@jbrowse/plugin-linear-genome-view 5.0.0-beta.11 → 5.0.0-beta.15

package/esm/displayKitTests/perRegionTestEnv.d.ts

@@ -245,6 +245,8 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
     };
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+    configProblemsOf(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): string[];
+    readonly liveNotices: string[];
 } & {
     setStatusMessage(status?: import("@jbrowse/core/util").RpcStatus): void;
     setError(error?: unknown): void;
@@ -263,15 +265,23 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
 } & {
     readonly plotKeys: string[];
     readonly plot: import("@jbrowse/core/configuration").Plot;
+    readonly configNotices: string[];
+    readonly notices: string[];
+    readonly cornerNotices: string[];
     readonly plotExamples: readonly import("@jbrowse/core/configuration").PlotExample[];
     readonly configDocsUrl: string;
-    liftPlot(draft: import("@jbrowse/core/configuration").Plot): import("@jbrowse/core/configuration").AnyConfigurationModel;
-    plotProblems(draft: import("@jbrowse/core/configuration").Plot): string[];
-    plotWrites(draft: import("@jbrowse/core/configuration").Plot): Record<string, unknown>;
+    liftPlot(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): import("@jbrowse/core/configuration").AnyConfigurationModel;
+    plotProblems(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): string[];
+    plotWrites(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): Record<string, unknown>;
 } & {
-    applyPlot(draft: import("@jbrowse/core/configuration").Plot): void;
+    applyPlot(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): void;
 } & {
     scrollTop: number;
+    hostHeight: number | undefined;
+} & {
+    readonly configuredHeight: number;
+} & {
+    readonly allottedHeight: number;
 } & {
     readonly height: number;
     readonly resizing: boolean;
@@ -281,6 +291,7 @@ declare function makeStateModel(control: PerRegionTestControl, gate: GateOptIns,
     readonly scrollableHeight: number;
 } & {
     setScrollTop(scrollTop: number): void;
+    setHostHeight(height: number | undefined): void;
     setHeight(displayHeight: number): number;
     resizeHeight(distance: number): number;
 } & {
@@ -772,6 +783,8 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
             };
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            configProblemsOf(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): string[];
+            readonly liveNotices: string[];
         } & {
             setStatusMessage(status?: import("@jbrowse/core/util").RpcStatus): void;
             setError(error?: unknown): void;
@@ -790,15 +803,23 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
         } & {
             readonly plotKeys: string[];
             readonly plot: import("@jbrowse/core/configuration").Plot;
+            readonly configNotices: string[];
+            readonly notices: string[];
+            readonly cornerNotices: string[];
             readonly plotExamples: readonly import("@jbrowse/core/configuration").PlotExample[];
             readonly configDocsUrl: string;
-            liftPlot(draft: import("@jbrowse/core/configuration").Plot): import("@jbrowse/core/configuration").AnyConfigurationModel;
-            plotProblems(draft: import("@jbrowse/core/configuration").Plot): string[];
-            plotWrites(draft: import("@jbrowse/core/configuration").Plot): Record<string, unknown>;
+            liftPlot(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): import("@jbrowse/core/configuration").AnyConfigurationModel;
+            plotProblems(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): string[];
+            plotWrites(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): Record<string, unknown>;
         } & {
-            applyPlot(draft: import("@jbrowse/core/configuration").Plot): void;
+            applyPlot(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): void;
         } & {
             scrollTop: number;
+            hostHeight: number | undefined;
+        } & {
+            readonly configuredHeight: number;
+        } & {
+            readonly allottedHeight: number;
         } & {
             readonly height: number;
             readonly resizing: boolean;
@@ -808,6 +829,7 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             readonly scrollableHeight: number;
         } & {
             setScrollTop(scrollTop: number): void;
+            setHostHeight(height: number | undefined): void;
             setHeight(displayHeight: number): number;
             resizeHeight(distance: number): number;
         } & {
@@ -1188,6 +1210,8 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
             };
             trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+            configProblemsOf(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): string[];
+            readonly liveNotices: string[];
         } & {
             setStatusMessage(status?: import("@jbrowse/core/util").RpcStatus): void;
             setError(error?: unknown): void;
@@ -1206,15 +1230,23 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
         } & {
             readonly plotKeys: string[];
             readonly plot: import("@jbrowse/core/configuration").Plot;
+            readonly configNotices: string[];
+            readonly notices: string[];
+            readonly cornerNotices: string[];
             readonly plotExamples: readonly import("@jbrowse/core/configuration").PlotExample[];
             readonly configDocsUrl: string;
-            liftPlot(draft: import("@jbrowse/core/configuration").Plot): import("@jbrowse/core/configuration").AnyConfigurationModel;
-            plotProblems(draft: import("@jbrowse/core/configuration").Plot): string[];
-            plotWrites(draft: import("@jbrowse/core/configuration").Plot): Record<string, unknown>;
+            liftPlot(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): import("@jbrowse/core/configuration").AnyConfigurationModel;
+            plotProblems(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): string[];
+            plotWrites(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): Record<string, unknown>;
         } & {
-            applyPlot(draft: import("@jbrowse/core/configuration").Plot): void;
+            applyPlot(draft: import("@jbrowse/core/configuration").Plot, options?: import("@jbrowse/core/configuration").PlotWriteOptions): void;
         } & {
             scrollTop: number;
+            hostHeight: number | undefined;
+        } & {
+            readonly configuredHeight: number;
+        } & {
+            readonly allottedHeight: number;
         } & {
             readonly height: number;
             readonly resizing: boolean;
@@ -1224,6 +1256,7 @@ export declare function createPerRegionTestEnvironment({ measuresBytes, gate, es
             readonly scrollableHeight: number;
         } & {
             setScrollTop(scrollTop: number): void;
+            setHostHeight(height: number | undefined): void;
             setHeight(displayHeight: number): number;
             resizeHeight(distance: number): number;
         } & {

package/esm/index.d.ts

@@ -5,6 +5,8 @@ export default class LinearGenomeViewPlugin extends Plugin {
     /**
      * #config LinearGenomeViewConfigSchema
      * #category root
+     * Sets defaults for every linear genome view, on the root config under
+     * `configuration.LinearGenomeViewPlugin`.
      */
     configurationSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly trackLabels: {
@@ -19,7 +21,7 @@ export default class LinearGenomeViewPlugin extends Plugin {
     configure(pluginManager: PluginManager): void;
 }
 export { DisplayChromeOverlayProvider, DisplayUIProvider, FloatingLegend, TrackControlProvider, plainChromeOverlays, plainTrackControl, useTrackControlMenu, } from '@jbrowse/display-ui';
-export type { DisplayBackgroundProgressModel, DisplayChromeOverlays, DisplayErrorBarModel, DisplayLoadingOverlayModel, LegendItem, LegendSection, TooLargeMessageModel, TrackControlComponent, TrackControlIcon, TrackControlMenu, TrackControlOption, TrackControlProps, } from '@jbrowse/display-ui';
+export type { BackgroundProgressProps, DisplayChromeOverlays, ErrorBarProps, LegendItem, LegendSection, LoadingProps, RenderErrorProps, TooLargeProps, TrackControlComponent, TrackControlIcon, TrackControlMenu, TrackControlOption, TrackControlProps, } from '@jbrowse/display-ui';
 export { HighlightChip, type LinearGenomeViewModel, type LinearGenomeViewStateModel, installLinkedViewSync, stateModelFactory as linearGenomeViewStateModelFactory, } from './LinearGenomeView/index.ts';
 export { default as SearchBox } from './LinearGenomeView/components/SearchBox.tsx';
 export { default as HeaderSearchBoxRow } from './LinearGenomeView/components/HeaderSearchBoxRow.tsx';
@@ -32,7 +34,7 @@ export { fetchResults, SearchResultsNotFoundError } from './searchUtils.ts';
 export type { LaunchLinearGenomeViewArgs } from './LaunchLinearGenomeView/index.ts';
 export type { BpOffset, ExportSvgOptions, HighlightInput, HighlightType, InitState, LinearGenomeViewLaunchProps, NavLocation, TrackLabelMode, ViewTrackLabelMode, VolatileGuide, } from './LinearGenomeView/types.ts';
 export type { ScalebarRefNameLabel } from './LinearGenomeView/util.ts';
-export type { HighlightRegion } from './LinearGenomeView/model.ts';
+export type { HighlightRegion, SearchPickerRow, SearchPickerState, } from './LinearGenomeView/model.ts';
 export type { RegionsOrientation } from './LinearGenomeView/util.ts';
 export type { RegionEdit } from './LinearGenomeView/util.ts';
 export { makeTicks } from './LinearGenomeView/util.ts';

package/esm/index.js

@@ -13,11 +13,13 @@ export default class LinearGenomeViewPlugin extends Plugin {
     /**
      * #config LinearGenomeViewConfigSchema
      * #category root
+     * Sets defaults for every linear genome view, on the root config under
+     * `configuration.LinearGenomeViewPlugin`.
      */
     configurationSchema = ConfigurationSchema('LinearGenomeViewConfigSchema', {
         /**
          * #slot configuration.LinearGenomeViewPlugin.trackLabels
-         * where a track's name is drawn: `offset` gives it its own line above the
+         * The placement of a track's name: `offset` gives it its own line above the
          * data, `overlapping` floats it over the top of the data to save vertical
          * space, `hidden` omits it. The view menu's "Track labels" submenu sets the
          * same thing per session

package/esm/searchUtils.js

@@ -170,6 +170,7 @@ export function notifySearchFailure(session, e) {
 // otherwise tell "showing it" from "asked you which one".
 export async function handleSelectedRegion({ input, model, assemblyName, grow, showHitTrack, }) {
     const { assemblyManager, textSearchManager } = getSession(model);
+    model.closeSearchPicker();
     // resolves only once regions/aliases are loaded, which isValidRefName needs
     // (it throws otherwise). A load failure is not this function's to report:
     // swallow it and let the input fall through to the text-search path below

package/esm/shared/RubberbandSpan.d.ts

@@ -4,7 +4,7 @@
  * single view reads one coordinate per edge and the multi-level rubberband reads
  * one per level.
  */
-export default function RubberbandSpan({ left, width, viewWidth, stickyTop, leftLabel, rightLabel, size, }: {
+declare const RubberbandSpan: ({ left, width, viewWidth, stickyTop, leftLabel, rightLabel, size, }: {
     left: number;
     width: number;
     viewWidth: number;
@@ -12,4 +12,5 @@ export default function RubberbandSpan({ left, width, viewWidth, stickyTop, left
     leftLabel: React.ReactNode;
     rightLabel: React.ReactNode;
     size?: React.ReactNode;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;
+export default RubberbandSpan;

package/esm/shared/RubberbandSpan.js

@@ -2,6 +2,7 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { alpha } from '@jbrowse/core/ui/palette';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Typography } from '@mui/material';
+import { observer } from 'mobx-react';
 import { LABEL_WIDTH, SpanEdgeLabels } from './coordLabels.js';
 const useStyles = makeStyles()(theme => ({
     rubberband: {
@@ -23,7 +24,7 @@ const useStyles = makeStyles()(theme => ({
  * single view reads one coordinate per edge and the multi-level rubberband reads
  * one per level.
  */
-export default function RubberbandSpan({ left, width, viewWidth, stickyTop, leftLabel, rightLabel, size, }) {
+const RubberbandSpan = observer(function RubberbandSpan({ left, width, viewWidth, stickyTop, leftLabel, rightLabel, size, }) {
     const { classes } = useStyles();
     // a label only moves inside its edge when the span can hold it, so a sliver of
     // a selection at a view border keeps both labels outside and takes the clip
@@ -31,4 +32,5 @@ export default function RubberbandSpan({ left, width, viewWidth, stickyTop, left
     return (_jsxs("div", { className: classes.rubberband, style: { transform: `translateX(${left}px)`, width }, children: [_jsx(SpanEdgeLabels, { stickyTop: stickyTop, left: leftLabel, right: rightLabel, insideLeft: fitsInside && left < LABEL_WIDTH, insideRight: fitsInside && left + width > viewWidth - LABEL_WIDTH }), size ? (_jsx(Typography, { variant: "h6", className: classes.rubberbandText, style: stickyTop === undefined
                     ? undefined
                     : { position: 'sticky', top: stickyTop }, children: size })) : null] }));
-}
+});
+export default RubberbandSpan;

package/esm/shared/coordLabels.d.ts

@@ -1,11 +1,11 @@
 export declare const LABEL_WIDTH = 100;
 /** A red vertical line at `coordX` with `children` labelled above it. */
-export declare function VerticalGuideLine({ coordX, viewWidth, stickyTop, children, }: {
+export declare const VerticalGuideLine: ({ coordX, viewWidth, stickyTop, children, }: {
     coordX: number;
     viewWidth: number;
     stickyTop: string | undefined;
     children: React.ReactNode;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;
 /**
  * The bp coordinate under a vertical guide, drawn just above the top of the
  * guide line so it covers neither the line nor the cursor hovering the scalebar
@@ -26,22 +26,22 @@ export declare function VerticalGuideLine({ coordX, viewWidth, stickyTop, childr
  * measured once per hover, not per mousemove — only `coordX` changes as the
  * mouse moves, and that needs no measurement.
  */
-export declare function GuideLabel({ coordX, viewWidth, stickyTop, children, }: {
+export declare const GuideLabel: ({ coordX, viewWidth, stickyTop, children, }: {
     coordX: number;
     viewWidth: number;
     stickyTop: string | undefined;
     children: React.ReactNode;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;
 /**
  * The bp coordinates of a rubberband selection, one label just outside each edge
  * of the span. Renders inside the span, so the edges are its own box. A label
  * with no room outside its edge flips inside instead, which is why the span it
  * has to fit in is a prop.
  */
-export declare function SpanEdgeLabels({ stickyTop, left, right, insideLeft, insideRight, }: {
+export declare const SpanEdgeLabels: ({ stickyTop, left, right, insideLeft, insideRight, }: {
     stickyTop: string | undefined;
     left: React.ReactNode;
     right: React.ReactNode;
     insideLeft: boolean;
     insideRight: boolean;
-}): import("react").JSX.Element;
+}) => import("react").JSX.Element;

package/esm/shared/coordLabels.js

@@ -3,6 +3,7 @@ import { useEffect, useRef, useState } from 'react';
 import { alpha } from '@jbrowse/core/ui/palette';
 import { MUI_TOOLTIP_Z_INDEX } from '@jbrowse/core/ui/zIndexes';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
+import { observer } from 'mobx-react';
 import { createPortal } from 'react-dom';
 // roughly how wide a coordinate label is. the guide clamps itself half of this
 // from either border, and a rubberband label that would hang off a border goes
@@ -62,10 +63,10 @@ const useStyles = makeStyles()(theme => ({
     },
 }));
 /** A red vertical line at `coordX` with `children` labelled above it. */
-export function VerticalGuideLine({ coordX, viewWidth, stickyTop, children, }) {
+export const VerticalGuideLine = observer(function VerticalGuideLine({ coordX, viewWidth, stickyTop, children, }) {
     const { classes } = useStyles();
     return (_jsxs(_Fragment, { children: [_jsx(GuideLabel, { coordX: coordX, viewWidth: viewWidth, stickyTop: stickyTop, children: children }), _jsx("div", { className: classes.guideLine, style: { transform: `translateX(${coordX}px)` } })] }));
-}
+});
 function anchorStyle(stickyTop) {
     return stickyTop === undefined
         ? { position: 'relative' }
@@ -91,7 +92,7 @@ function anchorStyle(stickyTop) {
  * measured once per hover, not per mousemove — only `coordX` changes as the
  * mouse moves, and that needs no measurement.
  */
-export function GuideLabel({ coordX, viewWidth, stickyTop, children, }) {
+export const GuideLabel = observer(function GuideLabel({ coordX, viewWidth, stickyTop, children, }) {
     const { classes, cx } = useStyles();
     const anchorRef = useRef(null);
     const [anchorPos, setAnchorPos] = useState();
@@ -120,14 +121,14 @@ export function GuideLabel({ coordX, viewWidth, stickyTop, children, }) {
                         bottom: anchorPos.viewportHeight - anchorPos.top + LABEL_GAP,
                     }, children: children }), document.body)
                 : null] }));
-}
+});
 /**
  * The bp coordinates of a rubberband selection, one label just outside each edge
  * of the span. Renders inside the span, so the edges are its own box. A label
  * with no room outside its edge flips inside instead, which is why the span it
  * has to fit in is a prop.
  */
-export function SpanEdgeLabels({ stickyTop, left, right, insideLeft, insideRight, }) {
+export const SpanEdgeLabels = observer(function SpanEdgeLabels({ stickyTop, left, right, insideLeft, insideRight, }) {
     const { classes, cx } = useStyles();
     return (_jsxs("div", { className: classes.anchor, style: anchorStyle(stickyTop), children: [_jsx("div", { className: cx(classes.label, classes.spanLabel, insideLeft ? classes.insideLeftEdge : classes.leftOfEdge), children: left }), _jsx("div", { className: cx(classes.label, classes.spanLabel, insideRight ? classes.insideRightEdge : classes.rightOfEdge), children: right })] }));
-}
+});

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "5.0.0-beta.11",
+  "version": "5.0.0-beta.15",
   "type": "module",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
@@ -21,15 +21,15 @@
     "esm"
   ],
   "dependencies": {
-    "@jbrowse/mobx-state-tree": "^6.7.0",
-    "@mui/icons-material": "^9.4.0",
-    "@mui/material": "^9.4.0",
-    "mobx": "^7.0.5",
+    "@jbrowse/mobx-state-tree": "^6.9.0",
+    "@mui/icons-material": "^9.5.0",
+    "@mui/material": "^9.5.0",
+    "mobx": "^7.0.6",
     "mobx-react": "^10.0.2",
-    "@jbrowse/display-kit": "^5.0.0-beta.11",
-    "@jbrowse/core": "^5.0.0-beta.11",
-    "@jbrowse/render-core": "^5.0.0-beta.11",
-    "@jbrowse/display-ui": "^5.0.0-beta.11"
+    "@jbrowse/display-kit": "^5.0.0-beta.15",
+    "@jbrowse/display-ui": "^5.0.0-beta.15",
+    "@jbrowse/core": "^5.0.0-beta.15",
+    "@jbrowse/render-core": "^5.0.0-beta.15"
   },
   "peerDependencies": {
     "react": ">=19.0.0",
@@ -40,7 +40,7 @@
   },
   "sideEffects": false,
   "devDependencies": {
-    "@jbrowse/display-test-utils": "^5.0.0-beta.11"
+    "@jbrowse/display-test-utils": "^5.0.0-beta.15"
   },
   "scripts": {
     "prebuild": "pnpm clean",