@jbrowse/plugin-linear-genome-view 2.11.0 → 2.11.1

package/dist/BaseLinearDisplay/components/Tooltip.js

@@ -40,6 +40,7 @@ const Tooltip = (0, mobx_react_1.observer)(function ({ model, clientMouseCoord,
     const y = clientMouseCoord[1];
     const { refs, floatingStyles, context } = (0, react_2.useFloating)({
         placement: 'right',
+        strategy: 'fixed',
     });
     const clientPoint = (0, react_2.useClientPoint)(context, { x, y });
     const { getFloatingProps } = (0, react_2.useInteractions)([clientPoint]);

package/dist/BasicTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function BasicTrackF(pm: PluginManager): void;

package/dist/BasicTrack/index.js

@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pm) => {
+function BasicTrackF(pm) {
     pm.addTrackType(() => {
         const configSchema = (0, configSchema_1.default)(pm);
         return new pluggableElementTypes_1.TrackType({
@@ -14,4 +14,5 @@ exports.default = (pm) => {
             stateModel: (0, pluggableElementTypes_1.createBaseTrackModel)(pm, 'BasicTrack', configSchema),
         });
     });
-};
+}
+exports.default = BasicTrackF;

package/dist/FeatureTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function FeatureTrackF(pm: PluginManager): void;

package/dist/FeatureTrack/index.js

@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pm) => {
+function FeatureTrackF(pm) {
     pm.addTrackType(() => {
         const configSchema = (0, configSchema_1.default)(pm);
         return new pluggableElementTypes_1.TrackType({
@@ -15,4 +15,5 @@ exports.default = (pm) => {
             stateModel: (0, pluggableElementTypes_1.createBaseTrackModel)(pm, 'FeatureTrack', configSchema),
         });
     });
-};
+}
+exports.default = FeatureTrackF;

package/dist/LaunchLinearGenomeView/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LaunchLinearGenomeViewF(pluginManager: PluginManager): void;

package/dist/LaunchLinearGenomeView/index.js

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const util_1 = require("@jbrowse/core/util");
 const searchUtils_1 = require("../searchUtils");
-exports.default = (pluginManager) => {
+function LaunchLinearGenomeViewF(pluginManager) {
     pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', 
     // @ts-expect-error
     async ({ session, assembly, loc, tracks = [], tracklist, nav, highlight, }) => {
@@ -51,7 +51,8 @@ exports.default = (pluginManager) => {
             throw e;
         }
     });
-};
+}
+exports.default = LaunchLinearGenomeViewF;
 function tryTrack(model, trackId, idsNotFound) {
     try {
         model.showTrack(trackId);

package/dist/LinearBareDisplay/index.d.ts

@@ -1,5 +1,4 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearBareDisplayF(pluginManager: PluginManager): void;
 export { configSchemaFactory } from './configSchema';
 export { stateModelFactory } from './model';

package/dist/LinearBareDisplay/index.js

@@ -6,7 +6,7 @@ const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const configSchema_1 = require("./configSchema");
 const model_1 = require("./model");
 const BaseLinearDisplay_1 = require("../BaseLinearDisplay/");
-exports.default = (pluginManager) => {
+function LinearBareDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.configSchemaFactory)(pluginManager);
         return new pluggableElementTypes_1.DisplayType({
@@ -19,7 +19,8 @@ exports.default = (pluginManager) => {
             ReactComponent: BaseLinearDisplay_1.BaseLinearDisplayComponent,
         });
     });
-};
+}
+exports.default = LinearBareDisplayF;
 var configSchema_2 = require("./configSchema");
 Object.defineProperty(exports, "configSchemaFactory", { enumerable: true, get: function () { return configSchema_2.configSchemaFactory; } });
 var model_2 = require("./model");

package/dist/LinearBasicDisplay/index.d.ts

@@ -1,5 +1,4 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearBasicDisplay(pluginManager: PluginManager): void;
 export { default as modelFactory } from './model';
 export { default as configSchema } from './configSchema';

package/dist/LinearBasicDisplay/index.js

@@ -9,7 +9,7 @@ const BaseLinearDisplay_1 = require("../BaseLinearDisplay");
 // locals
 const configSchema_1 = __importDefault(require("./configSchema"));
 const model_1 = __importDefault(require("./model"));
-exports.default = (pluginManager) => {
+function LinearBasicDisplay(pluginManager) {
     pluginManager.addDisplayType(() => {
         const config = (0, configSchema_1.default)(pluginManager);
         return new pluggableElementTypes_1.DisplayType({
@@ -22,7 +22,8 @@ exports.default = (pluginManager) => {
             ReactComponent: BaseLinearDisplay_1.BaseLinearDisplayComponent,
         });
     });
-};
+}
+exports.default = LinearBasicDisplay;
 var model_2 = require("./model");
 Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return __importDefault(model_2).default; } });
 var configSchema_2 = require("./configSchema");

package/dist/LinearGenomeView/components/Cytobands.js

@@ -8,6 +8,7 @@ const mobx_react_1 = require("mobx-react");
 // locals
 const __1 = require("..");
 const util_1 = require("./util");
+const util_2 = require("@jbrowse/core/util");
 // rounded rect from https://stackoverflow.com/a/45889603/2129219
 // prettier-ignore
 function rightRoundedRect(x, y, width, height, radius) {
@@ -68,28 +69,26 @@ const Cytobands = (0, mobx_react_1.observer)(function ({ overview, block, assemb
         const e = overview.bpToPx({ refName, coord: end }) || 0;
         const l = Math.min(s, e);
         const w = Math.abs(e - s);
-        const c = colorMap[type];
+        const c = colorMap[type] || 'black';
         if (type === 'acen' && !centromereSeen) {
             centromereSeen = true; // the next acen entry is drawn with different right triangle
-            const tri = reversed
-                ? rightTriangle(s - w, 0, w, h)
-                : leftTriangle(s, 0, w, h);
-            return react_1.default.createElement("polygon", { key: k, points: tri, fill: c });
+            return (react_1.default.createElement("polygon", { key: k, points: reversed
+                    ? rightTriangle(s - w, 0, w, h)
+                    : leftTriangle(s, 0, w, h), ...(0, util_2.getFillProps)(c) }));
         }
         else if (type === 'acen' && centromereSeen) {
-            const tri = reversed
-                ? leftTriangle(s - w, 0, w, h)
-                : rightTriangle(s, 0, w, h);
-            return react_1.default.createElement("polygon", { key: k, points: tri, fill: c });
+            return (react_1.default.createElement("polygon", { key: k, points: reversed
+                    ? leftTriangle(s - w, 0, w, h)
+                    : rightTriangle(s, 0, w, h), ...(0, util_2.getFillProps)(c) }));
         }
         else if (lcap === index) {
-            return react_1.default.createElement("path", { key: k, d: leftRoundedRect(l, 0, w, h, 8), fill: c });
+            return (react_1.default.createElement("path", { key: k, d: leftRoundedRect(l, 0, w, h, 8), ...(0, util_2.getFillProps)(c) }));
         }
         else if (rcap === index) {
-            return react_1.default.createElement("path", { key: k, d: rightRoundedRect(l, 0, w, h, 8), fill: c });
+            return (react_1.default.createElement("path", { key: k, d: rightRoundedRect(l, 0, w, h, 8), ...(0, util_2.getFillProps)(c) }));
         }
         else {
-            return react_1.default.createElement("rect", { key: k, x: l, y: 0, width: w, height: h, fill: c });
+            return (react_1.default.createElement("rect", { key: k, x: l, y: 0, width: w, height: h, ...(0, util_2.getFillProps)(c) }));
         }
     })));
 });

package/dist/LinearGenomeView/components/OverviewScalebarPolygon.js

@@ -8,6 +8,7 @@ const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 // locals
 const __1 = require("..");
+const util_1 = require("@jbrowse/core/util");
 const OverviewScalebarPolygon = (0, mobx_react_1.observer)(function ({ model, overview, useOffset = true, }) {
     const theme = (0, material_1.useTheme)();
     const multiplier = Number(useOffset);
@@ -41,6 +42,6 @@ const OverviewScalebarPolygon = (0, mobx_react_1.observer)(function ({ model, ov
         [topRight, 0],
         [topLeft, 0],
     ];
-    return (react_1.default.createElement("polygon", { points: points.toString(), fill: (0, material_1.alpha)(polygonColor, 0.3), stroke: (0, material_1.alpha)(polygonColor, 0.8) }));
+    return (react_1.default.createElement("polygon", { points: points.toString(), ...(0, util_1.getFillProps)((0, material_1.alpha)(polygonColor, 0.3)), ...(0, util_1.getStrokeProps)((0, material_1.alpha)(polygonColor, 0.8)) }));
 });
 exports.default = OverviewScalebarPolygon;

package/dist/LinearGenomeView/svgcomponents/SVGHeader.js

@@ -47,7 +47,7 @@ function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight, }) {
         react_1.default.createElement("text", { x: 0, y: 0, dominantBaseline: "hanging", fontSize: fontSize, fill: c }, assemblyName),
         showCytobands ? (react_1.default.createElement("g", { transform: `translate(0 ${rulerHeight})` },
             react_1.default.createElement(Cytobands_1.default, { overview: overview, assembly: assembly, block: block }),
-            react_1.default.createElement("rect", { stroke: "red", fill: "rgb(255,0,0,0.1)", width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: __1.HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
+            react_1.default.createElement("rect", { stroke: "red", fill: "rgb(255,0,0)", fillOpacity: 0.1, width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: __1.HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
             react_1.default.createElement("g", { transform: `translate(0,${__1.HEADER_OVERVIEW_HEIGHT})` },
                 react_1.default.createElement(OverviewScalebarPolygon_1.default, { overview: overview, model: model, useOffset: false })))) : null,
         react_1.default.createElement("g", { transform: `translate(0 ${fontSize + y})` },

package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.js

@@ -8,7 +8,7 @@ const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
 function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }) {
     const theme = (0, material_1.useTheme)();
-    const fill = theme.palette.text.primary;
+    const fill = (0, util_1.stripAlpha)(theme.palette.text.primary);
     const xoff = trackLabels === 'overlay' ? 5 : 0;
     const yoff = trackLabels === 'offset' ? 5 : 0;
     const name = (0, util_1.coarseStripHTML)(trackName);

package/esm/BaseLinearDisplay/components/Tooltip.js

@@ -35,6 +35,7 @@ const Tooltip = observer(function ({ model, clientMouseCoord, }) {
     const y = clientMouseCoord[1];
     const { refs, floatingStyles, context } = useFloating({
         placement: 'right',
+        strategy: 'fixed',
     });
     const clientPoint = useClientPoint(context, { x, y });
     const { getFloatingProps } = useInteractions([clientPoint]);

package/esm/BasicTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function BasicTrackF(pm: PluginManager): void;

package/esm/BasicTrack/index.js

@@ -1,6 +1,6 @@
 import { createBaseTrackModel, TrackType, } from '@jbrowse/core/pluggableElementTypes';
 import configSchemaF from './configSchema';
-export default (pm) => {
+export default function BasicTrackF(pm) {
     pm.addTrackType(() => {
         const configSchema = configSchemaF(pm);
         return new TrackType({
@@ -9,4 +9,4 @@ export default (pm) => {
             stateModel: createBaseTrackModel(pm, 'BasicTrack', configSchema),
         });
     });
-};
+}

package/esm/FeatureTrack/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pm: PluginManager) => void;
-export default _default;
+export default function FeatureTrackF(pm: PluginManager): void;

package/esm/FeatureTrack/index.js

@@ -1,6 +1,6 @@
 import { createBaseTrackModel, TrackType, } from '@jbrowse/core/pluggableElementTypes';
 import configSchemaF from './configSchema';
-export default (pm) => {
+export default function FeatureTrackF(pm) {
     pm.addTrackType(() => {
         const configSchema = configSchemaF(pm);
         return new TrackType({
@@ -10,4 +10,4 @@ export default (pm) => {
             stateModel: createBaseTrackModel(pm, 'FeatureTrack', configSchema),
         });
     });
-};
+}

package/esm/LaunchLinearGenomeView/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LaunchLinearGenomeViewF(pluginManager: PluginManager): void;

package/esm/LaunchLinearGenomeView/index.js

@@ -1,6 +1,6 @@
 import { when, parseLocString, } from '@jbrowse/core/util';
 import { handleSelectedRegion } from '../searchUtils';
-export default (pluginManager) => {
+export default function LaunchLinearGenomeViewF(pluginManager) {
     pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', 
     // @ts-expect-error
     async ({ session, assembly, loc, tracks = [], tracklist, nav, highlight, }) => {
@@ -49,7 +49,7 @@ export default (pluginManager) => {
             throw e;
         }
     });
-};
+}
 function tryTrack(model, trackId, idsNotFound) {
     try {
         model.showTrack(trackId);

package/esm/LinearBareDisplay/index.d.ts

@@ -1,5 +1,4 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearBareDisplayF(pluginManager: PluginManager): void;
 export { configSchemaFactory } from './configSchema';
 export { stateModelFactory } from './model';

package/esm/LinearBareDisplay/index.js

@@ -3,7 +3,7 @@ import { DisplayType } from '@jbrowse/core/pluggableElementTypes';
 import { configSchemaFactory } from './configSchema';
 import { stateModelFactory } from './model';
 import { BaseLinearDisplayComponent } from '../BaseLinearDisplay/';
-export default (pluginManager) => {
+export default function LinearBareDisplayF(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = configSchemaFactory(pluginManager);
         return new DisplayType({
@@ -16,6 +16,6 @@ export default (pluginManager) => {
             ReactComponent: BaseLinearDisplayComponent,
         });
     });
-};
+}
 export { configSchemaFactory } from './configSchema';
 export { stateModelFactory } from './model';

package/esm/LinearBasicDisplay/index.d.ts

@@ -1,5 +1,4 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function LinearBasicDisplay(pluginManager: PluginManager): void;
 export { default as modelFactory } from './model';
 export { default as configSchema } from './configSchema';

package/esm/LinearBasicDisplay/index.js

@@ -3,7 +3,7 @@ import { BaseLinearDisplayComponent } from '../BaseLinearDisplay';
 // locals
 import configSchema from './configSchema';
 import modelFactory from './model';
-export default (pluginManager) => {
+export default function LinearBasicDisplay(pluginManager) {
     pluginManager.addDisplayType(() => {
         const config = configSchema(pluginManager);
         return new DisplayType({
@@ -16,6 +16,6 @@ export default (pluginManager) => {
             ReactComponent: BaseLinearDisplayComponent,
         });
     });
-};
+}
 export { default as modelFactory } from './model';
 export { default as configSchema } from './configSchema';

package/esm/LinearGenomeView/components/Cytobands.js

@@ -3,6 +3,7 @@ import { observer } from 'mobx-react';
 // locals
 import { HEADER_OVERVIEW_HEIGHT } from '..';
 import { getCytobands } from './util';
+import { getFillProps } from '@jbrowse/core/util';
 // rounded rect from https://stackoverflow.com/a/45889603/2129219
 // prettier-ignore
 function rightRoundedRect(x, y, width, height, radius) {
@@ -63,28 +64,26 @@ const Cytobands = observer(function ({ overview, block, assembly, }) {
         const e = overview.bpToPx({ refName, coord: end }) || 0;
         const l = Math.min(s, e);
         const w = Math.abs(e - s);
-        const c = colorMap[type];
+        const c = colorMap[type] || 'black';
         if (type === 'acen' && !centromereSeen) {
             centromereSeen = true; // the next acen entry is drawn with different right triangle
-            const tri = reversed
-                ? rightTriangle(s - w, 0, w, h)
-                : leftTriangle(s, 0, w, h);
-            return React.createElement("polygon", { key: k, points: tri, fill: c });
+            return (React.createElement("polygon", { key: k, points: reversed
+                    ? rightTriangle(s - w, 0, w, h)
+                    : leftTriangle(s, 0, w, h), ...getFillProps(c) }));
         }
         else if (type === 'acen' && centromereSeen) {
-            const tri = reversed
-                ? leftTriangle(s - w, 0, w, h)
-                : rightTriangle(s, 0, w, h);
-            return React.createElement("polygon", { key: k, points: tri, fill: c });
+            return (React.createElement("polygon", { key: k, points: reversed
+                    ? leftTriangle(s - w, 0, w, h)
+                    : rightTriangle(s, 0, w, h), ...getFillProps(c) }));
         }
         else if (lcap === index) {
-            return React.createElement("path", { key: k, d: leftRoundedRect(l, 0, w, h, 8), fill: c });
+            return (React.createElement("path", { key: k, d: leftRoundedRect(l, 0, w, h, 8), ...getFillProps(c) }));
         }
         else if (rcap === index) {
-            return React.createElement("path", { key: k, d: rightRoundedRect(l, 0, w, h, 8), fill: c });
+            return (React.createElement("path", { key: k, d: rightRoundedRect(l, 0, w, h, 8), ...getFillProps(c) }));
         }
         else {
-            return React.createElement("rect", { key: k, x: l, y: 0, width: w, height: h, fill: c });
+            return (React.createElement("rect", { key: k, x: l, y: 0, width: w, height: h, ...getFillProps(c) }));
         }
     })));
 });

package/esm/LinearGenomeView/components/OverviewScalebarPolygon.js

@@ -3,6 +3,7 @@ import { useTheme, alpha } from '@mui/material';
 import { observer } from 'mobx-react';
 // locals
 import { HEADER_BAR_HEIGHT } from '..';
+import { getFillProps, getStrokeProps } from '@jbrowse/core/util';
 const OverviewScalebarPolygon = observer(function ({ model, overview, useOffset = true, }) {
     const theme = useTheme();
     const multiplier = Number(useOffset);
@@ -36,6 +37,6 @@ const OverviewScalebarPolygon = observer(function ({ model, overview, useOffset
         [topRight, 0],
         [topLeft, 0],
     ];
-    return (React.createElement("polygon", { points: points.toString(), fill: alpha(polygonColor, 0.3), stroke: alpha(polygonColor, 0.8) }));
+    return (React.createElement("polygon", { points: points.toString(), ...getFillProps(alpha(polygonColor, 0.3)), ...getStrokeProps(alpha(polygonColor, 0.8)) }));
 });
 export default OverviewScalebarPolygon;

package/esm/LinearGenomeView/svgcomponents/SVGHeader.js

@@ -42,7 +42,7 @@ export default function SVGHeader({ model, fontSize, cytobandHeight, rulerHeight
         React.createElement("text", { x: 0, y: 0, dominantBaseline: "hanging", fontSize: fontSize, fill: c }, assemblyName),
         showCytobands ? (React.createElement("g", { transform: `translate(0 ${rulerHeight})` },
             React.createElement(Cytobands, { overview: overview, assembly: assembly, block: block }),
-            React.createElement("rect", { stroke: "red", fill: "rgb(255,0,0,0.1)", width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
+            React.createElement("rect", { stroke: "red", fill: "rgb(255,0,0)", fillOpacity: 0.1, width: Math.max(lastOverviewPx - firstOverviewPx, 0.5), height: HEADER_OVERVIEW_HEIGHT - 1, x: firstOverviewPx, y: 0.5 }),
             React.createElement("g", { transform: `translate(0,${HEADER_OVERVIEW_HEIGHT})` },
                 React.createElement(OverviewScalebarPolygon, { overview: overview, model: model, useOffset: false })))) : null,
         React.createElement("g", { transform: `translate(0 ${fontSize + y})` },

package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.js

@@ -1,9 +1,9 @@
 import React from 'react';
 import { useTheme } from '@mui/material';
-import { coarseStripHTML } from '@jbrowse/core/util';
+import { coarseStripHTML, stripAlpha } from '@jbrowse/core/util';
 export default function SVGTrackLabel({ trackLabels, trackName, fontSize, trackLabelOffset, x, }) {
     const theme = useTheme();
-    const fill = theme.palette.text.primary;
+    const fill = stripAlpha(theme.palette.text.primary);
     const xoff = trackLabels === 'overlay' ? 5 : 0;
     const yoff = trackLabels === 'offset' ? 5 : 0;
     const name = coarseStripHTML(trackName);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.11.0",
+  "version": "2.11.1",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -63,5 +63,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
+  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
 }