@jbrowse/plugin-alignments 1.7.9 → 2.0.0

package/dist/LinearPileupDisplay/model.js.map

@@ -0,0 +1 @@
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package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -5,6 +5,6 @@ declare const SNPCoverageTooltip: (props: {
     height: number;
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;
-    clientRect?: DOMRect;
+    clientRect?: DOMRect | undefined;
 }) => JSX.Element | null;
 export default SNPCoverageTooltip;

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -1,62 +1,110 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _extends2 = _interopRequireDefault(require("@babel/runtime/helpers/extends"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _react = _interopRequireDefault(require("react"));
-
-var _mobxReact = require("mobx-react");
-
-var _pluginWiggle = require("@jbrowse/plugin-wiggle");
-
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+var __rest = (this && this.__rest) || function (s, e) {
+    var t = {};
+    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
+        t[p] = s[p];
+    if (s != null && typeof Object.getOwnPropertySymbols === "function")
+        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
+            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
+                t[p[i]] = s[p[i]];
+        }
+    return t;
+};
+var __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
 /* eslint-disable @typescript-eslint/no-explicit-any */
-var en = function en(n) {
-  return n.toLocaleString('en-US');
+var react_1 = __importDefault(require("react"));
+var mobx_react_1 = require("mobx-react");
+var plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+var en = function (n) { return n.toLocaleString('en-US'); };
+var toP = function (s) {
+    if (s === void 0) { s = 0; }
+    return +(+s).toFixed(1);
 };
-
-var TooltipContents = /*#__PURE__*/_react.default.forwardRef(function (_ref, ref) {
-  var feature = _ref.feature;
-  var start = feature.get('start');
-  var end = feature.get('end');
-  var name = feature.get('refName');
-  var info = feature.get('snpinfo');
-  var loc = [name, start === end ? en(start) : "".concat(en(start), "..").concat(en(end))].filter(function (f) {
-    return !!f;
-  }).join(':');
-  var total = info === null || info === void 0 ? void 0 : info.total;
-  return /*#__PURE__*/_react.default.createElement("div", {
-    ref: ref
-  }, /*#__PURE__*/_react.default.createElement("table", null, /*#__PURE__*/_react.default.createElement("caption", null, loc), /*#__PURE__*/_react.default.createElement("thead", null, /*#__PURE__*/_react.default.createElement("tr", null, /*#__PURE__*/_react.default.createElement("th", null, "Base"), /*#__PURE__*/_react.default.createElement("th", null, "Count"), /*#__PURE__*/_react.default.createElement("th", null, "% of Total"), /*#__PURE__*/_react.default.createElement("th", null, "Strands"), /*#__PURE__*/_react.default.createElement("th", null, "Source"))), /*#__PURE__*/_react.default.createElement("tbody", null, /*#__PURE__*/_react.default.createElement("tr", null, /*#__PURE__*/_react.default.createElement("td", null, "Total"), /*#__PURE__*/_react.default.createElement("td", null, info.total)), /*#__PURE__*/_react.default.createElement("tr", null, /*#__PURE__*/_react.default.createElement("td", null, "REF"), /*#__PURE__*/_react.default.createElement("td", null, info.ref), /*#__PURE__*/_react.default.createElement("td", null, info['-1'] ? "".concat(info['-1'], "(-)") : '', info['1'] ? "".concat(info['1'], "(+)") : ''), /*#__PURE__*/_react.default.createElement("td", null)), Object.entries(info).map(function (_ref2) {
-    var _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
-        key = _ref3[0],
-        entry = _ref3[1];
-
-    return Object.entries(entry).map(function (_ref4) {
-      var _ref5 = (0, _slicedToArray2.default)(_ref4, 2),
-          base = _ref5[0],
-          score = _ref5[1];
-
-      return /*#__PURE__*/_react.default.createElement("tr", {
-        key: base
-      }, /*#__PURE__*/_react.default.createElement("td", null, base.toUpperCase()), /*#__PURE__*/_react.default.createElement("td", null, score.total), /*#__PURE__*/_react.default.createElement("td", null, base === 'total' || base === 'skip' ? '---' : "".concat(Math.floor(score.total / (total || score.total || 1) * 100), "%")), /*#__PURE__*/_react.default.createElement("td", null, score['-1'] ? "".concat(score['-1'], "(-)") : '', score['1'] ? "".concat(score['1'], "(+)") : ''), /*#__PURE__*/_react.default.createElement("td", null, key));
-    });
-  }))));
+var pct = function (n, total) { return "".concat(toP((n / (total || 1)) * 100), "%"); };
+var TooltipContents = react_1.default.forwardRef(function (_a, reactRef) {
+    var feature = _a.feature;
+    var start = feature.get('start');
+    var end = feature.get('end');
+    var name = feature.get('refName');
+    var _b = feature.get('snpinfo'), refbase = _b.refbase, all = _b.all, total = _b.total, ref = _b.ref, rn1 = _b["-1"], r1 = _b["1"], r0 = _b["0"], info = __rest(_b, ["refbase", "all", "total", "ref", '-1', '1', '0']);
+    var loc = [name, start === end ? en(start) : "".concat(en(start), "..").concat(en(end))]
+        .filter(function (f) { return !!f; })
+        .join(':');
+    return (react_1.default.createElement("div", { ref: reactRef },
+        react_1.default.createElement("table", null,
+            react_1.default.createElement("caption", null, loc),
+            react_1.default.createElement("thead", null,
+                react_1.default.createElement("tr", null,
+                    react_1.default.createElement("th", null, "Base"),
+                    react_1.default.createElement("th", null, "Count"),
+                    react_1.default.createElement("th", null, "% of Total"),
+                    react_1.default.createElement("th", null, "Strands"),
+                    react_1.default.createElement("th", null, "Source"))),
+            react_1.default.createElement("tbody", null,
+                react_1.default.createElement("tr", null,
+                    react_1.default.createElement("td", null, "Total"),
+                    react_1.default.createElement("td", null, all)),
+                react_1.default.createElement("tr", null,
+                    react_1.default.createElement("td", null,
+                        "REF ",
+                        refbase ? "(".concat(refbase.toUpperCase(), ")") : ''),
+                    react_1.default.createElement("td", null, ref),
+                    react_1.default.createElement("td", null, pct(ref, all)),
+                    react_1.default.createElement("td", null,
+                        rn1 ? "".concat(rn1, "(-)") : '',
+                        r1 ? "".concat(r1, "(+)") : ''),
+                    react_1.default.createElement("td", null)),
+                Object.entries(info).map(function (_a) {
+                    var _b = __read(_a, 2), key = _b[0], entry = _b[1];
+                    return Object.entries(entry).map(function (_a) {
+                        var _b = __read(_a, 2), base = _b[0], score = _b[1];
+                        return (react_1.default.createElement("tr", { key: base },
+                            react_1.default.createElement("td", null, base.toUpperCase()),
+                            react_1.default.createElement("td", null, score.total),
+                            react_1.default.createElement("td", null, base === 'total' || base === 'skip'
+                                ? '---'
+                                : pct(score.total, all)),
+                            react_1.default.createElement("td", null,
+                                score['-1'] ? "".concat(score['-1'], "(-)") : '',
+                                score['1'] ? "".concat(score['1'], "(+)") : ''),
+                            react_1.default.createElement("td", null, key)));
+                    });
+                })))));
 });
-
-var SNPCoverageTooltip = (0, _mobxReact.observer)(function (props) {
-  var model = props.model;
-  var feat = model.featureUnderMouse;
-  return feat && feat.get('type') === 'skip' ? null : /*#__PURE__*/_react.default.createElement(_pluginWiggle.Tooltip, (0, _extends2.default)({
-    TooltipContents: TooltipContents
-  }, props));
+var SNPCoverageTooltip = (0, mobx_react_1.observer)(function (props) {
+    var model = props.model;
+    var feat = model.featureUnderMouse;
+    return feat && feat.get('type') === 'skip' ? null : (react_1.default.createElement(plugin_wiggle_1.Tooltip, __assign({ TooltipContents: TooltipContents }, props)));
 });
-var _default = SNPCoverageTooltip;
-exports.default = _default;
+exports.default = SNPCoverageTooltip;
+//# sourceMappingURL=Tooltip.js.map

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map

@@ -0,0 +1 @@
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package/dist/LinearSNPCoverageDisplay/index.js

@@ -1,30 +1,24 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = register;
-
-var _configSchema = _interopRequireDefault(require("./models/configSchema"));
-
-var _model = _interopRequireDefault(require("./models/model"));
-
-var _pluginWiggle = require("@jbrowse/plugin-wiggle");
-
-var _DisplayType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var configSchema_1 = __importDefault(require("./models/configSchema"));
+var model_1 = __importDefault(require("./models/model"));
+var plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+var DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 function register(pluginManager) {
-  pluginManager.addDisplayType(function () {
-    var configSchema = (0, _configSchema.default)(pluginManager);
-    return new _DisplayType.default({
-      name: 'LinearSNPCoverageDisplay',
-      configSchema: configSchema,
-      stateModel: (0, _model.default)(pluginManager, configSchema),
-      trackType: 'AlignmentsTrack',
-      viewType: 'LinearGenomeView',
-      ReactComponent: _pluginWiggle.LinearWiggleDisplayReactComponent
+    pluginManager.addDisplayType(function () {
+        var configSchema = (0, configSchema_1.default)(pluginManager);
+        return new DisplayType_1.default({
+            name: 'LinearSNPCoverageDisplay',
+            configSchema: configSchema,
+            stateModel: (0, model_1.default)(pluginManager, configSchema),
+            trackType: 'AlignmentsTrack',
+            viewType: 'LinearGenomeView',
+            ReactComponent: plugin_wiggle_1.LinearWiggleDisplayReactComponent,
+        });
     });
-  });
-}
+}
+exports.default = register;
+//# sourceMappingURL=index.js.map

package/dist/LinearSNPCoverageDisplay/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearSNPCoverageDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,uEAAuD;AACvD,yDAAyC;AACzC,wDAA0E;AAC1E,gGAAyE;AAEzE,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC;QAC3B,IAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,0BAA0B;YAChC,YAAY,cAAA;YACZ,UAAU,EAAE,IAAA,eAAY,EAAC,aAAa,EAAE,YAAY,CAAC;YACrD,SAAS,EAAE,iBAAiB;YAC5B,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,iDAAiC;SAClD,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC;AAZD,2BAYC"}

package/dist/LinearSNPCoverageDisplay/models/configSchema.js

@@ -1,57 +1,47 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = SNPCoverageConfigFactory;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _pluginLinearGenomeView = require("@jbrowse/plugin-linear-genome-view");
-
-var _mobxStateTree = require("mobx-state-tree");
-
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+var plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+var mobx_state_tree_1 = require("mobx-state-tree");
 function SNPCoverageConfigFactory(pluginManager) {
-  var SNPCoverageRendererConfigSchema = pluginManager.getRendererType('SNPCoverageRenderer').configSchema;
-  return (0, _configuration.ConfigurationSchema)('LinearSNPCoverageDisplay', {
-    autoscale: {
-      type: 'stringEnum',
-      defaultValue: 'local',
-      model: _mobxStateTree.types.enumeration('Autoscale type', ['local']),
-      description: 'performs local autoscaling (no other options for SNP Coverage available)'
-    },
-    minScore: {
-      type: 'number',
-      defaultValue: Number.MIN_VALUE,
-      description: 'minimum value for the y-scale'
-    },
-    maxScore: {
-      type: 'number',
-      description: 'maximum value for the y-scale',
-      defaultValue: Number.MAX_VALUE
-    },
-    scaleType: {
-      type: 'stringEnum',
-      model: _mobxStateTree.types.enumeration('Scale type', ['linear', 'log']),
-      // todo zscale
-      description: 'The type of scale to use',
-      defaultValue: 'linear'
-    },
-    inverted: {
-      type: 'boolean',
-      description: 'draw upside down',
-      defaultValue: false
-    },
-    multiTicks: {
-      type: 'boolean',
-      description: 'Display multiple values for the ticks',
-      defaultValue: false
-    },
-    renderers: (0, _configuration.ConfigurationSchema)('RenderersConfiguration', {
-      SNPCoverageRenderer: SNPCoverageRendererConfigSchema
-    })
-  }, {
-    baseConfiguration: _pluginLinearGenomeView.baseLinearDisplayConfigSchema,
-    explicitlyTyped: true
-  });
-}
+    var SNPCoverageRendererConfigSchema = pluginManager.getRendererType('SNPCoverageRenderer').configSchema;
+    return (0, configuration_1.ConfigurationSchema)('LinearSNPCoverageDisplay', {
+        autoscale: {
+            type: 'stringEnum',
+            defaultValue: 'local',
+            model: mobx_state_tree_1.types.enumeration('Autoscale type', ['local']),
+            description: 'performs local autoscaling (no other options for SNP Coverage available)',
+        },
+        minScore: {
+            type: 'number',
+            defaultValue: Number.MIN_VALUE,
+            description: 'minimum value for the y-scale',
+        },
+        maxScore: {
+            type: 'number',
+            description: 'maximum value for the y-scale',
+            defaultValue: Number.MAX_VALUE,
+        },
+        scaleType: {
+            type: 'stringEnum',
+            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']),
+            description: 'The type of scale to use',
+            defaultValue: 'linear',
+        },
+        inverted: {
+            type: 'boolean',
+            description: 'draw upside down',
+            defaultValue: false,
+        },
+        multiTicks: {
+            type: 'boolean',
+            description: 'Display multiple values for the ticks',
+            defaultValue: false,
+        },
+        renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
+            SNPCoverageRenderer: SNPCoverageRendererConfigSchema,
+        }),
+    }, { baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema, explicitlyTyped: true });
+}
+exports.default = SNPCoverageConfigFactory;
+//# sourceMappingURL=configSchema.js.map

package/dist/LinearSNPCoverageDisplay/models/configSchema.js.map

@@ -0,0 +1 @@
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package/dist/LinearSNPCoverageDisplay/models/model.d.ts

@@ -96,11 +96,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     error: unknown;
 } & {
     readonly RenderingComponent: import("react").FC<{
-        model: import("mobx-state-tree").ModelInstanceTypeProps<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }> & {
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -115,11 +115,11 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
         blockState?: Record<string, any> | undefined;
     }>;
     readonly DisplayBlurb: import("react").FC<{
-        model: import("mobx-state-tree").ModelInstanceTypeProps<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-            type: import("mobx-state-tree").ISimpleType<string>;
-            rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        }> & {
+        model: {
+            id: string;
+            type: string;
+            rpcDriverName: string | undefined;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
@@ -152,7 +152,7 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
-    readonly blockType: "staticBlocks" | "dynamicBlocks";
+    readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -205,7 +205,9 @@ declare const stateModelFactory: (pluginManager: PluginManager, configSchema: An
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     contextMenuItems(): {
         label: string;
-        icon: import("@material-ui/core/OverridableComponent").OverridableComponent<import("@material-ui/core").SvgIconTypeMap<{}, "svg">>;
+        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
+            muiName: string;
+        };
         onClick: () => void;
     }[];
     renderProps(): any;