npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.1.4 → 2.1.6 - Mend

@jbrowse/plugin-linear-genome-view 2.1.4 → 2.1.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (104) hide show

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

@@ -1,12 +1,11 @@
 import React from 'react';
-import { Instance } from 'mobx-state-tree';
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 import { ContentBlock } from '@jbrowse/core/util/blockTypes';
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
 import { LinearGenomeViewModel } from '..';
 declare const Polygon: ({ model, overview, useOffset, }: {
     model: LGV;
-    overview: Instance<Base1DViewModel>;
+    overview: Base1DViewModel;
     useOffset?: boolean | undefined;
 }) => JSX.Element | null;
 declare type LGV = LinearGenomeViewModel;
@@ -55,27 +54,20 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-        setRefNameAliases(refNameAliases: {
+        setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseRefNameAliases: {
+        }, lowerCase: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
         afterAttach(): void;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            forwardMap: {
-                [key: string]: string;
-            };
-            reverseMap: {
-                [key: string]: string;
-            };
-        }>;
+        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<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
     } & 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>>;
@@ -120,27 +112,20 @@ declare const Cytobands: ({ overview, block, assembly, }: {
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
-        setRefNameAliases(refNameAliases: {
+        setRefNameAliases(aliases: {
             [x: string]: string;
-        }, lowerCaseRefNameAliases: {
+        }, lowerCase: {
             [x: string]: string;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
         afterAttach(): void;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            forwardMap: {
-                [key: string]: string;
-            };
-            reverseMap: {
-                [key: string]: string;
-            };
-        }>;
+        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<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
         getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [key: string]: string;
+            [x: string]: string;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     block: ContentBlock;

package/dist/LinearGenomeView/components/OverviewScaleBar.js CHANGED Viewed

@@ -194,7 +194,7 @@ const Cytobands = (0, mobx_react_1.observer)(({ overview, block, assembly, }) =>
 exports.Cytobands = Cytobands;
 const OverviewBox = (0, mobx_react_1.observer)(({ scale, model, block, overview, }) => {
     const { classes, cx } = useStyles();
-    const { cytobandOffset, bpPerPx, showCytobands } = model;
+    const { cytobandOffset, showCytobands } = model;
     const { start, end, reversed, refName, assemblyName } = block;
     const { majorPitch } = (0, util_2.chooseGridPitch)(scale, 120, 15);
     const { assemblyManager } = (0, util_1.getSession)(model);
@@ -225,7 +225,7 @@ const OverviewBox = (0, mobx_react_1.observer)(({ scale, model, block, overview,
                         left: ((labelIdx + 1) * majorPitch) / scale,
                         pointerEvents: 'none',
                         color: refNameColor,
-                    } }, (0, util_1.getTickDisplayStr)(tickLabel, bpPerPx))))
+                    } }, (0, util_1.getTickDisplayStr)(tickLabel, overview.bpPerPx))))
                 : null,
             canDisplayCytobands ? (react_1.default.createElement("svg", { style: { width: '100%' } },
                 react_1.default.createElement(Cytobands, { overview: overview, assembly: assembly, block: block }))) : null)));

package/dist/LinearGenomeView/components/OverviewScaleBar.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearGenomeView/components/SearchResultsDialog.js CHANGED Viewed

@@ -24,7 +24,7 @@ function SearchResultsDialog({ model, optAssemblyName, handleClose, }) {
     var _a, _b;
     const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
-    const { pluginManager } = (0, mobx_state_tree_1.getEnv)(session);
+    const { pluginManager } = (0, util_1.getEnv)(session);
     const { assemblyManager } = session;
     let assemblyName = optAssemblyName;
     if (model.displayedRegions.length > 0) {
@@ -62,11 +62,9 @@ function SearchResultsDialog({ model, optAssemblyName, handleClose, }) {
     function getTrackName(trackId) {
         var _a;
         if (trackId) {
-            const trackConfigSchema = pluginManager.pluggableConfigSchemaType('track');
-            const configuration = (0, mobx_state_tree_1.resolveIdentifier)(trackConfigSchema, (0, mobx_state_tree_1.getRoot)(model), trackId);
-            if (configuration) {
-                return (_a = configuration.name) === null || _a === void 0 ? void 0 : _a.value;
-            }
+            const schema = pluginManager.pluggableConfigSchemaType('track');
+            const configuration = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(model), trackId);
+            return ((_a = configuration === null || configuration === void 0 ? void 0 : configuration.name) === null || _a === void 0 ? void 0 : _a.value) || '';
         }
         return '';
     }

package/dist/LinearGenomeView/components/SearchResultsDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearGenomeView/components/SequenceSearchDialog.d.ts CHANGED Viewed

@@ -1,7 +1,9 @@
 /// <reference types="react" />
-import { LinearGenomeViewModel } from '..';
 declare function SequenceDialog({ model, handleClose, }: {
-    model: LinearGenomeViewModel;
+    model: {
+        assemblyNames: string[];
+        toggleTrack(trackId: string): void;
+    };
     handleClose: () => void;
 }): JSX.Element;
 declare const _default: typeof SequenceDialog;

package/dist/LinearGenomeView/components/SequenceSearchDialog.js.map CHANGED Viewed

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

@@ -4,12 +4,13 @@ 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 mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const CascadingMenu_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenu"));
 const util_1 = require("@jbrowse/core/util");
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
+const tracks_1 = require("@jbrowse/core/util/tracks");
 const hooks_1 = require("material-ui-popup-state/hooks");
 // icons
 const MoreVert_1 = __importDefault(require("@mui/icons-material/MoreVert"));
@@ -44,17 +45,6 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         padding: theme.spacing(1),
     },
 }));
-function getTrackName(track, session) {
-    const trackName = (0, configuration_1.getConf)(track, 'name');
-    if ((0, configuration_1.getConf)(track, 'type') === 'ReferenceSequenceTrack') {
-        const asm = session.assemblies.find(a => a.sequence === track.configuration);
-        return (trackName ||
-            (asm
-                ? `Reference Sequence (${(0, configuration_1.readConfObject)(asm, 'displayName') || (0, configuration_1.readConfObject)(asm, 'name')})`
-                : 'Reference Sequence'));
-    }
-    return trackName;
-}
 const TrackLabel = react_1.default.forwardRef(({ track, className }, ref) => {
     var _a;
     const { classes, cx } = useStyles();
@@ -62,25 +52,24 @@ const TrackLabel = react_1.default.forwardRef(({ track, className }, ref) => {
     const session = (0, util_1.getSession)(track);
     const trackConf = track.configuration;
     const trackId = (0, configuration_1.getConf)(track, 'trackId');
-    const trackName = getTrackName(track, session);
+    const trackName = (0, tracks_1.getTrackName)(trackConf, session);
     const popupState = (0, hooks_1.usePopupState)({
         popupId: 'trackLabelMenu',
         variant: 'popover',
     });
-    const onDragStart = (event) => {
-        const target = event.currentTarget;
-        if (target.parentNode) {
-            const parent = target.parentNode;
-            event.dataTransfer.setDragImage(parent, 20, 20);
-            view.setDraggingTrackId(track.id);
-        }
-    };
     const items = [
         ...(((_a = session.getTrackActionMenuItems) === null || _a === void 0 ? void 0 : _a.call(session, trackConf)) || []),
         ...track.trackMenuItems(),
     ].sort((a, b) => (b.priority || 0) - (a.priority || 0));
     return (react_1.default.createElement(material_1.Paper, { ref: ref, className: cx(className, classes.root) },
-        react_1.default.createElement("span", { draggable: true, className: classes.dragHandle, onDragStart: onDragStart, onDragEnd: () => view.setDraggingTrackId(undefined), "data-testid": `dragHandle-${view.id}-${trackId}` },
+        react_1.default.createElement("span", { draggable: true, className: classes.dragHandle, onDragStart: event => {
+                const target = event.currentTarget;
+                if (target.parentNode) {
+                    const parent = target.parentNode;
+                    event.dataTransfer.setDragImage(parent, 20, 20);
+                    view.setDraggingTrackId(track.id);
+                }
+            }, onDragEnd: () => view.setDraggingTrackId(undefined), "data-testid": `dragHandle-${view.id}-${trackId}` },
             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" })),

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

	@@ -1 +1 @@
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package/dist/LinearGenomeView/components/TracksContainer.d.ts CHANGED Viewed

@@ -1,7 +1,6 @@
 import React from 'react';
-import { Instance } from 'mobx-state-tree';
-import { LinearGenomeViewStateModel } from '..';
-declare type LGV = Instance<LinearGenomeViewStateModel>;
+import { LinearGenomeViewModel } from '..';
+declare type LGV = LinearGenomeViewModel;
 declare function TracksContainer({ children, model, }: {
     children: React.ReactNode;
     model: LGV;

package/dist/LinearGenomeView/components/TracksContainer.js CHANGED Viewed

@@ -30,6 +30,7 @@ const react_1 = __importStar(require("react"));
 const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
 const normalize_wheel_1 = __importDefault(require("normalize-wheel"));
+// locals
 const __1 = require("..");
 const RubberBand_1 = __importDefault(require("./RubberBand"));
 const ScaleBar_1 = __importDefault(require("./ScaleBar"));

package/dist/LinearGenomeView/components/TracksContainer.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/LinearGenomeView/index.d.ts CHANGED Viewed

@@ -1,3 +1,4 @@
+import React from 'react';
 import { Region } from '@jbrowse/core/util/types';
 import { MenuItem } from '@jbrowse/core/ui';
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
@@ -7,6 +8,8 @@ import PluginManager from '@jbrowse/core/PluginManager';
 import { renderToSvg } from './components/LinearGenomeViewSvg';
 import RefNameAutocomplete from './components/RefNameAutocomplete';
 import SearchBox from './components/SearchBox';
+import ZoomControls from './components/ZoomControls';
+import LinearGenomeView from './components/LinearGenomeView';
 export interface BpOffset {
     refName?: string;
     index: number;
@@ -91,6 +94,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly interRegionPaddingWidth: number;
     readonly assemblyNames: string[];
 } & {
+    MiniControlsComponent(): React.FC<any>;
+    HeaderComponent(): React.FC<any>;
     readonly assemblyErrors: string;
     readonly assembliesInitialized: boolean;
     readonly initialized: boolean;
@@ -171,6 +176,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     showAllRegionsInAssembly(assemblyName?: string): void;
     setDraggingTrackId(idx?: string): void;
     setScaleFactor(factor: number): void;
+    clearView(): void;
+    exportSvg(opts?: ExportSvgOptions): Promise<void>;
 } & {
     slide: (viewWidths: number) => void;
 } & {
@@ -201,11 +208,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     readonly visibleLocStrings: string;
     readonly coarseVisibleLocStrings: string;
 } & {
-    clearView(): void;
     setCoarseDynamicBlocks(blocks: BlockSet): void;
     afterAttach(): void;
 } & {
-    exportSvg(opts?: ExportSvgOptions): Promise<void>;
     /**
      * offset is the base-pair-offset in the displayed region, index is the index of the
      * displayed region in the linear genome view
@@ -269,7 +274,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         reversed: boolean;
     } | undefined;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export { renderToSvg, RefNameAutocomplete, SearchBox };
+export { renderToSvg, RefNameAutocomplete, SearchBox, ZoomControls, LinearGenomeView, };
 export declare type LinearGenomeViewStateModel = ReturnType<typeof stateModelFactory>;
 export declare type LinearGenomeViewModel = Instance<LinearGenomeViewStateModel>;
 export { default as ReactComponent } from './components/LinearGenomeView';

package/dist/LinearGenomeView/index.js CHANGED Viewed

@@ -26,7 +26,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.ReactComponent = exports.SearchBox = exports.RefNameAutocomplete = exports.renderToSvg = exports.stateModelFactory = exports.WIDGET_HEIGHT = exports.SPACING = exports.INTER_REGION_PADDING_WIDTH = exports.RESIZE_HANDLE_HEIGHT = exports.SCALE_BAR_HEIGHT = exports.HEADER_OVERVIEW_HEIGHT = exports.HEADER_BAR_HEIGHT = void 0;
+exports.ReactComponent = exports.LinearGenomeView = exports.ZoomControls = exports.SearchBox = exports.RefNameAutocomplete = exports.renderToSvg = exports.stateModelFactory = exports.WIDGET_HEIGHT = exports.SPACING = exports.INTER_REGION_PADDING_WIDTH = exports.RESIZE_HANDLE_HEIGHT = exports.SCALE_BAR_HEIGHT = exports.HEADER_OVERVIEW_HEIGHT = exports.HEADER_BAR_HEIGHT = void 0;
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
@@ -59,6 +59,12 @@ exports.RefNameAutocomplete = RefNameAutocomplete_1.default;
 const SearchBox_1 = __importDefault(require("./components/SearchBox"));
 exports.SearchBox = SearchBox_1.default;
 const ExportSvgDialog_1 = __importDefault(require("./components/ExportSvgDialog"));
+const MiniControls_1 = __importDefault(require("./components/MiniControls"));
+const Header_1 = __importDefault(require("./components/Header"));
+const ZoomControls_1 = __importDefault(require("./components/ZoomControls"));
+exports.ZoomControls = ZoomControls_1.default;
+const LinearGenomeView_1 = __importDefault(require("./components/LinearGenomeView"));
+exports.LinearGenomeView = LinearGenomeView_1.default;
 const SequenceSearchDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SequenceSearchDialog'))));
 function calculateVisibleLocStrings(contentBlocks) {
     if (!contentBlocks.length) {
@@ -147,6 +153,14 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .views(self => ({
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        MiniControlsComponent() {
+            return MiniControls_1.default;
+        },
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        HeaderComponent() {
+            return Header_1.default;
+        },
         get assemblyErrors() {
             const { assemblyManager } = (0, util_1.getSession)(self);
             const { assemblyNames } = self;
@@ -518,6 +532,22 @@ function stateModelFactory(pluginManager) {
         setScaleFactor(factor) {
             self.scaleFactor = factor;
         },
+        // this "clears the view" and makes the view return to the import form
+        clearView() {
+            this.setDisplayedRegions([]);
+            self.tracks.clear();
+            // it is necessary to run these after setting displayed regions empty
+            // or else model.offsetPx gets set to Infinity and breaks
+            // mobx-state-tree snapshot
+            self.scrollTo(0);
+            self.zoomTo(10);
+        },
+        async exportSvg(opts = {}) {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            const html = await (0, LinearGenomeViewSvg_1.renderToSvg)(self, opts);
+            const blob = new Blob([html], { type: 'image/svg+xml' });
+            (0, file_saver_1.saveAs)(blob, opts.filename || 'image.svg');
+        },
     }))
         .actions(self => {
         let cancelLastAnimation = () => { };
@@ -572,6 +602,7 @@ function stateModelFactory(pluginManager) {
         .views(self => ({
         menuItems() {
             const { canShowCytobands, showCytobands } = self;
+            const session = (0, util_1.getSession)(self);
             const menuItems = [
                 {
                     label: 'Return to import form',
@@ -583,15 +614,19 @@ function stateModelFactory(pluginManager) {
                     },
                     icon: FolderOpen_1.default,
                 },
-                {
-                    label: 'Sequence search',
-                    onClick: () => {
-                        (0, util_1.getSession)(self).queueDialog(handleClose => [
-                            SequenceSearchDialog,
-                            { model: self, handleClose },
-                        ]);
-                    },
-                },
+                ...((0, util_1.isSessionWithAddTracks)(session)
+                    ? [
+                        {
+                            label: 'Sequence search',
+                            onClick: () => {
+                                (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                    SequenceSearchDialog,
+                                    { model: self, handleClose },
+                                ]);
+                            },
+                        },
+                    ]
+                    : []),
                 {
                     label: 'Export SVG',
                     icon: PhotoCamera_1.default,
@@ -737,16 +772,6 @@ function stateModelFactory(pluginManager) {
         };
     })
         .actions(self => ({
-        // this "clears the view" and makes the view return to the import form
-        clearView() {
-            self.setDisplayedRegions([]);
-            self.tracks.clear();
-            // it is necessary to run these after setting displayed regions empty
-            // or else model.offsetPx gets set to Infinity and breaks
-            // mobx-state-tree snapshot
-            self.scrollTo(0);
-            self.zoomTo(10);
-        },
         setCoarseDynamicBlocks(blocks) {
             self.coarseDynamicBlocks = blocks.contentBlocks;
             self.coarseTotalBp = blocks.totalBp;
@@ -760,12 +785,6 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .actions(self => ({
-        async exportSvg(opts = {}) {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            const html = await (0, LinearGenomeViewSvg_1.renderToSvg)(self, opts);
-            const blob = new Blob([html], { type: 'image/svg+xml' });
-            (0, file_saver_1.saveAs)(blob, opts.filename || 'image.svg');
-        },
         /**
          * offset is the base-pair-offset in the displayed region, index is the index of the
          * displayed region in the linear genome view
@@ -1013,6 +1032,6 @@ function stateModelFactory(pluginManager) {
     }));
 }
 exports.stateModelFactory = stateModelFactory;
-var LinearGenomeView_1 = require("./components/LinearGenomeView");
-Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(LinearGenomeView_1).default; } });
+var LinearGenomeView_2 = require("./components/LinearGenomeView");
+Object.defineProperty(exports, "ReactComponent", { enumerable: true, get: function () { return __importDefault(LinearGenomeView_2).default; } });
 //# sourceMappingURL=index.js.map