@jbrowse/plugin-circular-view 2.6.2 → 2.7.0

package/dist/BaseChordDisplay/components/BaseChordDisplay.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-declare const _default: ({ display, }: {
+declare const BaseChordDisplay: ({ display, }: {
     display: {
         filled: boolean;
         error: unknown;
@@ -9,4 +9,4 @@ declare const _default: ({ display, }: {
         };
     };
 }) => React.JSX.Element;
-export default _default;
+export default BaseChordDisplay;

package/dist/BaseChordDisplay/components/BaseChordDisplay.js

@@ -8,7 +8,7 @@ const mobx_react_1 = require("mobx-react");
 // locals
 const Loading_1 = __importDefault(require("./Loading"));
 const DisplayError_1 = __importDefault(require("./DisplayError"));
-exports.default = (0, mobx_react_1.observer)(function BaseChordDisplay({ display, }) {
+const BaseChordDisplay = (0, mobx_react_1.observer)(function ({ display, }) {
     if (display.error) {
         return react_1.default.createElement(DisplayError_1.default, { model: display });
     }
@@ -17,3 +17,4 @@ exports.default = (0, mobx_react_1.observer)(function BaseChordDisplay({ display
     }
     return display.reactElement;
 });
+exports.default = BaseChordDisplay;

package/dist/BaseChordDisplay/models/renderReaction.d.ts

@@ -3,10 +3,28 @@ export declare function renderReactionData(self: any): {
     rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
     renderProps: any;
     renderArgs: {
-        assemblyName: any;
+        assemblyName: string;
         adapterConfig: any;
         rendererType: any;
-        regions: any;
+        regions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
+            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").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+            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").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
         blockDefinitions: any;
         sessionId: string;
         timeout: number;

package/dist/CircularView/components/Controls.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { CircularViewModel } from '../models/CircularView';
-declare const _default: ({ model }: {
+declare const Controls: ({ model }: {
     model: CircularViewModel;
 }) => React.JSX.Element;
-export default _default;
+export default Controls;

package/dist/CircularView/components/Controls.js

@@ -52,7 +52,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         top: 0,
     },
 }));
-exports.default = (0, mobx_react_1.observer)(function ({ model }) {
+const Controls = (0, mobx_react_1.observer)(function ({ model }) {
     const { classes } = useStyles();
     const [anchorEl, setAnchorEl] = (0, react_1.useState)(null);
     return (react_1.default.createElement("div", { className: classes.controls },
@@ -87,3 +87,4 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
                 setAnchorEl(null);
             }, open: Boolean(anchorEl), onClose: () => setAnchorEl(null) })) : null));
 });
+exports.default = Controls;

package/dist/CircularView/components/Ruler.d.ts

@@ -1,8 +1,8 @@
 import React from 'react';
 import { Slice } from '../models/slices';
 import { CircularViewModel } from '../models/CircularView';
-declare const _default: ({ model, slice, }: {
+declare const Ruler: ({ model, slice, }: {
     model: CircularViewModel;
     slice: Slice;
 }) => React.JSX.Element;
-export default _default;
+export default Ruler;

package/dist/CircularView/components/Ruler.js

@@ -120,9 +120,10 @@ const RegionRulerArc = (0, mobx_react_1.observer)(function ({ model, slice, regi
         react_1.default.createElement(RulerLabel, { text: region.refName, view: model, maxWidthPx: widthPx, radians: centerRadians, radiusPx: radiusPx, color: color }),
         react_1.default.createElement("path", { d: sliceArcPath(slice, radiusPx + 1, region.start, region.end), stroke: color, strokeWidth: 2, fill: "none" })));
 });
-exports.default = (0, mobx_react_1.observer)(function ({ model, slice, }) {
+const Ruler = (0, mobx_react_1.observer)(function ({ model, slice, }) {
     if (slice.region.elided) {
         return (react_1.default.createElement(ElisionRulerArc, { key: (0, util_1.assembleLocString)(slice.region.regions[0]), model: model, region: slice.region, slice: slice }));
     }
     return (react_1.default.createElement(RegionRulerArc, { key: (0, util_1.assembleLocString)(slice.region), region: slice.region, model: model, slice: slice }));
 });
+exports.default = Ruler;

package/dist/CircularView/models/slices.d.ts

@@ -1,17 +1,17 @@
 import { Region } from '@jbrowse/core/util';
-export type SliceElidedRegion = {
+export interface SliceElidedRegion {
     elided: true;
     widthBp: number;
     regions: Region[];
-};
-export type SliceNonElidedRegion = {
+}
+export interface SliceNonElidedRegion {
     elided: false;
     widthBp: number;
     start: number;
     end: number;
     refName: string;
     assemblyName: string;
-};
+}
 export type SliceRegion = SliceNonElidedRegion | SliceElidedRegion;
 export declare class Slice {
     region: SliceRegion;

package/dist/CircularView/models/viewportVisibleRegion.js

@@ -86,8 +86,7 @@ function viewportVisibleSection(viewSides, circleCenter, circleRadius) {
             [viewR, viewB],
         ];
         let maxRho = -Infinity;
-        for (let i = 0; i < vertices.length; i += 1) {
-            const [x, y] = vertices[i];
+        for (const [x, y] of vertices) {
             const rho = Math.sqrt(x * x + y * y);
             if (rho > maxRho) {
                 maxRho = rho;
@@ -187,9 +186,8 @@ function viewportVisibleSection(viewSides, circleCenter, circleRadius) {
     let rhoMax = -Infinity;
     let thetaMin = Infinity;
     let thetaMax = -Infinity;
-    for (let i = 0; i < vertices.length; i += 1) {
+    for (const [vx, vy] of vertices) {
         // ignore vertex if outside the viewport
-        const [vx, vy] = vertices[i];
         if (vx >= viewL && vx <= viewR && vy >= viewT && vy <= viewB) {
             const [rho, theta] = cartesianToPolar(vx * reflect, vy * reflect);
             // ignore vertex if outside the circle

package/dist/CircularView/svgcomponents/SVGBackground.js

@@ -5,8 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
+const util_1 = require("@jbrowse/core/util");
 function SVGBackground({ width, height, shift, }) {
     const theme = (0, material_1.useTheme)();
-    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: (0, util_1.stripAlpha)(theme.palette.background.default) }));
 }
 exports.default = SVGBackground;

package/dist/LaunchCircularView/index.js

@@ -4,7 +4,7 @@ const mobx_1 = require("mobx");
 exports.default = (pluginManager) => {
     pluginManager.addToExtensionPoint('LaunchView-CircularView', 
     // @ts-expect-error
-    async ({ session, assembly, loc, tracks = [], }) => {
+    async ({ session, assembly, tracks = [], }) => {
         const { assemblyManager } = session;
         const view = session.addView('CircularView', {});
         await (0, mobx_1.when)(() => view.initialized);

package/esm/BaseChordDisplay/components/BaseChordDisplay.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-declare const _default: ({ display, }: {
+declare const BaseChordDisplay: ({ display, }: {
     display: {
         filled: boolean;
         error: unknown;
@@ -9,4 +9,4 @@ declare const _default: ({ display, }: {
         };
     };
 }) => React.JSX.Element;
-export default _default;
+export default BaseChordDisplay;

package/esm/BaseChordDisplay/components/BaseChordDisplay.js

@@ -3,7 +3,7 @@ import { observer } from 'mobx-react';
 // locals
 import Loading from './Loading';
 import DisplayError from './DisplayError';
-export default observer(function BaseChordDisplay({ display, }) {
+const BaseChordDisplay = observer(function ({ display, }) {
     if (display.error) {
         return React.createElement(DisplayError, { model: display });
     }
@@ -12,3 +12,4 @@ export default observer(function BaseChordDisplay({ display, }) {
     }
     return display.reactElement;
 });
+export default BaseChordDisplay;

package/esm/BaseChordDisplay/models/renderReaction.d.ts

@@ -3,10 +3,28 @@ export declare function renderReactionData(self: any): {
     rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
     renderProps: any;
     renderArgs: {
-        assemblyName: any;
+        assemblyName: string;
         adapterConfig: any;
         rendererType: any;
-        regions: any;
+        regions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
+            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").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
+            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").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
         blockDefinitions: any;
         sessionId: string;
         timeout: number;

package/esm/CircularView/components/Controls.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { CircularViewModel } from '../models/CircularView';
-declare const _default: ({ model }: {
+declare const Controls: ({ model }: {
     model: CircularViewModel;
 }) => React.JSX.Element;
-export default _default;
+export default Controls;

package/esm/CircularView/components/Controls.js

@@ -24,7 +24,7 @@ const useStyles = makeStyles()(theme => ({
         top: 0,
     },
 }));
-export default observer(function ({ model }) {
+const Controls = observer(function ({ model }) {
     const { classes } = useStyles();
     const [anchorEl, setAnchorEl] = useState(null);
     return (React.createElement("div", { className: classes.controls },
@@ -59,3 +59,4 @@ export default observer(function ({ model }) {
                 setAnchorEl(null);
             }, open: Boolean(anchorEl), onClose: () => setAnchorEl(null) })) : null));
 });
+export default Controls;

package/esm/CircularView/components/Ruler.d.ts

@@ -1,8 +1,8 @@
 import React from 'react';
 import { Slice } from '../models/slices';
 import { CircularViewModel } from '../models/CircularView';
-declare const _default: ({ model, slice, }: {
+declare const Ruler: ({ model, slice, }: {
     model: CircularViewModel;
     slice: Slice;
 }) => React.JSX.Element;
-export default _default;
+export default Ruler;

package/esm/CircularView/components/Ruler.js

@@ -115,9 +115,10 @@ const RegionRulerArc = observer(function ({ model, slice, region, }) {
         React.createElement(RulerLabel, { text: region.refName, view: model, maxWidthPx: widthPx, radians: centerRadians, radiusPx: radiusPx, color: color }),
         React.createElement("path", { d: sliceArcPath(slice, radiusPx + 1, region.start, region.end), stroke: color, strokeWidth: 2, fill: "none" })));
 });
-export default observer(function ({ model, slice, }) {
+const Ruler = observer(function ({ model, slice, }) {
     if (slice.region.elided) {
         return (React.createElement(ElisionRulerArc, { key: assembleLocString(slice.region.regions[0]), model: model, region: slice.region, slice: slice }));
     }
     return (React.createElement(RegionRulerArc, { key: assembleLocString(slice.region), region: slice.region, model: model, slice: slice }));
 });
+export default Ruler;

package/esm/CircularView/models/slices.d.ts

@@ -1,17 +1,17 @@
 import { Region } from '@jbrowse/core/util';
-export type SliceElidedRegion = {
+export interface SliceElidedRegion {
     elided: true;
     widthBp: number;
     regions: Region[];
-};
-export type SliceNonElidedRegion = {
+}
+export interface SliceNonElidedRegion {
     elided: false;
     widthBp: number;
     start: number;
     end: number;
     refName: string;
     assemblyName: string;
-};
+}
 export type SliceRegion = SliceNonElidedRegion | SliceElidedRegion;
 export declare class Slice {
     region: SliceRegion;

package/esm/CircularView/models/viewportVisibleRegion.js

@@ -81,8 +81,7 @@ export function viewportVisibleSection(viewSides, circleCenter, circleRadius) {
             [viewR, viewB],
         ];
         let maxRho = -Infinity;
-        for (let i = 0; i < vertices.length; i += 1) {
-            const [x, y] = vertices[i];
+        for (const [x, y] of vertices) {
             const rho = Math.sqrt(x * x + y * y);
             if (rho > maxRho) {
                 maxRho = rho;
@@ -182,9 +181,8 @@ export function viewportVisibleSection(viewSides, circleCenter, circleRadius) {
     let rhoMax = -Infinity;
     let thetaMin = Infinity;
     let thetaMax = -Infinity;
-    for (let i = 0; i < vertices.length; i += 1) {
+    for (const [vx, vy] of vertices) {
         // ignore vertex if outside the viewport
-        const [vx, vy] = vertices[i];
         if (vx >= viewL && vx <= viewR && vy >= viewT && vy <= viewB) {
             const [rho, theta] = cartesianToPolar(vx * reflect, vy * reflect);
             // ignore vertex if outside the circle

package/esm/CircularView/svgcomponents/SVGBackground.js

@@ -1,6 +1,7 @@
 import React from 'react';
 import { useTheme } from '@mui/material';
+import { stripAlpha } from '@jbrowse/core/util';
 export default function SVGBackground({ width, height, shift, }) {
     const theme = useTheme();
-    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: stripAlpha(theme.palette.background.default) }));
 }

package/esm/LaunchCircularView/index.js

@@ -2,7 +2,7 @@ import { when } from 'mobx';
 export default (pluginManager) => {
     pluginManager.addToExtensionPoint('LaunchView-CircularView', 
     // @ts-expect-error
-    async ({ session, assembly, loc, tracks = [], }) => {
+    async ({ session, assembly, tracks = [], }) => {
         const { assemblyManager } = session;
         const view = session.addView('CircularView', {});
         await when(() => view.initialized);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-circular-view",
-  "version": "2.6.2",
+  "version": "2.7.0",
   "description": "JBrowse 2 circular view",
   "keywords": [
     "jbrowse",
@@ -45,7 +45,7 @@
     "@jbrowse/core": "^2.0.0",
     "@mui/material": "^5.0.0",
     "mobx": "^6.0.0",
-    "mobx-react": "^7.0.0",
+    "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
     "react": ">=16.8.0",
     "react-dom": ">=16.8.0",
@@ -57,5 +57,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
+  "gitHead": "dbe7fb1af01fc89f833d2744635eb44a17365b41"
 }