@jbrowse/plugin-comparative-adapters 2.17.0 → 3.0.0

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

@@ -1,13 +1,15 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PAFAdapterF from './PAFAdapter';
-import PairwiseIndexedPAFAdapterF from './PairwiseIndexedPAFAdapter';
+import BlastTabularAdapter from './BlastTabularAdapter';
+import ChainAdapterF from './ChainAdapter';
+import ComparativeAddTrackComponentF from './ComparativeAddTrackComponent';
+import DeltaAdapterF from './DeltaAdapter';
+import GuessAdapterF from './GuessAdapter';
+import MCScanAddTrackComponentF from './MCScanAddTrackComponent';
 import MCScanAnchorsAdapterF from './MCScanAnchorsAdapter';
 import MCScanSimpleAnchorsAdapterF from './MCScanSimpleAnchorsAdapter';
 import MashMapAdapterF from './MashMapAdapter';
-import DeltaAdapterF from './DeltaAdapter';
-import ChainAdapterF from './ChainAdapter';
-import BlastTabularAdapter from './BlastTabularAdapter';
-import { getFileName, } from '@jbrowse/core/util/tracks';
+import PAFAdapterF from './PAFAdapter';
+import PairwiseIndexedPAFAdapterF from './PairwiseIndexedPAFAdapter';
 export default class ComparativeAdaptersPlugin extends Plugin {
     constructor() {
         super(...arguments);
@@ -22,24 +24,8 @@ export default class ComparativeAdaptersPlugin extends Plugin {
         MCScanSimpleAnchorsAdapterF(pluginManager);
         MashMapAdapterF(pluginManager);
         BlastTabularAdapter(pluginManager);
-        pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-            return (file, index, adapterHint) => {
-                const regexGuess = /\.paf/i;
-                const adapterName = 'PAFAdapter';
-                const fileName = getFileName(file);
-                if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                    return {
-                        type: adapterName,
-                        pafLocation: file,
-                    };
-                }
-                return adapterGuesser(file, index, adapterHint);
-            };
-        });
-        pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
-            return (adapterName) => adapterName === 'PAFAdapter'
-                ? 'SyntenyTrack'
-                : trackTypeGuesser(adapterName);
-        });
+        ComparativeAddTrackComponentF(pluginManager);
+        MCScanAddTrackComponentF(pluginManager);
+        GuessAdapterF(pluginManager);
     }
 }

package/esm/syntenyTypes.d.ts

@@ -0,0 +1,3 @@
+export declare const syntenyTypes: string[];
+export declare const pairwiseTypes: string[];
+export declare const mcscanTypes: string[];

package/esm/syntenyTypes.js

@@ -0,0 +1,22 @@
+export const syntenyTypes = [
+    'PAFAdapter',
+    'ChainAdapter',
+    'DeltaAdapter',
+    'BlastTabularAdapter',
+    'MashMapAdapter',
+    'MCScanAnchorsAdapter',
+    'MCScanSimpleAnchorsAdapter',
+    'PairwiseIndexedPAFAdapter',
+];
+export const pairwiseTypes = [
+    'PAFAdapter',
+    'ChainAdapter',
+    'DeltaAdapter',
+    'MashMapAdapter',
+    'BlastTabularAdapter',
+    'PairwiseIndexedPAFAdapter',
+];
+export const mcscanTypes = [
+    'MCScanAnchorsAdapter',
+    'MCScanSimpleAnchorsAdapter',
+];

package/esm/util.d.ts

@@ -1,7 +1,6 @@
-import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { GenericFilehandle } from 'generic-filehandle';
-import type { Buffer } from 'buffer';
-import { PAFRecord } from './PAFAdapter/util';
+import type { PAFRecord } from './PAFAdapter/util';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export declare function parseBed(text: string): Map<string | undefined, {
     refName: string | undefined;
     start: number;
@@ -12,7 +11,7 @@ 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<T>(buffer: Buffer, cb: (line: string) => T | undefined): T[];
+export declare function parseLineByLine<T>(buffer: Uint8Array, 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

@@ -1,4 +1,4 @@
-import { fetchAndMaybeUnzip } from '@jbrowse/core/util';
+import { fetchAndMaybeUnzipText } from '@jbrowse/core/util';
 export function parseBed(text) {
     return new Map(text
         .split(/\n|\r\n|\r/)
@@ -19,9 +19,7 @@ export function parseBed(text) {
     }));
 }
 export async function readFile(file, opts) {
-    const buf = await fetchAndMaybeUnzip(file, opts);
-    const decoder = new TextDecoder('utf8');
-    return decoder.decode(buf);
+    return fetchAndMaybeUnzipText(file, opts);
 }
 export function zip(a, b) {
     return a.map((e, i) => [e, b[i]]);
@@ -31,7 +29,7 @@ export function parseLineByLine(buffer, cb) {
     const entries = [];
     const decoder = new TextDecoder('utf8');
     while (blockStart < buffer.length) {
-        const n = buffer.indexOf('\n', blockStart);
+        const n = buffer.indexOf(10, blockStart);
         if (n === -1) {
             break;
         }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -36,9 +36,9 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/tabix": "^1.5.6",
-    "generic-filehandle": "^3.0.0"
+    "@gmod/bgzf-filehandle": "^2.0.1",
+    "@gmod/tabix": "^2.0.0",
+    "generic-filehandle2": "^1.0.0"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }