npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.2.0 → 2.2.1 - Mend

@jbrowse/plugin-linear-genome-view 2.2.0 → 2.2.1

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 (71) hide show

package/dist/LinearGenomeView/index.js CHANGED Viewed

@@ -65,6 +65,7 @@ const ZoomControls_1 = __importDefault(require("./components/ZoomControls"));
 exports.ZoomControls = ZoomControls_1.default;
 const LinearGenomeView_1 = __importDefault(require("./components/LinearGenomeView"));
 exports.LinearGenomeView = LinearGenomeView_1.default;
+// lazies
 const SequenceSearchDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SequenceSearchDialog'))));
 function calculateVisibleLocStrings(contentBlocks) {
     if (!contentBlocks.length) {
@@ -103,6 +104,9 @@ function stateModelFactory(pluginManager) {
         id: mst_1.ElementId,
         /**
          * #property
+         * this is a string instead of the const literal 'LinearGenomeView' to reduce some
+         * typescripting strictness, but you should pass the string 'LinearGenomeView' to
+         * the model explicitly
          */
         type: mobx_state_tree_1.types.literal('LinearGenomeView'),
         /**
@@ -216,14 +220,23 @@ function stateModelFactory(pluginManager) {
         },
     }))
         .views(self => ({
+        /**
+         * #method
+         */
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
         MiniControlsComponent() {
             return MiniControls_1.default;
         },
+        /**
+         * #method
+         */
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
         HeaderComponent() {
             return Header_1.default;
         },
+        /**
+         * #getter
+         */
         get assemblyErrors() {
             const { assemblyManager } = (0, util_1.getSession)(self);
             const { assemblyNames } = self;
@@ -232,23 +245,41 @@ function stateModelFactory(pluginManager) {
                 .filter(f => !!f)
                 .join(', ');
         },
+        /**
+         * #getter
+         */
         get assembliesInitialized() {
             const { assemblyManager } = (0, util_1.getSession)(self);
             const { assemblyNames } = self;
             return assemblyNames.every(a => { var _a; return (_a = assemblyManager.get(a)) === null || _a === void 0 ? void 0 : _a.initialized; });
         },
+        /**
+         * #getter
+         */
         get initialized() {
             return self.volatileWidth !== undefined && this.assembliesInitialized;
         },
+        /**
+         * #getter
+         */
         get hasDisplayedRegions() {
             return self.displayedRegions.length > 0;
         },
+        /**
+         * #getter
+         */
         get isSearchDialogDisplayed() {
             return self.searchResults !== undefined;
         },
+        /**
+         * #getter
+         */
         get scaleBarHeight() {
             return exports.SCALE_BAR_HEIGHT + exports.RESIZE_HANDLE_HEIGHT;
         },
+        /**
+         * #getter
+         */
         get headerHeight() {
             if (self.hideHeader) {
                 return 0;
@@ -258,44 +289,77 @@ function stateModelFactory(pluginManager) {
             }
             return exports.HEADER_BAR_HEIGHT + exports.HEADER_OVERVIEW_HEIGHT;
         },
+        /**
+         * #getter
+         */
         get trackHeights() {
             return self.tracks
                 .map(t => t.displays[0].height)
                 .reduce((a, b) => a + b, 0);
         },
+        /**
+         * #getter
+         */
         get trackHeightsWithResizeHandles() {
             return this.trackHeights + self.tracks.length * exports.RESIZE_HANDLE_HEIGHT;
         },
+        /**
+         * #getter
+         */
         get height() {
             return (this.trackHeightsWithResizeHandles +
                 this.headerHeight +
                 this.scaleBarHeight);
         },
+        /**
+         * #getter
+         */
         get totalBp() {
             return self.displayedRegions.reduce((a, b) => a + b.end - b.start, 0);
         },
+        /**
+         * #getter
+         */
         get maxBpPerPx() {
             return this.totalBp / (self.width * 0.9);
         },
+        /**
+         * #getter
+         */
         get minBpPerPx() {
             return 1 / 50;
         },
+        /**
+         * #getter
+         */
         get error() {
             return self.volatileError || this.assemblyErrors;
         },
+        /**
+         * #getter
+         */
         get maxOffset() {
             // objectively determined to keep the linear genome on the main screen
             const leftPadding = 10;
             return this.displayedRegionsTotalPx - leftPadding;
         },
+        /**
+         * #getter
+         */
         get minOffset() {
             // objectively determined to keep the linear genome on the main screen
             const rightPadding = 30;
             return -self.width + rightPadding;
         },
+        /**
+         * #getter
+         */
         get displayedRegionsTotalPx() {
             return this.totalBp / self.bpPerPx;
         },
+        /**
+         * #method
+         */
         renderProps() {
             return {
                 ...(0, tracks_1.getParentRenderProps)(self),
@@ -303,6 +367,9 @@ function stateModelFactory(pluginManager) {
                 highResolutionScaling: (0, configuration_1.getConf)((0, util_1.getSession)(self), 'highResolutionScaling'),
             };
         },
+        /**
+         * #method
+         */
         searchScope(assemblyName) {
             return {
                 assemblyName,
@@ -310,9 +377,15 @@ function stateModelFactory(pluginManager) {
                 tracks: self.tracks,
             };
         },
+        /**
+         * #method
+         */
         getTrack(id) {
             return self.tracks.find(t => t.configuration.trackId === id);
         },
+        /**
+         * #method
+         */
         rankSearchResults(results) {
             // order of rank
             const openTrackIds = self.tracks.map(track => track.configuration.trackId);
@@ -323,7 +396,10 @@ function stateModelFactory(pluginManager) {
             });
             return results;
         },
-        // modifies view menu action onClick to apply to all tracks of same type
+        /**
+         * #method
+         * modifies view menu action onClick to apply to all tracks of same type
+         */
         rewriteOnClicks(trackType, viewMenuActions) {
             viewMenuActions.forEach(action => {
                 // go to lowest level menu
@@ -342,6 +418,9 @@ function stateModelFactory(pluginManager) {
                 }
             });
         },
+        /**
+         * #getter
+         */
         get trackTypeActions() {
             const allActions = new Map();
             self.tracks.forEach(track => {
@@ -503,6 +582,9 @@ function stateModelFactory(pluginManager) {
             }
             return t[0];
         },
+        /**
+         * #action
+         */
         hideTrack(trackId) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const conf = (0, mobx_state_tree_1.resolveIdentifier)(schema, (0, mobx_state_tree_1.getRoot)(self), trackId);
@@ -686,7 +768,7 @@ function stateModelFactory(pluginManager) {
          * this "clears the view" and makes the view return to the import form
          */
         clearView() {
-            this.setDisplayedRegions([]);
+            self.displayedRegions.clear();
             self.tracks.clear();
             // it is necessary to run these after setting displayed regions empty
             // or else model.offsetPx gets set to Infinity and breaks
@@ -828,59 +910,57 @@ function stateModelFactory(pluginManager) {
                     icon: SyncAlt_1.default,
                     onClick: self.horizontallyFlip,
                 },
-                { type: 'divider' },
-                {
-                    label: 'Show all regions in assembly',
-                    icon: Visibility_1.default,
-                    onClick: self.showAllRegionsInAssembly,
-                },
-                {
-                    label: 'Show center line',
-                    icon: Visibility_1.default,
-                    type: 'checkbox',
-                    checked: self.showCenterLine,
-                    onClick: self.toggleCenterLine,
-                },
-                {
-                    label: 'Show header',
-                    icon: Visibility_1.default,
-                    type: 'checkbox',
-                    checked: !self.hideHeader,
-                    onClick: self.toggleHeader,
-                },
                 {
-                    label: 'Show header overview',
+                    label: 'Show...',
                     icon: Visibility_1.default,
-                    type: 'checkbox',
-                    checked: !self.hideHeaderOverview,
-                    onClick: self.toggleHeaderOverview,
-                    disabled: self.hideHeader,
-                },
-                {
-                    label: 'Show no tracks active button',
-                    icon: Visibility_1.default,
-                    type: 'checkbox',
-                    checked: !self.hideNoTracksActive,
-                    onClick: self.toggleNoTracksActive,
-                },
-                {
-                    label: 'Show guidelines',
-                    icon: Visibility_1.default,
-                    type: 'checkbox',
-                    checked: self.showGridlines,
-                    onClick: self.toggleShowGridlines,
-                },
-                ...(canShowCytobands
-                    ? [
+                    subMenu: [
                         {
-                            label: 'Show ideogram',
-                            icon: Visibility_1.default,
+                            label: 'Show all regions in assembly',
+                            onClick: self.showAllRegionsInAssembly,
+                        },
+                        {
+                            label: 'Show center line',
                             type: 'checkbox',
-                            checked: self.showCytobands,
-                            onClick: () => self.setShowCytobands(!showCytobands),
+                            checked: self.showCenterLine,
+                            onClick: self.toggleCenterLine,
                         },
-                    ]
-                    : []),
+                        {
+                            label: 'Show header',
+                            type: 'checkbox',
+                            checked: !self.hideHeader,
+                            onClick: self.toggleHeader,
+                        },
+                        {
+                            label: 'Show header overview',
+                            type: 'checkbox',
+                            checked: !self.hideHeaderOverview,
+                            onClick: self.toggleHeaderOverview,
+                            disabled: self.hideHeader,
+                        },
+                        {
+                            label: 'Show no tracks active button',
+                            type: 'checkbox',
+                            checked: !self.hideNoTracksActive,
+                            onClick: self.toggleNoTracksActive,
+                        },
+                        {
+                            label: 'Show guidelines',
+                            type: 'checkbox',
+                            checked: self.showGridlines,
+                            onClick: self.toggleShowGridlines,
+                        },
+                        ...(canShowCytobands
+                            ? [
+                                {
+                                    label: 'Show ideogram',
+                                    type: 'checkbox',
+                                    checked: self.showCytobands,
+                                    onClick: () => self.setShowCytobands(!showCytobands),
+                                },
+                            ]
+                            : []),
+                    ],
+                },
                 {
                     label: 'Track labels',
                     icon: Label_1.default,
@@ -1173,31 +1253,31 @@ function stateModelFactory(pluginManager) {
                         this.moveTo({ index, offset: f.reversed ? f.end - e : s - f.start }, { index, offset: f.reversed ? f.end - s : e - f.start });
                         return;
                     }
-                    let locationIndex = 0;
-                    let locationStart = 0;
-                    let locationEnd = 0;
-                    for (locationIndex; locationIndex < locations.length; locationIndex++) {
-                        const location = locations[locationIndex];
-                        const region = self.displayedRegions[index + locationIndex];
-                        locationStart = location.start || region.start;
-                        locationEnd = location.end || region.end;
+                    let idx = 0;
+                    let start = 0;
+                    let end = 0;
+                    for (idx; idx < locations.length; idx++) {
+                        const location = locations[idx];
+                        const region = self.displayedRegions[index + idx];
+                        start = location.start || region.start;
+                        end = location.end || region.end;
                         if (location.refName !== region.refName) {
                             throw new Error(`Entered location ${(0, util_1.assembleLocString)(location)} does not match with displayed regions`);
                         }
                     }
-                    locationIndex -= 1;
+                    idx -= 1;
                     const startDisplayedRegion = self.displayedRegions[index];
-                    const endDisplayedRegion = self.displayedRegions[index + locationIndex];
+                    const endDisplayedRegion = self.displayedRegions[index + idx];
                     this.moveTo({
                         index,
                         offset: startDisplayedRegion.reversed
                             ? startDisplayedRegion.end - e
                             : s - startDisplayedRegion.start,
                     }, {
-                        index: index + locationIndex,
+                        index: index + idx,
                         offset: endDisplayedRegion.reversed
-                            ? endDisplayedRegion.end - locationStart
-                            : locationEnd - endDisplayedRegion.start,
+                            ? endDisplayedRegion.end - start
+                            : end - endDisplayedRegion.start,
                     });
                     return;
                 }

package/dist/LinearGenomeView/index.js.map CHANGED Viewed

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

@@ -611,7 +611,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
             model: {
                 id: string;
                 displayName: string | undefined;
-                type: "LinearGenomeView";
+                minimized: boolean;
+                type: string;
                 offsetPx: number;
                 bpPerPx: number;
                 displayedRegions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
@@ -649,6 +650,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -808,9 +810,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
                 id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
             } & {
                 id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                type: import("mobx-state-tree").ISimpleType<"LinearGenomeView">;
+                type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -839,6 +842,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1001,7 +1005,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
             model: {
                 id: string;
                 displayName: string | undefined;
-                type: "LinearGenomeView";
+                minimized: boolean;
+                type: string;
                 offsetPx: number;
                 bpPerPx: number;
                 displayedRegions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
@@ -1039,6 +1044,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1198,9 +1204,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
                 id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
             } & {
                 id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                type: import("mobx-state-tree").ISimpleType<"LinearGenomeView">;
+                type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -1229,6 +1236,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1391,7 +1399,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
             model: {
                 id: string;
                 displayName: string | undefined;
-                type: "LinearGenomeView";
+                minimized: boolean;
+                type: string;
                 offsetPx: number;
                 bpPerPx: number;
                 displayedRegions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
@@ -1429,6 +1438,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;
@@ -1588,9 +1598,10 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
                 id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
                 displayName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+                minimized: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
             } & {
                 id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-                type: import("mobx-state-tree").ISimpleType<"LinearGenomeView">;
+                type: import("mobx-state-tree").IType<string | undefined, string, string>;
                 offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
                 displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
@@ -1619,6 +1630,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
             } & {
                 setDisplayName(name: string): void;
                 setWidth(newWidth: number): void;
+                setMinimized(flag: boolean): void;
             } & {
                 volatileWidth: number | undefined;
                 minimumBlockWidth: number;

package/esm/BaseLinearDisplay/components/Tooltip.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 /// <reference types="react" />
 import { BaseLinearDisplayModel } from '../models/BaseLinearDisplayModel';
-declare type Coord = [number, number];
+type Coord = [number, number];
 declare const Tooltip: ({ model, clientMouseCoord, }: {
     model: BaseLinearDisplayModel;
     clientMouseCoord: Coord;