@jbrowse/plugin-wiggle 3.3.0 → 3.4.0

package/dist/BigWigAdapter/BigWigAdapter.d.ts

@@ -21,6 +21,5 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;
     }>;
-    freeResources(): void;
 }
 export {};

package/dist/BigWigAdapter/BigWigAdapter.js

@@ -72,7 +72,6 @@ class BigWigAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             featureDensity: 0,
         };
     }
-    freeResources() { }
 }
 BigWigAdapter.capabilities = [
     'hasResolution',

package/dist/LinearWiggleDisplay/model.d.ts

@@ -212,7 +212,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/dist/MultiLinearWiggleDisplay/components/YScaleBars.js

@@ -22,7 +22,7 @@ const Wrapper = (0, mobx_react_1.observer)(function ({ children, model, exportSV
 });
 exports.YScaleBars = (0, mobx_react_1.observer)(function (props) {
     const { model, orientation, exportSVG } = props;
-    const { stats, needsFullHeightScalebar, sources } = model;
-    return stats && sources ? ((0, jsx_runtime_1.jsx)(Wrapper, { ...props, children: needsFullHeightScalebar ? ((0, jsx_runtime_1.jsx)(FullHeightScaleBar_1.default, { model: model, orientation: orientation, exportSVG: exportSVG })) : ((0, jsx_runtime_1.jsx)(IndividualScaleBars_1.default, { model: model, orientation: orientation, exportSVG: exportSVG })) })) : null;
+    const { showSidebar, stats, needsFullHeightScalebar, sources } = model;
+    return stats && sources ? ((0, jsx_runtime_1.jsx)(Wrapper, { ...props, children: showSidebar ? (needsFullHeightScalebar ? ((0, jsx_runtime_1.jsx)(FullHeightScaleBar_1.default, { model: model, orientation: orientation, exportSVG: exportSVG })) : ((0, jsx_runtime_1.jsx)(IndividualScaleBars_1.default, { model: model, orientation: orientation, exportSVG: exportSVG }))) : null })) : null;
 });
 exports.default = exports.YScaleBars;

package/dist/MultiLinearWiggleDisplay/model.d.ts

@@ -101,6 +101,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
 } & {
     type: import("mobx-state-tree").ISimpleType<"MultiLinearWiggleDisplay">;
     layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
+    showSidebar: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -213,7 +214,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
@@ -327,6 +328,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
     featureUnderMouseVolatile: Feature | undefined;
     sourcesVolatile: Source[] | undefined;
 } & {
+    setShowSidebar(arg: boolean): void;
     setSourcesLoading(str: string): void;
     setLayout(layout: Source[]): void;
     clearLayout(): void;

package/dist/MultiLinearWiggleDisplay/model.js

@@ -63,6 +63,7 @@ function stateModelFactory(_pluginManager, configSchema) {
         .compose('MultiLinearWiggleDisplay', (0, SharedWiggleMixin_1.default)(configSchema), mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('MultiLinearWiggleDisplay'),
         layout: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), []),
+        showSidebar: true,
     }))
         .volatile(() => ({
         sourcesLoadingStopToken: undefined,
@@ -70,6 +71,9 @@ function stateModelFactory(_pluginManager, configSchema) {
         sourcesVolatile: undefined,
     }))
         .actions(self => ({
+        setShowSidebar(arg) {
+            self.showSidebar = arg;
+        },
         setSourcesLoading(str) {
             if (self.sourcesLoadingStopToken) {
                 (0, stopToken_1.stopStopToken)(self.sourcesLoadingStopToken);
@@ -353,6 +357,14 @@ function stateModelFactory(_pluginManager, configSchema) {
                             ]);
                         },
                     },
+                    {
+                        label: 'Show sidebar',
+                        type: 'checkbox',
+                        checked: self.showSidebar,
+                        onClick: () => {
+                            self.setShowSidebar(!self.showSidebar);
+                        },
+                    },
                     {
                         label: 'Edit colors/arrangement...',
                         onClick: () => {

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.d.ts

@@ -26,6 +26,5 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
         name: string;
         __name: unknown;
     }[]>;
-    freeResources(): void;
 }
 export {};

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js

@@ -76,7 +76,6 @@ class MultiWiggleAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             ...rest,
         }));
     }
-    freeResources() { }
 }
 MultiWiggleAdapter.capabilities = [
     'hasResolution',

package/dist/WiggleBaseRenderer.d.ts

@@ -33,7 +33,7 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        canvasRecordedData: any;
+        canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -41,15 +41,15 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        reactElement: import("react/jsx-runtime").JSX.Element;
+        imageData: any;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<string, Feature>;
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
+        reactElement: React.ReactElement;
         html?: string;
     }>;
     abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): Promise<Record<string, unknown> | undefined>;

package/dist/drawDensity.js

@@ -39,15 +39,21 @@ function drawDensity(ctx, props) {
             start = performance.now();
         }
         const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+        if (Math.floor(leftPx) !== Math.floor(prevLeftPx) || rightPx - leftPx > 1) {
             reducedFeatures.push(feature);
             prevLeftPx = leftPx;
         }
         const score = feature.get('score');
         hasClipping = hasClipping || score > niceMax || score < niceMin;
         const w = rightPx - leftPx + fudgeFactor;
-        ctx.fillStyle = cb(feature, score);
-        ctx.fillRect(leftPx, 0, w, height);
+        if (score >= scaleOpts.domain[0]) {
+            ctx.fillStyle = cb(feature, score);
+            ctx.fillRect(leftPx, 0, w, height);
+        }
+        else {
+            ctx.fillStyle = '#eee';
+            ctx.fillRect(leftPx, 0, w, height);
+        }
     }
     ctx.save();
     if (hasClipping) {
@@ -69,5 +75,7 @@ function drawDensity(ctx, props) {
         }
     }
     ctx.restore();
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/dist/drawLine.js

@@ -28,7 +28,7 @@ function drawLine(ctx, props) {
             start = performance.now();
         }
         const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+        if (Math.floor(leftPx) !== Math.floor(prevLeftPx) || rightPx - leftPx > 1) {
             reducedFeatures.push(feature);
             prevLeftPx = leftPx;
         }
@@ -71,5 +71,7 @@ function drawLine(ctx, props) {
             ctx.stroke();
         }
     }
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/dist/drawXY.js

@@ -92,7 +92,8 @@ function drawXY(ctx, props) {
                         .toString())
                 : c;
             const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
-            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+            if (Math.floor(leftPx) !== Math.floor(prevLeftPx) ||
+                rightPx - leftPx > 1) {
                 reducedFeatures.push(feature);
                 prevLeftPx = leftPx;
             }
@@ -131,7 +132,8 @@ function drawXY(ctx, props) {
                 start = performance.now();
             }
             const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
-            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+            if (Math.floor(leftPx) !== Math.floor(prevLeftPx) ||
+                rightPx - leftPx > 1) {
                 reducedFeatures.push(feature);
                 prevLeftPx = leftPx;
             }
@@ -183,5 +185,7 @@ function drawXY(ctx, props) {
             ctx.stroke();
         }
     }
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/dist/shared/SharedWiggleMixin.d.ts

@@ -206,7 +206,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/esm/BigWigAdapter/BigWigAdapter.d.ts

@@ -21,6 +21,5 @@ export default class BigWigAdapter extends BaseFeatureDataAdapter {
     getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;
     }>;
-    freeResources(): void;
 }
 export {};

package/esm/BigWigAdapter/BigWigAdapter.js

@@ -70,7 +70,6 @@ class BigWigAdapter extends BaseFeatureDataAdapter {
             featureDensity: 0,
         };
     }
-    freeResources() { }
 }
 BigWigAdapter.capabilities = [
     'hasResolution',

package/esm/LinearWiggleDisplay/model.d.ts

@@ -212,7 +212,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/esm/MultiLinearWiggleDisplay/components/YScaleBars.js

@@ -16,7 +16,7 @@ const Wrapper = observer(function ({ children, model, exportSVG, }) {
 });
 export const YScaleBars = observer(function (props) {
     const { model, orientation, exportSVG } = props;
-    const { stats, needsFullHeightScalebar, sources } = model;
-    return stats && sources ? (_jsx(Wrapper, { ...props, children: needsFullHeightScalebar ? (_jsx(FullHeightScaleBar, { model: model, orientation: orientation, exportSVG: exportSVG })) : (_jsx(IndividualScaleBars, { model: model, orientation: orientation, exportSVG: exportSVG })) })) : null;
+    const { showSidebar, stats, needsFullHeightScalebar, sources } = model;
+    return stats && sources ? (_jsx(Wrapper, { ...props, children: showSidebar ? (needsFullHeightScalebar ? (_jsx(FullHeightScaleBar, { model: model, orientation: orientation, exportSVG: exportSVG })) : (_jsx(IndividualScaleBars, { model: model, orientation: orientation, exportSVG: exportSVG }))) : null })) : null;
 });
 export default YScaleBars;

package/esm/MultiLinearWiggleDisplay/model.d.ts

@@ -101,6 +101,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
 } & {
     type: import("mobx-state-tree").ISimpleType<"MultiLinearWiggleDisplay">;
     layout: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<Source[], Source[], Source[]>, [undefined]>;
+    showSidebar: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -213,7 +214,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
@@ -327,6 +328,7 @@ export declare function stateModelFactory(_pluginManager: PluginManager, configS
     featureUnderMouseVolatile: Feature | undefined;
     sourcesVolatile: Source[] | undefined;
 } & {
+    setShowSidebar(arg: boolean): void;
     setSourcesLoading(str: string): void;
     setLayout(layout: Source[]): void;
     clearLayout(): void;

package/esm/MultiLinearWiggleDisplay/model.js

@@ -24,6 +24,7 @@ export function stateModelFactory(_pluginManager, configSchema) {
         .compose('MultiLinearWiggleDisplay', SharedWiggleMixin(configSchema), types.model({
         type: types.literal('MultiLinearWiggleDisplay'),
         layout: types.optional(types.frozen(), []),
+        showSidebar: true,
     }))
         .volatile(() => ({
         sourcesLoadingStopToken: undefined,
@@ -31,6 +32,9 @@ export function stateModelFactory(_pluginManager, configSchema) {
         sourcesVolatile: undefined,
     }))
         .actions(self => ({
+        setShowSidebar(arg) {
+            self.showSidebar = arg;
+        },
         setSourcesLoading(str) {
             if (self.sourcesLoadingStopToken) {
                 stopStopToken(self.sourcesLoadingStopToken);
@@ -314,6 +318,14 @@ export function stateModelFactory(_pluginManager, configSchema) {
                             ]);
                         },
                     },
+                    {
+                        label: 'Show sidebar',
+                        type: 'checkbox',
+                        checked: self.showSidebar,
+                        onClick: () => {
+                            self.setShowSidebar(!self.showSidebar);
+                        },
+                    },
                     {
                         label: 'Edit colors/arrangement...',
                         onClick: () => {

package/esm/MultiWiggleAdapter/MultiWiggleAdapter.d.ts

@@ -26,6 +26,5 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
         name: string;
         __name: unknown;
     }[]>;
-    freeResources(): void;
 }
 export {};

package/esm/MultiWiggleAdapter/MultiWiggleAdapter.js

@@ -74,7 +74,6 @@ class MultiWiggleAdapter extends BaseFeatureDataAdapter {
             ...rest,
         }));
     }
-    freeResources() { }
 }
 MultiWiggleAdapter.capabilities = [
     'hasResolution',

package/esm/WiggleBaseRenderer.d.ts

@@ -33,7 +33,7 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        canvasRecordedData: any;
+        canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -41,15 +41,15 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        reactElement: import("react/jsx-runtime").JSX.Element;
+        imageData: any;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<string, Feature>;
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
+        reactElement: React.ReactElement;
         html?: string;
     }>;
     abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): Promise<Record<string, unknown> | undefined>;

package/esm/drawDensity.js

@@ -36,15 +36,21 @@ export function drawDensity(ctx, props) {
             start = performance.now();
         }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+        if (Math.floor(leftPx) !== Math.floor(prevLeftPx) || rightPx - leftPx > 1) {
             reducedFeatures.push(feature);
             prevLeftPx = leftPx;
         }
         const score = feature.get('score');
         hasClipping = hasClipping || score > niceMax || score < niceMin;
         const w = rightPx - leftPx + fudgeFactor;
-        ctx.fillStyle = cb(feature, score);
-        ctx.fillRect(leftPx, 0, w, height);
+        if (score >= scaleOpts.domain[0]) {
+            ctx.fillStyle = cb(feature, score);
+            ctx.fillRect(leftPx, 0, w, height);
+        }
+        else {
+            ctx.fillStyle = '#eee';
+            ctx.fillRect(leftPx, 0, w, height);
+        }
     }
     ctx.save();
     if (hasClipping) {
@@ -66,5 +72,7 @@ export function drawDensity(ctx, props) {
         }
     }
     ctx.restore();
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/esm/drawLine.js

@@ -25,7 +25,7 @@ export function drawLine(ctx, props) {
             start = performance.now();
         }
         const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-        if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+        if (Math.floor(leftPx) !== Math.floor(prevLeftPx) || rightPx - leftPx > 1) {
             reducedFeatures.push(feature);
             prevLeftPx = leftPx;
         }
@@ -68,5 +68,7 @@ export function drawLine(ctx, props) {
             ctx.stroke();
         }
     }
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/esm/drawXY.js

@@ -89,7 +89,8 @@ export function drawXY(ctx, props) {
                         .toString())
                 : c;
             const w = Math.max(rightPx - leftPx + fudgeFactor, minSize);
-            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+            if (Math.floor(leftPx) !== Math.floor(prevLeftPx) ||
+                rightPx - leftPx > 1) {
                 reducedFeatures.push(feature);
                 prevLeftPx = leftPx;
             }
@@ -128,7 +129,8 @@ export function drawXY(ctx, props) {
                 start = performance.now();
             }
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-            if (Math.floor(leftPx) !== Math.floor(prevLeftPx)) {
+            if (Math.floor(leftPx) !== Math.floor(prevLeftPx) ||
+                rightPx - leftPx > 1) {
                 reducedFeatures.push(feature);
                 prevLeftPx = leftPx;
             }
@@ -180,5 +182,7 @@ export function drawXY(ctx, props) {
             ctx.stroke();
         }
     }
-    return { reducedFeatures };
+    return {
+        reducedFeatures,
+    };
 }

package/esm/shared/SharedWiggleMixin.d.ts

@@ -206,7 +206,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "3.3.0",
+  "version": "3.4.0",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -36,10 +36,10 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bbi": "^6.0.0",
-    "@jbrowse/core": "^3.3.0",
-    "@jbrowse/plugin-data-management": "^3.3.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.3.0",
+    "@gmod/bbi": "^7.0.0",
+    "@jbrowse/core": "^3.4.0",
+    "@jbrowse/plugin-data-management": "^3.4.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.4.0",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "@mui/x-charts-vendor": "^8.0.0",
@@ -62,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
+  "gitHead": "a9f1ac35fc2dd810bae92cdaf1fc19995bee4413"
 }