@jbrowse/core 1.5.0 → 1.5.4

package/BaseFeatureWidget/BaseFeatureDetail.d.ts

@@ -4,19 +4,21 @@ import { BaseCardProps, BaseProps } from './types';
 import { SimpleFeatureSerialized } from '../util/simpleFeature';
 export declare const useStyles: (props?: any) => import("@material-ui/styles").ClassNameMap<"expandIcon" | "expansionPanelDetails" | "field" | "fieldDescription" | "fieldName" | "fieldValue" | "fieldSubvalue">;
 export declare function BaseCard({ children, title, defaultExpanded, }: BaseCardProps): JSX.Element;
-export declare const FieldName: ({ description, name, prefix, }: {
+export declare const FieldName: ({ description, name, prefix, width, }: {
     description?: React.ReactNode;
     name: string;
     prefix?: string[] | undefined;
+    width?: number | undefined;
 }) => JSX.Element;
 export declare const BasicValue: ({ value }: {
     value: string | React.ReactNode;
 }) => JSX.Element;
-export declare const SimpleValue: ({ name, value, description, prefix, }: {
+export declare const SimpleValue: ({ name, value, description, prefix, width, }: {
     description?: React.ReactNode;
     name: string;
     value: any;
     prefix?: string[] | undefined;
+    width?: number | undefined;
 }) => JSX.Element | null;
 export declare const BaseCoreDetails: (props: BaseProps) => JSX.Element;
 interface AttributeProps {

package/BaseFeatureWidget/BaseFeatureDetail.js

@@ -7,8 +7,9 @@ var _typeof = require("@babel/runtime/helpers/typeof");
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
+exports.BaseAttributes = exports.Attributes = void 0;
 exports.BaseCard = BaseCard;
-exports.default = exports.FeatureDetails = exports.BaseAttributes = exports.Attributes = exports.BaseCoreDetails = exports.SimpleValue = exports.BasicValue = exports.FieldName = exports.useStyles = void 0;
+exports.useStyles = exports.default = exports.SimpleValue = exports.FieldName = exports.FeatureDetails = exports.BasicValue = exports.BaseCoreDetails = void 0;
 
 var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
 
@@ -54,11 +55,12 @@ function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "functio
 
 function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
+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 = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
+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; }
+
+var MAX_FIELD_NAME_WIDTH = 170; // these are always omitted as too detailed
 
-// these are always omitted as too detailed
 var globalOmit = ['length', 'position', 'subfeatures', 'uniqueId', 'exonFrames', 'parentId', 'thickStart', 'thickEnd']; // coreDetails are omitted in some circumstances
 
 var coreDetails = ['name', 'start', 'end', 'strand', 'refName', 'description', 'type'];
@@ -83,7 +85,6 @@ var useStyles = (0, _styles.makeStyles)(function (theme) {
     fieldName: {
       wordBreak: 'break-all',
       minWidth: '90px',
-      maxWidth: '150px',
       borderBottom: '1px solid #0003',
       background: theme.palette.grey[200],
       marginRight: theme.spacing(1),
@@ -145,7 +146,8 @@ var FieldName = function FieldName(_ref2) {
   var description = _ref2.description,
       name = _ref2.name,
       _ref2$prefix = _ref2.prefix,
-      prefix = _ref2$prefix === void 0 ? [] : _ref2$prefix;
+      prefix = _ref2$prefix === void 0 ? [] : _ref2$prefix,
+      width = _ref2.width;
   var classes = useStyles();
   var val = [].concat((0, _toConsumableArray2.default)(prefix), [name]).join('.');
   return description ? /*#__PURE__*/_react.default.createElement(_core.Tooltip, {
@@ -154,7 +156,10 @@ var FieldName = function FieldName(_ref2) {
   }, /*#__PURE__*/_react.default.createElement("div", {
     className: (0, _clsx.default)(classes.fieldDescription, classes.fieldName)
   }, val)) : /*#__PURE__*/_react.default.createElement("div", {
-    className: classes.fieldName
+    className: classes.fieldName,
+    style: {
+      width: width
+    }
   }, val);
 };
 
@@ -176,14 +181,16 @@ var SimpleValue = function SimpleValue(_ref4) {
   var name = _ref4.name,
       value = _ref4.value,
       description = _ref4.description,
-      prefix = _ref4.prefix;
+      prefix = _ref4.prefix,
+      width = _ref4.width;
   var classes = useStyles();
   return value !== null && value !== undefined ? /*#__PURE__*/_react.default.createElement("div", {
     className: classes.field
   }, /*#__PURE__*/_react.default.createElement(FieldName, {
     prefix: prefix,
     description: description,
-    name: name
+    name: name,
+    width: width
   }), /*#__PURE__*/_react.default.createElement(BasicValue, {
     value: value
   })) : null;
@@ -370,6 +377,17 @@ function accessNested(arr) {
   return typeof obj === 'string' ? obj : typeof ((_obj = obj) === null || _obj === void 0 ? void 0 : _obj.Description) === 'string' ? obj.Description : undefined;
 }
 
+function generateMaxWidth(array, prefix) {
+  // @ts-ignore
+  var arr = [];
+  array.forEach(function (key, value) {
+    var val = [].concat((0, _toConsumableArray2.default)(prefix), [key[0]]).join('.');
+    arr.push((0, _util.measureText)(val, 12));
+  }); // @ts-ignore
+
+  return Math.ceil(Math.max.apply(Math, arr)) + 10;
+}
+
 var Attributes = function Attributes(props) {
   var attributes = props.attributes,
       _props$omit = props.omit,
@@ -382,16 +400,24 @@ var Attributes = function Attributes(props) {
       _props$prefix = props.prefix,
       prefix = _props$prefix === void 0 ? [] : _props$prefix;
   var omits = [].concat((0, _toConsumableArray2.default)(omit), globalOmit);
-  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, Object.entries(attributes).filter(function (_ref14) {
+  var maxLabelWidth = generateMaxWidth(Object.entries(attributes).filter(function (_ref14) {
     var _ref15 = (0, _slicedToArray2.default)(_ref14, 2),
         k = _ref15[0],
         v = _ref15[1];
 
     return v !== undefined && !omits.includes(k);
-  }).map(function (_ref16) {
+  }), prefix);
+  var labelWidth = maxLabelWidth <= MAX_FIELD_NAME_WIDTH ? maxLabelWidth : MAX_FIELD_NAME_WIDTH;
+  return /*#__PURE__*/_react.default.createElement(_react.default.Fragment, null, Object.entries(attributes).filter(function (_ref16) {
     var _ref17 = (0, _slicedToArray2.default)(_ref16, 2),
-        key = _ref17[0],
-        value = _ref17[1];
+        k = _ref17[0],
+        v = _ref17[1];
+
+    return v !== undefined && !omits.includes(k);
+  }).map(function (_ref18) {
+    var _ref19 = (0, _slicedToArray2.default)(_ref18, 2),
+        key = _ref19[0],
+        value = _ref19[1];
 
     if (Array.isArray(value) && value.length > 2 && value.every(function (val) {
       return (0, _isObject.default)(val);
@@ -431,7 +457,8 @@ var Attributes = function Attributes(props) {
       name: key,
       value: formatter(value, key),
       description: description,
-      prefix: prefix
+      prefix: prefix,
+      width: labelWidth
     });
   }));
 };
@@ -479,8 +506,8 @@ 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(_ref18) {
-      var error = _ref18.error;
+    FallbackComponent: function FallbackComponent(_ref20) {
+      var error = _ref20.error;
       return /*#__PURE__*/_react.default.createElement(_core.Typography, {
         color: "error"
       }, "Failed to fetch sequence for feature: ", "".concat(error));

package/BaseFeatureWidget/SequenceFeatureDetails.js

@@ -7,8 +7,8 @@ var _typeof = require("@babel/runtime/helpers/typeof");
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.default = SequenceFeatureDetails;
 exports.SequencePanel = void 0;
+exports.default = SequenceFeatureDetails;
 
 var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
 
@@ -38,9 +38,9 @@ function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "functio
 
 function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
 
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
+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 = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
+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; }
 
 var useStyles = (0, _core.makeStyles)(function (theme) {
   return {
@@ -192,7 +192,8 @@ var SequencePanel = /*#__PURE__*/_react.default.forwardRef(function (_ref4, ref)
   }, /*#__PURE__*/_react.default.createElement("div", {
     style: {
       fontFamily: 'monospace',
-      wordWrap: 'break-word'
+      wordWrap: 'break-word',
+      maxWidth: 600
     }
   }, ">".concat(feature.name || feature.id || 'unknown', "-").concat(mode, "\n"), mode === 'cds' ? /*#__PURE__*/_react.default.createElement(GeneCDS, {
     cds: cds,

package/BaseFeatureWidget/index.js

@@ -3,8 +3,8 @@
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.stateModelFactory = exports.default = stateModelFactory;
 exports.configSchema = void 0;
+exports.stateModelFactory = exports.default = stateModelFactory;
 
 var _mobxStateTree = require("mobx-state-tree");
 

package/BaseFeatureWidget/util.js

@@ -5,19 +5,19 @@ var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefau
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
-exports.stitch = stitch;
-exports.dedupe = dedupe;
-exports.revlist = revlist;
 exports.calculateUTRs = calculateUTRs;
+exports.dedupe = dedupe;
 exports.ellipses = ellipses;
+exports.revlist = revlist;
+exports.stitch = stitch;
 
 var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
 
 var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
 
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); if (enumerableOnly) { symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; }); } keys.push.apply(keys, symbols); } return keys; }
+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 = arguments[i] != null ? arguments[i] : {}; if (i % 2) { ownKeys(Object(source), true).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }); } else if (Object.getOwnPropertyDescriptors) { Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)); } else { ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } } return target; }
+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; }
 
 function stitch(subfeats, sequence) {
   return subfeats.map(function (sub) {

package/CorePlugin.d.ts

@@ -1,6 +1,5 @@
 import Plugin from './Plugin';
 import PluginManager from './PluginManager';
-/** the core plugin, which registers types that ALL JBrowse applications are expected to need. */
 export default class CorePlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/CorePlugin.js

@@ -29,10 +29,14 @@ var _BaseFeatureWidget = require("./BaseFeatureWidget");
 
 var _Plugin2 = _interopRequireDefault(require("./Plugin"));
 
+var _AdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
+
 var coreRpcMethods = _interopRequireWildcard(require("./rpc/coreRpcMethods"));
 
 var _WidgetType = _interopRequireDefault(require("./pluggableElementTypes/WidgetType"));
 
+var _CytobandAdapter = require("./data_adapters/CytobandAdapter");
+
 function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
 
 function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
@@ -41,7 +45,8 @@ function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflec
 
 function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
 
-/** the core plugin, which registers types that ALL JBrowse applications are expected to need. */
+// the core plugin, which registers types that ALL JBrowse applications are
+// expected to need.
 var CorePlugin = /*#__PURE__*/function (_Plugin) {
   (0, _inherits2.default)(CorePlugin, _Plugin);
 
@@ -70,6 +75,13 @@ var CorePlugin = /*#__PURE__*/function (_Plugin) {
           return new RpcMethod(pluginManager);
         });
       });
+      pluginManager.addAdapterType(function () {
+        return new _AdapterType.default({
+          name: 'CytobandAdapter',
+          configSchema: _CytobandAdapter.configSchema,
+          AdapterClass: _CytobandAdapter.DataAdapter
+        });
+      });
       pluginManager.addWidgetType(function () {
         return new _WidgetType.default({
           name: 'BaseFeatureWidget',

package/PluginLoader.d.ts

@@ -1,17 +1,40 @@
 import { PluginConstructor } from './Plugin';
 export declare const PluginSourceConfigurationSchema: import("./configuration/configurationSchema").AnyConfigurationSchemaType;
-export interface PluginDefinition {
-    name?: string;
+export interface UMDPluginDefinition {
+    umdUrl: string;
+    name: string;
+}
+export interface LegacyUMDPluginDefinition {
     url: string;
+    name: string;
+}
+export declare function isUMDPluginDefinition(pluginDefinition: PluginDefinition): pluginDefinition is UMDPluginDefinition | LegacyUMDPluginDefinition;
+export interface ESMPluginDefinition {
+    esmUrl: string;
+}
+export declare function isESMPluginDefinition(pluginDefinition: PluginDefinition): pluginDefinition is ESMPluginDefinition;
+export interface CJSPluginDefinition {
+    cjsUrl: string;
+}
+export declare function isCJSPluginDefinition(pluginDefinition: PluginDefinition): pluginDefinition is CJSPluginDefinition;
+export interface PluginDefinition extends Partial<UMDPluginDefinition>, Partial<LegacyUMDPluginDefinition>, Partial<ESMPluginDefinition>, Partial<CJSPluginDefinition> {
 }
 export interface PluginRecord {
     plugin: PluginConstructor;
     definition: PluginDefinition;
 }
+export interface LoadedPlugin {
+    default: PluginConstructor;
+}
 export default class PluginLoader {
     definitions: PluginDefinition[];
     constructor(pluginDefinitions?: PluginDefinition[]);
     loadScript(scriptUrl: string): Promise<void>;
+    loadCJSPlugin(pluginDefinition: CJSPluginDefinition): Promise<LoadedPlugin>;
+    loadESMPlugin(pluginDefinition: ESMPluginDefinition): Promise<LoadedPlugin>;
+    loadUMDPlugin(pluginDefinition: UMDPluginDefinition | LegacyUMDPluginDefinition): Promise<{
+        default: PluginConstructor;
+    }>;
     loadPlugin(definition: PluginDefinition): Promise<PluginConstructor>;
     installGlobalReExports(target: WindowOrWorkerGlobalScope): void;
     load(): Promise<PluginRecord[]>;