@jbrowse/plugin-gtf 3.0.0 → 3.0.2

package/dist/GtfAdapter/GtfAdapter.d.ts

@@ -2,7 +2,8 @@ import IntervalTree from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature } from '@jbrowse/core/util';
-import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import type { Region } from '@jbrowse/core/util/types';
+import type { Observer } from 'rxjs';
 type StatusCallback = (arg: string) => void;
 export default class GtfAdapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;
@@ -14,7 +15,14 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
     private loadData;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
-    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery, }: {
+        query: Region;
+        opts: BaseOptions;
+        observer: Observer<Feature>;
+        allowRedispatch: boolean;
+        originalQuery?: Region;
+    }): Promise<void>;
     freeResources(): void;
 }
 export {};

package/dist/GtfAdapter/GtfAdapter.js

@@ -57,11 +57,8 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     const intervalTree = new interval_tree_1.default();
                     (0, gtf_nostream_1.parseStringSync)(lines)
                         .flat()
-                        .map((f, i) => new util_1.SimpleFeature({
-                        data: (0, util_2.featureData)(f),
-                        id: `${this.id}-${refName}-${i}`,
-                    }))
-                        .forEach(obj => intervalTree.insert([obj.get('start'), obj.get('end')], obj));
+                        .map((f, i) => (0, util_2.featureData)(f, `${this.id}-${refName}-${i}`))
+                        .forEach(obj => intervalTree.insert([obj.start, obj.end], obj));
                     this.calculatedIntervalTreeMap[refName] = intervalTree;
                 }
                 return this.calculatedIntervalTreeMap[refName];
@@ -91,20 +88,101 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     getFeatures(query, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            var _a;
             try {
-                const { start, end, refName } = query;
-                const { intervalTreeMap } = await this.loadData(opts);
-                (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([start, end]).forEach(f => {
-                    observer.next(f);
+                await this.getFeaturesHelper({
+                    query,
+                    opts,
+                    observer,
+                    allowRedispatch: true,
                 });
-                observer.complete();
             }
             catch (e) {
                 observer.error(e);
             }
         }, opts.stopToken);
     }
+    async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
+        var _a;
+        const aggregateField = this.getConf('aggregateField');
+        const { start, end, refName } = query;
+        const { intervalTreeMap } = await this.loadData(opts);
+        const feats = (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
+            start,
+            end,
+        ]);
+        if (feats) {
+            if (allowRedispatch && feats.length) {
+                let minStart = Number.POSITIVE_INFINITY;
+                let maxEnd = Number.NEGATIVE_INFINITY;
+                let hasAnyAggregateField = false;
+                for (const feat of feats) {
+                    if (feat.start < minStart) {
+                        minStart = feat.start;
+                    }
+                    if (feat.end > maxEnd) {
+                        maxEnd = feat.end;
+                    }
+                    if (feat[aggregateField]) {
+                        hasAnyAggregateField = true;
+                    }
+                }
+                if (hasAnyAggregateField &&
+                    (maxEnd > query.end || minStart < query.start)) {
+                    await this.getFeaturesHelper({
+                        query: {
+                            ...query,
+                            start: minStart,
+                            end: maxEnd,
+                        },
+                        opts,
+                        observer,
+                        allowRedispatch: false,
+                        originalQuery: query,
+                    });
+                    return;
+                }
+            }
+            const parentAggregation = {};
+            if (feats.some(f => f.uniqueId === undefined)) {
+                throw new Error('found uniqueId undefined');
+            }
+            for (const feat of feats) {
+                const aggr = feat[aggregateField];
+                if (!parentAggregation[aggr]) {
+                    parentAggregation[aggr] = [];
+                }
+                if (aggr) {
+                    parentAggregation[aggr].push(feat);
+                }
+                else {
+                    observer.next(new util_1.SimpleFeature({
+                        id: feat.uniqueId,
+                        data: feat,
+                    }));
+                }
+            }
+            Object.entries(parentAggregation).map(([name, subfeatures]) => {
+                const s = (0, util_1.min)(subfeatures.map(f => f.start));
+                const e = (0, util_1.max)(subfeatures.map(f => f.end));
+                if ((0, util_1.doesIntersect2)(s, e, originalQuery.start, originalQuery.end)) {
+                    const { uniqueId, strand } = subfeatures[0];
+                    observer.next(new util_1.SimpleFeature({
+                        id: `${uniqueId}-parent`,
+                        data: {
+                            type: 'gene',
+                            subfeatures,
+                            strand,
+                            name,
+                            start: s,
+                            end: e,
+                            refName: query.refName,
+                        },
+                    }));
+                }
+            });
+        }
+        observer.complete();
+    }
     freeResources() { }
 }
 exports.default = GtfAdapter;

package/dist/GtfAdapter/configSchema.d.ts

@@ -6,5 +6,9 @@ declare const GtfAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
+    aggregateField: {
+        type: string;
+        defaultValue: string;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default GtfAdapter;

package/dist/GtfAdapter/configSchema.js

@@ -7,5 +7,9 @@ const GtfAdapter = (0, configuration_1.ConfigurationSchema)('GtfAdapter', {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.gtf', locationType: 'UriLocation' },
     },
+    aggregateField: {
+        type: 'string',
+        defaultValue: 'gene_name',
+    },
 }, { explicitlyTyped: true });
 exports.default = GtfAdapter;

package/dist/util.d.ts

@@ -10,4 +10,4 @@ export interface FeatureLoc {
     derived_features: unknown;
     attributes: Record<string, unknown[]>;
 }
-export declare function featureData(data: FeatureLoc): Record<string, unknown>;
+export declare function featureData(data: FeatureLoc, id?: string): Record<string, unknown>;

package/dist/util.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.featureData = featureData;
-function featureData(data) {
+function featureData(data, id) {
     const f = { ...data };
     f.start -= 1;
     f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand];
@@ -52,5 +52,8 @@ function featureData(data) {
     if (f.transcript_id) {
         f.name = f.transcript_id;
     }
+    if (id !== undefined) {
+        f.uniqueId = id;
+    }
     return f;
 }

package/esm/GtfAdapter/GtfAdapter.d.ts

@@ -2,7 +2,8 @@ import IntervalTree from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature } from '@jbrowse/core/util';
-import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
+import type { Region } from '@jbrowse/core/util/types';
+import type { Observer } from 'rxjs';
 type StatusCallback = (arg: string) => void;
 export default class GtfAdapter extends BaseFeatureDataAdapter {
     calculatedIntervalTreeMap: Record<string, IntervalTree>;
@@ -14,7 +15,14 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
     private loadData;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
-    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
+    getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery, }: {
+        query: Region;
+        opts: BaseOptions;
+        observer: Observer<Feature>;
+        allowRedispatch: boolean;
+        originalQuery?: Region;
+    }): Promise<void>;
     freeResources(): void;
 }
 export {};

package/esm/GtfAdapter/GtfAdapter.js

@@ -1,6 +1,6 @@
 import IntervalTree from '@flatten-js/interval-tree';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { SimpleFeature, fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { SimpleFeature, doesIntersect2, fetchAndMaybeUnzip, max, min, } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { parseStringSync } from 'gtf-nostream';
@@ -52,11 +52,8 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
                     const intervalTree = new IntervalTree();
                     parseStringSync(lines)
                         .flat()
-                        .map((f, i) => new SimpleFeature({
-                        data: featureData(f),
-                        id: `${this.id}-${refName}-${i}`,
-                    }))
-                        .forEach(obj => intervalTree.insert([obj.get('start'), obj.get('end')], obj));
+                        .map((f, i) => featureData(f, `${this.id}-${refName}-${i}`))
+                        .forEach(obj => intervalTree.insert([obj.start, obj.end], obj));
                     this.calculatedIntervalTreeMap[refName] = intervalTree;
                 }
                 return this.calculatedIntervalTreeMap[refName];
@@ -86,19 +83,100 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
     }
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {
-            var _a;
             try {
-                const { start, end, refName } = query;
-                const { intervalTreeMap } = await this.loadData(opts);
-                (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([start, end]).forEach(f => {
-                    observer.next(f);
+                await this.getFeaturesHelper({
+                    query,
+                    opts,
+                    observer,
+                    allowRedispatch: true,
                 });
-                observer.complete();
             }
             catch (e) {
                 observer.error(e);
             }
         }, opts.stopToken);
     }
+    async getFeaturesHelper({ query, opts, observer, allowRedispatch, originalQuery = query, }) {
+        var _a;
+        const aggregateField = this.getConf('aggregateField');
+        const { start, end, refName } = query;
+        const { intervalTreeMap } = await this.loadData(opts);
+        const feats = (_a = intervalTreeMap[refName]) === null || _a === void 0 ? void 0 : _a.call(intervalTreeMap, opts.statusCallback).search([
+            start,
+            end,
+        ]);
+        if (feats) {
+            if (allowRedispatch && feats.length) {
+                let minStart = Number.POSITIVE_INFINITY;
+                let maxEnd = Number.NEGATIVE_INFINITY;
+                let hasAnyAggregateField = false;
+                for (const feat of feats) {
+                    if (feat.start < minStart) {
+                        minStart = feat.start;
+                    }
+                    if (feat.end > maxEnd) {
+                        maxEnd = feat.end;
+                    }
+                    if (feat[aggregateField]) {
+                        hasAnyAggregateField = true;
+                    }
+                }
+                if (hasAnyAggregateField &&
+                    (maxEnd > query.end || minStart < query.start)) {
+                    await this.getFeaturesHelper({
+                        query: {
+                            ...query,
+                            start: minStart,
+                            end: maxEnd,
+                        },
+                        opts,
+                        observer,
+                        allowRedispatch: false,
+                        originalQuery: query,
+                    });
+                    return;
+                }
+            }
+            const parentAggregation = {};
+            if (feats.some(f => f.uniqueId === undefined)) {
+                throw new Error('found uniqueId undefined');
+            }
+            for (const feat of feats) {
+                const aggr = feat[aggregateField];
+                if (!parentAggregation[aggr]) {
+                    parentAggregation[aggr] = [];
+                }
+                if (aggr) {
+                    parentAggregation[aggr].push(feat);
+                }
+                else {
+                    observer.next(new SimpleFeature({
+                        id: feat.uniqueId,
+                        data: feat,
+                    }));
+                }
+            }
+            Object.entries(parentAggregation).map(([name, subfeatures]) => {
+                const s = min(subfeatures.map(f => f.start));
+                const e = max(subfeatures.map(f => f.end));
+                if (doesIntersect2(s, e, originalQuery.start, originalQuery.end)) {
+                    const { uniqueId, strand } = subfeatures[0];
+                    observer.next(new SimpleFeature({
+                        id: `${uniqueId}-parent`,
+                        data: {
+                            type: 'gene',
+                            subfeatures,
+                            strand,
+                            name,
+                            start: s,
+                            end: e,
+                            refName: query.refName,
+                        },
+                    }));
+                }
+            });
+        }
+        observer.complete();
+    }
     freeResources() { }
 }

package/esm/GtfAdapter/configSchema.d.ts

@@ -6,5 +6,9 @@ declare const GtfAdapter: import("@jbrowse/core/configuration/configurationSchem
             locationType: string;
         };
     };
+    aggregateField: {
+        type: string;
+        defaultValue: string;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default GtfAdapter;

package/esm/GtfAdapter/configSchema.js

@@ -5,5 +5,9 @@ const GtfAdapter = ConfigurationSchema('GtfAdapter', {
         type: 'fileLocation',
         defaultValue: { uri: '/path/to/my.gtf', locationType: 'UriLocation' },
     },
+    aggregateField: {
+        type: 'string',
+        defaultValue: 'gene_name',
+    },
 }, { explicitlyTyped: true });
 export default GtfAdapter;

package/esm/util.d.ts

@@ -10,4 +10,4 @@ export interface FeatureLoc {
     derived_features: unknown;
     attributes: Record<string, unknown[]>;
 }
-export declare function featureData(data: FeatureLoc): Record<string, unknown>;
+export declare function featureData(data: FeatureLoc, id?: string): Record<string, unknown>;

package/esm/util.js

@@ -1,4 +1,4 @@
-export function featureData(data) {
+export function featureData(data, id) {
     const f = { ...data };
     f.start -= 1;
     f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand];
@@ -49,5 +49,8 @@ export function featureData(data) {
     if (f.transcript_id) {
         f.name = f.transcript_id;
     }
+    if (id !== undefined) {
+        f.uniqueId = id;
+    }
     return f;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "3.0.0",
+  "version": "3.0.2",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -38,23 +38,23 @@
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
     "@gmod/bgzf-filehandle": "^2.0.1",
-    "gtf-nostream": "^1.0.0"
-  },
-  "peerDependencies": {
-    "@jbrowse/core": "^2.0.0",
-    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@jbrowse/core": "^3.0.2",
+    "@jbrowse/plugin-linear-genome-view": "^3.0.2",
     "@mui/material": "^6.0.0",
+    "gtf-nostream": "^1.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
-    "react": ">=16.8.0",
     "rxjs": "^7.0.0"
   },
+  "peerDependencies": {
+    "react": ">=18.0.0"
+  },
   "publishConfig": {
     "access": "public"
   },
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
+  "gitHead": "c01a35edcb2612e94661af8793f09c95c0b13c75"
 }