@jbrowse/plugin-linear-genome-view 2.1.7 → 2.2.1

package/dist/LinearGenomeView/components/LinearGenomeViewSvg.js.map

@@ -1 +1 @@
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package/dist/LinearGenomeView/components/OverviewRubberBand.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 import { LinearGenomeViewModel } from '..';
-declare type LGV = LinearGenomeViewModel;
+type LGV = LinearGenomeViewModel;
 declare function OverviewRubberBand({ model, overview, ControlComponent, }: {
     model: LGV;
     overview: Base1DViewModel;

package/dist/LinearGenomeView/components/OverviewScaleBar.d.ts

@@ -8,14 +8,16 @@ declare const Polygon: ({ model, overview, useOffset, }: {
     overview: Base1DViewModel;
     useOffset?: boolean | undefined;
 }) => JSX.Element | null;
-declare type LGV = LinearGenomeViewModel;
+type LGV = LinearGenomeViewModel;
 declare const Cytobands: ({ overview, block, assembly, }: {
     overview: Base1DViewModel;
     assembly?: ({
         configuration: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        error: Error | undefined;
-        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        error: unknown;
+        loaded: boolean;
+        loadingP: Promise<void> | undefined;
+        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         refNameAliases: {
             [x: string]: string;
         } | undefined;
@@ -26,41 +28,35 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     } & {
         readonly initialized: boolean;
         readonly name: string;
+        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         readonly aliases: string[];
         readonly displayName: string | undefined;
         hasName(name: string): boolean;
         readonly allAliases: string[];
-        readonly refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
+    } & {
+        readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-            adapterRegionsWithAssembly: import("@jbrowse/core/util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("@jbrowse/core/util").Feature[];
-        }): void;
-        setError(e: Error): void;
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+        setError(e: unknown): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCase: {
+        }, lcAliases: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        afterAttach(): void;
+        setLoadingP(p?: Promise<void> | undefined): void;
+        load(): Promise<void>;
+        loadPre(): Promise<void>;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
@@ -72,8 +68,10 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     }, {
-        error: Error | undefined;
-        regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        error: unknown;
+        loaded: boolean;
+        loadingP: Promise<void> | undefined;
+        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         refNameAliases: {
             [x: string]: string;
         } | undefined;
@@ -84,41 +82,35 @@ declare const Cytobands: ({ overview, block, assembly, }: {
     } & {
         readonly initialized: boolean;
         readonly name: string;
+        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         readonly aliases: string[];
         readonly displayName: string | undefined;
         hasName(name: string): boolean;
         readonly allAliases: string[];
-        readonly refNames: string[] | undefined;
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
         readonly rpcManager: any;
         readonly refNameColors: string[];
+    } & {
+        readonly refNames: string[] | undefined;
     } & {
         getCanonicalRefName(refName: string): string;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
-        setLoading(): void;
-        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: {
-            adapterRegionsWithAssembly: import("@jbrowse/core/util").Region[];
-            refNameAliases: {
-                [x: string]: string;
-            };
-            lowerCaseRefNameAliases: {
-                [x: string]: string;
-            };
-            cytobands: import("@jbrowse/core/util").Feature[];
-        }): void;
-        setError(e: Error): void;
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+        setError(e: unknown): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
         setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCase: {
+        }, lcAliases: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
-        afterAttach(): void;
+        setLoadingP(p?: Promise<void> | undefined): void;
+        load(): Promise<void>;
+        loadPre(): Promise<void>;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
         getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{

package/dist/LinearGenomeView/components/RubberBand.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { LinearGenomeViewModel } from '..';
-declare type LGV = LinearGenomeViewModel;
+type LGV = LinearGenomeViewModel;
 declare function RubberBand({ model, ControlComponent, }: {
     model: LGV;
     ControlComponent?: React.ReactElement;

package/dist/LinearGenomeView/components/ScaleBar.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { LinearGenomeViewModel } from '..';
-declare type LGV = LinearGenomeViewModel;
+type LGV = LinearGenomeViewModel;
 interface ScaleBarProps {
     model: LGV;
     style?: React.CSSProperties;

package/dist/LinearGenomeView/components/TrackContainer.d.ts

@@ -1,7 +1,7 @@
 /// <reference types="react" />
 import { BaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { LinearGenomeViewModel } from '..';
-declare type LGV = LinearGenomeViewModel;
+type LGV = LinearGenomeViewModel;
 declare function TrackContainer({ model, track, }: {
     model: LGV;
     track: BaseTrackModel;

package/dist/LinearGenomeView/components/TrackContainer.js

@@ -33,6 +33,7 @@ const mobx_react_1 = require("mobx-react");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
+const react_error_boundary_1 = require("react-error-boundary");
 const util_1 = require("@jbrowse/core/util");
 const TrackLabel_1 = __importDefault(require("./TrackLabel"));
 const useStyles = (0, mui_1.makeStyles)()({
@@ -98,6 +99,7 @@ function TrackContainer({ model, track, }) {
     const trackId = (0, configuration_1.getConf)(track, 'trackId');
     const ref = (0, react_1.useRef)(null);
     const dimmed = draggingTrackId !== undefined && draggingTrackId !== display.id;
+    const minimized = track.minimized;
     const debouncedOnDragEnter = (0, util_1.useDebouncedCallback)(() => {
         if ((0, mobx_state_tree_1.isAlive)(display) && dimmed) {
             moveTrack(draggingTrackId, track.id);
@@ -113,15 +115,16 @@ function TrackContainer({ model, track, }) {
     }, [model.trackRefs, trackId]);
     return (react_1.default.createElement(material_1.Paper, { className: classes.root, variant: "outlined" },
         react_1.default.createElement(TrackContainerLabel, { model: track, view: model }),
-        react_1.default.createElement("div", { className: classes.trackRenderingContainer, style: { height }, onScroll: event => display.setScrollTop(event.currentTarget.scrollTop), onDragEnter: debouncedOnDragEnter, "data-testid": `trackRenderingContainer-${model.id}-${trackId}` },
-            react_1.default.createElement("div", { ref: ref, className: classes.renderingComponentContainer, style: { transform: `scaleX(${model.scaleFactor})` } },
-                react_1.default.createElement(RenderingComponent, { model: display, onHorizontalScroll: horizontalScroll })),
-            DisplayBlurb ? (react_1.default.createElement("div", { style: {
-                    position: 'absolute',
-                    left: 0,
-                    top: display.height - 20,
-                } },
-                react_1.default.createElement(DisplayBlurb, { model: display }))) : null),
+        react_1.default.createElement(react_error_boundary_1.ErrorBoundary, { key: track.id, FallbackComponent: ({ error }) => react_1.default.createElement(ui_1.ErrorMessage, { error: error }) },
+            react_1.default.createElement("div", { className: classes.trackRenderingContainer, style: { height: minimized ? 20 : height }, onScroll: evt => display.setScrollTop(evt.currentTarget.scrollTop), onDragEnter: debouncedOnDragEnter, "data-testid": `trackRenderingContainer-${model.id}-${trackId}` }, !minimized ? (react_1.default.createElement(react_1.default.Fragment, null,
+                react_1.default.createElement("div", { ref: ref, className: classes.renderingComponentContainer, style: { transform: `scaleX(${model.scaleFactor})` } },
+                    react_1.default.createElement(RenderingComponent, { model: display, onHorizontalScroll: horizontalScroll })),
+                DisplayBlurb ? (react_1.default.createElement("div", { style: {
+                        position: 'absolute',
+                        left: 0,
+                        top: display.height - 20,
+                    } },
+                    react_1.default.createElement(DisplayBlurb, { model: display }))) : null)) : null)),
         react_1.default.createElement("div", { className: classes.overlay, style: {
                 height: display.height,
                 background: dimmed ? 'rgba(0, 0, 0, 0.4)' : undefined,

package/dist/LinearGenomeView/components/TrackContainer.js.map

@@ -1 +1 @@
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package/dist/LinearGenomeView/components/TrackLabel.js

@@ -16,6 +16,8 @@ const hooks_1 = require("material-ui-popup-state/hooks");
 const MoreVert_1 = __importDefault(require("@mui/icons-material/MoreVert"));
 const DragIndicator_1 = __importDefault(require("@mui/icons-material/DragIndicator"));
 const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const Minimize_1 = __importDefault(require("@mui/icons-material/Minimize"));
+const Add_1 = __importDefault(require("@mui/icons-material/Add"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     root: {
         background: (0, material_1.alpha)(theme.palette.background.paper, 0.8),
@@ -51,6 +53,7 @@ const TrackLabel = react_1.default.forwardRef(({ track, className }, ref) => {
     const view = (0, util_1.getContainingView)(track);
     const session = (0, util_1.getSession)(track);
     const trackConf = track.configuration;
+    const minimized = track.minimized;
     const trackId = (0, configuration_1.getConf)(track, 'trackId');
     const trackName = (0, tracks_1.getTrackName)(trackConf, session);
     const popupState = (0, hooks_1.usePopupState)({
@@ -58,6 +61,11 @@ const TrackLabel = react_1.default.forwardRef(({ track, className }, ref) => {
         variant: 'popover',
     });
     const items = [
+        {
+            label: minimized ? 'Restore track' : 'Minimize track',
+            icon: minimized ? Add_1.default : Minimize_1.default,
+            onClick: () => track.setMinimized(!minimized),
+        },
         ...(((_a = session.getTrackActionMenuItems) === null || _a === void 0 ? void 0 : _a.call(session, trackConf)) || []),
         ...track.trackMenuItems(),
     ].sort((a, b) => (b.priority || 0) - (a.priority || 0));
@@ -73,7 +81,7 @@ const TrackLabel = react_1.default.forwardRef(({ track, className }, ref) => {
             react_1.default.createElement(DragIndicator_1.default, { className: classes.dragHandleIcon, fontSize: "small" })),
         react_1.default.createElement(material_1.IconButton, { onClick: () => view.hideTrack(trackId), className: classes.iconButton, title: "close this track", color: "secondary" },
             react_1.default.createElement(Close_1.default, { fontSize: "small" })),
-        react_1.default.createElement(material_1.Typography, { variant: "body1", component: "span", className: classes.trackName }, trackName),
+        react_1.default.createElement(material_1.Typography, { variant: "body1", component: "span", className: classes.trackName }, trackName + (minimized ? ' (minimized)' : '')),
         react_1.default.createElement(material_1.IconButton, { ...(0, hooks_1.bindTrigger)(popupState), className: classes.iconButton, color: "secondary", "data-testid": "track_menu_icon", disabled: !items.length },
             react_1.default.createElement(MoreVert_1.default, { fontSize: "small" })),
         react_1.default.createElement(CascadingMenu_1.default, { ...(0, hooks_1.bindPopover)(popupState), onMenuItemClick: (_, callback) => callback(), menuItems: items, popupState: popupState })));

package/dist/LinearGenomeView/components/TrackLabel.js.map

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+{"version":3,"file":"TrackLabel.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/TrackLabel.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAoE;AACpE,uCAA0C;AAC1C,2CAAqC;AACrC,+DAAqD;AACrD,mFAA0D;AAC1D,6CAAkE;AAClE,sDAAwD;AAGxD,yDAIsC;AAEtC,QAAQ;AACR,4EAAuD;AACvD,sFAAwD;AACxD,sEAAiD;AACjD,4EAAuD;AACvD,kEAA6C;AAI7C,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,UAAU,EAAE,IAAA,gBAAK,EAAC,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK,EAAE,GAAG,CAAC;QACtD,SAAS,EAAE;YACT,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,UAAU,CAAC,KAAK;SAC3C;QACD,UAAU,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC,YAAY,CAAC,EAAE;YACnD,QAAQ,EAAE,KAAK,CAAC,WAAW,CAAC,QAAQ,CAAC,QAAQ;SAC9C,CAAC;KACH;IACD,SAAS,EAAE;QACT,MAAM,EAAE,QAAQ;QAChB,KAAK,EAAE,KAAK;QACZ,QAAQ,EAAE,QAAQ;QAClB,aAAa,EAAE,MAAM;KACtB;IACD,UAAU,EAAE;QACV,MAAM,EAAE,MAAM;QACd,KAAK,EAAE,SAAS;KACjB;IACD,cAAc,EAAE;QACd,OAAO,EAAE,cAAc;QACvB,aAAa,EAAE,QAAQ;QACvB,aAAa,EAAE,MAAM;KACtB;IACD,UAAU,EAAE;QACV,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAC1B;CACF,CAAC,CAAC,CAAA;AASH,MAAM,UAAU,GAAG,eAAK,CAAC,UAAU,CACjC,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,EAAE,GAAG,EAAE,EAAE;;IAC5B,MAAM,EAAE,OAAO,EAAE,EAAE,EAAE,GAAG,SAAS,EAAE,CAAA;IACnC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,KAAK,CAAQ,CAAA;IAC5C,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,SAAS,GAAG,KAAK,CAAC,aAAa,CAAA;IACrC,MAAM,SAAS,GAAG,KAAK,CAAC,SAAS,CAAA;IACjC,MAAM,OAAO,GAAG,IAAA,uBAAO,EAAC,KAAK,EAAE,SAAS,CAAC,CAAA;IACzC,MAAM,SAAS,GAAG,IAAA,qBAAY,EAAC,SAAS,EAAE,OAAO,CAAC,CAAA;IAElD,MAAM,UAAU,GAAG,IAAA,qBAAa,EAAC;QAC/B,OAAO,EAAE,gBAAgB;QACzB,OAAO,EAAE,SAAS;KACnB,CAAC,CAAA;IAEF,MAAM,KAAK,GAAG;QACZ;YACE,KAAK,EAAE,SAAS,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,gBAAgB;YACrD,IAAI,EAAE,SAAS,CAAC,CAAC,CAAC,aAAO,CAAC,CAAC,CAAC,kBAAY;YACxC,OAAO,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,SAAS,CAAC;SAC9C;QACD,GAAG,CAAC,CAAA,MAAA,OAAO,CAAC,uBAAuB,wDAAG,SAAS,CAAC,KAAI,EAAE,CAAC;QACvD,GAAG,KAAK,CAAC,cAAc,EAAE;KAC1B,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,IAAI,CAAC,CAAC,CAAC,CAAA;IAEvD,OAAO,CACL,8BAAC,gBAAK,IAAC,GAAG,EAAE,GAAG,EAAE,SAAS,EAAE,EAAE,CAAC,SAAS,EAAE,OAAO,CAAC,IAAI,CAAC;QACrD,wCACE,SAAS,QACT,SAAS,EAAE,OAAO,CAAC,UAAU,EAC7B,WAAW,EAAE,KAAK,CAAC,EAAE;gBACnB,MAAM,MAAM,GAAG,KAAK,CAAC,aAAa,CAAA;gBAClC,IAAI,MAAM,CAAC,UAAU,EAAE;oBACrB,MAAM,MAAM,GAAG,MAAM,CAAC,UAAyB,CAAA;oBAC/C,KAAK,CAAC,YAAY,CAAC,YAAY,CAAC,MAAM,EAAE,EAAE,EAAE,EAAE,CAAC,CAAA;oBAC/C,IAAI,CAAC,kBAAkB,CAAC,KAAK,CAAC,EAAE,CAAC,CAAA;iBAClC;YACH,CAAC,EACD,SAAS,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,kBAAkB,CAAC,SAAS,CAAC,iBACtC,cAAc,IAAI,CAAC,EAAE,IAAI,OAAO,EAAE;YAE/C,8BAAC,uBAAQ,IAAC,SAAS,EAAE,OAAO,CAAC,cAAc,EAAE,QAAQ,EAAC,OAAO,GAAG,CAC3D;QACP,8BAAC,qBAAU,IACT,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,EACtC,SAAS,EAAE,OAAO,CAAC,UAAU,EAC7B,KAAK,EAAC,kBAAkB,EACxB,KAAK,EAAC,WAAW;YAEjB,8BAAC,eAAS,IAAC,QAAQ,EAAC,OAAO,GAAG,CACnB;QAEb,8BAAC,qBAAU,IACT,OAAO,EAAC,OAAO,EACf,SAAS,EAAC,MAAM,EAChB,SAAS,EAAE,OAAO,CAAC,SAAS,IAE3B,SAAS,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC,CACnC;QACb,8BAAC,qBAAU,OACL,IAAA,mBAAW,EAAC,UAAU,CAAC,EAC3B,SAAS,EAAE,OAAO,CAAC,UAAU,EAC7B,KAAK,EAAC,WAAW,iBACL,iBAAiB,EAC7B,QAAQ,EAAE,CAAC,KAAK,CAAC,MAAM;YAEvB,8BAAC,kBAAY,IAAC,QAAQ,EAAC,OAAO,GAAG,CACtB;QACb,8BAAC,uBAAa,OACR,IAAA,mBAAW,EAAC,UAAU,CAAC,EAC3B,eAAe,EAAE,CAAC,CAAU,EAAE,QAAkB,EAAE,EAAE,CAAC,QAAQ,EAAE,EAC/D,SAAS,EAAE,KAAK,EAChB,UAAU,EAAE,UAAU,GACtB,CACI,CACT,CAAA;AACH,CAAC,CACF,CAAA;AAED,kBAAe,IAAA,qBAAQ,EAAC,UAAU,CAAC,CAAA"}

package/dist/LinearGenomeView/components/TracksContainer.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { LinearGenomeViewModel } from '..';
-declare type LGV = LinearGenomeViewModel;
+type LGV = LinearGenomeViewModel;
 declare function TracksContainer({ children, model, }: {
     children: React.ReactNode;
     model: LGV;