@jbrowse/core 2.0.0 → 2.0.1

package/BaseFeatureWidget/BaseFeatureDetail.d.ts

@@ -34,7 +34,7 @@ export declare const BaseCoreDetails: (props: BaseProps) => JSX.Element;
 interface AttributeProps {
     attributes: Record<string, any>;
     omit?: string[];
-    formatter?: (val: unknown, key: string) => React.ReactElement;
+    formatter?: (val: unknown, key: string) => React.ReactNode;
     descriptions?: Record<string, React.ReactNode>;
     prefix?: string[];
 }
@@ -44,14 +44,14 @@ export interface BaseInputProps extends BaseCardProps {
     omit?: string[];
     model: any;
     descriptions?: Record<string, React.ReactNode>;
-    formatter?: (val: unknown, key: string) => React.ReactElement;
+    formatter?: (val: unknown, key: string) => React.ReactNode;
 }
 export declare const FeatureDetails: (props: {
     model: IAnyStateTreeNode;
     feature: SimpleFeatureSerialized;
     depth?: number | undefined;
     omit?: string[] | undefined;
-    formatter?: ((val: unknown, key: string) => React.ReactElement) | undefined;
+    formatter?: ((val: unknown, key: string) => React.ReactNode) | undefined;
 }) => JSX.Element;
 declare const BaseFeatureDetails: (props: BaseInputProps) => JSX.Element | null;
 export default BaseFeatureDetails;

package/BaseFeatureWidget/BaseFeatureDetail.js

@@ -292,22 +292,33 @@ function CoreDetails(props) {
     position: "".concat(refName, ":").concat(toLocale(start + 1), "..").concat(toLocale(end), " ").concat(str)
   });
 
-  var coreRenderedDetails = ['Position', 'Description', 'Name', 'Length', 'Type'];
-  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, coreRenderedDetails.map(function (key) {
-    return [key, displayedDetails[key.toLowerCase()]];
-  }).filter(function (_ref6) {
+  var coreRenderedDetails = {
+    position: 'Position',
+    description: 'Description',
+    name: 'Name',
+    length: 'Length',
+    type: 'Type',
+    assemblyName: 'Assembly name'
+  };
+  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, Object.entries(coreRenderedDetails).map(function (_ref6) {
     var _ref7 = (0, _slicedToArray2.default)(_ref6, 2),
-        value = _ref7[1];
+        key = _ref7[0],
+        name = _ref7[1];
 
-    return value !== null && value !== undefined;
-  }).map(function (_ref8) {
+    return [name, displayedDetails[key]];
+  }).filter(function (_ref8) {
     var _ref9 = (0, _slicedToArray2.default)(_ref8, 2),
-        key = _ref9[0],
         value = _ref9[1];
 
+    return value !== null && value !== undefined;
+  }).map(function (_ref10) {
+    var _ref11 = (0, _slicedToArray2.default)(_ref10, 2),
+        name = _ref11[0],
+        value = _ref11[1];
+
     return /*#__PURE__*/_react.default.createElement(SimpleValue, {
-      key: key,
-      name: key,
+      key: name,
+      name: name,
       value: value
     });
   }));
@@ -321,10 +332,10 @@ var BaseCoreDetails = function BaseCoreDetails(props) {
 
 exports.BaseCoreDetails = BaseCoreDetails;
 
-var DataGridDetails = function DataGridDetails(_ref10) {
-  var value = _ref10.value,
-      prefix = _ref10.prefix,
-      name = _ref10.name;
+var DataGridDetails = function DataGridDetails(_ref12) {
+  var value = _ref12.value,
+      prefix = _ref12.prefix,
+      name = _ref12.name;
   var keys = Object.keys(value[0]).sort();
   var unionKeys = new Set(keys);
   value.forEach(function (val) {
@@ -335,10 +346,10 @@ var DataGridDetails = function DataGridDetails(_ref10) {
 
   if (unionKeys.size < keys.length + 5) {
     // avoids key 'id' from being used in row data
-    var rows = Object.entries(value).map(function (_ref11) {
-      var _ref12 = (0, _slicedToArray2.default)(_ref11, 2),
-          k = _ref12[0],
-          val = _ref12[1];
+    var rows = Object.entries(value).map(function (_ref13) {
+      var _ref14 = (0, _slicedToArray2.default)(_ref13, 2),
+          k = _ref14[0],
+          val = _ref14[1];
 
       var id = val.id,
           rest = (0, _objectWithoutProperties2.default)(val, _excluded);
@@ -422,10 +433,10 @@ function generateMaxWidth(array, prefix) {
   return Math.ceil(Math.max.apply(Math, arr)) + 10;
 }
 
-function UriAttribute(_ref13) {
-  var value = _ref13.value,
-      prefix = _ref13.prefix,
-      name = _ref13.name;
+function UriAttribute(_ref15) {
+  var value = _ref15.value,
+      prefix = _ref15.prefix,
+      name = _ref15.name;
 
   var _useStyles6 = useStyles(),
       classes = _useStyles6.classes;
@@ -468,23 +479,23 @@ function Attributes(props) {
 
   var formattedAttributes = _objectSpread(_objectSpread({}, rest), __jbrowsefmt);
 
-  var maxLabelWidth = generateMaxWidth(Object.entries(formattedAttributes).filter(function (_ref14) {
-    var _ref15 = (0, _slicedToArray2.default)(_ref14, 2),
-        k = _ref15[0],
-        v = _ref15[1];
-
-    return v !== undefined && !omits.includes(k);
-  }), prefix);
-  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, Object.entries(formattedAttributes).filter(function (_ref16) {
+  var maxLabelWidth = generateMaxWidth(Object.entries(formattedAttributes).filter(function (_ref16) {
     var _ref17 = (0, _slicedToArray2.default)(_ref16, 2),
         k = _ref17[0],
         v = _ref17[1];
 
     return v !== undefined && !omits.includes(k);
-  }).map(function (_ref18) {
+  }), prefix);
+  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, Object.entries(formattedAttributes).filter(function (_ref18) {
     var _ref19 = (0, _slicedToArray2.default)(_ref18, 2),
-        key = _ref19[0],
-        value = _ref19[1];
+        k = _ref19[0],
+        v = _ref19[1];
+
+    return v !== undefined && !omits.includes(k);
+  }).map(function (_ref20) {
+    var _ref21 = (0, _slicedToArray2.default)(_ref20, 2),
+        key = _ref21[0],
+        value = _ref21[1];
 
     var description = accessNested([].concat((0, _toConsumableArray2.default)(prefix), [key]), descriptions);
 
@@ -511,13 +522,13 @@ function Attributes(props) {
         name: key,
         prefix: prefix,
         value: value
-      }) : /*#__PURE__*/_react.default.createElement(Attributes, {
+      }) : /*#__PURE__*/_react.default.createElement(Attributes, (0, _extends2.default)({}, props, {
         omit: omits,
         key: key,
         attributes: value,
         descriptions: descriptions,
         prefix: [].concat((0, _toConsumableArray2.default)(prefix), [key])
-      });
+      }));
     } else {
       return /*#__PURE__*/_react.default.createElement(SimpleValue, {
         key: key,
@@ -576,8 +587,8 @@ var FeatureDetails = function FeatureDetails(props) {
   }, props, {
     omit: [].concat((0, _toConsumableArray2.default)(omit), coreDetails)
   })), sequenceTypes.includes(feature.type) ? /*#__PURE__*/_react.default.createElement(_reactErrorBoundary.ErrorBoundary, {
-    FallbackComponent: function FallbackComponent(_ref20) {
-      var error = _ref20.error;
+    FallbackComponent: function FallbackComponent(_ref22) {
+      var error = _ref22.error;
       return /*#__PURE__*/_react.default.createElement(_material.Typography, {
         color: "error"
       }, "".concat(error));

package/BaseFeatureWidget/SequenceFeatureDetails.js

@@ -195,6 +195,7 @@ var SequencePanel = /*#__PURE__*/_react.default.forwardRef(function (_ref4, ref)
     style: {
       fontFamily: 'monospace',
       wordWrap: 'break-word',
+      fontSize: 12,
       maxWidth: 600
     }
   }, ">".concat(feature.name || feature.id || 'unknown', "-").concat(mode, "\n"), mode === 'cds' ? /*#__PURE__*/_react.default.createElement(GeneCDS, {

package/BaseFeatureWidget/types.d.ts

@@ -4,6 +4,7 @@ import { SimpleFeatureSerialized } from '../util/simpleFeature';
 import { AbstractViewModel } from '../util';
 export interface BaseProps extends BaseCardProps {
     feature: SimpleFeatureSerialized;
+    formatter?: (val: unknown, key: string) => React.ReactNode;
     descriptions?: Record<string, React.ReactNode>;
     model?: IAnyStateTreeNode & {
         view?: AbstractViewModel & {

package/PluginManager.d.ts

@@ -162,30 +162,22 @@ export default class PluginManager {
             readonly maxOffset: number;
             readonly minOffset: number;
             readonly totalBp: number;
+        } & {
+            readonly dynamicBlocks: import("./util/blockTypes").BlockSet;
+            readonly staticBlocks: import("./util/blockTypes").BlockSet;
+            readonly currBp: number;
+        } & {
             pxToBp(px: number): {
-                oob: boolean;
-                coord: number;
-                offset: number;
-                index: number;
-                refName: string;
-                start: number;
-                end: number;
-                reversed: boolean;
-                assemblyName: string;
-            } | {
                 coord: number;
                 index: number;
-                start: number;
                 refName: string;
                 oob: boolean;
                 assemblyName: string;
                 offset: number;
+                start: number;
+                end: number;
                 reversed: boolean;
             };
-        } & {
-            readonly dynamicBlocks: import("./util/blockTypes").BlockSet;
-            readonly staticBlocks: import("./util/blockTypes").BlockSet;
-            readonly currBp: number;
             bpToPx({ refName, coord, regionNumber, }: {
                 refName: string;
                 coord: number;
@@ -193,15 +185,15 @@ export default class PluginManager {
             }): number | undefined;
         } & {
             setFeatures(features: import("./util").Feature[]): void;
-            zoomToDisplayedRegions(leftPx: import("./util/Base1DViewModel").BpOffset | undefined, rightPx: import("./util/Base1DViewModel").BpOffset | undefined): void;
             showAllRegions(): void;
-            moveTo(start: import("./util/Base1DViewModel").BpOffset, end: import("./util/Base1DViewModel").BpOffset): void;
             zoomOut(): void;
             zoomIn(): void;
-            zoomTo(newBpPerPx: number, offset?: number): void;
+            zoomTo(newBpPerPx: number, offset?: number): number;
             scrollTo(offsetPx: number): number;
-            centerAt(coord: number, refName: string, regionNumber: number): void;
+            centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
             scroll(distance: number): number;
+        } & {
+            moveTo(start?: import("./util/Base1DUtils").BpOffset | undefined, end?: import("./util/Base1DUtils").BpOffset | undefined): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
         '@jbrowse/core/util/io': typeof import("./util/io");
         '@jbrowse/core/util/mst-reflection': typeof import("./util/mst-reflection");

package/ReExports/modules.d.ts

@@ -86,30 +86,22 @@ declare const libs: {
         readonly maxOffset: number;
         readonly minOffset: number;
         readonly totalBp: number;
+    } & {
+        readonly dynamicBlocks: import("../util/blockTypes").BlockSet;
+        readonly staticBlocks: import("../util/blockTypes").BlockSet;
+        readonly currBp: number;
+    } & {
         pxToBp(px: number): {
-            oob: boolean;
-            coord: number;
-            offset: number;
-            index: number;
-            refName: string;
-            start: number;
-            end: number;
-            reversed: boolean;
-            assemblyName: string;
-        } | {
             coord: number;
             index: number;
-            start: number;
             refName: string;
             oob: boolean;
             assemblyName: string;
             offset: number;
+            start: number;
+            end: number;
             reversed: boolean;
         };
-    } & {
-        readonly dynamicBlocks: import("../util/blockTypes").BlockSet;
-        readonly staticBlocks: import("../util/blockTypes").BlockSet;
-        readonly currBp: number;
         bpToPx({ refName, coord, regionNumber, }: {
             refName: string;
             coord: number;
@@ -117,15 +109,15 @@ declare const libs: {
         }): number | undefined;
     } & {
         setFeatures(features: coreUtil.Feature[]): void;
-        zoomToDisplayedRegions(leftPx: import("../util/Base1DViewModel").BpOffset | undefined, rightPx: import("../util/Base1DViewModel").BpOffset | undefined): void;
         showAllRegions(): void;
-        moveTo(start: import("../util/Base1DViewModel").BpOffset, end: import("../util/Base1DViewModel").BpOffset): void;
         zoomOut(): void;
         zoomIn(): void;
-        zoomTo(newBpPerPx: number, offset?: number): void;
+        zoomTo(newBpPerPx: number, offset?: number): number;
         scrollTo(offsetPx: number): number;
-        centerAt(coord: number, refName: string, regionNumber: number): void;
+        centerAt(coord: number, refName: string | undefined, regionNumber: number): void;
         scroll(distance: number): number;
+    } & {
+        moveTo(start?: import("../util/Base1DUtils").BpOffset | undefined, end?: import("../util/Base1DUtils").BpOffset | undefined): void;
     }, mst._NotCustomized, mst._NotCustomized>;
     '@jbrowse/core/util/io': typeof coreIo;
     '@jbrowse/core/util/mst-reflection': typeof coreMstReflection;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/core",
-  "version": "2.0.0",
+  "version": "2.0.1",
   "description": "JBrowse 2 core libraries used by plugins",
   "keywords": [
     "jbrowse",
@@ -74,5 +74,5 @@
     "access": "public",
     "directory": "dist"
   },
-  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
+  "gitHead": "ed935bf5612af3818abdc8ef52d100d5d81d33a2"
 }

package/pluggableElementTypes/renderers/FeatureRendererType.js

@@ -35,6 +35,8 @@ var _dataAdapterCache = require("../../data_adapters/dataAdapterCache");
 
 var _ServerSideRendererType = _interopRequireDefault(require("./ServerSideRendererType"));
 
+var _BaseAdapter = require("../../data_adapters/BaseAdapter");
+
 function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
 
 function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
@@ -159,16 +161,25 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
               case 3:
                 _yield$getAdapter = _context.sent;
                 dataAdapter = _yield$getAdapter.dataAdapter;
+
+                if ((0, _BaseAdapter.isFeatureAdapter)(dataAdapter)) {
+                  _context.next = 7;
+                  break;
+                }
+
+                throw new Error('Adapter does not support retrieving features');
+
+              case 7:
                 features = new Map();
 
                 if (!(!regions || regions.length === 0)) {
-                  _context.next = 8;
+                  _context.next = 10;
                   break;
                 }
 
                 return _context.abrupt("return", features);
 
-              case 8:
+              case 10:
                 requestRegions = regions.map(function (r) {
                   // make sure the requested region's start and end are integers, if
                   // there is a region specification.
@@ -185,13 +196,11 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
                   return requestRegion;
                 });
                 region = requestRegions[0];
-                featureObservable = requestRegions.length === 1 ? dataAdapter.getFeatures(this.getExpandedRegion(region, renderArgs), // @ts-ignore
-                renderArgs) : // @ts-ignore
-                dataAdapter.getFeaturesInMultipleRegions(requestRegions, renderArgs);
-                _context.next = 13;
+                featureObservable = requestRegions.length === 1 ? dataAdapter.getFeatures(this.getExpandedRegion(region, renderArgs), renderArgs) : dataAdapter.getFeaturesInMultipleRegions(requestRegions, renderArgs);
+                _context.next = 15;
                 return featureObservable.pipe((0, _operators.toArray)()).toPromise();
 
-              case 13:
+              case 15:
                 feats = _context.sent;
                 (0, _util.checkAbortSignal)(signal);
                 return _context.abrupt("return", new Map(feats.filter(function (feat) {
@@ -200,7 +209,7 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
                   return [feat.id(), feat];
                 })));
 
-              case 16:
+              case 18:
               case "end":
                 return _context.stop();
             }

package/rpc/coreRpcMethods.d.ts

@@ -72,9 +72,7 @@ export declare class CoreEstimateRegionStats extends RpcMethodType {
         signal?: RemoteAbortSignal;
         headers?: Record<string, string>;
         sessionId: string;
-    }, rpcDriverClassName: string): Promise<import("../data_adapters/BaseAdapter").Stats | {
-        featureDensity: number;
-    }>;
+    }, rpcDriverClassName: string): Promise<import("../data_adapters/BaseAdapter").Stats>;
 }
 /**
  * fetches features from an adapter and call a renderer with them

package/rpc/coreRpcMethods.js

@@ -91,7 +91,7 @@ var CoreGetRefNames = /*#__PURE__*/function (_RpcMethodType) {
                 _yield$getAdapter = _context.sent;
                 dataAdapter = _yield$getAdapter.dataAdapter;
 
-                if (!(dataAdapter instanceof _BaseAdapter.BaseFeatureDataAdapter)) {
+                if (!(0, _BaseAdapter.isFeatureAdapter)(dataAdapter)) {
                   _context.next = 10;
                   break;
                 }
@@ -378,7 +378,7 @@ var CoreGetFeatures = /*#__PURE__*/function (_RpcMethodType4) {
                   break;
                 }
 
-                return _context6.abrupt("return", []);
+                throw new Error('Adapter does not support retrieving features');
 
               case 10:
                 ret = dataAdapter.getFeaturesInMultipleRegions(regions, _objectSpread(_objectSpread({}, opts), {}, {
@@ -590,15 +590,15 @@ var CoreEstimateRegionStats = /*#__PURE__*/function (_RpcMethodType6) {
                 _yield$getAdapter5 = _context10.sent;
                 dataAdapter = _yield$getAdapter5.dataAdapter;
 
-                if (!(dataAdapter instanceof _BaseAdapter.BaseFeatureDataAdapter)) {
+                if ((0, _BaseAdapter.isFeatureAdapter)(dataAdapter)) {
                   _context10.next = 10;
                   break;
                 }
 
-                return _context10.abrupt("return", dataAdapter.estimateRegionsStats(regions, deserializedArgs));
+                throw new Error('Adapter does not support retrieving features');
 
               case 10:
-                throw new Error('Data adapter not found');
+                return _context10.abrupt("return", dataAdapter.estimateRegionsStats(regions, deserializedArgs));
 
               case 11:
               case "end":