@jbrowse/plugin-sequence 1.5.8 → 1.6.2

package/dist/IndexedFastaAdapter/IndexedFastaAdapter.d.ts

@@ -1,11 +1,11 @@
 import { IndexedFasta } from '@gmod/indexedfasta';
-import { BaseFeatureDataAdapter, SequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseSequenceAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-export default class extends BaseFeatureDataAdapter implements SequenceAdapter {
+export default class extends BaseSequenceAdapter {
     protected fasta: IndexedFasta;
     private seqCache;
     constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);

package/dist/LinearReferenceSequenceDisplay/model.d.ts

@@ -53,6 +53,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearReferenceSequenceDisplay">;
     configuration: import("mobx-state-tree").ITypeUnion<any, any, any>;
@@ -113,15 +114,17 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     setRpcDriverName(rpcDriverName: string): void;
     reload(): void;
 } & {
+    currBpPerPx: number;
     message: string;
     featureIdUnderMouse: string | undefined;
     contextMenuFeature: import("@jbrowse/core/util/simpleFeature").Feature | undefined;
     scrollTop: number;
+    estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
+    estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
     readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
-    readonly maxViewBpPerPx: any;
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
     readonly selectedFeatureId: string | undefined;
@@ -132,14 +135,28 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     getFeatureOverlapping(blockKey: string, x: number, y: number): any;
     getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    readonly currentBytesRequested: number;
+    readonly currentFeatureScreenDensity: number;
+    readonly maxFeatureScreenDensity: any;
+    readonly estimatedStatsReady: boolean;
+    readonly maxAllowableBytes: number;
 } & {
+    setMessage(message: string): void;
     afterAttach(): void;
+    estimateRegionsStats(regions: import("@jbrowse/core/util").Region[], opts: {
+        headers?: Record<string, string> | undefined;
+        signal?: AbortSignal | undefined;
+        filters?: string[] | undefined;
+    }): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    setRegionStatsP(p?: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined): void;
+    setRegionStats(estimatedRegionStats?: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined): void;
+    clearRegionStats(): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
     setScrollTop(scrollTop: number): void;
-    setUserBpPerPxLimit(limit: number): void;
-    setMessage(message: string): void;
+    updateStatsLimit(stats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats): void;
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
+    setCurrBpPerPx(n: number): void;
     deleteBlock(key: string): void;
     selectFeature(feature: import("@jbrowse/core/util/simpleFeature").Feature): void;
     clearFeatureSelection(): void;
@@ -147,7 +164,13 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     reload(): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util/simpleFeature").Feature | undefined): void;
 } & {
-    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Zoom in to see features";
+    readonly regionTooLarge: boolean;
+    readonly regionTooLargeReason: string;
+} & {
+    reload(): Promise<void>;
+    afterAttach(): void;
+} & {
+    regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): JSX.Element | undefined;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
@@ -157,7 +180,7 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     }[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").ExportSvgOptions & {
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view/dist/LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
     }): Promise<JSX.Element>;
 } & {
@@ -181,4 +204,5 @@ export declare function modelFactory(configSchema: AnyConfigurationSchemaType):
     rpcDriverName: string | undefined;
     height: number;
     userBpPerPxLimit: number | undefined;
+    userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;

package/dist/TwoBitAdapter/TwoBitAdapter.d.ts

@@ -1,10 +1,10 @@
-import { BaseFeatureDataAdapter, SequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import { NoAssemblyRegion } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
-export default class TwoBitAdapter extends BaseFeatureDataAdapter implements SequenceAdapter {
+export default class TwoBitAdapter extends BaseSequenceAdapter {
     private twobit;
     protected chromSizesData: Promise<Record<string, number> | undefined>;
     private initChromSizes;

package/dist/plugin-sequence.cjs.development.js

@@ -12,10 +12,10 @@ var Plugin = _interopDefault(require('@jbrowse/core/Plugin'));
 var pluginLinearGenomeView = require('@jbrowse/plugin-linear-genome-view');
 var tracks = require('@jbrowse/core/util/tracks');
 var configuration = require('@jbrowse/core/configuration');
+var React = _interopDefault(require('react'));
 var color = require('@jbrowse/core/util/color');
 var ui = require('@jbrowse/core/ui');
 var mobxReact = require('mobx-react');
-var React = _interopDefault(require('react'));
 var util = require('@jbrowse/core/util');
 var mobxStateTree = require('mobx-state-tree');
 var BaseAdapter = require('@jbrowse/core/data_adapters/BaseAdapter');
@@ -135,14 +135,14 @@ function _inherits(subClass, superClass) {
     throw new TypeError("Super expression must either be null or a function");
   }
 
+  subClass.prototype = Object.create(superClass && superClass.prototype, {
+    constructor: {
+      value: subClass,
+      writable: true,
+      configurable: true
+    }
+  });
   Object.defineProperty(subClass, "prototype", {
-    value: Object.create(superClass && superClass.prototype, {
-      constructor: {
-        value: subClass,
-        writable: true,
-        configurable: true
-      }
-    }),
     writable: false
   });
   if (superClass) _setPrototypeOf(subClass, superClass);
@@ -512,6 +512,7 @@ var Wrapper = function Wrapper(_ref3) {
       totalHeight = _ref3.totalHeight,
       children = _ref3.children;
   return exportSVG ? React.createElement(React.Fragment, null, children) : React.createElement("svg", {
+    "data-testid": "sequence_track",
     width: width,
     height: totalHeight,
     style: {
@@ -834,12 +835,15 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           var regexGuess = /\.2bit$/i;
           var adapterName = 'TwoBitAdapter';
           var fileName = tracks.getFileName(file);
+          var obj = {
+            type: adapterName,
+            twoBitLocation: file
+          };
 
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              twoBitLocation: file
-            };
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
           }
 
           return adapterGuesser(file, index, adapterHint);
@@ -893,13 +897,16 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           var regexGuess = /\.(fa|fasta|fas|fna|mfa)$/i;
           var adapterName = 'IndexedFastaAdapter';
           var fileName = tracks.getFileName(file);
+          var obj = {
+            type: adapterName,
+            fastaLocation: file,
+            faiLocation: index || tracks.makeIndex(file, '.fai')
+          };
 
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              fastaLocation: file,
-              faiLocation: index || tracks.makeIndex(file, '.fai')
-            };
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
           }
 
           return adapterGuesser(file, index, adapterHint);
@@ -936,13 +943,16 @@ var SequencePlugin = /*#__PURE__*/function (_Plugin) {
           var regexGuess = /\.(fa|fasta|fas|fna|mfa)\.b?gz$/i;
           var adapterName = 'BgzipFastaAdapter';
           var fileName = tracks.getFileName(file);
+          var obj = {
+            type: adapterName,
+            faiLocation: tracks.makeIndex(file, '.fai'),
+            gziLocation: tracks.makeIndex(file, '.gzi')
+          };
 
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              faiLocation: tracks.makeIndex(file, '.fai'),
-              gziLocation: tracks.makeIndex(file, '.gzi')
-            };
+          if (regexGuess.test(fileName) && !adapterHint) {
+            return obj;
+          } else if (adapterHint === adapterName) {
+            return obj;
           }
 
           return adapterGuesser(file, index, adapterHint);
@@ -1836,8 +1846,9 @@ var default_1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
       this.gcMode = 'content';
       return rxjs.ObservableCreate( /*#__PURE__*/function () {
         var _ref = _asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee3(observer) {
-          var sequenceAdapter, hw, f, queryStart, queryEnd, ret, _yield$ret$pipe$toPro, _yield$ret$pipe$toPro2, feat, residues, i, r, nc, ng, len, j, pos, score;
+          var _feats$;
 
+          var sequenceAdapter, hw, f, queryStart, queryEnd, ret, feats, residues, i, r, nc, ng, len, j, pos, score;
           return runtime_1.wrap(function _callee3$(_context3) {
             while (1) {
               switch (_context3.prev = _context3.next) {
@@ -1866,15 +1877,13 @@ var default_1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                   ret = sequenceAdapter.getFeatures(_objectSpread2(_objectSpread2({}, query), {}, {
                     start: queryStart,
                     end: queryEnd
-                  }), opts);
+                  }));
                   _context3.next = 14;
                   return ret.pipe(operators.toArray()).toPromise();
 
                 case 14:
-                  _yield$ret$pipe$toPro = _context3.sent;
-                  _yield$ret$pipe$toPro2 = _slicedToArray(_yield$ret$pipe$toPro, 1);
-                  feat = _yield$ret$pipe$toPro2[0];
-                  residues = feat.get('seq');
+                  feats = _context3.sent;
+                  residues = ((_feats$ = feats[0]) === null || _feats$ === void 0 ? void 0 : _feats$.get('seq')) || '';
 
                   for (i = hw; i < residues.length - hw; i += _this2.windowDelta) {
                     r = f ? residues[i] : residues.slice(i - hw, i + hw);
@@ -1901,20 +1910,19 @@ var default_1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
                       score = (ng + nc) / (len || 1);
                     } else if (_this2.gcMode === 'skew') {
                       score = (ng - nc) / (ng + nc || 1);
-                    } // if (r[Math.floor(r.length / 2)] !== 'N') {
-
+                    }
 
                     observer.next(new SimpleFeature({
                       uniqueId: "".concat(_this2.id, "_").concat(pos + i),
                       start: pos + i,
                       end: pos + i + _this2.windowDelta,
                       score: score
-                    })); // }
+                    }));
                   }
 
                   observer.complete();
 
-                case 20:
+                case 18:
                 case "end":
                   return _context3.stop();
               }
@@ -1949,8 +1957,8 @@ var GCContentAdapter = {
   'default': default_1
 };
 
-var TwoBitAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  _inherits(TwoBitAdapter, _BaseFeatureDataAdapt);
+var TwoBitAdapter = /*#__PURE__*/function (_BaseSequenceAdapter) {
+  _inherits(TwoBitAdapter, _BaseSequenceAdapter);
 
   var _super = /*#__PURE__*/_createSuper(TwoBitAdapter);
 
@@ -2188,7 +2196,7 @@ var TwoBitAdapter = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }]);
 
   return TwoBitAdapter;
-}(BaseAdapter.BaseFeatureDataAdapter);
+}(BaseAdapter.BaseSequenceAdapter);
 
 var TwoBitAdapter$1 = {
   __proto__: null,
@@ -2324,8 +2332,8 @@ var ChromSizesAdapter = {
   'default': _default
 };
 
-var _default$1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
-  _inherits(_default, _BaseFeatureDataAdapt);
+var _default$1 = /*#__PURE__*/function (_BaseSequenceAdapter) {
+  _inherits(_default, _BaseSequenceAdapter);
 
   var _super = /*#__PURE__*/_createSuper(_default);
 
@@ -2505,7 +2513,7 @@ var _default$1 = /*#__PURE__*/function (_BaseFeatureDataAdapt) {
   }]);
 
   return _default;
-}(BaseAdapter.BaseFeatureDataAdapter);
+}(BaseAdapter.BaseSequenceAdapter);
 
 var IndexedFastaAdapter = {
   __proto__: null,