@jbrowse/plugin-wiggle 2.12.3 → 2.13.1

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

@@ -24,9 +24,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree" /**
-             * #getter
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {

package/dist/MultiDensityRenderer/MultiDensityRenderer.js

@@ -9,11 +9,9 @@ const drawDensity_1 = require("../drawDensity");
 class MultiXYPlotRenderer extends WiggleBaseRenderer_1.default {
     // @ts-expect-error
     async draw(ctx, props) {
-        const { bpPerPx, sources, regions, features } = props;
-        const [region] = regions;
+        const { sources, features } = props;
         const groups = (0, util_1.groupBy)(features.values(), f => f.get('source'));
         const height = props.height / sources.length;
-        const width = (region.end - region.start) / bpPerPx;
         let feats = [];
         ctx.save();
         sources.forEach(source => {
@@ -23,11 +21,6 @@ class MultiXYPlotRenderer extends WiggleBaseRenderer_1.default {
                 features,
                 height,
             });
-            ctx.strokeStyle = 'rgba(200,200,200,0.8)';
-            ctx.beginPath();
-            ctx.moveTo(0, height);
-            ctx.lineTo(width, height);
-            ctx.stroke();
             ctx.translate(0, height);
             feats = feats.concat(reducedFeatures);
         });

package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js

@@ -7,7 +7,7 @@ const react_1 = __importDefault(require("react"));
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const mobx_react_1 = require("mobx-react");
 const YScaleBars_1 = __importDefault(require("./YScaleBars"));
-const MultiLinearWiggleDisplayComponent = (0, mobx_react_1.observer)((props) => {
+const MultiLinearWiggleDisplayComponent = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     return (react_1.default.createElement("div", null,
         react_1.default.createElement(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props }),

package/dist/shared/modelShared.d.ts

@@ -21,9 +21,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             end: import("mobx-state-tree").ISimpleType<number>;
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
-            assemblyName: import("mobx-state-tree" /**
-             * #property
-             */).ISimpleType<string>;
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/util.js

@@ -101,11 +101,10 @@ function getNiceDomain({ scaleType, domain, bounds, }) {
         }
     }
     if (scaleType === 'log') {
-        // if the min is 0, assume that it's just something
-        // with no read coverage and that we should ignore it in calculations
-        // if it's greater than 1 pin to 1 for the full range also
-        // otherwise, we may see bigwigs with fractional values
-        if (min === 0 || min > 1) {
+        // for min>0 and max>1, set log min to 1, which works for most coverage
+        // types tracks. if max is not >1, might be like raw p-values so then it'll
+        // display negative values
+        if (min >= 0 && max > 1) {
             min = 1;
         }
     }

package/esm/LinearWiggleDisplay/models/model.d.ts

@@ -24,9 +24,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             refName: import("mobx-state-tree").ISimpleType<string>;
             start: import("mobx-state-tree").ISimpleType<number>;
             end: import("mobx-state-tree").ISimpleType<number>;
-            reversed: import("mobx-state-tree" /**
-             * #getter
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
             assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {

package/esm/MultiDensityRenderer/MultiDensityRenderer.js

@@ -4,11 +4,9 @@ import { drawDensity } from '../drawDensity';
 export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
     // @ts-expect-error
     async draw(ctx, props) {
-        const { bpPerPx, sources, regions, features } = props;
-        const [region] = regions;
+        const { sources, features } = props;
         const groups = groupBy(features.values(), f => f.get('source'));
         const height = props.height / sources.length;
-        const width = (region.end - region.start) / bpPerPx;
         let feats = [];
         ctx.save();
         sources.forEach(source => {
@@ -18,11 +16,6 @@ export default class MultiXYPlotRenderer extends WiggleBaseRenderer {
                 features,
                 height,
             });
-            ctx.strokeStyle = 'rgba(200,200,200,0.8)';
-            ctx.beginPath();
-            ctx.moveTo(0, height);
-            ctx.lineTo(width, height);
-            ctx.stroke();
             ctx.translate(0, height);
             feats = feats.concat(reducedFeatures);
         });

package/esm/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js

@@ -2,7 +2,7 @@ import React from 'react';
 import { BaseLinearDisplayComponent } from '@jbrowse/plugin-linear-genome-view';
 import { observer } from 'mobx-react';
 import YScaleBars from './YScaleBars';
-const MultiLinearWiggleDisplayComponent = observer((props) => {
+const MultiLinearWiggleDisplayComponent = observer(function (props) {
     const { model } = props;
     return (React.createElement("div", null,
         React.createElement(BaseLinearDisplayComponent, { ...props }),

package/esm/shared/modelShared.d.ts

@@ -21,9 +21,7 @@ export default function SharedWiggleMixin(configSchema: AnyConfigurationSchemaTy
             end: import("mobx-state-tree").ISimpleType<number>;
             reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
         } & {
-            assemblyName: import("mobx-state-tree" /**
-             * #property
-             */).ISimpleType<string>;
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
         }, {
             setRefName(newRefName: string): void;
         }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/util.js

@@ -90,11 +90,10 @@ export function getNiceDomain({ scaleType, domain, bounds, }) {
         }
     }
     if (scaleType === 'log') {
-        // if the min is 0, assume that it's just something
-        // with no read coverage and that we should ignore it in calculations
-        // if it's greater than 1 pin to 1 for the full range also
-        // otherwise, we may see bigwigs with fractional values
-        if (min === 0 || min > 1) {
+        // for min>0 and max>1, set log min to 1, which works for most coverage
+        // types tracks. if max is not >1, might be like raw p-values so then it'll
+        // display negative values
+        if (min >= 0 && max > 1) {
             min = 1;
         }
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-wiggle",
-  "version": "2.12.3",
+  "version": "2.13.1",
   "description": "JBrowse 2 wiggle adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -66,5 +66,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "2775490221cde56af344acebb0afa7e14531cd81"
+  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
 }