@jbrowse/plugin-alignments 1.6.9 → 1.7.3

package/dist/LinearSNPCoverageDisplay/models/model.js

@@ -0,0 +1,237 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+
+var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
+
+var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+var _mobxStateTree = require("mobx-state-tree");
+
+var _mobx = require("mobx");
+
+var _configuration = require("@jbrowse/core/configuration");
+
+var _pluginWiggle = require("@jbrowse/plugin-wiggle");
+
+var _util = require("@jbrowse/core/util");
+
+var _Tooltip = _interopRequireDefault(require("../components/Tooltip"));
+
+var _shared = require("../../shared");
+
+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; }
+
+// using a map because it preserves order
+var rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
+
+var stateModelFactory = function stateModelFactory(pluginManager, configSchema) {
+  return _mobxStateTree.types.compose('LinearSNPCoverageDisplay', (0, _pluginWiggle.linearWiggleDisplayModelFactory)(pluginManager, configSchema), _mobxStateTree.types.model({
+    type: _mobxStateTree.types.literal('LinearSNPCoverageDisplay'),
+    drawInterbaseCounts: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
+    drawIndicators: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
+    drawArcs: _mobxStateTree.types.maybe(_mobxStateTree.types["boolean"]),
+    filterBy: _mobxStateTree.types.optional(_mobxStateTree.types.model({
+      flagInclude: _mobxStateTree.types.optional(_mobxStateTree.types.number, 0),
+      flagExclude: _mobxStateTree.types.optional(_mobxStateTree.types.number, 1540),
+      readName: _mobxStateTree.types.maybe(_mobxStateTree.types.string),
+      tagFilter: _mobxStateTree.types.maybe(_mobxStateTree.types.model({
+        tag: _mobxStateTree.types.string,
+        value: _mobxStateTree.types.string
+      }))
+    }), {}),
+    colorBy: _mobxStateTree.types.maybe(_mobxStateTree.types.model({
+      type: _mobxStateTree.types.string,
+      tag: _mobxStateTree.types.maybe(_mobxStateTree.types.string)
+    }))
+  }))["volatile"](function () {
+    return {
+      modificationTagMap: _mobx.observable.map({})
+    };
+  }).actions(function (self) {
+    return {
+      setConfig: function setConfig(configuration) {
+        self.configuration = configuration;
+      },
+      setFilterBy: function setFilterBy(filter) {
+        self.filterBy = (0, _mobxStateTree.cast)(filter);
+      },
+      setColorBy: function setColorBy(colorBy) {
+        self.colorBy = (0, _mobxStateTree.cast)(colorBy);
+      },
+      updateModificationColorMap: function updateModificationColorMap(uniqueModifications) {
+        var colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
+        var i = 0;
+        uniqueModifications.forEach(function (value) {
+          if (!self.modificationTagMap.has(value)) {
+            var newColor = colorPalette[i++];
+            self.modificationTagMap.set(value, newColor);
+          }
+        });
+      }
+    };
+  }).views(function (self) {
+    var superRenderProps = self.renderProps;
+    return {
+      get rendererConfig() {
+        var configBlob = (0, _configuration.getConf)(self, ['renderers', self.rendererTypeName]) || {};
+        return self.rendererType.configSchema.create(_objectSpread(_objectSpread({}, configBlob), {}, {
+          drawInterbaseCounts: self.drawInterbaseCounts === undefined ? configBlob.drawInterbaseCounts : self.drawInterbaseCounts,
+          drawIndicators: self.drawIndicators === undefined ? configBlob.drawIndicators : self.drawIndicators,
+          drawArcs: self.drawArcs === undefined ? configBlob.drawArcs : self.drawArcs
+        }), (0, _mobxStateTree.getEnv)(self));
+      },
+
+      get drawArcsSetting() {
+        return self.drawArcs !== undefined ? self.drawArcs : (0, _configuration.readConfObject)(this.rendererConfig, 'drawArcs');
+      },
+
+      get drawInterbaseCountsSetting() {
+        return self.drawInterbaseCounts !== undefined ? self.drawInterbaseCounts : (0, _configuration.readConfObject)(this.rendererConfig, 'drawInterbaseCounts');
+      },
+
+      get drawIndicatorsSetting() {
+        return self.drawIndicators !== undefined ? self.drawIndicators : (0, _configuration.readConfObject)(this.rendererConfig, 'drawIndicators');
+      },
+
+      get modificationsReady() {
+        var _self$colorBy;
+
+        return ((_self$colorBy = self.colorBy) === null || _self$colorBy === void 0 ? void 0 : _self$colorBy.type) === 'modifications' ? Object.keys(JSON.parse(JSON.stringify(self.modificationTagMap))).length > 0 : true;
+      },
+
+      renderProps: function renderProps() {
+        var superProps = superRenderProps();
+        return _objectSpread(_objectSpread({}, superProps), {}, {
+          notReady: superProps.notReady || !this.modificationsReady,
+          modificationTagMap: JSON.parse(JSON.stringify(self.modificationTagMap)),
+          // must use getSnapshot because otherwise changes to e.g. just the
+          // colorBy.type are not read
+          colorBy: self.colorBy ? (0, _mobxStateTree.getSnapshot)(self.colorBy) : undefined,
+          filterBy: self.filterBy
+        });
+      }
+    };
+  }).actions(function (self) {
+    return {
+      toggleDrawIndicators: function toggleDrawIndicators() {
+        self.drawIndicators = !self.drawIndicatorsSetting;
+      },
+      toggleDrawInterbaseCounts: function toggleDrawInterbaseCounts() {
+        self.drawInterbaseCounts = !self.drawInterbaseCountsSetting;
+      },
+      toggleDrawArcs: function toggleDrawArcs() {
+        self.drawArcs = !self.drawArcsSetting;
+      },
+      afterAttach: function afterAttach() {
+        (0, _mobxStateTree.addDisposer)(self, (0, _mobx.autorun)( /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_regenerator["default"].mark(function _callee() {
+          var colorBy, _ref2, staticBlocks, vals;
+
+          return _regenerator["default"].wrap(function _callee$(_context) {
+            while (1) {
+              switch (_context.prev = _context.next) {
+                case 0:
+                  _context.prev = 0;
+                  colorBy = self.colorBy;
+                  _ref2 = (0, _util.getContainingView)(self), staticBlocks = _ref2.staticBlocks;
+
+                  if (!((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications')) {
+                    _context.next = 8;
+                    break;
+                  }
+
+                  _context.next = 6;
+                  return (0, _shared.getUniqueModificationValues)(self, (0, _configuration.getConf)(self.parentTrack, 'adapter'), colorBy, staticBlocks);
+
+                case 6:
+                  vals = _context.sent;
+                  self.updateModificationColorMap(vals);
+
+                case 8:
+                  _context.next = 14;
+                  break;
+
+                case 10:
+                  _context.prev = 10;
+                  _context.t0 = _context["catch"](0);
+                  console.error(_context.t0);
+                  self.setError(_context.t0);
+
+                case 14:
+                case "end":
+                  return _context.stop();
+              }
+            }
+          }, _callee, null, [[0, 10]]);
+        })), {
+          delay: 1000
+        }));
+      }
+    };
+  }).views(function (self) {
+    var superTrackMenuItems = self.trackMenuItems;
+    return {
+      get TooltipComponent() {
+        return _Tooltip["default"];
+      },
+
+      get adapterConfig() {
+        var subadapter = (0, _configuration.getConf)(self.parentTrack, 'adapter');
+        return {
+          type: 'SNPCoverageAdapter',
+          subadapter: subadapter
+        };
+      },
+
+      get rendererTypeName() {
+        return rendererTypes.get('snpcoverage');
+      },
+
+      get needsScalebar() {
+        return true;
+      },
+
+      contextMenuItems: function contextMenuItems() {
+        return [];
+      },
+      trackMenuItems: function trackMenuItems() {
+        return [].concat((0, _toConsumableArray2["default"])(superTrackMenuItems()), [{
+          label: 'Draw insertion/clipping indicators',
+          type: 'checkbox',
+          checked: self.drawIndicatorsSetting,
+          onClick: function onClick() {
+            self.toggleDrawIndicators();
+          }
+        }, {
+          label: 'Draw insertion/clipping counts',
+          type: 'checkbox',
+          checked: self.drawInterbaseCountsSetting,
+          onClick: function onClick() {
+            self.toggleDrawInterbaseCounts();
+          }
+        }, {
+          label: 'Draw arcs',
+          type: 'checkbox',
+          checked: self.drawArcsSetting,
+          onClick: function onClick() {
+            self.toggleDrawArcs();
+          }
+        }]);
+      }
+    };
+  });
+};
+
+var _default = stateModelFactory;
+exports["default"] = _default;

package/dist/NestedFrequencyTable.d.ts

@@ -1,14 +1,14 @@
-export default class NestedFrequencyTable {
-    categories: {
-        [key: string]: any;
-    };
-    constructor(initialData?: {});
-    total(): number;
-    decrement(slotName: string, amount: number): any;
-    increment(slotName: string, amount: number): any;
-    get(slotName: string): any;
-    getNested(path: string | string[]): any;
-    toString(): string;
-    valueOf(): number;
-    forEach(func: Function, ctx: any): void;
-}
+export default class NestedFrequencyTable {
+    categories: {
+        [key: string]: any;
+    };
+    constructor(initialData?: {});
+    total(): number;
+    decrement(slotName: string, amount: number): any;
+    increment(slotName: string, amount: number): any;
+    get(slotName: string): any;
+    getNested(path: string | string[]): any;
+    toString(): string;
+    valueOf(): number;
+    forEach(func: Function, ctx: any): void;
+}

package/dist/NestedFrequencyTable.js

@@ -0,0 +1,152 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports["default"] = void 0;
+
+var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+
+var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+
+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); 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; }
+
+/* eslint-disable @typescript-eslint/no-explicit-any */
+// see perf results on object.keys vs for-in loop
+// https://jsperf.com/object-keys-vs-hasownproperty/55
+var NestedFrequencyTable = /*#__PURE__*/function () {
+  function NestedFrequencyTable() {
+    var initialData = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};
+    (0, _classCallCheck2["default"])(this, NestedFrequencyTable);
+    (0, _defineProperty2["default"])(this, "categories", void 0);
+    this.categories = _objectSpread({}, initialData);
+  } // get the sum of all the category counts
+
+
+  (0, _createClass2["default"])(NestedFrequencyTable, [{
+    key: "total",
+    value: function total() {
+      // calculate total if necessary
+      var t = 0;
+
+      for (var k in this.categories) {
+        var v = this.categories[k];
+        t += v.total ? v.total() : v;
+      }
+
+      return t;
+    } // decrement the count for the given category
+
+  }, {
+    key: "decrement",
+    value: function decrement(slotName, amount) {
+      if (!amount) {
+        amount = 1;
+      }
+
+      if (!slotName) {
+        slotName = 'default';
+      } else {
+        slotName = slotName.toString();
+      }
+
+      if (this.categories[slotName]) {
+        this.categories[slotName] = Math.max(0, this.categories[slotName] - amount);
+        return this.categories[slotName];
+      }
+
+      return 0;
+    } // increment the count for the given category
+
+  }, {
+    key: "increment",
+    value: function increment(slotName, amount) {
+      if (!amount) {
+        amount = 1;
+      }
+
+      if (!slotName) {
+        slotName = 'default';
+      } else {
+        slotName = slotName.toString();
+      }
+
+      this.categories[slotName] = (this.categories[slotName] || 0) + amount;
+      return this.categories[slotName];
+    } // get the value of the given category.  may be a number or a
+    // frequency table.
+
+  }, {
+    key: "get",
+    value: function get(slotName) {
+      return this.categories[slotName] || 0;
+    } // get a given category as a frequency table
+
+  }, {
+    key: "getNested",
+    value: function getNested(path) {
+      if (typeof path === 'string') {
+        path = path.split('/');
+      }
+
+      if (!path.length) {
+        return this;
+      }
+
+      var slotName = path[0].toString();
+      var slot = this.categories[slotName];
+
+      if (!slot || !slot.categories) {
+        this.categories[slotName] = new NestedFrequencyTable(slot ? {
+          "default": slot + 0
+        } : {});
+      }
+
+      slot = this.categories[slotName];
+
+      if (path.length > 1) {
+        return slot.getNested(path.slice(1));
+      }
+
+      return slot;
+    }
+  }, {
+    key: "toString",
+    value: function toString() {
+      return this.total().toPrecision(6).toString().replace(/\.?0+$/, '');
+    }
+  }, {
+    key: "valueOf",
+    value: function valueOf() {
+      return this.total();
+    } // iterate through the categories and counts, call like:
+    //
+    //   tbl.forEach( function( count, categoryName ) {
+    //      // do something
+    //   }, this );
+    //
+
+  }, {
+    key: "forEach",
+    value: function forEach(func, ctx) {
+      if (ctx) {
+        for (var slotName in this.categories) {
+          func.call(ctx, this.categories[slotName], slotName);
+        }
+      } else {
+        for (var _slotName in this.categories) {
+          func(this.categories[_slotName], _slotName);
+        }
+      }
+    }
+  }]);
+  return NestedFrequencyTable;
+}();
+
+exports["default"] = NestedFrequencyTable;

package/dist/PileupRPC/rpcMethods.d.ts

@@ -1,34 +1,34 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-import { Region } from '@jbrowse/core/util/types';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
-export declare class PileupGetGlobalValueForTag extends RpcMethodType {
-    name: string;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: Function;
-    }, rpcDriverClassName: string): Promise<{}>;
-    execute(args: {
-        adapterConfig: {};
-        signal?: RemoteAbortSignal;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriverClassName: string): Promise<string[]>;
-}
-export declare class PileupGetVisibleModifications extends RpcMethodType {
-    name: string;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: Function;
-    }, rpcDriverClassName: string): Promise<{}>;
-    execute(args: {
-        adapterConfig: {};
-        signal?: RemoteAbortSignal;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriverClassName: string): Promise<string[]>;
-}
+import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
+import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
+import { Region } from '@jbrowse/core/util/types';
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
+export declare class PileupGetGlobalValueForTag extends RpcMethodType {
+    name: string;
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: Function;
+    }, rpcDriverClassName: string): Promise<{}>;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sessionId: string;
+        tag: string;
+    }, rpcDriverClassName: string): Promise<string[]>;
+}
+export declare class PileupGetVisibleModifications extends RpcMethodType {
+    name: string;
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: Function;
+    }, rpcDriverClassName: string): Promise<{}>;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        headers?: Record<string, string>;
+        regions: Region[];
+        sessionId: string;
+        tag: string;
+    }, rpcDriverClassName: string): Promise<string[]>;
+}