@jbrowse/plugin-comparative-adapters 2.16.1 → 2.18.0

package/esm/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.d.ts

@@ -1,10 +1,11 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import PluginManager from '@jbrowse/core/PluginManager';
 import { TabixIndexedFile } from '@gmod/tabix';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
 interface PAFOptions extends BaseOptions {
     config?: AnyConfigurationModel;
 }

package/esm/PairwiseIndexedPAFAdapter/PairwiseIndexedPAFAdapter.js

@@ -1,10 +1,9 @@
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import { openLocation } from '@jbrowse/core/util/io';
 import { TabixIndexedFile } from '@gmod/tabix';
-// locals
-import { parsePAFLine } from '../util';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SyntenyFeature from '../SyntenyFeature';
+import { parsePAFLine } from '../util';
 class PAFAdapter extends BaseFeatureDataAdapter {
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
@@ -93,12 +92,12 @@ class PAFAdapter extends BaseFeatureDataAdapter {
                         },
                     }));
                 },
-                signal: opts.signal,
+                stopToken: opts.stopToken,
             });
             observer.complete();
         });
     }
-    freeResources( /* { query } */) { }
+    freeResources() { }
 }
 PAFAdapter.capabilities = ['getFeatures', 'getRefNames'];
 export default PAFAdapter;

package/esm/PairwiseIndexedPAFAdapter/configSchema.d.ts

@@ -1,31 +1,19 @@
 declare const PairwiseIndexedPAFAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];
         description: string;
     };
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: string;
         defaultValue: string;
         description: string;
     };
-    /**
-     * #slot
-     */
     pifGzLocation: {
         type: string;
         description: string;
@@ -34,21 +22,12 @@ declare const PairwiseIndexedPAFAdapter: import("@jbrowse/core/configuration/con
             locationType: string;
         };
     };
-    /**
-     * #slot
-     */
     index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: import("mobx-state-tree").ISimpleType<string>;
             type: string;
             defaultValue: string;
         };
-        /**
-         * #slot index.location
-         */
         location: {
             type: string;
             defaultValue: {

package/esm/PairwiseIndexedPAFAdapter/configSchema.js

@@ -1,37 +1,22 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { types } from 'mobx-state-tree';
-/**
- * #config PairwiseIndexedPAFAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const PairwiseIndexedPAFAdapter = ConfigurationSchema('PairwiseIndexedPAFAdapter', {
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second',
     },
-    /**
-     * #slot
-     */
     targetAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the target assembly name',
     },
-    /**
-     * #slot
-     */
     queryAssembly: {
         type: 'string',
         defaultValue: '',
         description: 'Alternative to assemblyNames: the query assembly name',
     },
-    /**
-     * #slot
-     */
     pifGzLocation: {
         type: 'fileLocation',
         description: 'location of pairwise tabix indexed PAF (pif)',
@@ -40,21 +25,12 @@ const PairwiseIndexedPAFAdapter = ConfigurationSchema('PairwiseIndexedPAFAdapter
             locationType: 'UriLocation',
         },
     },
-    /**
-     * #slot
-     */
     index: ConfigurationSchema('TabixIndex', {
-        /**
-         * #slot index.indexType
-         */
         indexType: {
             model: types.enumeration('IndexType', ['TBI', 'CSI']),
             type: 'stringEnum',
             defaultValue: 'TBI',
         },
-        /**
-         * #slot index.location
-         */
         location: {
             type: 'fileLocation',
             defaultValue: {

package/esm/PairwiseIndexedPAFAdapter/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function PairwiseIndexedPAFAdapterF(pluginManager: PluginManager): void;

package/esm/SyntenyFeature/index.js

@@ -1,6 +1,5 @@
 import { SimpleFeature } from '@jbrowse/core/util';
 import { MismatchParser } from '@jbrowse/plugin-alignments';
-// locals
 const { getMismatches } = MismatchParser;
 export default class SyntenyFeature extends SimpleFeature {
     get(arg) {

package/esm/index.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 default class ComparativeAdaptersPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,12 +1,13 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PAFAdapterF from './PAFAdapter';
-import PairwiseIndexedPAFAdapterF from './PairwiseIndexedPAFAdapter';
+import { getFileName } from '@jbrowse/core/util/tracks';
+import BlastTabularAdapter from './BlastTabularAdapter';
+import ChainAdapterF from './ChainAdapter';
+import DeltaAdapterF from './DeltaAdapter';
 import MCScanAnchorsAdapterF from './MCScanAnchorsAdapter';
 import MCScanSimpleAnchorsAdapterF from './MCScanSimpleAnchorsAdapter';
 import MashMapAdapterF from './MashMapAdapter';
-import DeltaAdapterF from './DeltaAdapter';
-import ChainAdapterF from './ChainAdapter';
-import { getFileName, } from '@jbrowse/core/util/tracks';
+import PAFAdapterF from './PAFAdapter';
+import PairwiseIndexedPAFAdapterF from './PairwiseIndexedPAFAdapter';
 export default class ComparativeAdaptersPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -20,6 +21,7 @@ export default class ComparativeAdaptersPlugin extends Plugin {
         MCScanAnchorsAdapterF(pluginManager);
         MCScanSimpleAnchorsAdapterF(pluginManager);
         MashMapAdapterF(pluginManager);
+        BlastTabularAdapter(pluginManager);
         pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
             return (file, index, adapterHint) => {
                 const regexGuess = /\.paf/i;

package/esm/util.d.ts

@@ -1,7 +1,7 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { GenericFilehandle } from 'generic-filehandle';
+import type { PAFRecord } from './PAFAdapter/util';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Buffer } from 'buffer';
-import { PAFRecord } from './PAFAdapter/util';
+import type { GenericFilehandle } from 'generic-filehandle';
 export declare function parseBed(text: string): Map<string | undefined, {
     refName: string | undefined;
     start: number;
@@ -12,7 +12,7 @@ export declare function parseBed(text: string): Map<string | undefined, {
 }>;
 export declare function readFile(file: GenericFilehandle, opts?: BaseOptions): Promise<string>;
 export declare function zip(a: number[], b: number[]): [number, number][];
-export declare function parseLineByLine(buffer: Buffer, cb: (line: string) => PAFRecord): PAFRecord[];
+export declare function parseLineByLine<T>(buffer: Buffer, cb: (line: string) => T | undefined): T[];
 export declare function parsePAFLine(line: string): PAFRecord;
 export declare function flipCigar(cigar: string[]): (string | undefined)[];
 export declare function swapIndelCigar(cigar: string): string;

package/esm/util.js

@@ -1,5 +1,4 @@
-import { unzip } from '@gmod/bgzf-filehandle';
-import { isGzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
 export function parseBed(text) {
     return new Map(text
         .split(/\n|\r\n|\r/)
@@ -20,25 +19,29 @@ export function parseBed(text) {
     }));
 }
 export async function readFile(file, opts) {
-    const buffer = (await file.readFile(opts));
-    return new TextDecoder('utf8', { fatal: true }).decode(isGzip(buffer) ? await unzip(buffer) : buffer);
+    const buf = await fetchAndMaybeUnzip(file, opts);
+    const decoder = new TextDecoder('utf8');
+    return decoder.decode(buf);
 }
 export function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
 }
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
 export function parseLineByLine(buffer, cb) {
     let blockStart = 0;
     const entries = [];
+    const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
         const n = buffer.indexOf('\n', blockStart);
         if (n === -1) {
             break;
         }
         const b = buffer.subarray(blockStart, n);
-        const line = ((decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString()).trim();
+        const line = decoder.decode(b).trim();
         if (line) {
-            entries.push(cb(line));
+            const entry = cb(line);
+            if (entry) {
+                entries.push(entry);
+            }
         }
         blockStart = n + 1;
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }