAndDeleteChildFeature } from './DeleteFeatureChange.js';
+import { SplitExonChange } from './SplitExonChange.js';
+export class UndoSplitExonChange extends FeatureChange {
     typeName = 'UndoSplitExonChange';
     changes;
     constructor(json, options) {
@@ -54,7 +51,7 @@ class UndoSplitExonChange extends common_1.FeatureChange {
             const childIds = this.getChildFeatureIds(exonToRestore);
             topLevelFeature.allIds.push(exonToRestore._id, ...childIds);
             topLevelFeature.allIds = topLevelFeature.allIds.filter((id) => !idsToDelete.includes(id));
-            idsToDelete.map((id) => (0, DeleteFeatureChange_1.findAndDeleteChildFeature)(topLevelFeature, id, this));
+            idsToDelete.map((id) => findAndDeleteChildFeature(topLevelFeature, id, this));
             await topLevelFeature.save();
         }
     }
@@ -99,7 +96,7 @@ class UndoSplitExonChange extends common_1.FeatureChange {
             leftExonId: undoSplitExonChange.leftExonId,
             rightExonId: undoSplitExonChange.rightExonId,
         }));
-        return new SplitExonChange_1.SplitExonChange({
+        return new SplitExonChange({
             changedIds: inverseChangedIds,
             typeName: 'SplitExonChange',
             changes: inverseChanges,
@@ -107,5 +104,4 @@ class UndoSplitExonChange extends common_1.FeatureChange {
         }, { logger });
     }
 }
-exports.UndoSplitExonChange = UndoSplitExonChange;
 //# sourceMappingURL=UndoSplitExonChange.js.map

package/dist/Changes/UndoSplitExonChange.js.map

@@ -1 +1 @@
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+{"version":3,"file":"UndoSplitExonChange.js","sourceRoot":"","sources":["../../src/Changes/UndoSplitExonChange.ts"],"names":[],"mappings":"AAAA,qDAAqD;AAErD,OAAO,EAGL,aAAa,GAId,MAAM,2BAA2B,CAAA;AAGlC,OAAO,EAAE,yBAAyB,EAAE,MAAM,0BAA0B,CAAA;AACpE,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AA4BtD,MAAM,OAAO,mBAAoB,SAAQ,aAAa;IACpD,QAAQ,GAAG,qBAA8B,CAAA;IACzC,OAAO,CAA8B;IAErC,YAAY,IAAmC,EAAE,OAAuB;QACtE,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAC1D,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,UAAU,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACxD,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,MAAM,CACJ,EACE,aAAa,EACb,eAAe,EACf,WAAW,EACX,WAAW,EACX,aAAa,EACb,UAAU,EACV,WAAW,GACZ,EACF,GAAG,OAAO,CAAA;YAEX,OAAO;gBACL,QAAQ;gBACR,UAAU;gBACV,QAAQ;gBACR,aAAa;gBACb,eAAe;gBACf,WAAW;gBACX,WAAW;gBACX,aAAa;gBACb,UAAU;gBACV,WAAW;aACZ,CAAA;QACH,CAAC;QACD,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAA;IACpD,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;QACzC,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;QACxB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,EAAE,aAAa,EAAE,eAAe,EAAE,WAAW,EAAE,GAAG,MAAM,CAAA;YAC9D,MAAM,eAAe,GAAG,MAAM,YAAY;iBACvC,OAAO,CAAC,EAAE,MAAM,EAAE,eAAe,EAAE,CAAC;iBACpC,OAAO,CAAC,OAAO,CAAC;iBAChB,IAAI,EAAE,CAAA;YACT,IAAI,CAAC,eAAe,EAAE,CAAC;gBACrB,MAAM,IAAI,KAAK,CAAC,mCAAmC,eAAe,GAAG,CAAC,CAAA;YACxE,CAAC;YACD,MAAM,aAAa,GAAG,IAAI,CAAC,gBAAgB,CACzC,eAAe,EACf,eAAe,CAChB,CAAA;YACD,IAAI,CAAC,aAAa,EAAE,CAAC;gBACnB,MAAM,IAAI,KAAK,CACb,mCAAmC,eAAe,iBAAiB,eAAe,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CACrG,CAAA;YACH,CAAC;YACD,IAAI,CAAC,aAAa,CAAC,QAAQ,EAAE,CAAC;gBAC5B,aAAa,CAAC,QAAQ,GAAG,IAAI,GAAG,EAAE,CAAA;YACpC,CAAC;YAED,IAAI,CAAC,QAAQ,CAAC,aAAa,EAAE,aAAa,CAAC,CAAA;YAC3C,MAAM,QAAQ,GAAG,IAAI,CAAC,kBAAkB,CAAC,aAAa,CAAC,CAAA;YACvD,eAAe,CAAC,MAAM,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,EAAE,GAAG,QAAQ,CAAC,CAAA;YAC3D,eAAe,CAAC,MAAM,GAAG,eAAe,CAAC,MAAM,CAAC,MAAM,CACpD,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,WAAW,CAAC,QAAQ,CAAC,EAAE,CAAC,CAClC,CAAA;YACD,WAAW,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CACrB,yBAAyB,CAAC,eAAe,EAAE,EAAE,EAAE,IAAI,CAAC,CACrD,CAAA;YACD,MAAM,eAAe,CAAC,IAAI,EAAE,CAAA;QAC9B,CAAC;IACH,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,QAA4B;QACnD,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,SAA0B;QAC9C,uEAAuE;QACvE,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;QAClC,CAAC;QACD,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;QACxB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,EAAE,aAAa,EAAE,eAAe,EAAE,WAAW,EAAE,GAAG,MAAM,CAAA;YAC9D,IAAI,CAAC,eAAe,EAAE,CAAC;gBACrB,MAAM,IAAI,KAAK,CAAC,sBAAsB,CAAC,CAAA;YACzC,CAAC;YACD,MAAM,aAAa,GAAG,SAAS,CAAC,UAAU,CAAC,eAAe,CAAC,CAAA;YAC3D,IAAI,CAAC,aAAa,EAAE,CAAC;gBACnB,MAAM,IAAI,KAAK,CAAC,kCAAkC,eAAe,GAAG,CAAC,CAAA;YACvE,CAAC;YACD,8DAA8D;YAC9D,IAAI,CAAC,aAAa,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;gBACzC,aAAa,CAAC,YAAY,CAAC,KAAK,EAAE,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAA;YACxD,CAAC;YACD,aAAa,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAA;YACrC,WAAW,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE;gBACrB,aAAa,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YAC/B,CAAC,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IAED,UAAU;QACR,MAAM,EAAE,QAAQ,EAAE,UAAU,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QACtD,MAAM,iBAAiB,GAAG,CAAC,GAAG,UAAU,CAAC,CAAC,OAAO,EAAE,CAAA;QACnD,MAAM,cAAc,GAAG,CAAC,GAAG,OAAO,CAAC;aAChC,OAAO,EAAE;aACT,GAAG,CAAC,CAAC,mBAAmB,EAAE,EAAE,CAAC,CAAC;YAC7B,eAAe,EAAE,mBAAmB,CAAC,eAAe;YACpD,aAAa,EAAE,mBAAmB,CAAC,aAAa;YAChD,WAAW,EAAE,mBAAmB,CAAC,WAAW;YAC5C,aAAa,EAAE,mBAAmB,CAAC,aAAa;YAChD,UAAU,EAAE,mBAAmB,CAAC,UAAU;YAC1C,WAAW,EAAE,mBAAmB,CAAC,WAAW;SAC7C,CAAC,CAAC,CAAA;QAEL,OAAO,IAAI,eAAe,CACxB;YACE,UAAU,EAAE,iBAAiB;YAC7B,QAAQ,EAAE,iBAAiB;YAC3B,OAAO,EAAE,cAAc;YACvB,QAAQ;SACT,EACD,EAAE,MAAM,EAAE,CACX,CAAA;IACH,CAAC;CACF"}

package/dist/Changes/UserChange.d.ts

@@ -23,3 +23,4 @@ export declare class UserChange extends Change {
     executeOnClient(_dataStore: ClientDataStore): Promise<void>;
     getInverse(): UserChange;
 }
+//# sourceMappingURL=UserChange.d.ts.map

package/dist/Changes/UserChange.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"UserChange.d.ts","sourceRoot":"","sources":["../../src/Changes/UserChange.ts"],"names":[],"mappings":"AACA,OAAO,EACL,MAAM,EACN,KAAK,aAAa,EAClB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,gBAAgB,EACrB,KAAK,eAAe,EACrB,MAAM,2BAA2B,CAAA;AAElC,MAAM,WAAW,wBAAyB,SAAQ,gBAAgB;IAChE,QAAQ,EAAE,YAAY,CAAA;IACtB,MAAM,EAAE,MAAM,CAAA;CACf;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,OAAO,GAAG,MAAM,GAAG,UAAU,CAAA;CACpC;AAED,MAAM,WAAW,0BACf,SAAQ,wBAAwB,EAC9B,iBAAiB;CAAG;AAExB,MAAM,WAAW,4BAA6B,SAAQ,wBAAwB;IAC5E,OAAO,EAAE,iBAAiB,EAAE,CAAA;CAC7B;AAED,MAAM,MAAM,oBAAoB,GAC5B,0BAA0B,GAC1B,4BAA4B,CAAA;AAEhC,qBAAa,UAAW,SAAQ,MAAM;IACpC,QAAQ,eAAwB;IAChC,OAAO,EAAE,iBAAiB,EAAE,CAAA;IAC5B,MAAM,EAAE,MAAM,CAAA;gBAEF,IAAI,EAAE,oBAAoB,EAAE,OAAO,CAAC,EAAE,aAAa;IAM/D,MAAM,IAAI,oBAAoB;IASxB,eAAe,CAAC,OAAO,EAAE,eAAe;IAmBxC,kBAAkB,CAAC,QAAQ,EAAE,kBAAkB;IAK/C,eAAe,CAAC,UAAU,EAAE,eAAe;IAEjD,UAAU;CAIX"}

package/dist/Changes/UserChange.js

@@ -1,9 +1,6 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.UserChange = void 0;
 /* eslint-disable @typescript-eslint/require-await */
-const common_1 = require("@apollo-annotation/common");
-class UserChange extends common_1.Change {
+import { Change, } from '@apollo-annotation/common';
+export class UserChange extends Change {
     typeName = 'UserChange';
     changes;
     userId;
@@ -47,5 +44,4 @@ class UserChange extends common_1.Change {
         return new UserChange({ typeName, changes, userId }, { logger });
     }
 }
-exports.UserChange = UserChange;
 //# sourceMappingURL=UserChange.js.map

package/dist/Changes/UserChange.js.map

@@ -1 +1 @@
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package/dist/Changes/index.d.ts

@@ -1,26 +1,26 @@
-import { AddAssemblyAliasesChange } from './AddAssemblyAliasesChange';
-import { AddAssemblyAndFeaturesFromFileChange } from './AddAssemblyAndFeaturesFromFileChange';
-import { AddAssemblyFromExternalChange } from './AddAssemblyFromExternalChange';
-import { AddAssemblyFromFileChange } from './AddAssemblyFromFileChange';
-import { AddFeatureChange } from './AddFeatureChange';
-import { AddFeaturesFromFileChange } from './AddFeaturesFromFileChange';
-import { AddRefSeqAliasesChange } from './AddRefSeqAliasesChange';
-import { DeleteAssemblyChange } from './DeleteAssemblyChange';
-import { DeleteFeatureChange } from './DeleteFeatureChange';
-import { DeleteUserChange } from './DeleteUserChange';
-import { FeatureAttributeChange } from './FeatureAttributeChange';
-import { ImportJBrowseConfigChange } from './ImportJBrowseConfigChange';
-import { LocationEndChange } from './LocationEndChange';
-import { LocationStartChange } from './LocationStartChange';
-import { MergeExonsChange } from './MergeExonsChange';
-import { MergeTranscriptsChange } from './MergeTranscriptsChange';
-import { SplitExonChange } from './SplitExonChange';
-import { StrandChange } from './StrandChange';
-import { TypeChange } from './TypeChange';
-import { UndoMergeExonsChange } from './UndoMergeExonsChange';
-import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange';
-import { UndoSplitExonChange } from './UndoSplitExonChange';
-import { UserChange } from './UserChange';
+import { AddAssemblyAliasesChange } from './AddAssemblyAliasesChange.js';
+import { AddAssemblyAndFeaturesFromFileChange } from './AddAssemblyAndFeaturesFromFileChange.js';
+import { AddAssemblyFromExternalChange } from './AddAssemblyFromExternalChange.js';
+import { AddAssemblyFromFileChange } from './AddAssemblyFromFileChange.js';
+import { AddFeatureChange } from './AddFeatureChange.js';
+import { AddFeaturesFromFileChange } from './AddFeaturesFromFileChange.js';
+import { AddRefSeqAliasesChange } from './AddRefSeqAliasesChange.js';
+import { DeleteAssemblyChange } from './DeleteAssemblyChange.js';
+import { DeleteFeatureChange } from './DeleteFeatureChange.js';
+import { DeleteUserChange } from './DeleteUserChange.js';
+import { FeatureAttributeChange } from './FeatureAttributeChange.js';
+import { ImportJBrowseConfigChange } from './ImportJBrowseConfigChange.js';
+import { LocationEndChange } from './LocationEndChange.js';
+import { LocationStartChange } from './LocationStartChange.js';
+import { MergeExonsChange } from './MergeExonsChange.js';
+import { MergeTranscriptsChange } from './MergeTranscriptsChange.js';
+import { SplitExonChange } from './SplitExonChange.js';
+import { StrandChange } from './StrandChange.js';
+import { TypeChange } from './TypeChange.js';
+import { UndoMergeExonsChange } from './UndoMergeExonsChange.js';
+import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange.js';
+import { UndoSplitExonChange } from './UndoSplitExonChange.js';
+import { UserChange } from './UserChange.js';
 export declare const changes: {
     AddAssemblyAndFeaturesFromFileChange: typeof AddAssemblyAndFeaturesFromFileChange;
     AddAssemblyFromFileChange: typeof AddAssemblyFromFileChange;
@@ -46,26 +46,27 @@ export declare const changes: {
     AddRefSeqAliasesChange: typeof AddRefSeqAliasesChange;
     AddAssemblyAliasesChange: typeof AddAssemblyAliasesChange;
 };
-export * from './AddAssemblyAndFeaturesFromFileChange';
-export * from './AddAssemblyFromFileChange';
-export * from './AddAssemblyFromExternalChange';
-export * from './AddFeatureChange';
-export * from './AddFeaturesFromFileChange';
-export * from './DeleteAssemblyChange';
-export * from './DeleteFeatureChange';
-export * from './DeleteUserChange';
-export * from './FeatureAttributeChange';
-export * from './ImportJBrowseConfigChange';
-export * from './LocationEndChange';
-export * from './LocationStartChange';
-export * from './MergeExonsChange';
-export * from './SplitExonChange';
-export * from './MergeTranscriptsChange';
-export * from './UndoMergeExonsChange';
-export * from './UndoSplitExonChange';
-export * from './UndoMergeTranscriptsChange';
-export * from './StrandChange';
-export * from './TypeChange';
-export * from './UserChange';
-export * from './AddRefSeqAliasesChange';
-export * from './AddAssemblyAliasesChange';
+export * from './AddAssemblyAndFeaturesFromFileChange.js';
+export * from './AddAssemblyFromFileChange.js';
+export * from './AddAssemblyFromExternalChange.js';
+export * from './AddFeatureChange.js';
+export * from './AddFeaturesFromFileChange.js';
+export * from './DeleteAssemblyChange.js';
+export * from './DeleteFeatureChange.js';
+export * from './DeleteUserChange.js';
+export * from './FeatureAttributeChange.js';
+export * from './ImportJBrowseConfigChange.js';
+export * from './LocationEndChange.js';
+export * from './LocationStartChange.js';
+export * from './MergeExonsChange.js';
+export * from './SplitExonChange.js';
+export * from './MergeTranscriptsChange.js';
+export * from './UndoMergeExonsChange.js';
+export * from './UndoSplitExonChange.js';
+export * from './UndoMergeTranscriptsChange.js';
+export * from './StrandChange.js';
+export * from './TypeChange.js';
+export * from './UserChange.js';
+export * from './AddRefSeqAliasesChange.js';
+export * from './AddAssemblyAliasesChange.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/Changes/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/Changes/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,wBAAwB,EAAE,MAAM,+BAA+B,CAAA;AACxE,OAAO,EAAE,oCAAoC,EAAE,MAAM,2CAA2C,CAAA;AAChG,OAAO,EAAE,6BAA6B,EAAE,MAAM,oCAAoC,CAAA;AAClF,OAAO,EAAE,yBAAyB,EAAE,MAAM,gCAAgC,CAAA;AAC1E,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,yBAAyB,EAAE,MAAM,gCAAgC,CAAA;AAC1E,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAA;AACpE,OAAO,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAA;AAChE,OAAO,EAAE,mBAAmB,EAAE,MAAM,0BAA0B,CAAA;AAC9D,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAA;AACpE,OAAO,EAAE,yBAAyB,EAAE,MAAM,gCAAgC,CAAA;AAC1E,OAAO,EAAE,iBAAiB,EAAE,MAAM,wBAAwB,CAAA;AAC1D,OAAO,EAAE,mBAAmB,EAAE,MAAM,0BAA0B,CAAA;AAC9D,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAA;AACxD,OAAO,EAAE,sBAAsB,EAAE,MAAM,6BAA6B,CAAA;AACpE,OAAO,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AACtD,OAAO,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAA;AAChD,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAA;AAC5C,OAAO,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAA;AAChE,OAAO,EAAE,0BAA0B,EAAE,MAAM,iCAAiC,CAAA;AAC5E,OAAO,EAAE,mBAAmB,EAAE,MAAM,0BAA0B,CAAA;AAC9D,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAA;AAE5C,eAAO,MAAM,OAAO;;;;;;;;;;;;;;;;;;;;;;;;CAwBnB,CAAA;AAED,cAAc,2CAA2C,CAAA;AACzD,cAAc,gCAAgC,CAAA;AAC9C,cAAc,oCAAoC,CAAA;AAClD,cAAc,uBAAuB,CAAA;AACrC,cAAc,gCAAgC,CAAA;AAC9C,cAAc,2BAA2B,CAAA;AACzC,cAAc,0BAA0B,CAAA;AACxC,cAAc,uBAAuB,CAAA;AACrC,cAAc,6BAA6B,CAAA;AAC3C,cAAc,gCAAgC,CAAA;AAC9C,cAAc,wBAAwB,CAAA;AACtC,cAAc,0BAA0B,CAAA;AACxC,cAAc,uBAAuB,CAAA;AACrC,cAAc,sBAAsB,CAAA;AACpC,cAAc,6BAA6B,CAAA;AAC3C,cAAc,2BAA2B,CAAA;AACzC,cAAc,0BAA0B,CAAA;AACxC,cAAc,iCAAiC,CAAA;AAC/C,cAAc,mBAAmB,CAAA;AACjC,cAAc,iBAAiB,CAAA;AAC/B,cAAc,iBAAiB,CAAA;AAC/B,cAAc,6BAA6B,CAAA;AAC3C,cAAc,+BAA+B,CAAA"}

package/dist/Changes/index.js

@@ -1,76 +1,72 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.changes = void 0;
-const tslib_1 = require("tslib");
-const AddAssemblyAliasesChange_1 = require("./AddAssemblyAliasesChange");
-const AddAssemblyAndFeaturesFromFileChange_1 = require("./AddAssemblyAndFeaturesFromFileChange");
-const AddAssemblyFromExternalChange_1 = require("./AddAssemblyFromExternalChange");
-const AddAssemblyFromFileChange_1 = require("./AddAssemblyFromFileChange");
-const AddFeatureChange_1 = require("./AddFeatureChange");
-const AddFeaturesFromFileChange_1 = require("./AddFeaturesFromFileChange");
-const AddRefSeqAliasesChange_1 = require("./AddRefSeqAliasesChange");
-const DeleteAssemblyChange_1 = require("./DeleteAssemblyChange");
-const DeleteFeatureChange_1 = require("./DeleteFeatureChange");
-const DeleteUserChange_1 = require("./DeleteUserChange");
-const FeatureAttributeChange_1 = require("./FeatureAttributeChange");
-const ImportJBrowseConfigChange_1 = require("./ImportJBrowseConfigChange");
-const LocationEndChange_1 = require("./LocationEndChange");
-const LocationStartChange_1 = require("./LocationStartChange");
-const MergeExonsChange_1 = require("./MergeExonsChange");
-const MergeTranscriptsChange_1 = require("./MergeTranscriptsChange");
-const SplitExonChange_1 = require("./SplitExonChange");
-const StrandChange_1 = require("./StrandChange");
-const TypeChange_1 = require("./TypeChange");
-const UndoMergeExonsChange_1 = require("./UndoMergeExonsChange");
-const UndoMergeTranscriptsChange_1 = require("./UndoMergeTranscriptsChange");
-const UndoSplitExonChange_1 = require("./UndoSplitExonChange");
-const UserChange_1 = require("./UserChange");
-exports.changes = {
-    AddAssemblyAndFeaturesFromFileChange: AddAssemblyAndFeaturesFromFileChange_1.AddAssemblyAndFeaturesFromFileChange,
-    AddAssemblyFromFileChange: AddAssemblyFromFileChange_1.AddAssemblyFromFileChange,
-    AddAssemblyFromExternalChange: AddAssemblyFromExternalChange_1.AddAssemblyFromExternalChange,
-    AddFeatureChange: AddFeatureChange_1.AddFeatureChange,
-    AddFeaturesFromFileChange: AddFeaturesFromFileChange_1.AddFeaturesFromFileChange,
-    DeleteAssemblyChange: DeleteAssemblyChange_1.DeleteAssemblyChange,
-    DeleteFeatureChange: DeleteFeatureChange_1.DeleteFeatureChange,
-    DeleteUserChange: DeleteUserChange_1.DeleteUserChange,
-    FeatureAttributeChange: FeatureAttributeChange_1.FeatureAttributeChange,
-    ImportJBrowseConfigChange: ImportJBrowseConfigChange_1.ImportJBrowseConfigChange,
-    LocationEndChange: LocationEndChange_1.LocationEndChange,
-    LocationStartChange: LocationStartChange_1.LocationStartChange,
-    MergeExonsChange: MergeExonsChange_1.MergeExonsChange,
-    SplitExonChange: SplitExonChange_1.SplitExonChange,
-    MergeTranscriptsChange: MergeTranscriptsChange_1.MergeTranscriptsChange,
-    UndoMergeExonsChange: UndoMergeExonsChange_1.UndoMergeExonsChange,
-    UndoSplitExonChange: UndoSplitExonChange_1.UndoSplitExonChange,
-    UndoMergeTranscriptsChange: UndoMergeTranscriptsChange_1.UndoMergeTranscriptsChange,
-    StrandChange: StrandChange_1.StrandChange,
-    TypeChange: TypeChange_1.TypeChange,
-    UserChange: UserChange_1.UserChange,
-    AddRefSeqAliasesChange: AddRefSeqAliasesChange_1.AddRefSeqAliasesChange,
-    AddAssemblyAliasesChange: AddAssemblyAliasesChange_1.AddAssemblyAliasesChange,
+import { AddAssemblyAliasesChange } from './AddAssemblyAliasesChange.js';
+import { AddAssemblyAndFeaturesFromFileChange } from './AddAssemblyAndFeaturesFromFileChange.js';
+import { AddAssemblyFromExternalChange } from './AddAssemblyFromExternalChange.js';
+import { AddAssemblyFromFileChange } from './AddAssemblyFromFileChange.js';
+import { AddFeatureChange } from './AddFeatureChange.js';
+import { AddFeaturesFromFileChange } from './AddFeaturesFromFileChange.js';
+import { AddRefSeqAliasesChange } from './AddRefSeqAliasesChange.js';
+import { DeleteAssemblyChange } from './DeleteAssemblyChange.js';
+import { DeleteFeatureChange } from './DeleteFeatureChange.js';
+import { DeleteUserChange } from './DeleteUserChange.js';
+import { FeatureAttributeChange } from './FeatureAttributeChange.js';
+import { ImportJBrowseConfigChange } from './ImportJBrowseConfigChange.js';
+import { LocationEndChange } from './LocationEndChange.js';
+import { LocationStartChange } from './LocationStartChange.js';
+import { MergeExonsChange } from './MergeExonsChange.js';
+import { MergeTranscriptsChange } from './MergeTranscriptsChange.js';
+import { SplitExonChange } from './SplitExonChange.js';
+import { StrandChange } from './StrandChange.js';
+import { TypeChange } from './TypeChange.js';
+import { UndoMergeExonsChange } from './UndoMergeExonsChange.js';
+import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange.js';
+import { UndoSplitExonChange } from './UndoSplitExonChange.js';
+import { UserChange } from './UserChange.js';
+export const changes = {
+    AddAssemblyAndFeaturesFromFileChange,
+    AddAssemblyFromFileChange,
+    AddAssemblyFromExternalChange,
+    AddFeatureChange,
+    AddFeaturesFromFileChange,
+    DeleteAssemblyChange,
+    DeleteFeatureChange,
+    DeleteUserChange,
+    FeatureAttributeChange,
+    ImportJBrowseConfigChange,
+    LocationEndChange,
+    LocationStartChange,
+    MergeExonsChange,
+    SplitExonChange,
+    MergeTranscriptsChange,
+    UndoMergeExonsChange,
+    UndoSplitExonChange,
+    UndoMergeTranscriptsChange,
+    StrandChange,
+    TypeChange,
+    UserChange,
+    AddRefSeqAliasesChange,
+    AddAssemblyAliasesChange,
 };
-tslib_1.__exportStar(require("./AddAssemblyAndFeaturesFromFileChange"), exports);
-tslib_1.__exportStar(require("./AddAssemblyFromFileChange"), exports);
-tslib_1.__exportStar(require("./AddAssemblyFromExternalChange"), exports);
-tslib_1.__exportStar(require("./AddFeatureChange"), exports);
-tslib_1.__exportStar(require("./AddFeaturesFromFileChange"), exports);
-tslib_1.__exportStar(require("./DeleteAssemblyChange"), exports);
-tslib_1.__exportStar(require("./DeleteFeatureChange"), exports);
-tslib_1.__exportStar(require("./DeleteUserChange"), exports);
-tslib_1.__exportStar(require("./FeatureAttributeChange"), exports);
-tslib_1.__exportStar(require("./ImportJBrowseConfigChange"), exports);
-tslib_1.__exportStar(require("./LocationEndChange"), exports);
-tslib_1.__exportStar(require("./LocationStartChange"), exports);
-tslib_1.__exportStar(require("./MergeExonsChange"), exports);
-tslib_1.__exportStar(require("./SplitExonChange"), exports);
-tslib_1.__exportStar(require("./MergeTranscriptsChange"), exports);
-tslib_1.__exportStar(require("./UndoMergeExonsChange"), exports);
-tslib_1.__exportStar(require("./UndoSplitExonChange"), exports);
-tslib_1.__exportStar(require("./UndoMergeTranscriptsChange"), exports);
-tslib_1.__exportStar(require("./StrandChange"), exports);
-tslib_1.__exportStar(require("./TypeChange"), exports);
-tslib_1.__exportStar(require("./UserChange"), exports);
-tslib_1.__exportStar(require("./AddRefSeqAliasesChange"), exports);
-tslib_1.__exportStar(require("./AddAssemblyAliasesChange"), exports);
+export * from './AddAssemblyAndFeaturesFromFileChange.js';
+export * from './AddAssemblyFromFileChange.js';
+export * from './AddAssemblyFromExternalChange.js';
+export * from './AddFeatureChange.js';
+export * from './AddFeaturesFromFileChange.js';
+export * from './DeleteAssemblyChange.js';
+export * from './DeleteFeatureChange.js';
+export * from './DeleteUserChange.js';
+export * from './FeatureAttributeChange.js';
+export * from './ImportJBrowseConfigChange.js';
+export * from './LocationEndChange.js';
+export * from './LocationStartChange.js';
+export * from './MergeExonsChange.js';
+export * from './SplitExonChange.js';
+export * from './MergeTranscriptsChange.js';
+export * from './UndoMergeExonsChange.js';
+export * from './UndoSplitExonChange.js';
+export * from './UndoMergeTranscriptsChange.js';
+export * from './StrandChange.js';
+export * from './TypeChange.js';
+export * from './UserChange.js';
+export * from './AddRefSeqAliasesChange.js';
+export * from './AddAssemblyAliasesChange.js';
 //# sourceMappingURL=index.js.map

package/dist/Changes/index.js.map

@@ -1 +1 @@
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package/dist/Checks/CDSCheck.d.ts

@@ -1,5 +1,5 @@
 import { Check } from '@apollo-annotation/common';
-import { type AnnotationFeatureSnapshot, type CheckResultSnapshot } from '@apollo-annotation/mst';
+import type { AnnotationFeatureSnapshot, CheckResultSnapshot } from '@apollo-annotation/mst';
 export declare class CDSCheck extends Check {
     name: string;
     causes: string[];
@@ -7,3 +7,4 @@ export declare class CDSCheck extends Check {
     isDefault: boolean;
     checkFeature(feature: AnnotationFeatureSnapshot, getSequence: (start: number, end: number) => Promise<string>): Promise<CheckResultSnapshot[]>;
 }
+//# sourceMappingURL=CDSCheck.d.ts.map

package/dist/Checks/CDSCheck.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"CDSCheck.d.ts","sourceRoot":"","sources":["../../src/Checks/CDSCheck.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,2BAA2B,CAAA;AACjD,OAAO,KAAK,EACV,yBAAyB,EACzB,mBAAmB,EACpB,MAAM,wBAAwB,CAAA;AAuR/B,qBAAa,QAAS,SAAQ,KAAK;IACjC,IAAI,SAAa;IACjB,MAAM,WAAc;IACpB,OAAO,SAAI;IACX,SAAS,UAAO;IAEV,YAAY,CAChB,OAAO,EAAE,yBAAyB,EAClC,WAAW,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,GAC3D,OAAO,CAAC,mBAAmB,EAAE,CAAC;CAelC"}

package/dist/Checks/CDSCheck.js

@@ -1,11 +1,7 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.CDSCheck = void 0;
-const tslib_1 = require("tslib");
-const common_1 = require("@apollo-annotation/common");
-const util_1 = require("@jbrowse/core/util");
-const bson_objectid_1 = tslib_1.__importDefault(require("bson-objectid"));
-const util_2 = require("./util");
+import { Check } from '@apollo-annotation/common';
+import { intersection2 } from '@jbrowse/core/util';
+import ObjectID from 'bson-objectid';
+import { getPrintableId } from './util.js';
 var STOP_CODONS;
 (function (STOP_CODONS) {
     STOP_CODONS[STOP_CODONS["TAG"] = 0] = "TAG";
@@ -79,13 +75,9 @@ function cmp(pos, max, strand) {
 }
 function getOriginalCodonLocation(cdsLocation, strand, index) {
     // Index 0 is the start codon, so reverse the CDS locations if strand is -1
-    const sortedLocation = structuredClone(cdsLocation);
-    if (strand === -1) {
-        sortedLocation.sort((a, b) => (a.min < b.min ? 1 : -1));
-    }
-    else {
-        sortedLocation.sort((a, b) => (a.min < b.min ? -1 : 1));
-    }
+    const sortedLocation = strand === -1
+        ? cdsLocation.toSorted((a, b) => (a.min < b.min ? 1 : -1))
+        : cdsLocation.toSorted((a, b) => (a.min < b.min ? -1 : 1));
     let i = 0;
     let currentStart = undefined;
     let currentEnd = undefined;
@@ -137,40 +129,40 @@ async function checkMRNA(feature, getSequence) {
                     : cdsLocation.at(0)?.min ?? min;
                 cdsStart = strand === -1 ? cdsStart - 3 : cdsStart;
                 checkResults.push({
-                    _id: new bson_objectid_1.default().toHexString(),
+                    _id: new ObjectID().toHexString(),
                     name: CHECK_NAME,
                     cause: CAUSES[CAUSES.MissingStartCodon],
                     ids,
                     refSeq: refSeq.toString(),
                     start: cdsStart,
                     end: cdsStart,
-                    message: `Unexpected start codon "${start_codon}" in feature "${(0, util_2.getPrintableId)(feature)}": `,
+                    message: `Unexpected start codon "${start_codon}" in feature "${getPrintableId(feature)}": `,
                 });
             }
             const lastCodon = codons.at(-1); // Last codon is supposed to be a stop
             if (lastCodon && !(lastCodon.toUpperCase() in STOP_CODONS)) {
                 checkResults.push({
-                    _id: new bson_objectid_1.default().toHexString(),
+                    _id: new ObjectID().toHexString(),
                     name: CHECK_NAME,
                     cause: CAUSES[CAUSES.MissingStopCodon],
                     ids,
                     refSeq: refSeq.toString(),
                     start: cdsEnd,
                     end: cdsEnd,
-                    message: `Missing stop codon in feature "${(0, util_2.getPrintableId)(feature)}"`,
+                    message: `Missing stop codon in feature "${getPrintableId(feature)}"`,
                 });
             }
         }
         else {
             checkResults.push({
-                _id: new bson_objectid_1.default().toHexString(),
+                _id: new ObjectID().toHexString(),
                 name: CHECK_NAME,
                 cause: CAUSES[CAUSES.MissingStopCodon],
                 ids,
                 refSeq: refSeq.toString(),
                 start: cdsEnd,
                 end: cdsEnd,
-                message: `Missing stop codon in feature "${(0, util_2.getPrintableId)(feature)}"`,
+                message: `Missing stop codon in feature "${getPrintableId(feature)}"`,
             });
         }
         for (const [idx, codon] of codons.entries()) {
@@ -182,14 +174,14 @@ async function checkMRNA(feature, getSequence) {
             if (location && codon.toUpperCase() in STOP_CODONS) {
                 const [codonStart, codonEnd] = location;
                 checkResults.push({
-                    _id: new bson_objectid_1.default().toHexString(),
+                    _id: new ObjectID().toHexString(),
                     name: CHECK_NAME,
                     cause: CAUSES[CAUSES.InternalStopCodon],
                     ids,
                     refSeq: refSeq.toString(),
                     start: codonStart,
                     end: codonEnd,
-                    message: `Internal stop codon in feature "${(0, util_2.getPrintableId)(feature)}"`,
+                    message: `Internal stop codon in feature "${getPrintableId(feature)}"`,
                 });
             }
         }
@@ -216,7 +208,7 @@ function getCDSLocations(feature) {
             if (child.type !== 'exon') {
                 continue;
             }
-            const [start, end] = (0, util_1.intersection2)(cdsMin, cdsMax, child.min, child.max);
+            const [start, end] = intersection2(cdsMin, cdsMax, child.min, child.max);
             if (start !== undefined && end !== undefined) {
                 locs.push({ min: start, max: end });
             }
@@ -242,7 +234,7 @@ function getCDSLocations(feature) {
 function getCauses() {
     return Object.values(CAUSES).filter((x) => Number.isNaN(Number(x)));
 }
-class CDSCheck extends common_1.Check {
+export class CDSCheck extends Check {
     name = CHECK_NAME;
     causes = getCauses();
     version = 1;
@@ -261,5 +253,4 @@ class CDSCheck extends common_1.Check {
         return checkResults;
     }
 }
-exports.CDSCheck = CDSCheck;
 //# sourceMappingURL=CDSCheck.js.map

package/dist/Checks/CDSCheck.js.map

@@ -1 +1 @@
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package/dist/Checks/TranscriptCheck.d.ts

@@ -1,5 +1,5 @@
 import { Check } from '@apollo-annotation/common';
-import { type AnnotationFeatureSnapshot, type CheckResultSnapshot } from '@apollo-annotation/mst';
+import type { AnnotationFeatureSnapshot, CheckResultSnapshot } from '@apollo-annotation/mst';
 export declare class TranscriptCheck extends Check {
     name: string;
     causes: string[];
@@ -7,3 +7,4 @@ export declare class TranscriptCheck extends Check {
     isDefault: boolean;
     checkFeature(feature: AnnotationFeatureSnapshot, getSequence: (start: number, end: number) => Promise<string>): Promise<CheckResultSnapshot[]>;
 }
+//# sourceMappingURL=TranscriptCheck.d.ts.map

package/dist/Checks/TranscriptCheck.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"TranscriptCheck.d.ts","sourceRoot":"","sources":["../../src/Checks/TranscriptCheck.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,2BAA2B,CAAA;AACjD,OAAO,KAAK,EACV,yBAAyB,EACzB,mBAAmB,EACpB,MAAM,wBAAwB,CAAA;AAyG/B,qBAAa,eAAgB,SAAQ,KAAK;IACxC,IAAI,SAAoB;IACxB,MAAM,WAAc;IACpB,OAAO,SAAI;IACX,SAAS,UAAO;IAEV,YAAY,CAChB,OAAO,EAAE,yBAAyB,EAClC,WAAW,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,KAAK,OAAO,CAAC,MAAM,CAAC,GAC3D,OAAO,CAAC,mBAAmB,EAAE,CAAC;CAmBlC"}