@jbrowse/plugin-config 2.8.0 → 2.10.0

package/dist/FromConfigAdapter/FromConfigAdapter.d.ts

@@ -1,19 +1,13 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import SimpleFeature, { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-/**
- * Adapter that just returns the features defined in its `features` configuration
- * key, like:
- *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
- */
+export declare function makeFeatures(fdata: SimpleFeatureSerialized[]): Map<string, Feature[]>;
 export default class FromConfigAdapter extends BaseFeatureDataAdapter {
     protected features: Map<string, Feature[]>;
     constructor(conf: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    static makeFeatures(fdata: SimpleFeatureSerialized[]): Map<string, Feature[]>;
-    static makeFeature(data: SimpleFeatureSerialized): SimpleFeature;
     getRefNames(): Promise<string[]>;
     getRefNameAliases(): Promise<{
         refName: string;

package/dist/FromConfigAdapter/FromConfigAdapter.js

@@ -3,43 +3,37 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.makeFeatures = void 0;
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * Adapter that just returns the features defined in its `features` configuration
- * key, like:
- *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
- */
+function makeFeatures(fdata) {
+    const features = new Map();
+    for (const entry of fdata) {
+        if (entry) {
+            const f = new simpleFeature_1.default(entry);
+            const refName = f.get('refName');
+            let bucket = features.get(refName);
+            if (!bucket) {
+                bucket = [];
+                features.set(refName, bucket);
+            }
+            bucket.push(f);
+        }
+    }
+    // sort the features on each reference sequence by start coordinate
+    for (const refFeatures of features.values()) {
+        refFeatures.sort((a, b) => a.get('start') - b.get('start'));
+    }
+    return features;
+}
+exports.makeFeatures = makeFeatures;
 class FromConfigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     constructor(conf, getSubAdapter, pluginManager) {
         super(conf, getSubAdapter, pluginManager);
         const feats = (0, configuration_1.readConfObject)(conf, 'features');
-        this.features = FromConfigAdapter.makeFeatures(feats || []);
-    }
-    static makeFeatures(fdata) {
-        const features = new Map();
-        for (const entry of fdata) {
-            if (entry) {
-                const f = this.makeFeature(entry);
-                const refName = f.get('refName');
-                let bucket = features.get(refName);
-                if (!bucket) {
-                    bucket = [];
-                    features.set(refName, bucket);
-                }
-                bucket.push(f);
-            }
-        }
-        // sort the features on each reference sequence by start coordinate
-        for (const refFeatures of features.values()) {
-            refFeatures.sort((a, b) => a.get('start') - b.get('start'));
-        }
-        return features;
-    }
-    static makeFeature(data) {
-        return new simpleFeature_1.default(data);
+        this.features = makeFeatures(feats || []);
     }
     async getRefNames() {
         return [...this.features.keys()];

package/dist/FromConfigRegionsAdapter/FromConfigRegionsAdapter.js

@@ -1,11 +1,8 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const configuration_1 = require("@jbrowse/core/configuration");
-const FromConfigAdapter_1 = __importDefault(require("../FromConfigAdapter/FromConfigAdapter"));
+const FromConfigAdapter_1 = require("../FromConfigAdapter/FromConfigAdapter");
 /**
  * Adapter that just returns the features defined in its `features` configuration
  * key, like:
@@ -14,8 +11,8 @@ const FromConfigAdapter_1 = __importDefault(require("../FromConfigAdapter/FromCo
 class FromConfigRegionsAdapter extends BaseAdapter_1.BaseAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
-        const features = (0, configuration_1.readConfObject)(config, 'features');
-        this.features = FromConfigAdapter_1.default.makeFeatures(features || []);
+        const f = (0, configuration_1.readConfObject)(config, 'features');
+        this.features = (0, FromConfigAdapter_1.makeFeatures)(f || []);
     }
     /**
      * Get refName, start, and end for all features after collapsing any overlaps

package/esm/FromConfigAdapter/FromConfigAdapter.d.ts

@@ -1,19 +1,13 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
-import SimpleFeature, { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
+import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-/**
- * Adapter that just returns the features defined in its `features` configuration
- * key, like:
- *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
- */
+export declare function makeFeatures(fdata: SimpleFeatureSerialized[]): Map<string, Feature[]>;
 export default class FromConfigAdapter extends BaseFeatureDataAdapter {
     protected features: Map<string, Feature[]>;
     constructor(conf: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
-    static makeFeatures(fdata: SimpleFeatureSerialized[]): Map<string, Feature[]>;
-    static makeFeature(data: SimpleFeatureSerialized): SimpleFeature;
     getRefNames(): Promise<string[]>;
     getRefNameAliases(): Promise<{
         refName: string;

package/esm/FromConfigAdapter/FromConfigAdapter.js

@@ -2,39 +2,31 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { readConfObject, } from '@jbrowse/core/configuration';
-/**
- * Adapter that just returns the features defined in its `features` configuration
- * key, like:
- *   `"features": [ { "refName": "ctgA", "start":1, "end":20 }, ... ]`
- */
+export function makeFeatures(fdata) {
+    const features = new Map();
+    for (const entry of fdata) {
+        if (entry) {
+            const f = new SimpleFeature(entry);
+            const refName = f.get('refName');
+            let bucket = features.get(refName);
+            if (!bucket) {
+                bucket = [];
+                features.set(refName, bucket);
+            }
+            bucket.push(f);
+        }
+    }
+    // sort the features on each reference sequence by start coordinate
+    for (const refFeatures of features.values()) {
+        refFeatures.sort((a, b) => a.get('start') - b.get('start'));
+    }
+    return features;
+}
 export default class FromConfigAdapter extends BaseFeatureDataAdapter {
     constructor(conf, getSubAdapter, pluginManager) {
         super(conf, getSubAdapter, pluginManager);
         const feats = readConfObject(conf, 'features');
-        this.features = FromConfigAdapter.makeFeatures(feats || []);
-    }
-    static makeFeatures(fdata) {
-        const features = new Map();
-        for (const entry of fdata) {
-            if (entry) {
-                const f = this.makeFeature(entry);
-                const refName = f.get('refName');
-                let bucket = features.get(refName);
-                if (!bucket) {
-                    bucket = [];
-                    features.set(refName, bucket);
-                }
-                bucket.push(f);
-            }
-        }
-        // sort the features on each reference sequence by start coordinate
-        for (const refFeatures of features.values()) {
-            refFeatures.sort((a, b) => a.get('start') - b.get('start'));
-        }
-        return features;
-    }
-    static makeFeature(data) {
-        return new SimpleFeature(data);
+        this.features = makeFeatures(feats || []);
     }
     async getRefNames() {
         return [...this.features.keys()];

package/esm/FromConfigRegionsAdapter/FromConfigRegionsAdapter.js

@@ -1,6 +1,6 @@
 import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { readConfObject, } from '@jbrowse/core/configuration';
-import FromConfigAdapter from '../FromConfigAdapter/FromConfigAdapter';
+import { makeFeatures } from '../FromConfigAdapter/FromConfigAdapter';
 /**
  * Adapter that just returns the features defined in its `features` configuration
  * key, like:
@@ -9,8 +9,8 @@ import FromConfigAdapter from '../FromConfigAdapter/FromConfigAdapter';
 export default class FromConfigRegionsAdapter extends BaseAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
-        const features = readConfObject(config, 'features');
-        this.features = FromConfigAdapter.makeFeatures(features || []);
+        const f = readConfObject(config, 'features');
+        this.features = makeFeatures(f || []);
     }
     /**
      * Get refName, start, and end for all features after collapsing any overlaps

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "2.8.0",
+  "version": "2.10.0",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "ee8c2bdc8bd4f1a70b1eefda984f04a2830d9ca0"
+  "gitHead": "223d8bfb68fd1bacaf22852639ad5920f1b7f43b"
 }