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/esm/LinearGenomeView/index.js CHANGED Viewed

@@ -31,6 +31,7 @@ import MiniControls from './components/MiniControls';
 import Header from './components/Header';
 import ZoomControls from './components/ZoomControls';
 import LinearGenomeView from './components/LinearGenomeView';
+// lazies
 const SequenceSearchDialog = lazy(() => import('./components/SequenceSearchDialog'));
 function calculateVisibleLocStrings(contentBlocks) {
     if (!contentBlocks.length) {
@@ -69,6 +70,9 @@ export function stateModelFactory(pluginManager) {
         id: 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: types.literal('LinearGenomeView'),
         /**
@@ -182,14 +186,23 @@ export function stateModelFactory(pluginManager) {
         },
     }))
         .views(self => ({
+        /**
+         * #method
+         */
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
         MiniControlsComponent() {
             return MiniControls;
         },
+        /**
+         * #method
+         */
         // eslint-disable-next-line @typescript-eslint/no-explicit-any
         HeaderComponent() {
             return Header;
         },
+        /**
+         * #getter
+         */
         get assemblyErrors() {
             const { assemblyManager } = getSession(self);
             const { assemblyNames } = self;
@@ -198,23 +211,41 @@ export function stateModelFactory(pluginManager) {
                 .filter(f => !!f)
                 .join(', ');
         },
+        /**
+         * #getter
+         */
         get assembliesInitialized() {
             const { assemblyManager } = 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 SCALE_BAR_HEIGHT + RESIZE_HANDLE_HEIGHT;
         },
+        /**
+         * #getter
+         */
         get headerHeight() {
             if (self.hideHeader) {
                 return 0;
@@ -224,44 +255,77 @@ export function stateModelFactory(pluginManager) {
             }
             return HEADER_BAR_HEIGHT + 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 * 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 {
                 ...getParentRenderProps(self),
@@ -269,6 +333,9 @@ export function stateModelFactory(pluginManager) {
                 highResolutionScaling: getConf(getSession(self), 'highResolutionScaling'),
             };
         },
+        /**
+         * #method
+         */
         searchScope(assemblyName) {
             return {
                 assemblyName,
@@ -276,9 +343,15 @@ export 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);
@@ -289,7 +362,10 @@ export 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
@@ -308,6 +384,9 @@ export function stateModelFactory(pluginManager) {
                 }
             });
         },
+        /**
+         * #getter
+         */
         get trackTypeActions() {
             const allActions = new Map();
             self.tracks.forEach(track => {
@@ -469,6 +548,9 @@ export function stateModelFactory(pluginManager) {
             }
             return t[0];
         },
+        /**
+         * #action
+         */
         hideTrack(trackId) {
             const schema = pluginManager.pluggableConfigSchemaType('track');
             const conf = resolveIdentifier(schema, getRoot(self), trackId);
@@ -652,7 +734,7 @@ export 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
@@ -794,59 +876,57 @@ export function stateModelFactory(pluginManager) {
                     icon: SyncAltIcon,
                     onClick: self.horizontallyFlip,
                 },
-                { type: 'divider' },
-                {
-                    label: 'Show all regions in assembly',
-                    icon: VisibilityIcon,
-                    onClick: self.showAllRegionsInAssembly,
-                },
-                {
-                    label: 'Show center line',
-                    icon: VisibilityIcon,
-                    type: 'checkbox',
-                    checked: self.showCenterLine,
-                    onClick: self.toggleCenterLine,
-                },
-                {
-                    label: 'Show header',
-                    icon: VisibilityIcon,
-                    type: 'checkbox',
-                    checked: !self.hideHeader,
-                    onClick: self.toggleHeader,
-                },
                 {
-                    label: 'Show header overview',
+                    label: 'Show...',
                     icon: VisibilityIcon,
-                    type: 'checkbox',
-                    checked: !self.hideHeaderOverview,
-                    onClick: self.toggleHeaderOverview,
-                    disabled: self.hideHeader,
-                },
-                {
-                    label: 'Show no tracks active button',
-                    icon: VisibilityIcon,
-                    type: 'checkbox',
-                    checked: !self.hideNoTracksActive,
-                    onClick: self.toggleNoTracksActive,
-                },
-                {
-                    label: 'Show guidelines',
-                    icon: VisibilityIcon,
-                    type: 'checkbox',
-                    checked: self.showGridlines,
-                    onClick: self.toggleShowGridlines,
-                },
-                ...(canShowCytobands
-                    ? [
+                    subMenu: [
                         {
-                            label: 'Show ideogram',
-                            icon: VisibilityIcon,
+                            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: LabelIcon,
@@ -1139,31 +1219,31 @@ export 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 ${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/esm/LinearGenomeView/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/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/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.2.0",
+  "version": "2.2.1",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -65,5 +65,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
+  "gitHead": "896d175c5d9345049faea8e1155f243c912aac42"
 }