@jbrowse/plugin-wiggle 2.0.1 → 2.1.0

package/dist/WiggleBaseRenderer.js

@@ -61,6 +61,17 @@ var __generator = (this && this.__generator) || function (thisArg, body) {
         if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
     }
 };
+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;
@@ -82,7 +93,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 var FeatureRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType"));
-var offscreenCanvasUtils_1 = require("@jbrowse/core/util/offscreenCanvasUtils");
+var util_1 = require("@jbrowse/core/util");
 var WiggleBaseRenderer = /** @class */ (function (_super) {
     __extends(WiggleBaseRenderer, _super);
     function WiggleBaseRenderer() {
@@ -92,25 +103,27 @@ var WiggleBaseRenderer = /** @class */ (function (_super) {
     }
     WiggleBaseRenderer.prototype.render = function (renderProps) {
         return __awaiter(this, void 0, void 0, function () {
-            var features, height, regions, bpPerPx, _a, region, width, res, results;
+            var features, height, regions, bpPerPx, _a, region, width, _b, reducedFeatures, rest, results;
             var _this = this;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
+            return __generator(this, function (_c) {
+                switch (_c.label) {
                     case 0: return [4 /*yield*/, this.getFeatures(renderProps)];
                     case 1:
-                        features = _b.sent();
+                        features = _c.sent();
                         height = renderProps.height, regions = renderProps.regions, bpPerPx = renderProps.bpPerPx;
                         _a = __read(regions, 1), region = _a[0];
                         width = (region.end - region.start) / bpPerPx;
-                        return [4 /*yield*/, (0, offscreenCanvasUtils_1.renderToAbstractCanvas)(width, height, renderProps, function (ctx) {
+                        return [4 /*yield*/, (0, util_1.renderToAbstractCanvas)(width, height, renderProps, function (ctx) {
                                 return _this.draw(ctx, __assign(__assign({}, renderProps), { features: features }));
                             })];
                     case 2:
-                        res = _b.sent();
-                        return [4 /*yield*/, _super.prototype.render.call(this, __assign(__assign(__assign({}, renderProps), res), { features: features, height: height, width: width }))];
+                        _b = _c.sent(), reducedFeatures = _b.reducedFeatures, rest = __rest(_b, ["reducedFeatures"]);
+                        return [4 /*yield*/, _super.prototype.render.call(this, __assign(__assign(__assign({}, renderProps), rest), { features: features, height: height, width: width }))];
                     case 3:
-                        results = _b.sent();
-                        return [2 /*return*/, __assign(__assign(__assign({}, results), res), { features: features, containsNoTransferables: true, height: height, width: width })];
+                        results = _c.sent();
+                        return [2 /*return*/, __assign(__assign(__assign({}, results), rest), { 
+                                // @ts-ignore
+                                features: reducedFeatures || results.features, containsNoTransferables: true, height: height, width: width })];
                 }
             });
         });

package/dist/WiggleBaseRenderer.js.map

@@ -1 +1 @@
-{"version":3,"file":"WiggleBaseRenderer.js","sourceRoot":"","sources":["../src/WiggleBaseRenderer.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,0HAO0E;AAC1E,gFAAgF;AA8BhF;IAAyD,sCAAmB;IAA5E;QAAA,qEA8CC;QA7CC,iBAAW,GAAG,IAAI,CAAA;;IA6CpB,CAAC;IA3CO,mCAAM,GAAZ,UAAa,WAAmC;;;;;;4BAC7B,qBAAM,IAAI,CAAC,WAAW,CAAC,WAAW,CAAC,EAAA;;wBAA9C,QAAQ,GAAG,SAAmC;wBAC5C,MAAM,GAAuB,WAAW,OAAlC,EAAE,OAAO,GAAc,WAAW,QAAzB,EAAE,OAAO,GAAK,WAAW,QAAhB,CAAgB;wBAC1C,KAAA,OAAW,OAAO,IAAA,EAAjB,MAAM,QAAA,CAAW;wBAClB,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;wBAEvC,qBAAM,IAAA,6CAAsB,EACtC,KAAK,EACL,MAAM,EACN,WAAW,EACX,UAAC,GAA6B;gCAC5B,OAAA,KAAI,CAAC,IAAI,CAAC,GAAG,wBACR,WAAW,KACd,QAAQ,UAAA,IACR;4BAHF,CAGE,CACL,EAAA;;wBATK,GAAG,GAAG,SASX;wBAEe,qBAAM,iBAAM,MAAM,2CAC7B,WAAW,GACX,GAAG,KACN,QAAQ,UAAA,EACR,MAAM,QAAA,EACN,KAAK,OAAA,IACL,EAAA;;wBANI,OAAO,GAAG,SAMd;wBAEF,qDACK,OAAO,GACP,GAAG,KACN,QAAQ,UAAA,EACR,uBAAuB,EAAE,IAAI,EAC7B,MAAM,QAAA,EACN,KAAK,OAAA,KACN;;;;KACF;IAUH,yBAAC;AAAD,CAAC,AA9CD,CAAyD,6BAAmB,GA8C3E"}
+{"version":3,"file":"WiggleBaseRenderer.js","sourceRoot":"","sources":["../src/WiggleBaseRenderer.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,0HAO0E;AAC1E,2CAAoE;AAmCpE;IAAyD,sCAAmB;IAA5E;QAAA,qEAgDC;QA/CC,iBAAW,GAAG,IAAI,CAAA;;IA+CpB,CAAC;IA7CO,mCAAM,GAAZ,UAAa,WAAmC;;;;;;4BAC7B,qBAAM,IAAI,CAAC,WAAW,CAAC,WAAW,CAAC,EAAA;;wBAA9C,QAAQ,GAAG,SAAmC;wBAC5C,MAAM,GAAuB,WAAW,OAAlC,EAAE,OAAO,GAAc,WAAW,QAAzB,EAAE,OAAO,GAAK,WAAW,QAAhB,CAAgB;wBAC1C,KAAA,OAAW,OAAO,IAAA,EAAjB,MAAM,QAAA,CAAW;wBAClB,KAAK,GAAG,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;wBAGd,qBAAM,IAAA,6BAAsB,EAC/D,KAAK,EACL,MAAM,EACN,WAAW,EACX,UAAA,GAAG;gCACD,OAAA,KAAI,CAAC,IAAI,CAAC,GAAG,wBACR,WAAW,KACd,QAAQ,UAAA,IACR;4BAHF,CAGE,CACL,EAAA;;wBATK,KAA+B,SASpC,EATO,eAAe,qBAAA,EAAK,IAAI,cAA1B,mBAA4B,CAAF;wBAWhB,qBAAM,iBAAM,MAAM,2CAC7B,WAAW,GACX,IAAI,KACP,QAAQ,UAAA,EACR,MAAM,QAAA,EACN,KAAK,OAAA,IACL,EAAA;;wBANI,OAAO,GAAG,SAMd;wBAEF,qDACK,OAAO,GACP,IAAI;gCACP,aAAa;gCACb,QAAQ,EAAE,eAAe,IAAI,OAAO,CAAC,QAAQ,EAC7C,uBAAuB,EAAE,IAAI,EAC7B,MAAM,QAAA,EACN,KAAK,OAAA,KACN;;;;KACF;IAUH,yBAAC;AAAD,CAAC,AAhDD,CAAyD,6BAAmB,GAgD3E"}

package/dist/WiggleRPC/rpcMethods.d.ts

@@ -1,6 +1,6 @@
 import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
 import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-import { Region } from '@jbrowse/core/util/types';
+import { Region } from '@jbrowse/core/util';
 import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
 import { FeatureStats } from '@jbrowse/core/util/stats';
 export declare class WiggleGetGlobalStats extends RpcMethodType {
@@ -29,3 +29,19 @@ export declare class WiggleGetMultiRegionStats extends RpcMethodType {
         bpPerPx: number;
     }, rpcDriverClassName: string): Promise<FeatureStats>;
 }
+export declare class MultiWiggleGetSources extends RpcMethodType {
+    name: string;
+    deserializeArguments(args: any, rpcDriverClassName: string): Promise<any>;
+    serializeArguments(args: RenderArgs & {
+        signal?: AbortSignal;
+        statusCallback?: Function;
+    }, rpcDriverClassName: string): Promise<{}>;
+    execute(args: {
+        adapterConfig: {};
+        signal?: RemoteAbortSignal;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<any>;
+}

package/dist/WiggleRPC/rpcMethods.js

@@ -65,12 +65,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.WiggleGetMultiRegionStats = exports.WiggleGetGlobalStats = void 0;
-var dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
+exports.MultiWiggleGetSources = exports.WiggleGetMultiRegionStats = exports.WiggleGetGlobalStats = void 0;
 var RpcMethodType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/RpcMethodType"));
+var serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
+var dataAdapterCache_1 = require("@jbrowse/core/data_adapters/dataAdapterCache");
 var util_1 = require("@jbrowse/core/util");
 var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-var serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
 var WiggleGetGlobalStats = /** @class */ (function (_super) {
     __extends(WiggleGetGlobalStats, _super);
     function WiggleGetGlobalStats() {
@@ -98,14 +98,16 @@ var WiggleGetGlobalStats = /** @class */ (function (_super) {
     };
     WiggleGetGlobalStats.prototype.execute = function (args, rpcDriverClassName) {
         return __awaiter(this, void 0, void 0, function () {
-            var deserializedArgs, adapterConfig, sessionId, dataAdapter;
+            var pm, deserializedArgs, adapterConfig, sessionId, dataAdapter;
             return __generator(this, function (_a) {
                 switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.deserializeArguments(args, rpcDriverClassName)];
+                    case 0:
+                        pm = this.pluginManager;
+                        return [4 /*yield*/, this.deserializeArguments(args, rpcDriverClassName)];
                     case 1:
                         deserializedArgs = _a.sent();
                         adapterConfig = deserializedArgs.adapterConfig, sessionId = deserializedArgs.sessionId;
-                        return [4 /*yield*/, (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)
+                        return [4 /*yield*/, (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig)
                             // @ts-ignore
                         ];
                     case 2:
@@ -145,19 +147,20 @@ var WiggleGetMultiRegionStats = /** @class */ (function (_super) {
         });
     };
     WiggleGetMultiRegionStats.prototype.serializeArguments = function (args, rpcDriverClassName) {
-        var _a, _b;
+        var _a, _b, _c;
         return __awaiter(this, void 0, void 0, function () {
-            var assemblyManager, renamedArgs;
-            return __generator(this, function (_c) {
-                switch (_c.label) {
+            var pm, assemblyManager, renamedArgs;
+            return __generator(this, function (_d) {
+                switch (_d.label) {
                     case 0:
-                        assemblyManager = (_b = (_a = this.pluginManager.rootModel) === null || _a === void 0 ? void 0 : _a.session) === null || _b === void 0 ? void 0 : _b.assemblyManager;
+                        pm = this.pluginManager;
+                        assemblyManager = (_b = (_a = pm.rootModel) === null || _a === void 0 ? void 0 : _a.session) === null || _b === void 0 ? void 0 : _b.assemblyManager;
                         if (!assemblyManager) {
                             return [2 /*return*/, args];
                         }
-                        return [4 /*yield*/, (0, util_1.renameRegionsIfNeeded)(assemblyManager, __assign(__assign({}, args), { filters: args.filters && args.filters.toJSON().filters }))];
+                        return [4 /*yield*/, (0, util_1.renameRegionsIfNeeded)(assemblyManager, __assign(__assign({}, args), { filters: (_c = args.filters) === null || _c === void 0 ? void 0 : _c.toJSON().filters }))];
                     case 1:
-                        renamedArgs = _c.sent();
+                        renamedArgs = _d.sent();
                         return [2 /*return*/, _super.prototype.serializeArguments.call(this, renamedArgs, rpcDriverClassName)];
                 }
             });
@@ -165,14 +168,16 @@ var WiggleGetMultiRegionStats = /** @class */ (function (_super) {
     };
     WiggleGetMultiRegionStats.prototype.execute = function (args, rpcDriverClassName) {
         return __awaiter(this, void 0, void 0, function () {
-            var deserializedArgs, regions, adapterConfig, sessionId, dataAdapter;
+            var pm, deserializedArgs, regions, adapterConfig, sessionId, dataAdapter;
             return __generator(this, function (_a) {
                 switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.deserializeArguments(args, rpcDriverClassName)];
+                    case 0:
+                        pm = this.pluginManager;
+                        return [4 /*yield*/, this.deserializeArguments(args, rpcDriverClassName)];
                     case 1:
                         deserializedArgs = _a.sent();
                         regions = deserializedArgs.regions, adapterConfig = deserializedArgs.adapterConfig, sessionId = deserializedArgs.sessionId;
-                        return [4 /*yield*/, (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig)];
+                        return [4 /*yield*/, (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig)];
                     case 2:
                         dataAdapter = (_a.sent()).dataAdapter;
                         if (dataAdapter instanceof BaseAdapter_1.BaseFeatureDataAdapter) {
@@ -186,4 +191,74 @@ var WiggleGetMultiRegionStats = /** @class */ (function (_super) {
     return WiggleGetMultiRegionStats;
 }(RpcMethodType_1.default));
 exports.WiggleGetMultiRegionStats = WiggleGetMultiRegionStats;
+var MultiWiggleGetSources = /** @class */ (function (_super) {
+    __extends(MultiWiggleGetSources, _super);
+    function MultiWiggleGetSources() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.name = 'MultiWiggleGetSources';
+        return _this;
+    }
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    MultiWiggleGetSources.prototype.deserializeArguments = function (args, rpcDriverClassName) {
+        return __awaiter(this, void 0, void 0, function () {
+            var l;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, _super.prototype.deserializeArguments.call(this, args, rpcDriverClassName)];
+                    case 1:
+                        l = _a.sent();
+                        return [2 /*return*/, __assign(__assign({}, l), { filters: args.filters
+                                    ? new serializableFilterChain_1.default({
+                                        filters: args.filters,
+                                    })
+                                    : undefined })];
+                }
+            });
+        });
+    };
+    MultiWiggleGetSources.prototype.serializeArguments = function (args, rpcDriverClassName) {
+        var _a, _b, _c;
+        return __awaiter(this, void 0, void 0, function () {
+            var pm, assemblyManager, renamedArgs;
+            return __generator(this, function (_d) {
+                switch (_d.label) {
+                    case 0:
+                        pm = this.pluginManager;
+                        assemblyManager = (_b = (_a = pm.rootModel) === null || _a === void 0 ? void 0 : _a.session) === null || _b === void 0 ? void 0 : _b.assemblyManager;
+                        if (!assemblyManager) {
+                            return [2 /*return*/, args];
+                        }
+                        return [4 /*yield*/, (0, util_1.renameRegionsIfNeeded)(assemblyManager, __assign(__assign({}, args), { filters: (_c = args.filters) === null || _c === void 0 ? void 0 : _c.toJSON().filters }))];
+                    case 1:
+                        renamedArgs = _d.sent();
+                        return [2 /*return*/, _super.prototype.serializeArguments.call(this, renamedArgs, rpcDriverClassName)];
+                }
+            });
+        });
+    };
+    MultiWiggleGetSources.prototype.execute = function (args, rpcDriverClassName) {
+        return __awaiter(this, void 0, void 0, function () {
+            var pm, deserializedArgs, regions, adapterConfig, sessionId, dataAdapter;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        pm = this.pluginManager;
+                        return [4 /*yield*/, this.deserializeArguments(args, rpcDriverClassName)];
+                    case 1:
+                        deserializedArgs = _a.sent();
+                        regions = deserializedArgs.regions, adapterConfig = deserializedArgs.adapterConfig, sessionId = deserializedArgs.sessionId;
+                        return [4 /*yield*/, (0, dataAdapterCache_1.getAdapter)(pm, sessionId, adapterConfig)
+                            // @ts-ignore
+                        ];
+                    case 2:
+                        dataAdapter = (_a.sent()).dataAdapter;
+                        // @ts-ignore
+                        return [2 /*return*/, dataAdapter.getSources(regions, deserializedArgs)];
+                }
+            });
+        });
+    };
+    return MultiWiggleGetSources;
+}(RpcMethodType_1.default));
+exports.MultiWiggleGetSources = MultiWiggleGetSources;
 //# sourceMappingURL=rpcMethods.js.map

package/dist/WiggleRPC/rpcMethods.js.map

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package/dist/WiggleRendering.d.ts

@@ -1,6 +1,6 @@
 /// <reference types="react" />
 import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Feature } from '@jbrowse/core/util';
 declare function WiggleRendering(props: {
     regions: Region[];
     features: Map<string, Feature>;

package/dist/WiggleRendering.js

@@ -82,7 +82,9 @@ function WiggleRendering(props) {
         try {
             for (var _b = __values(features.values()), _c = _b.next(); !_c.done; _c = _b.next()) {
                 var feature = _c.value;
-                if (clientBp <= feature.get('end') && clientBp >= feature.get('start')) {
+                // bpPerPx added to the end to accomodate "reduced features" (one feature per px)
+                if (clientBp <= feature.get('end') + bpPerPx &&
+                    clientBp >= feature.get('start')) {
                     featureUnderMouse = feature;
                     break;
                 }
@@ -97,13 +99,7 @@ function WiggleRendering(props) {
         }
         return featureUnderMouse;
     }
-    return (react_1.default.createElement("div", { ref: ref, "data-testid": "wiggle-rendering-test", onMouseMove: function (event) {
-            var featureUnderMouse = getFeatureUnderMouse(event.clientX);
-            onMouseMove(event, featureUnderMouse ? featureUnderMouse.id() : undefined);
-        }, onClick: function (event) {
-            var featureUnderMouse = getFeatureUnderMouse(event.clientX);
-            onFeatureClick(event, featureUnderMouse ? featureUnderMouse.id() : undefined);
-        }, onMouseLeave: function (event) { return onMouseLeave(event); }, role: "presentation", className: "WiggleRendering", style: {
+    return (react_1.default.createElement("div", { ref: ref, "data-testid": "wiggle-rendering-test", onMouseMove: function (event) { var _a; return onMouseMove(event, (_a = getFeatureUnderMouse(event.clientX)) === null || _a === void 0 ? void 0 : _a.id()); }, onClick: function (event) { var _a; return onFeatureClick(event, (_a = getFeatureUnderMouse(event.clientX)) === null || _a === void 0 ? void 0 : _a.id()); }, onMouseLeave: function (event) { return onMouseLeave(event); }, style: {
             overflow: 'visible',
             position: 'relative',
             height: height,

package/dist/WiggleRendering.js.map

@@ -1 +1 @@
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package/dist/XYPlotRenderer/XYPlotRenderer.d.ts

@@ -1,4 +1,7 @@
+import { Feature } from '@jbrowse/core/util';
 import WiggleBaseRenderer, { RenderArgsDeserializedWithFeatures } from '../WiggleBaseRenderer';
 export default class XYPlotRenderer extends WiggleBaseRenderer {
-    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;
+    draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<{
+        reducedFeatures: Feature[];
+    }>;
 }

package/dist/XYPlotRenderer/XYPlotRenderer.js

@@ -100,40 +100,23 @@ var __read = (this && this.__read) || function (o, n) {
     }
     return ar;
 };
-var __values = (this && this.__values) || function(o) {
-    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
-    if (m) return m.call(o);
-    if (o && typeof o.length === "number") return {
-        next: function () {
-            if (o && i >= o.length) o = void 0;
-            return { value: o && o[i++], done: !o };
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
         }
-    };
-    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
 };
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 var configuration_1 = require("@jbrowse/core/configuration");
-var util_1 = require("@jbrowse/core/util");
-var util_2 = require("../util");
+var drawxy_1 = require("../drawxy");
 var WiggleBaseRenderer_1 = __importDefault(require("../WiggleBaseRenderer"));
-var model_1 = require("../LinearWiggleDisplay/models/model");
-function fillRect(ctx, x, y, width, height, color) {
-    if (color) {
-        ctx.fillStyle = String(color);
-    }
-    if (width < 0) {
-        x += width;
-        width = -width;
-    }
-    if (height < 0) {
-        y += height;
-        height = -height;
-    }
-    ctx.fillRect(x, y, width, height);
-}
+var util_1 = require("../util");
 var XYPlotRenderer = /** @class */ (function (_super) {
     __extends(XYPlotRenderer, _super);
     function XYPlotRenderer() {
@@ -141,110 +124,24 @@ var XYPlotRenderer = /** @class */ (function (_super) {
     }
     XYPlotRenderer.prototype.draw = function (ctx, props) {
         return __awaiter(this, void 0, void 0, function () {
-            var features, bpPerPx, regions, scaleOpts, unadjustedHeight, config, ticks, displayCrossHatches, Color, _a, region, width, rc, offset, height, pivotValue, negColor, posColor, filled, clipColor, highlightColor, summaryScoreMode, scale, originY, _b, niceMin, niceMax, toY, toHeight, colorCallback, crossingOrigin, _c, _d, feature, _e, leftPx, rightPx, score, maxr, minr, lowClipping, highClipping, w, summary, c;
-            var e_1, _f;
-            return __generator(this, function (_g) {
-                switch (_g.label) {
+            var features, config, pivotValue, negColor, posColor, Color;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
                     case 0:
-                        features = props.features, bpPerPx = props.bpPerPx, regions = props.regions, scaleOpts = props.scaleOpts, unadjustedHeight = props.height, config = props.config, ticks = props.ticks, displayCrossHatches = props.displayCrossHatches;
+                        features = props.features, config = props.config;
+                        pivotValue = (0, configuration_1.readConfObject)(config, 'bicolorPivotValue');
+                        negColor = (0, configuration_1.readConfObject)(config, 'negColor');
+                        posColor = (0, configuration_1.readConfObject)(config, 'posColor');
                         return [4 /*yield*/, Promise.resolve().then(function () { return __importStar(require('color')); }).then(function (f) { return f.default; })];
                     case 1:
-                        Color = _g.sent();
-                        _a = __read(regions, 1), region = _a[0];
-                        width = (region.end - region.start) / bpPerPx;
-                        rc = function (s, rest) {
-                            return (0, configuration_1.readConfObject)(config, s, rest);
-                        };
-                        offset = model_1.YSCALEBAR_LABEL_OFFSET;
-                        height = unadjustedHeight - offset * 2;
-                        pivotValue = rc('bicolorPivotValue');
-                        negColor = rc('negColor');
-                        posColor = rc('posColor');
-                        filled = rc('filled');
-                        clipColor = rc('clipColor');
-                        highlightColor = rc('highlightColor');
-                        summaryScoreMode = rc('summaryScoreMode');
-                        scale = (0, util_2.getScale)(__assign(__assign({}, scaleOpts), { range: [0, height] }));
-                        originY = (0, util_2.getOrigin)(scaleOpts.scaleType);
-                        _b = __read(scale.domain(), 2), niceMin = _b[0], niceMax = _b[1];
-                        toY = function (n) { return height - (scale(n) || 0) + offset; };
-                        toHeight = function (n) { return toY(originY) - toY(n); };
-                        colorCallback = rc('color') === '#f0f'
-                            ? function (_, score) {
-                                return score < pivotValue ? negColor : posColor;
-                            }
-                            : function (feature, _score) { return rc('color', { feature: feature }); };
-                        crossingOrigin = niceMin < pivotValue && niceMax > pivotValue;
-                        try {
-                            for (_c = __values(features.values()), _d = _c.next(); !_d.done; _d = _c.next()) {
-                                feature = _d.value;
-                                _e = __read((0, util_1.featureSpanPx)(feature, region, bpPerPx), 2), leftPx = _e[0], rightPx = _e[1];
-                                score = feature.get('score');
-                                maxr = feature.get('maxScore');
-                                minr = feature.get('minScore');
-                                lowClipping = score < niceMin;
-                                highClipping = score > niceMax;
-                                w = rightPx - leftPx + 0.4 // fudge factor for subpixel rendering
-                                ;
-                                summary = feature.get('summary');
-                                if (summaryScoreMode === 'max') {
-                                    score = summary ? maxr : score;
-                                    fillRect(ctx, leftPx, toY(score), w, filled ? toHeight(score) : 1, colorCallback(feature, score));
-                                }
-                                else if (summaryScoreMode === 'min') {
-                                    score = summary ? minr : score;
-                                    fillRect(ctx, leftPx, toY(score), w, filled ? toHeight(score) : 1, colorCallback(feature, score));
-                                }
-                                else if (summaryScoreMode === 'whiskers') {
-                                    c = colorCallback(feature, score);
-                                    if (summary) {
-                                        fillRect(ctx, leftPx, toY(maxr), w, filled ? toHeight(maxr) - toHeight(score) : 1, crossingOrigin
-                                            ? colorCallback(feature, maxr)
-                                            : Color(c).lighten(0.6));
-                                    }
-                                    // normal
-                                    fillRect(ctx, leftPx, toY(score), w, filled ? toHeight(score) - (summary ? toHeight(minr) : 0) : 1, crossingOrigin && summary
-                                        ? Color(colorCallback(feature, maxr)).mix(Color(colorCallback(feature, minr)))
-                                        : c);
-                                    // min
-                                    if (summary) {
-                                        fillRect(ctx, leftPx, toY(minr), w, filled ? toHeight(minr) : 1, crossingOrigin
-                                            ? colorCallback(feature, minr)
-                                            : Color(c).darken(0.6));
+                        Color = _a.sent();
+                        return [2 /*return*/, (0, drawxy_1.drawXY)(ctx, __assign(__assign({}, props), { colorCallback: (0, configuration_1.readConfObject)(config, 'color') === '#f0f'
+                                    ? function (_, score) {
+                                        return score < pivotValue ? negColor : posColor;
                                     }
-                                }
-                                else {
-                                    fillRect(ctx, leftPx, toY(score), w, filled ? toHeight(score) : 1, colorCallback(feature, score));
-                                }
-                                if (highClipping) {
-                                    fillRect(ctx, leftPx, 0, w, 4, clipColor);
-                                }
-                                else if (lowClipping && scaleOpts.scaleType !== 'log') {
-                                    fillRect(ctx, leftPx, unadjustedHeight - 4, w, 4, clipColor);
-                                }
-                                if (feature.get('highlighted')) {
-                                    fillRect(ctx, leftPx, 0, w, height, highlightColor);
-                                }
-                            }
-                        }
-                        catch (e_1_1) { e_1 = { error: e_1_1 }; }
-                        finally {
-                            try {
-                                if (_d && !_d.done && (_f = _c.return)) _f.call(_c);
-                            }
-                            finally { if (e_1) throw e_1.error; }
-                        }
-                        if (displayCrossHatches) {
-                            ctx.lineWidth = 1;
-                            ctx.strokeStyle = 'rgba(200,200,200,0.8)';
-                            ticks.values.forEach(function (tick) {
-                                ctx.beginPath();
-                                ctx.moveTo(0, Math.round(toY(tick)));
-                                ctx.lineTo(width, Math.round(toY(tick)));
-                                ctx.stroke();
-                            });
-                        }
-                        return [2 /*return*/];
+                                    : function (feature, _score) {
+                                        return (0, configuration_1.readConfObject)(config, 'color', { feature: feature });
+                                    }, offset: util_1.YSCALEBAR_LABEL_OFFSET, features: __spreadArray([], __read(features.values()), false), Color: Color }))];
                 }
             });
         });

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package/dist/XYPlotRenderer/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default configSchema;

package/dist/XYPlotRenderer/configSchema.js

@@ -0,0 +1,31 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+var configSchema_1 = __importDefault(require("../configSchema"));
+var mobx_state_tree_1 = require("mobx-state-tree");
+var configSchema = (0, configuration_1.ConfigurationSchema)('XYPlotRenderer', {
+    filled: {
+        type: 'boolean',
+        defaultValue: true,
+    },
+    displayCrossHatches: {
+        type: 'boolean',
+        description: 'choose to draw cross hatches (sideways lines)',
+        defaultValue: false,
+    },
+    summaryScoreMode: {
+        type: 'stringEnum',
+        model: mobx_state_tree_1.types.enumeration('Score type', ['max', 'min', 'avg', 'whiskers']),
+        description: 'choose whether to use max/min/average or whiskers which combines all three into the same rendering',
+        defaultValue: 'whiskers',
+    },
+    minSize: {
+        type: 'number',
+        defaultValue: 0,
+    },
+}, { baseConfiguration: configSchema_1.default, explicitlyTyped: true });
+exports.default = configSchema;
+//# sourceMappingURL=configSchema.js.map

package/dist/XYPlotRenderer/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/XYPlotRenderer/configSchema.ts"],"names":[],"mappings":";;;;;AAAA,6DAAiE;AACjE,iEAA0C;AAC1C,mDAAuC;AAEvC,IAAM,YAAY,GAAG,IAAA,mCAAmB,EACtC,gBAAgB,EAChB;IACE,MAAM,EAAE;QACN,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,IAAI;KACnB;IACD,mBAAmB,EAAE;QACnB,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,+CAA+C;QAC5D,YAAY,EAAE,KAAK;KACpB;IACD,gBAAgB,EAAE;QAChB,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,YAAY,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,UAAU,CAAC,CAAC;QACzE,WAAW,EACT,oGAAoG;QACtG,YAAY,EAAE,UAAU;KACzB;IACD,OAAO,EAAE;QACP,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,iBAAiB,EAAE,sBAAY,EAAE,eAAe,EAAE,IAAI,EAAE,CAC3D,CAAA;AAED,kBAAe,YAAY,CAAA"}

package/dist/XYPlotRenderer/index.d.ts

@@ -1,3 +1,7 @@
-export { default as ReactComponent } from '../WiggleRendering';
-export { default } from './XYPlotRenderer';
-export declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+import ReactComponent from '../WiggleRendering';
+import PluginManager from '@jbrowse/core/PluginManager';
+import XYPlotRenderer from './XYPlotRenderer';
+import configSchema from './configSchema';
+export { XYPlotRenderer, configSchema, ReactComponent };
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;