@apollo-annotation/shared 0.3.5 → 0.3.7

package/dist/Changes/UndoMergeTranscriptsChange.js

@@ -0,0 +1,104 @@
+"use strict";
+/* eslint-disable @typescript-eslint/require-await */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.UndoMergeTranscriptsChange = void 0;
+const common_1 = require("@apollo-annotation/common");
+const MergeTranscriptsChange_1 = require("./MergeTranscriptsChange");
+class UndoMergeTranscriptsChange extends common_1.FeatureChange {
+    typeName = 'UndoMergeTranscriptsChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    toJSON() {
+        const { assembly, changedIds, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ transcriptsToRestore, parentFeatureId }] = changes;
+            return {
+                typeName,
+                changedIds,
+                assembly,
+                transcriptsToRestore,
+                parentFeatureId,
+            };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    async executeOnServer(backend) {
+        const { featureModel, session } = backend;
+        const { changes } = this;
+        for (const change of changes) {
+            const { transcriptsToRestore, parentFeatureId } = change;
+            if (transcriptsToRestore.length !== 2) {
+                throw new Error(`Expected exactly two transcripts to restore. Got :${transcriptsToRestore.length}`);
+            }
+            const topLevelFeature = await featureModel
+                .findOne({ allIds: parentFeatureId })
+                .session(session)
+                .exec();
+            if (!topLevelFeature) {
+                throw new Error(`Could not find feature with ID "${parentFeatureId}"`);
+            }
+            const parentFeature = this.getFeatureFromId(topLevelFeature, parentFeatureId);
+            if (!parentFeature) {
+                throw new Error(`Could not find feature with ID "${parentFeatureId}" in feature "${topLevelFeature._id.toString()}"`);
+            }
+            if (!parentFeature.children) {
+                parentFeature.children = new Map();
+            }
+            for (const transcript of transcriptsToRestore) {
+                this.addChild(parentFeature, transcript);
+                const childIds = this.getChildFeatureIds(transcript);
+                topLevelFeature.allIds.push(transcript._id, ...childIds);
+            }
+            await topLevelFeature.save();
+        }
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        const { changes } = this;
+        for (const change of changes) {
+            const { transcriptsToRestore, parentFeatureId } = change;
+            if (!parentFeatureId) {
+                throw new Error('Parent ID is missing');
+            }
+            const parentFeature = dataStore.getFeature(parentFeatureId);
+            if (!parentFeature) {
+                throw new Error(`Could not find parent feature "${parentFeatureId}"`);
+            }
+            // create an ID for the parent feature if it does not have one
+            if (!parentFeature.attributes.get('_id')) {
+                parentFeature.setAttribute('_id', [parentFeature._id]);
+            }
+            for (const transcript of transcriptsToRestore) {
+                parentFeature.addChild(transcript);
+            }
+        }
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes]
+            .reverse()
+            .map((undoMergeTranscriptsChange) => ({
+            firstTranscript: undoMergeTranscriptsChange.transcriptsToRestore[0],
+            secondTranscript: undoMergeTranscriptsChange.transcriptsToRestore[1],
+            parentFeatureId: undoMergeTranscriptsChange.parentFeatureId,
+        }));
+        return new MergeTranscriptsChange_1.MergeTranscriptsChange({
+            changedIds: inverseChangedIds,
+            typeName: 'MergeTranscriptsChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+exports.UndoMergeTranscriptsChange = UndoMergeTranscriptsChange;
+//# sourceMappingURL=UndoMergeTranscriptsChange.js.map

package/dist/Changes/UndoMergeTranscriptsChange.js.map

@@ -0,0 +1 @@
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package/dist/Changes/UndoSplitExonChange.d.ts

@@ -0,0 +1,32 @@
+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';
+interface SerializedUndoSplitExonChangeBase extends SerializedFeatureChange {
+    typeName: 'UndoSplitExonChange';
+}
+export interface UndoSplitExonChangeDetails {
+    exonToRestore: AnnotationFeatureSnapshot;
+    parentFeatureId: string;
+    idsToDelete: string[];
+    upstreamCut: number;
+    downstreamCut: number;
+    leftExonId: string;
+    rightExonId: string;
+}
+interface SerializedUndoSplitExonChangeSingle extends SerializedUndoSplitExonChangeBase, UndoSplitExonChangeDetails {
+}
+interface SerializedUndoSplitExonChangeMultiple extends SerializedUndoSplitExonChangeBase {
+    changes: UndoSplitExonChangeDetails[];
+}
+export type SerializedUndoSplitExonChange = SerializedUndoSplitExonChangeSingle | SerializedUndoSplitExonChangeMultiple;
+export declare class UndoSplitExonChange extends FeatureChange {
+    typeName: "UndoSplitExonChange";
+    changes: UndoSplitExonChangeDetails[];
+    constructor(json: SerializedUndoSplitExonChange, options?: ChangeOptions);
+    toJSON(): SerializedUndoSplitExonChange;
+    executeOnServer(backend: ServerDataStore): Promise<void>;
+    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
+    executeOnClient(dataStore: ClientDataStore): Promise<void>;
+    getInverse(): SplitExonChange;
+}
+export {};

package/dist/Changes/UndoSplitExonChange.js

@@ -0,0 +1,111 @@
+"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 {
+    typeName = 'UndoSplitExonChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    toJSON() {
+        const { assembly, changedIds, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ exonToRestore, parentFeatureId, idsToDelete, upstreamCut, downstreamCut, leftExonId, rightExonId, },] = changes;
+            return {
+                typeName,
+                changedIds,
+                assembly,
+                exonToRestore,
+                parentFeatureId,
+                idsToDelete,
+                upstreamCut,
+                downstreamCut,
+                leftExonId,
+                rightExonId,
+            };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    async executeOnServer(backend) {
+        const { featureModel, session } = backend;
+        const { changes } = this;
+        for (const change of changes) {
+            const { exonToRestore, parentFeatureId, idsToDelete } = change;
+            const topLevelFeature = await featureModel
+                .findOne({ allIds: parentFeatureId })
+                .session(session)
+                .exec();
+            if (!topLevelFeature) {
+                throw new Error(`Could not find feature with ID "${parentFeatureId}"`);
+            }
+            const parentFeature = this.getFeatureFromId(topLevelFeature, parentFeatureId);
+            if (!parentFeature) {
+                throw new Error(`Could not find feature with ID "${parentFeatureId}" in feature "${topLevelFeature._id.toString()}"`);
+            }
+            if (!parentFeature.children) {
+                parentFeature.children = new Map();
+            }
+            this.addChild(parentFeature, exonToRestore);
+            const childIds = this.getChildFeatureIds(exonToRestore);
+            topLevelFeature.allIds.push(exonToRestore._id, ...childIds);
+            topLevelFeature.allIds = topLevelFeature.allIds.filter((id) => !idsToDelete.includes(id));
+            idsToDelete.map((id) => (0, DeleteFeatureChange_1.findAndDeleteChildFeature)(topLevelFeature, id, this));
+            await topLevelFeature.save();
+        }
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        const { changes } = this;
+        for (const change of changes) {
+            const { exonToRestore, parentFeatureId, idsToDelete } = change;
+            if (!parentFeatureId) {
+                throw new Error('Parent ID is missing');
+            }
+            const parentFeature = dataStore.getFeature(parentFeatureId);
+            if (!parentFeature) {
+                throw new Error(`Could not find parent feature "${parentFeatureId}"`);
+            }
+            // create an ID for the parent feature if it does not have one
+            if (!parentFeature.attributes.get('_id')) {
+                parentFeature.setAttribute('_id', [parentFeature._id]);
+            }
+            parentFeature.addChild(exonToRestore);
+            idsToDelete.map((id) => {
+                parentFeature.deleteChild(id);
+            });
+        }
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes]
+            .reverse()
+            .map((undoSplitExonChange) => ({
+            parentFeatureId: undoSplitExonChange.parentFeatureId,
+            exonToBeSplit: undoSplitExonChange.exonToRestore,
+            upstreamCut: undoSplitExonChange.upstreamCut,
+            downstreamCut: undoSplitExonChange.downstreamCut,
+            leftExonId: undoSplitExonChange.leftExonId,
+            rightExonId: undoSplitExonChange.rightExonId,
+        }));
+        return new SplitExonChange_1.SplitExonChange({
+            changedIds: inverseChangedIds,
+            typeName: 'SplitExonChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+exports.UndoSplitExonChange = UndoSplitExonChange;
+//# sourceMappingURL=UndoSplitExonChange.js.map

package/dist/Changes/UndoSplitExonChange.js.map

@@ -0,0 +1 @@
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package/dist/Changes/UserChange.d.ts

@@ -1,4 +1,4 @@
-import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedChange, ServerDataStore } from '@apollo-annotation/common';
+import { Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedChange, type ServerDataStore } from '@apollo-annotation/common';
 export interface SerializedUserChangeBase extends SerializedChange {
     typeName: 'UserChange';
     userId: string;

package/dist/Changes/index.d.ts

@@ -1,3 +1,4 @@
+import { AddAssemblyAliasesChange } from './AddAssemblyAliasesChange';
 import { AddAssemblyAndFeaturesFromFileChange } from './AddAssemblyAndFeaturesFromFileChange';
 import { AddAssemblyFromExternalChange } from './AddAssemblyFromExternalChange';
 import { AddAssemblyFromFileChange } from './AddAssemblyFromFileChange';
@@ -11,8 +12,14 @@ 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';
 export declare const changes: {
     AddAssemblyAndFeaturesFromFileChange: typeof AddAssemblyAndFeaturesFromFileChange;
@@ -27,10 +34,17 @@ export declare const changes: {
     ImportJBrowseConfigChange: typeof ImportJBrowseConfigChange;
     LocationEndChange: typeof LocationEndChange;
     LocationStartChange: typeof LocationStartChange;
+    MergeExonsChange: typeof MergeExonsChange;
+    SplitExonChange: typeof SplitExonChange;
+    MergeTranscriptsChange: typeof MergeTranscriptsChange;
+    UndoMergeExonsChange: typeof UndoMergeExonsChange;
+    UndoSplitExonChange: typeof UndoSplitExonChange;
+    UndoMergeTranscriptsChange: typeof UndoMergeTranscriptsChange;
     StrandChange: typeof StrandChange;
     TypeChange: typeof TypeChange;
     UserChange: typeof UserChange;
     AddRefSeqAliasesChange: typeof AddRefSeqAliasesChange;
+    AddAssemblyAliasesChange: typeof AddAssemblyAliasesChange;
 };
 export * from './AddAssemblyAndFeaturesFromFileChange';
 export * from './AddAssemblyFromFileChange';
@@ -44,7 +58,14 @@ 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';

package/dist/Changes/index.js

@@ -2,6 +2,7 @@
 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");
@@ -15,8 +16,14 @@ 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,
@@ -31,10 +38,17 @@ exports.changes = {
     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,
 };
 tslib_1.__exportStar(require("./AddAssemblyAndFeaturesFromFileChange"), exports);
 tslib_1.__exportStar(require("./AddAssemblyFromFileChange"), exports);
@@ -48,8 +62,15 @@ 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);
 //# sourceMappingURL=index.js.map

package/dist/Changes/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Changes/index.ts"],"names":[],"mappings":";;;;AAAA,yEAAqE;AACrE,iGAA6F;AAC7F,mFAA+E;AAC/E,2EAAuE;AACvE,yDAAqD;AACrD,2EAAuE;AACvE,qEAAiE;AACjE,iEAA6D;AAC7D,+DAA2D;AAC3D,yDAAqD;AACrD,qEAAiE;AACjE,2EAAuE;AACvE,2DAAuD;AACvD,+DAA2D;AAC3D,yDAAqD;AACrD,qEAAiE;AACjE,uDAAmD;AACnD,iDAA6C;AAC7C,6CAAyC;AACzC,iEAA6D;AAC7D,6EAAyE;AACzE,+DAA2D;AAC3D,6CAAyC;AAE5B,QAAA,OAAO,GAAG;IACrB,oCAAoC,EAApC,2EAAoC;IACpC,yBAAyB,EAAzB,qDAAyB;IACzB,6BAA6B,EAA7B,6DAA6B;IAC7B,gBAAgB,EAAhB,mCAAgB;IAChB,yBAAyB,EAAzB,qDAAyB;IACzB,oBAAoB,EAApB,2CAAoB;IACpB,mBAAmB,EAAnB,yCAAmB;IACnB,gBAAgB,EAAhB,mCAAgB;IAChB,sBAAsB,EAAtB,+CAAsB;IACtB,yBAAyB,EAAzB,qDAAyB;IACzB,iBAAiB,EAAjB,qCAAiB;IACjB,mBAAmB,EAAnB,yCAAmB;IACnB,gBAAgB,EAAhB,mCAAgB;IAChB,eAAe,EAAf,iCAAe;IACf,sBAAsB,EAAtB,+CAAsB;IACtB,oBAAoB,EAApB,2CAAoB;IACpB,mBAAmB,EAAnB,yCAAmB;IACnB,0BAA0B,EAA1B,uDAA0B;IAC1B,YAAY,EAAZ,2BAAY;IACZ,UAAU,EAAV,uBAAU;IACV,UAAU,EAAV,uBAAU;IACV,sBAAsB,EAAtB,+CAAsB;IACtB,wBAAwB,EAAxB,mDAAwB;CACzB,CAAA;AAED,iFAAsD;AACtD,sEAA2C;AAC3C,0EAA+C;AAC/C,6DAAkC;AAClC,sEAA2C;AAC3C,iEAAsC;AACtC,gEAAqC;AACrC,6DAAkC;AAClC,mEAAwC;AACxC,sEAA2C;AAC3C,8DAAmC;AACnC,gEAAqC;AACrC,6DAAkC;AAClC,4DAAiC;AACjC,mEAAwC;AACxC,iEAAsC;AACtC,gEAAqC;AACrC,uEAA4C;AAC5C,yDAA8B;AAC9B,uDAA4B;AAC5B,uDAA4B;AAC5B,mEAAwC;AACxC,qEAA0C"}

package/dist/Checks/CDSCheck.d.ts

@@ -1,5 +1,5 @@
 import { Check } from '@apollo-annotation/common';
-import { AnnotationFeatureSnapshot, CheckResultSnapshot } from '@apollo-annotation/mst';
+import { type AnnotationFeatureSnapshot, type CheckResultSnapshot } from '@apollo-annotation/mst';
 export declare class CDSCheck extends Check {
     name: string;
     causes: string[];

package/dist/GFF3/annotationFeatureToGFF3.d.ts

@@ -1,3 +1,3 @@
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { GFF3Feature } from '@gmod/gff';
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { type GFF3Feature } from '@gmod/gff';
 export declare function annotationFeatureToGFF3(feature: AnnotationFeatureSnapshot, parentId?: string, refSeqNames?: Record<string, string | undefined>): GFF3Feature;

package/dist/GFF3/annotationFeatureToGFF3.js

@@ -205,7 +205,13 @@ function getTranscriptParts(feature) {
     return transcriptParts;
 }
 function getCdsLocations(feature) {
-    const transcriptParts = getTranscriptParts(feature);
+    let transcriptParts = [];
+    try {
+        transcriptParts = getTranscriptParts(feature);
+    }
+    catch {
+        return [];
+    }
     return transcriptParts.map((transcript) => transcript.filter((transcriptPart) => transcriptPart.type === 'CDS'));
 }
 //# sourceMappingURL=annotationFeatureToGFF3.js.map

package/dist/GFF3/annotationFeatureToGFF3.js.map

@@ -1 +1 @@
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package/dist/GFF3/annotationFeatureToGFF3.test.js

@@ -4,8 +4,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 /* eslint-disable @typescript-eslint/no-floating-promises */
 const node_test_1 = require("node:test");
 const chai_1 = require("chai");
-const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test");
 const annotationFeatureToGFF3_1 = require("./annotationFeatureToGFF3");
+const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test");
 (0, node_test_1.describe)('annotationFeatureToGFF3', () => {
     (0, node_test_1.it)('Test mandatory columns', () => {
         const annotationFeature = (0, gff3ToAnnotationFeature_test_1.readAnnotationFeatureSnapshot)('test_data/gene.json');

package/dist/GFF3/annotationFeatureToGFF3.test.js.map

@@ -1 +1 @@
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package/dist/GFF3/gff3ToAnnotationFeature.d.ts

@@ -1,3 +1,3 @@
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { GFF3Feature } from '@gmod/gff';
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { type GFF3Feature } from '@gmod/gff';
 export declare function gff3ToAnnotationFeature(gff3Feature: GFF3Feature, refSeq?: string, featureIds?: string[]): AnnotationFeatureSnapshot;

package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts

@@ -1,2 +1,2 @@
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
 export declare function readAnnotationFeatureSnapshot(fn: string): AnnotationFeatureSnapshot;

package/dist/GFF3/gff3ToAnnotationFeature.test.js

@@ -3,8 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.readAnnotationFeatureSnapshot = readAnnotationFeatureSnapshot;
 const tslib_1 = require("tslib");
 /* eslint-disable @typescript-eslint/no-floating-promises */
-const node_test_1 = require("node:test");
 const node_fs_1 = require("node:fs");
+const node_test_1 = require("node:test");
 const gff_1 = tslib_1.__importDefault(require("@gmod/gff"));
 const chai_1 = require("chai");
 const chai_exclude_1 = tslib_1.__importDefault(require("chai-exclude"));

package/dist/GFF3/gff3ToAnnotationFeature.test.js.map

@@ -1 +1 @@
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package/dist/GFF3/gffReservedKeys.d.ts

@@ -3,3 +3,10 @@ export type GFFInternalAttribute = 'gff_id' | 'gff_name' | 'gff_alias' | 'gff_pa
 export declare const gffToInternal: Record<GFFReservedAttribute, GFFInternalAttribute>;
 export declare function isGFFReservedAttribute(attribute: string): attribute is GFFReservedAttribute;
 export declare const internalToGFF: Record<GFFInternalAttribute, GFFReservedAttribute>;
+export declare function isGFFInternalAttribute(attribute: string): attribute is GFFInternalAttribute;
+export type GFFColumn = 'score' | 'source';
+export type GFFColumnInternal = 'gff_score' | 'gff_source';
+export declare const gffColumnToInternal: Record<GFFColumn, GFFColumnInternal>;
+export declare function isGFFColumn(attribute: string): attribute is GFFColumn;
+export declare const gffInternalToColumn: Record<GFFColumnInternal, GFFColumn>;
+export declare function isGFFColumnInternal(column: string): column is GFFColumnInternal;

package/dist/GFF3/gffReservedKeys.js

@@ -1,7 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.internalToGFF = exports.gffToInternal = void 0;
+exports.gffInternalToColumn = exports.gffColumnToInternal = exports.internalToGFF = exports.gffToInternal = void 0;
 exports.isGFFReservedAttribute = isGFFReservedAttribute;
+exports.isGFFInternalAttribute = isGFFInternalAttribute;
+exports.isGFFColumn = isGFFColumn;
+exports.isGFFColumnInternal = isGFFColumnInternal;
 exports.gffToInternal = {
     ID: 'gff_id',
     Name: 'gff_name',
@@ -31,4 +34,21 @@ exports.internalToGFF = {
     gff_ontology_term: 'Ontology_term',
     gff_is_circular: 'Is_circular',
 };
+function isGFFInternalAttribute(attribute) {
+    return attribute in exports.internalToGFF;
+}
+exports.gffColumnToInternal = {
+    score: 'gff_score',
+    source: 'gff_source',
+};
+function isGFFColumn(attribute) {
+    return attribute in exports.gffColumnToInternal;
+}
+exports.gffInternalToColumn = {
+    gff_score: 'score',
+    gff_source: 'source',
+};
+function isGFFColumnInternal(column) {
+    return column in exports.gffInternalToColumn;
+}
 //# sourceMappingURL=gffReservedKeys.js.map

package/dist/GFF3/gffReservedKeys.js.map

@@ -1 +1 @@
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