@jbrowse/plugin-alignments 2.1.0 → 2.1.2

package/dist/LinearPileupDisplay/model.js.map

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

@@ -8,6 +8,6 @@ declare const SNPCoverageTooltip: (props: {
     height: number;
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;
-    clientRect?: DOMRect | undefined;
+    clientRect?: DOMRect;
 }) => JSX.Element | null;
 export default SNPCoverageTooltip;

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -1,63 +1,21 @@
 "use strict";
-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 });
-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 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; })
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+const en = (n) => n.toLocaleString('en-US');
+const toP = (s = 0) => +(+s).toFixed(1);
+const pct = (n, total) => `${toP((n / (total || 1)) * 100)}%`;
+const TooltipContents = react_1.default.forwardRef(({ feature }, reactRef) => {
+    const start = feature.get('start');
+    const end = feature.get('end');
+    const name = feature.get('refName');
+    const { refbase, all, total, ref, '-1': rn1, '1': r1, '0': r0, ...info } = feature.get('snpinfo');
+    const loc = [name, start === end ? en(start) : `${en(start)}..${en(end)}`]
+        .filter(f => !!f)
         .join(':');
     return (react_1.default.createElement("div", { ref: reactRef },
         react_1.default.createElement("table", null,
@@ -76,34 +34,28 @@ var TooltipContents = react_1.default.forwardRef(function (_a, reactRef) {
                 react_1.default.createElement("tr", null,
                     react_1.default.createElement("td", null,
                         "REF ",
-                        refbase ? "(".concat(refbase.toUpperCase(), ")") : ''),
+                        refbase ? `(${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, "(+)") : ''),
+                        rn1 ? `${rn1}(-)` : '',
+                        r1 ? `${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)));
-                    });
-                })))));
+                Object.entries(info).map(([key, entry]) => Object.entries(entry).map(([base, score]) => (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'] ? `${score['-1']}(-)` : '',
+                        score['1'] ? `${score['1']}(+)` : ''),
+                    react_1.default.createElement("td", null, key)))))))));
 });
-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)));
+const SNPCoverageTooltip = (0, mobx_react_1.observer)((props) => {
+    const { model } = props;
+    const { featureUnderMouse: feat } = model;
+    return feat && feat.get('type') === 'skip' ? null : (react_1.default.createElement(plugin_wiggle_1.Tooltip, { TooltipContents: TooltipContents, ...props }));
 });
 exports.default = SNPCoverageTooltip;
 //# sourceMappingURL=Tooltip.js.map

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

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

@@ -3,16 +3,16 @@ 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"));
+const configSchema_1 = __importDefault(require("./models/configSchema"));
+const model_1 = __importDefault(require("./models/model"));
+const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
 function register(pluginManager) {
-    pluginManager.addDisplayType(function () {
-        var configSchema = (0, configSchema_1.default)(pluginManager);
+    pluginManager.addDisplayType(() => {
+        const configSchema = (0, configSchema_1.default)(pluginManager);
         return new DisplayType_1.default({
             name: 'LinearSNPCoverageDisplay',
-            configSchema: configSchema,
+            configSchema,
             stateModel: (0, model_1.default)(pluginManager, configSchema),
             trackType: 'AlignmentsTrack',
             viewType: 'LinearGenomeView',

package/dist/LinearSNPCoverageDisplay/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearSNPCoverageDisplay/index.ts"],"names":[],"mappings":";;;;;AACA,yEAAuD;AACvD,2DAAyC;AACzC,0DAA0E;AAC1E,kGAAyE;AAEzE,SAAwB,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,sBAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,qBAAW,CAAC;YACrB,IAAI,EAAE,0BAA0B;YAChC,YAAY;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

@@ -1,10 +1,10 @@
 "use strict";
 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");
+const configuration_1 = require("@jbrowse/core/configuration");
+const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function SNPCoverageConfigFactory(pluginManager) {
-    var SNPCoverageRendererConfigSchema = pluginManager.getRendererType('SNPCoverageRenderer').configSchema;
+    const SNPCoverageRendererConfigSchema = pluginManager.getRendererType('SNPCoverageRenderer').configSchema;
     return (0, configuration_1.ConfigurationSchema)('LinearSNPCoverageDisplay', {
         autoscale: {
             type: 'stringEnum',

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

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/models/configSchema.ts"],"names":[],"mappings":";;AAAA,+DAAiE;AACjE,kFAAkF;AAClF,qDAAuC;AAGvC,SAAwB,wBAAwB,CAAC,aAA4B;IAC3E,MAAM,+BAA+B,GAAG,aAAa,CAAC,eAAe,CACnE,qBAAqB,CACtB,CAAC,YAAY,CAAA;IAEd,OAAO,IAAA,mCAAmB,EACxB,0BAA0B,EAC1B;QACE,SAAS,EAAE;YACT,IAAI,EAAE,YAAY;YAClB,YAAY,EAAE,OAAO;YACrB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,gBAAgB,EAAE,CAAC,OAAO,CAAC,CAAC;YACrD,WAAW,EACT,0EAA0E;SAC7E;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,YAAY,EAAE,MAAM,CAAC,SAAS;YAC9B,WAAW,EAAE,+BAA+B;SAC7C;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,+BAA+B;YAC5C,YAAY,EAAE,MAAM,CAAC,SAAS;SAC/B;QACD,SAAS,EAAE;YACT,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,YAAY,EAAE,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAC;YACzD,WAAW,EAAE,0BAA0B;YACvC,YAAY,EAAE,QAAQ;SACvB;QACD,QAAQ,EAAE;YACR,IAAI,EAAE,SAAS;YACf,WAAW,EAAE,kBAAkB;YAC/B,YAAY,EAAE,KAAK;SACpB;QAED,UAAU,EAAE;YACV,IAAI,EAAE,SAAS;YACf,WAAW,EAAE,uCAAuC;YACpD,YAAY,EAAE,KAAK;SACpB;QAED,SAAS,EAAE,IAAA,mCAAmB,EAAC,wBAAwB,EAAE;YACvD,mBAAmB,EAAE,+BAA+B;SACrD,CAAC;KACH,EACD,EAAE,iBAAiB,EAAE,yDAA6B,EAAE,eAAe,EAAE,IAAI,EAAE,CAC5E,CAAA;AACH,CAAC;AAjDD,2CAiDC"}

package/dist/LinearSNPCoverageDisplay/models/model.d.ts

@@ -153,7 +153,7 @@ 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;