@apollo-annotation/common 0.3.5 → 0.3.7

package/dist/ApolloPlugin.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export type ApolloPluginConstructor = new (...args: unknown[]) => ApolloPlugin;
 export interface ApolloPluginManager {
     addToExtensionPoint: PluginManager['addToExtensionPoint'];

package/dist/AssemblySpecificChange.d.ts

@@ -1,4 +1,4 @@
-import { Change, ChangeOptions, SerializedChange } from './Change';
+import { Change, type ChangeOptions, type SerializedChange } from './Change';
 export interface SerializedAssemblySpecificChange extends SerializedChange {
     assembly: string;
 }

package/dist/AssemblySpecificChange.js.map

@@ -1 +1 @@
-{"version":3,"file":"AssemblySpecificChange.js","sourceRoot":"","sources":["../src/AssemblySpecificChange.ts"],"names":[],"mappings":";;;AAOA,4DAOC;AAdD,gEAAgE;AAChE,qCAA4E;AAM5E,SAAgB,wBAAwB;AACtC,8DAA8D;AAC9D,KAAU;IAEV,OAAO,CACL,IAAA,iBAAQ,EAAC,KAAK,CAAC,IAAK,KAAgC,CAAC,QAAQ,KAAK,SAAS,CAC5E,CAAA;AACH,CAAC;AAED,MAAsB,sBAAuB,SAAQ,eAAM;IAGzD,YAAY,IAAsC,EAAE,OAAuB;QACzE,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAA;IAC/B,CAAC;CACF;AAPD,wDAOC"}
+{"version":3,"file":"AssemblySpecificChange.js","sourceRoot":"","sources":["../src/AssemblySpecificChange.ts"],"names":[],"mappings":";;;AAYA,4DAOC;AAnBD,gEAAgE;AAChE,qCAKiB;AAMjB,SAAgB,wBAAwB;AACtC,8DAA8D;AAC9D,KAAU;IAEV,OAAO,CACL,IAAA,iBAAQ,EAAC,KAAK,CAAC,IAAK,KAAgC,CAAC,QAAQ,KAAK,SAAS,CAC5E,CAAA;AACH,CAAC;AAED,MAAsB,sBAAuB,SAAQ,eAAM;IAGzD,YAAY,IAAsC,EAAE,OAAuB;QACzE,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAA;IAC/B,CAAC;CACF;AAPD,wDAOC"}

package/dist/Change.d.ts

@@ -1,6 +1,6 @@
-import { AnnotationFeature, AnnotationFeatureSnapshot, ApolloAssemblyI, BackendDriverType, CheckResultI, CheckResultSnapshot } from '@apollo-annotation/mst';
-import { AppRootModel, Region } from '@jbrowse/core/util';
-import { BackendDataStore, Operation, OperationOptions, SerializedOperation } from './Operation';
+import { type AnnotationFeature, type AnnotationFeatureSnapshot, type ApolloAssemblyI, type BackendDriverType, type CheckResultI, type CheckResultSnapshot } from '@apollo-annotation/mst';
+import { type AppRootModel, type Region } from '@jbrowse/core/util';
+import { type BackendDataStore, Operation, type OperationOptions, type SerializedOperation } from './Operation';
 export interface ClientDataStore {
     typeName: 'Client';
     assemblies: Map<string | number, ApolloAssemblyI>;

package/dist/ChangeTypeRegistry.d.ts

@@ -1,4 +1,4 @@
-import { Change } from './Change';
+import { type Change } from './Change';
 type ChangeType = new (...args: any[]) => Change;
 declare class ChangeTypeRegistry {
     changes: Map<string, ChangeType>;

package/dist/Check.d.ts

@@ -1,4 +1,4 @@
-import { AnnotationFeatureSnapshot, CheckResultSnapshot } from '@apollo-annotation/mst';
+import { type AnnotationFeatureSnapshot, type CheckResultSnapshot } from '@apollo-annotation/mst';
 export declare abstract class Check {
     abstract name: string;
     abstract version: number;

package/dist/CheckRegistry.d.ts

@@ -1,4 +1,4 @@
-import { Check } from './Check';
+import { type Check } from './Check';
 declare class CheckRegistry {
     checks: Map<string, Check>;
     registerCheck(name: string, check: Check): void;

package/dist/FeatureChange.d.ts

@@ -1,7 +1,7 @@
-import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { Feature } from '@apollo-annotation/schemas';
-import { AssemblySpecificChange, SerializedAssemblySpecificChange } from './AssemblySpecificChange';
-import { ChangeOptions } from './Change';
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { type Feature } from '@apollo-annotation/schemas';
+import { AssemblySpecificChange, type SerializedAssemblySpecificChange } from './AssemblySpecificChange';
+import { type ChangeOptions } from './Change';
 export interface SerializedFeatureChange extends SerializedAssemblySpecificChange {
     /** The IDs of features that were changed in this operation */
     changedIds: string[];
@@ -29,4 +29,13 @@ export declare abstract class FeatureChange extends AssemblySpecificChange {
      * @param featureIds -
      */
     generateNewIds(feature: Feature | AnnotationFeatureSnapshot, featureIds: string[]): AnnotationFeatureSnapshot;
+    addChild(parentFeature: Feature, child: AnnotationFeatureSnapshot): void;
+    /**
+     * Delete feature's subfeatures that match an ID and return the IDs of any
+     * sub-subfeatures that were deleted
+     * @param feature -
+     * @param featureIdToDelete -
+     * @returns - list of deleted feature IDs
+     */
+    findAndDeleteChildFeature(feature: Feature, featureIdToDelete: string): string[];
 }

package/dist/FeatureChange.js

@@ -84,6 +84,63 @@ class FeatureChange extends AssemblySpecificChange_1.AssemblySpecificChange {
             _id: newId,
         };
     }
+    addChild(parentFeature, child) {
+        var _a;
+        if (!((_a = parentFeature.attributes) === null || _a === void 0 ? void 0 : _a._id)) {
+            let { attributes } = parentFeature;
+            if (!attributes) {
+                attributes = {};
+            }
+            // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+            attributes = {
+                _id: [parentFeature._id.toString()],
+                // eslint-disable-next-line unicorn/prefer-structured-clone
+                ...JSON.parse(JSON.stringify(attributes)),
+            };
+            parentFeature.attributes = attributes;
+        }
+        const { _id } = child;
+        if (!parentFeature.children) {
+            parentFeature.children = new Map();
+        }
+        parentFeature.children.set(_id, {
+            allIds: [],
+            ...child,
+            // eslint-disable-next-line @typescript-eslint/ban-ts-comment
+            // @ts-expect-error
+            _id,
+        });
+        // Child features should be sorted for click and drag of gene glyphs to work properly
+        parentFeature.children = new Map([...parentFeature.children.entries()].sort((a, b) => a[1].min - b[1].min));
+    }
+    /**
+     * Delete feature's subfeatures that match an ID and return the IDs of any
+     * sub-subfeatures that were deleted
+     * @param feature -
+     * @param featureIdToDelete -
+     * @returns - list of deleted feature IDs
+     */
+    findAndDeleteChildFeature(feature, featureIdToDelete) {
+        if (!feature.children) {
+            throw new Error(`Feature ${feature._id.toHexString()} has no children`);
+        }
+        const { _id, children } = feature;
+        const child = children.get(featureIdToDelete);
+        if (child) {
+            const deletedIds = this.getChildFeatureIds(child);
+            children.delete(featureIdToDelete);
+            return deletedIds;
+        }
+        for (const [, childFeature] of children) {
+            try {
+                return this.findAndDeleteChildFeature(childFeature, featureIdToDelete);
+            }
+            catch {
+                // pass
+            }
+        }
+        throw new Error(`Feature "${featureIdToDelete}" not found in ${_id.toHexString()}`);
+    }
 }
 exports.FeatureChange = FeatureChange;
 //# sourceMappingURL=FeatureChange.js.map

package/dist/FeatureChange.js.map

@@ -1 +1 @@
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package/dist/Operation.d.ts

@@ -1,9 +1,9 @@
-import type { ReadStream } from 'node:fs';
-import type { FileHandle } from 'node:fs/promises';
-import { AssemblyDocument, FeatureDocument, FileDocument, RefSeqChunkDocument, RefSeqDocument, JBrowseConfigDocument, UserDocument, CheckDocument } from '@apollo-annotation/schemas';
-import type { LoggerService } from '@nestjs/common';
-import type { ClientSession, Model } from 'mongoose';
-import { GenericFilehandle } from 'generic-filehandle';
+import { type ReadStream } from 'node:fs';
+import { type FileHandle } from 'node:fs/promises';
+import { type AssemblyDocument, type CheckDocument, type FeatureDocument, type FileDocument, type JBrowseConfigDocument, type RefSeqChunkDocument, type RefSeqDocument, type UserDocument } from '@apollo-annotation/schemas';
+import { type LoggerService } from '@nestjs/common';
+import { type GenericFilehandle } from 'generic-filehandle';
+import { type ClientSession, type Model } from 'mongoose';
 export interface LocalGFF3DataStore {
     typeName: 'LocalGFF3';
     gff3Handle: FileHandle;

package/dist/OperationTypeRegistry.d.ts

@@ -1,4 +1,4 @@
-import { Operation } from './Operation';
+import { type Operation } from './Operation';
 type OperationType = new (...args: any[]) => Operation;
 declare class OperationTypeRegistry {
     operations: Map<string, OperationType>;

package/dist/Validation.d.ts

@@ -1,8 +1,8 @@
-import { FeatureDocument } from '@apollo-annotation/schemas';
-import type { ExecutionContext } from '@nestjs/common';
-import type { Reflector } from '@nestjs/core';
-import { ClientSession, Model } from 'mongoose';
-import { Change, ClientDataStore } from './Change';
+import { type FeatureDocument } from '@apollo-annotation/schemas';
+import { type ExecutionContext } from '@nestjs/common';
+import { type Reflector } from '@nestjs/core';
+import { type ClientSession, type Model } from 'mongoose';
+import { type Change, type ClientDataStore } from './Change';
 export interface Context {
     context: ExecutionContext;
     reflector: Reflector;