@jbrowse/plugin-comparative-adapters 2.17.0 → 2.18.0

package/esm/PAFAdapter/configSchema.d.ts

@@ -1,31 +1,19 @@
 declare const PAFAdapter: 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
-     */
     pafLocation: {
         type: string;
         defaultValue: {

package/esm/PAFAdapter/configSchema.js

@@ -1,36 +1,21 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config PAFAdapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 const PAFAdapter = ConfigurationSchema('PAFAdapter', {
-    /**
-     * #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
-     */
     pafLocation: {
         type: 'fileLocation',
         defaultValue: {

package/esm/PAFAdapter/index.d.ts

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

package/esm/PAFAdapter/util.js

@@ -1,38 +1,4 @@
 import { zip } from '../util';
-// based on "weighted mean" method from https://github.com/tpoorten/dotPlotly
-// License reproduced here
-//
-// MIT License
-// Copyright (c) 2017 Tom Poorten
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to deal
-// in the Software without restriction, including without limitation the rights
-// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-// copies of the Software, and to permit persons to whom the Software is
-// furnished to do so, subject to the following conditions:
-// The above copyright notice and this permission notice shall be included in all
-// copies or substantial portions of the Software.
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-// SOFTWARE.
-//
-// Notes: in the weighted mean longer alignments factor in more heavily of all
-// the fragments of a query vs the reference that it mapped to
-//
-// this uses a combined key query+'-'+ref to iteratively map all the alignments
-// that match a particular ref from a particular query (so 1d array of what
-// could be a 2d map)
-//
-// the result is a single number that says e.g. chr5 from human mapped to chr5
-// on mouse with 0.8 quality, and that0.8 is then attached to all the pieces of
-// chr5 on human that mapped to chr5 on mouse. if chr5 on human also more
-// weakly mapped to chr6 on mouse, then it would have another value e.g. 0.6.
-// this can show strong and weak levels of synteny, especially in polyploidy
-// situations
 export function getWeightedMeans(ret) {
     const scoreMap = {};
     for (const entry of ret) {
@@ -67,7 +33,6 @@ export function getWeightedMeans(ret) {
     }
     return ret;
 }
-// https://gist.github.com/stekhn/a12ed417e91f90ecec14bcfa4c2ae16a
 function weightedMean(tuples) {
     const [valueSum, weightSum] = tuples.reduce(([valueSum, weightSum], [value, weight]) => [
         valueSum + value * weight,

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

@@ -1,13 +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 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);

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;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-comparative-adapters",
-  "version": "2.17.0",
+  "version": "2.18.0",
   "description": "JBrowse 2 comparative adapters",
   "keywords": [
     "jbrowse",
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }