@jbrowse/plugin-linear-genome-view 5.0.0-beta.1 → 5.0.0-beta.11

package/esm/FeatureTrack/configSchema.d.ts

@@ -40,85 +40,177 @@ import type PluginManager from '@jbrowse/core/PluginManager';
  * }
  * ```
  */
-declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const configSchema: (pluginManager: PluginManager) => import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
+    assemblyNames: {
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
+    };
+    category: {
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
+    };
+    description: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+    displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly config: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly hideUris: {
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly feature: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly subfeatures: {
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly depth: {
+            type: "maybeNumber";
+        };
+        readonly maxDepth: {
+            type: "maybeNumber";
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+    metadata: {
+        type: "frozen";
+    } & {
+        defaultValue: unknown;
+    };
+    name: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        readonly indexingAttributes: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly indexingFeatureTypesToExclude: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly indexingFeatureTypesToInclude: {
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
+        };
+        readonly textSearchAdapter: import("@jbrowse/mobx-state-tree").ITypeUnion<any, any, import("@jbrowse/core/configuration").PluggableConfigNode | undefined>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+    trackId: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     readonly name: {
-        readonly description: "descriptive name of the track, falls back to the trackId when unset";
-        readonly type: "string";
-        readonly defaultValue: "";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
     readonly assemblyNames: {
-        readonly description: "name of the assembly (or assemblies) track belongs to";
-        readonly type: "stringArray";
-        readonly defaultValue: readonly ["assemblyName"];
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
     readonly description: {
-        readonly description: "a description of the track";
-        readonly type: "string";
-        readonly defaultValue: "";
+        type: "string";
+    } & {
+        defaultValue: string;
     };
     readonly category: {
-        readonly description: "the category and sub-categories of a track";
-        readonly type: "stringArray";
-        readonly defaultValue: readonly [];
+        type: "stringArray";
+    } & {
+        defaultValue: unknown;
     };
     readonly metadata: {
-        readonly type: "frozen";
-        readonly description: "anything to add about this track";
-        readonly defaultValue: {};
+        type: "frozen";
+    } & {
+        defaultValue: unknown;
     };
-    readonly adapter: import("@jbrowse/mobx-state-tree").IAnyType;
+    readonly adapter: import("@jbrowse/core/PluginManager").PluggableConfigSchemaType;
     readonly textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly indexingAttributes: {
-            readonly type: "stringArray";
-            readonly description: "list of which feature attributes to index for text searching";
-            readonly defaultValue: readonly ["Name", "ID", "symbol"];
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
         };
         readonly indexingFeatureTypesToExclude: {
-            readonly type: "stringArray";
-            readonly description: "list of feature types to exclude in text search index";
-            readonly defaultValue: readonly ["CDS", "exon"];
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
         };
         readonly indexingFeatureTypesToInclude: {
-            readonly type: "stringArray";
-            readonly description: "the only feature types to index; empty means index every type not excluded";
-            readonly defaultValue: readonly [];
+            type: "stringArray";
+        } & {
+            defaultValue: unknown;
         };
-        readonly textSearchAdapter: import("@jbrowse/mobx-state-tree").IAnyType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    readonly displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyType>;
+        readonly textSearchAdapter: import("@jbrowse/mobx-state-tree").ITypeUnion<any, any, import("@jbrowse/core/configuration").PluggableConfigNode | undefined>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+    readonly displays: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/core/PluginManager").PluggableConfigSchemaType>;
     readonly formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly feature: {
-            readonly type: "frozen";
-            readonly description: "adds extra fields to the feature details";
-            readonly defaultValue: {};
-            readonly contextVariable: ["feature"];
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
         };
         readonly subfeatures: {
-            readonly type: "frozen";
-            readonly description: "adds extra fields to the subfeatures of a feature";
-            readonly defaultValue: {};
-            readonly contextVariable: ["feature"];
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
         };
         readonly depth: {
-            readonly type: "maybeNumber";
-            readonly description: "levels of subfeature the formatDetails.subfeatures callback runs on, default 2";
+            type: "maybeNumber";
         };
         readonly maxDepth: {
-            readonly type: "maybeNumber";
-            readonly description: "hide subfeatures nested deeper than this, default no limit";
+            type: "maybeNumber";
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
     readonly formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly config: {
-            readonly type: "frozen";
-            readonly description: "formats configuration object in about dialog";
-            readonly defaultValue: {};
-            readonly contextVariable: ["config"];
+            type: "frozen";
+        } & {
+            defaultValue: unknown;
         };
         readonly hideUris: {
-            readonly type: "boolean";
-            readonly defaultValue: false;
+            type: "boolean";
+        } & {
+            defaultValue: boolean;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, "trackId">>;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined, undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
+    type: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+    trackId: {
+        type: "string";
+    } & {
+        defaultValue: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId", true, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>, "trackId", undefined, import("@jbrowse/core/configuration").ConfigurationSchemaRequirement<Partial<Record<string, string[]>>, string>, any>>;
 export default configSchema;

package/esm/LaunchLinearGenomeView/index.js

@@ -1,22 +1,11 @@
-import { linearGenomeViewPropKeys, partitionLaunchKeys, warnUnknownLaunchKeys, } from '../LinearGenomeView/initKeys.js';
 export default function LaunchLinearGenomeViewF(pluginManager) {
     /** #extensionPoint LaunchView-LinearGenomeView | async | Programmatically launch a linear genome view */
     pluginManager.addToExtensionPoint('LaunchView-LinearGenomeView', args => {
-        const { session, id, ...spec } = args;
+        const { session, ...spec } = args;
         if (!spec.assembly) {
             throw new Error('No assembly provided when launching linear genome view');
         }
-        // Resolution keys go into the one-shot `init` blob afterAttach applies and
-        // discards; plain props go straight onto the view snapshot, where MST
-        // restores them natively (and, except for the purely localStorage-backed
-        // showCenterLine, persist on save). Anything in neither set is a typo — MST
-        // drops unknown snapshot keys and `init` is a frozen blob, so nothing
-        // downstream would notice.
-        const { init, viewProps, unknown } = partitionLaunchKeys(spec, linearGenomeViewPropKeys(pluginManager));
-        warnUnknownLaunchKeys('LaunchView-LinearGenomeView', unknown);
-        // A provided id is passed top-level so MST's optional identifier honors it
-        // (undefined falls back to an auto-generated id).
-        session.addView('LinearGenomeView', { id, ...viewProps, init });
+        session.addView('LinearGenomeView', spec);
         return args;
     });
 }

package/esm/LinearGenomeView/afterAttach.d.ts

@@ -1,17 +1,17 @@
 import type { LinearGenomeViewModel } from './model.ts';
 import type { InitState } from './types.ts';
-import type { AssemblyHost, NotificationSink } from '@jbrowse/core/util';
+import type { AbstractSessionModel, AssemblyHost, NotificationSink } from '@jbrowse/core/util';
 /**
- * Apply an init blob's `highlight` entries to a view, coercing each locstring
- * or wire-format object and reporting a bad one without taking out its
- * siblings.
+ * Add an init blob's `highlight` entries to the session, coercing each
+ * locstring or wire-format object and reporting a bad one without taking out
+ * its siblings. An entry without an assembly takes the launch's.
  *
  * Exported because a LinearSyntenyView row is a LinearGenomeView that does NOT
  * go through this file's init autorun — the synteny view builds each row's
  * snapshot and navigates it itself — so the row's own `highlight` had nowhere
  * to be applied and was dropped in silence.
  */
-export declare function applyInitHighlights(self: LinearGenomeViewModel, session: AssemblyHost & NotificationSink, init: Pick<InitState, 'highlight' | 'assembly'>): void;
+export declare function applyInitHighlights(session: AssemblyHost & NotificationSink & Pick<AbstractSessionModel, 'addHighlight'>, init: Pick<InitState, 'highlight' | 'assembly'>): void;
 /**
  * Autorun that handles the init state - navigating to initial location,
  * showing tracks, etc.

package/esm/LinearGenomeView/afterAttach.js

@@ -1,19 +1,10 @@
 import { getSession, isSessionModelWithWidgets, localStorageSetItem, resolveNamedRegions, } from '@jbrowse/core/util';
 import { coerceHighlight } from '@jbrowse/core/util/highlights';
 import { installInitAutorun } from '@jbrowse/core/util/installInitAutorun';
-import { normalizeTrackInit } from '@jbrowse/core/util/tracks';
-import { addDisposer, getPropertyMembers } from '@jbrowse/mobx-state-tree';
-import { autorun, when } from 'mobx';
+import { normalizeTrackInit, warmTrackDisplayGeneric, } from '@jbrowse/core/util/tracks';
+import { addDisposer } from '@jbrowse/mobx-state-tree';
+import { autorun, untracked, when } from 'mobx';
 import { SearchResultsNotFoundError } from '../searchUtils.js';
-import { partitionLaunchKeys, warnUnknownLaunchKeys } from './initKeys.js';
-function warnInitKeyProblems(self, init) {
-    const { viewProps, unknown } = partitionLaunchKeys(init, new Set(Object.keys(getPropertyMembers(self).properties)));
-    const viewPropKeys = Object.keys(viewProps);
-    warnUnknownLaunchKeys('LinearGenomeView init', unknown);
-    if (viewPropKeys.length) {
-        console.warn(`LinearGenomeView init ignored view prop(s): ${viewPropKeys.join(', ')} — set these on the view alongside init, not inside it`);
-    }
-}
 // `init` is a frozen blob that often comes from hand-authored JSON, where a
 // lone entry gets written bare (`tracks: 'genes'`). A string is iterable, so
 // looping over it directly walked its characters — one track opened per letter.
@@ -30,24 +21,17 @@ async function openTracklist(self, session, superseded) {
     // activateTrackSelector throws without widget support, which would abort the
     // rest of init (navigation included) over an optional extra
     if (isSessionModelWithWidgets(session)) {
-        // `poppedOut` — the visible widget rendered in a modal, leaving the drawer
-        // column free — lives on SessionWithDrawerWidgets, whose type guard is
-        // product-core's, so duck-type it here rather than take an upward
-        // dependency. A session without the key has no modal to pop out into, so
-        // false is the right answer for it.
-        const poppedOut = 'poppedOut' in session && session.poppedOut === true;
-        // the same line App.tsx draws to decide whether to render the drawer column
-        // at all. A *minimized* drawer still holds a visibleWidget while taking no
-        // width, and showWidget un-minimizes it (product-core's DrawerWidgets), so
-        // `!!visibleWidget` alone reads "already open", skips the wait below, and
-        // hands navigation the pre-drawer width — the exact thing this is here to
-        // prevent.
-        const drawerWasOpen = !!session.visibleWidget && !session.minimized && !poppedOut;
+        // `drawerVisible` is the line App.tsx draws to render the drawer column at
+        // all: a minimized, popped-out or modal-only widget takes no width. It
+        // lives on SessionWithDrawerWidgets, whose type guard is product-core's, so
+        // it is duck-typed rather than taken as an upward dependency; a session
+        // without it has no drawer column.
+        const drawerVisible = () => 'drawerVisible' in session && session.drawerVisible === true;
+        const drawerWasVisible = drawerVisible();
         const widthBefore = self.volatileWidth;
         self.activateTrackSelector();
-        // a width change is only coming if the drawer is about to start taking
-        // space; popped out it never does, so don't sit out the timeout for it
-        if (!drawerWasOpen && !poppedOut) {
+        // a width change is only coming if the drawer just started taking space
+        if (!drawerWasVisible && drawerVisible()) {
             // Bounded so init can't wedge here if the drawer doesn't shrink the view
             // (e.g. embedded or modal-drawer layouts, where no width change is
             // coming), and superseded so a re-launch landing mid-wait isn't held
@@ -103,7 +87,11 @@ async function navigateInit(self, session, init) {
             // navToLocString waits for the assembly itself, and this autorun only
             // runs once `initialized` confirms init.assembly has loaded regions, so
             // no explicit waitForAssembly is needed here
-            await self.navToLocString(init.loc, init.assembly, init.grow);
+            // a spec that listed its tracks gets those tracks; one that only named
+            // a gene gets the track the gene was found in, as the search box would
+            await self.navToLocString(init.loc, init.assembly, init.grow, {
+                showHitTrack: init.showHitTrack ?? asArray(init.tracks).length === 0,
+            });
         }
         else if (init.displayedRegionNames?.length) {
             // an explicit region list is a navigation request just like `loc`, so it
@@ -134,44 +122,33 @@ async function navigateInit(self, session, init) {
         }
     }
 }
-// showTrack funnels through showTrackGeneric, which surfaces any failure
-// (unresolved id, bad config, etc) as its own snackbar
-function showInitTracks(self, init) {
+// launchTrack funnels through showTrackGeneric, which surfaces any failure
+// (unresolved id, bad config, etc) as its own snackbar, and loads the picked
+// display's state model first when it is registered lazily
+async function showInitTracks(self, init) {
     for (const t of asArray(init.tracks)) {
         const { trackId, trackSnapshot, displaySnapshot } = normalizeTrackInit(t);
-        self.showTrack(trackId, trackSnapshot, displaySnapshot);
-    }
-}
-// backfill assemblyName on any session-authored highlights that omitted it so
-// downstream code (bookmark widget grid, addBookmark, etc) doesn't have to keep
-// falling back
-function backfillHighlightAssemblies(self) {
-    const fallback = self.assemblyNames[0];
-    if (self.highlight.length && fallback) {
-        const normalized = self.highlight.map(h => h.assemblyName ? h : { ...h, assemblyName: fallback });
-        if (normalized.some((h, i) => h !== self.highlight[i])) {
-            self.setHighlight(normalized);
-        }
+        await self.launchTrack(trackId, trackSnapshot, displaySnapshot);
     }
 }
 /**
- * Apply an init blob's `highlight` entries to a view, coercing each locstring
- * or wire-format object and reporting a bad one without taking out its
- * siblings.
+ * Add an init blob's `highlight` entries to the session, coercing each
+ * locstring or wire-format object and reporting a bad one without taking out
+ * its siblings. An entry without an assembly takes the launch's.
  *
  * Exported because a LinearSyntenyView row is a LinearGenomeView that does NOT
  * go through this file's init autorun — the synteny view builds each row's
  * snapshot and navigates it itself — so the row's own `highlight` had nowhere
  * to be applied and was dropped in silence.
  */
-export function applyInitHighlights(self, session, init) {
+export function applyInitHighlights(session, init) {
     for (const h of asArray(init.highlight)) {
         // parseLocString throws on an unknown refName or a malformed locstring, and
         // one bad entry must take out neither its siblings nor the rest of init
         try {
             const highlight = coerceHighlight(h, init.assembly, refName => session.assemblyManager.isValidRefName(refName, init.assembly));
             if (highlight) {
-                self.addToHighlights(highlight);
+                session.addHighlight(highlight);
             }
         }
         catch (e) {
@@ -180,20 +157,24 @@ export function applyInitHighlights(self, session, init) {
         }
     }
 }
-async function applyInit(self, init, { superseded }) {
+async function applyInit(self, pending, { superseded }) {
     const session = getSession(self);
-    warnInitKeyProblems(self, init);
+    // A re-launch of a view already showing an assembly need not restate it:
+    // jb.setSession writes `loc` and track entries beside the built state, and
+    // the readiness gate resolved the same default before letting this run.
+    const init = pending.assembly
+        ? pending
+        : { ...pending, assembly: self.launchAssemblyName ?? pending.assembly };
     if (init.tracklist) {
         await openTracklist(self, session, superseded);
     }
     // `superseded`, not a bare isAlive: it subsumes the liveness check (the view
     // may have been removed while the drawer or the navigation resolved, and
     // reading or mutating a detached node throws) and also covers the case
-    // isAlive misses — a newer setInit landed mid-apply, so the rest of *this*
+    // isAlive misses — a newer setLaunch landed mid-apply, so the rest of *this*
     // blob is stale. Finishing it anyway appends its tracks and highlights under
-    // the one that replaced it, and addToHighlights pushes, so a re-launch of the
-    // same spec (a StrictMode remount) doubles the bands. The drain loop applies
-    // the newer init next either way.
+    // the one that replaced it. The drain loop applies the newer init next either
+    // way.
     //
     // Checked after each await rather than once at the top, and as early returns
     // rather than nesting, so a step added later takes a guard beside it instead
@@ -205,12 +186,44 @@ async function applyInit(self, init, { superseded }) {
     if (superseded()) {
         return;
     }
-    showInitTracks(self, init);
+    await showInitTracks(self, init);
+    if (superseded()) {
+        return;
+    }
     if (init.nav !== undefined) {
         self.setHideHeader(!init.nav);
     }
-    backfillHighlightAssemblies(self);
-    applyInitHighlights(self, session, init);
+    applyInitHighlights(session, init);
+}
+/**
+ * The init autorun below waits for the view's width, which exists only once its
+ * component has rendered, and then loads the assembly and launches the tracks
+ * one at a time. The assembly and the display code each pending track needs can
+ * start loading now, all at once.
+ */
+function setupInitWarmup(self) {
+    addDisposer(self, autorun(function initWarmupAutorun() {
+        const pending = self.pendingLaunch;
+        const tracks = asArray(pending?.tracks);
+        // eslint-disable-next-line no-restricted-syntax -- EFFECT INPUT: the assembly and track configs only feed the loads started here; the pending launch is the key
+        untracked(() => {
+            const assembly = pending?.assembly ?? self.launchAssemblyName;
+            if (pending && assembly) {
+                try {
+                    getSession(self)
+                        .assemblyManager.waitForAssembly(assembly)
+                        .catch(() => { });
+                }
+                catch {
+                    // navigation reports an assembly that cannot load
+                }
+            }
+            for (const t of tracks) {
+                const { trackId, displaySnapshot } = normalizeTrackInit(t);
+                warmTrackDisplayGeneric(self, trackId, displaySnapshot, assembly);
+            }
+        });
+    }, { name: 'LGVInitWarmup' }));
 }
 /**
  * Autorun that handles the init state - navigating to initial location,
@@ -221,9 +234,8 @@ export function setupInitAutorun(self) {
         name: 'LGVInit',
         // `init` is what makes hasSomethingToShow / awaitingInitNavigation report
         // "loading"
-        // until navigation populates displayedRegions, so the alternative gate
-        // (clearing `init` up front, the way SpreadsheetView does) would flash the
-        // import form mid-load.
+        // until navigation populates displayedRegions, so clearing `init` up front
+        // would flash the import form mid-load.
         ready: () => self.initialized,
         // No pre-materialization phase to protect: the view is its own single row,
         // and `error` already derives a failed init assembly declaratively (via
@@ -271,6 +283,7 @@ function setupLocalStorageAutorun(self) {
  * Sets up all afterAttach autoruns for the LinearGenomeView
  */
 export function doAfterAttach(self) {
+    setupInitWarmup(self);
     setupInitAutorun(self);
     setupCoarseDynamicBlocksAutorun(self);
     setupLocalStorageAutorun(self);

package/esm/LinearGenomeView/components/CenterLine.js

@@ -1,4 +1,6 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { clamp } from '@jbrowse/core/util';
+import { basePaintedAt } from '@jbrowse/core/util/Base1DUtils';
 import { makeStyles } from '@jbrowse/core/util/tss-react';
 import CloseIcon from '@mui/icons-material/Close';
 import { IconButton, Tooltip } from '@mui/material';
@@ -18,6 +20,7 @@ const useStyles = makeStyles()(theme => ({
     centerLineText: {
         position: 'absolute',
         left: 0,
+        bottom: 0,
         display: 'flex',
         alignItems: 'center',
         gap: 2,
@@ -31,7 +34,7 @@ const useStyles = makeStyles()(theme => ({
     },
 }));
 const CenterLine = observer(function CenterLine({ model }) {
-    const { bpPerPx, centerLineInfo, trackHeights, tracks, width } = model;
+    const { bpPerPx, centerLineInfo, tracks, width } = model;
     const { classes } = useStyles();
     const startingPosition = width / 2;
     return tracks.length ? (_jsx("div", { "data-testid": "centerline_container", className: classes.centerLineContainer, role: "presentation", style: {
@@ -39,8 +42,7 @@ const CenterLine = observer(function CenterLine({ model }) {
             width: Math.max(1 / bpPerPx, 1),
         }, children: centerLineInfo && (_jsxs("div", { "data-testid": "centerline_text", className: classes.centerLineText, role: "presentation", style: {
                 transform: `translateX(${Math.max(1 / bpPerPx, 1) + 5}px)`,
-                top: trackHeights,
-            }, children: [centerLineInfo.refName, ":", ' ', Math.max(Math.round(centerLineInfo.offset) + 1, 0).toLocaleString('en-US'), _jsx(Tooltip, { title: "Hide center line", children: _jsx(IconButton, { className: classes.dismiss, onClick: () => {
+            }, children: [centerLineInfo.refName, ":", ' ', (clamp(basePaintedAt(centerLineInfo, centerLineInfo.offset), centerLineInfo.start, centerLineInfo.end - 1) + 1).toLocaleString('en-US'), _jsx(Tooltip, { title: "Hide center line", children: _jsx(IconButton, { className: classes.dismiss, onClick: () => {
                             model.setShowCenterLine(false);
                         }, children: _jsx(CloseIcon, { fontSize: "inherit" }) }) })] })) })) : null;
 });

package/esm/LinearGenomeView/components/CrisprGuidePanel.js

@@ -64,15 +64,14 @@ const CrisprGuidePanel = observer(function CrisprGuidePanel({ model, handleClose
     const [pamLocation, setPamLocation] = useState(DEFAULT_PRESET.pamLocation);
     const [guideLengthStr, setGuideLengthStr] = useState(String(DEFAULT_PRESET.guideLength));
     const [cutOffsetStr, setCutOffsetStr] = useState(String(DEFAULT_PRESET.cutOffset));
-    // presets carry this; Custom is treated as a blunt cutter, so the panel does
-    // not grow a second offset field for a case config can express directly
-    const [cutOffsetBottom, setCutOffsetBottom] = useState(DEFAULT_PRESET.cutOffsetBottom);
     const [searchForward, setSearchForward] = useState(true);
     const [searchReverse, setSearchReverse] = useState(true);
     const [filterQuality, setFilterQuality] = useState(false);
     // `Number('')` is 0, so an emptied field would otherwise read as a valid zero
     const guideLength = toBpCount(guideLengthStr);
     const cutOffset = toBpCount(cutOffsetStr);
+    // Custom is a blunt cutter: config can express a staggered one directly
+    const cutOffsetBottom = ENZYME_PRESETS[enzyme]?.cutOffsetBottom ?? cutOffset;
     // both are bp counts used for fixed-length string slicing, so a fractional
     // value would silently truncate and skew the placement
     const guideLengthValid = Number.isInteger(guideLength) && guideLength > 0;
@@ -101,7 +100,6 @@ const CrisprGuidePanel = observer(function CrisprGuidePanel({ model, handleClose
             setPamLocation(preset.pamLocation);
             setGuideLengthStr(String(preset.guideLength));
             setCutOffsetStr(String(preset.cutOffset));
-            setCutOffsetBottom(preset.cutOffsetBottom);
         }
     }
     function handleSubmit() {
@@ -116,7 +114,7 @@ const CrisprGuidePanel = observer(function CrisprGuidePanel({ model, handleClose
                 guideLength,
                 pamLocation,
                 cutOffset,
-                cutOffsetBottom: enzyme === 'Custom' ? cutOffset : cutOffsetBottom,
+                cutOffsetBottom,
                 searchForward,
                 searchReverse,
                 excludePolyT: filterQuality,

package/esm/LinearGenomeView/components/ExportSvgDialog.d.ts

@@ -1,11 +1,12 @@
-import type { TrackLabelMode } from '../types.ts';
+import type { TrackLabelMode, ViewTrackLabelMode } from '../types.ts';
 import type { BaseExportSvgOptions } from '@jbrowse/core/ui';
 export default function ExportSvgDialog({ model, handleClose, }: {
     model: {
+        effectiveTrackLabels?: ViewTrackLabelMode;
         exportSvg(opts: BaseExportSvgOptions & {
             trackLabels: TrackLabelMode;
             showGridlines: boolean;
-        }): Promise<void>;
+        }): Promise<unknown>;
     };
     handleClose: () => void;
 }): import("react").JSX.Element;

package/esm/LinearGenomeView/components/ExportSvgDialog.js

@@ -4,11 +4,15 @@ import { MenuItem, TextField } from '@mui/material';
 // Shared track-label + gridlines export dialog. Used by LGV, linear-synteny and
 // breakpoint-split views (their lazyDialogs re-export this).
 export default function ExportSvgDialog({ model, handleClose, }) {
-    const [trackLabels, setTrackLabels] = useExportSvgPreference('tracklabels', 'offset');
+    // The view's own setting is already an export mode, so a user who has not
+    // picked one here gets the figure their screen shows. The key is `-mode`
+    // because the modes were once spelled `overlay`/`none`, and a stored one of
+    // those would select nothing in the dropdown.
+    const [trackLabels, setTrackLabels] = useExportSvgPreference('tracklabels-mode', model.effectiveTrackLabels ?? 'offset');
     const [showGridlines, setShowGridlines] = useExportSvgPreference('gridlines', false);
     return (_jsx(BaseExportSvgDialog, { model: model, handleClose: handleClose, exportSvg: opts => model.exportSvg({ ...opts, trackLabels, showGridlines }), checkboxes: _jsx(LabeledCheckbox, { checked: showGridlines, onChange: val => {
                 setShowGridlines(val);
             }, label: "Show gridlines" }), children: _jsxs(TextField, { select: true, label: "Track label positioning", variant: "outlined", style: { minWidth: 200 }, value: trackLabels, onChange: event => {
                 setTrackLabels(event.target.value);
-            }, children: [_jsx(MenuItem, { value: "offset", children: "Offset" }), _jsx(MenuItem, { value: "overlay", children: "Overlay" }), _jsx(MenuItem, { value: "left", children: "Left" }), _jsx(MenuItem, { value: "none", children: "None" })] }) }));
+            }, children: [_jsx(MenuItem, { value: "offset", children: "Offset" }), _jsx(MenuItem, { value: "overlapping", children: "Overlapping" }), _jsx(MenuItem, { value: "left", children: "Left" }), _jsx(MenuItem, { value: "hidden", children: "Hidden" })] }) }));
 }

package/esm/LinearGenomeView/components/GetSequenceDialog.js

@@ -32,12 +32,12 @@ const GetSequenceDialog = observer(function GetSequenceDialog({ model, regions,
     // a selection this dialog will happily take is a whole chromosome of
     // sequence, so both handles are forwarded: closing the dialog stops the
     // read rather than leaving the worker on it, and the wait is named
-    async (_name, _locs, stopToken, statusCallback) => {
+    async (_name, _locs, signal, statusCallback) => {
         if (regions.length === 0) {
             throw new Error('Selected region is out of bounds');
         }
         const chunks = await fetchSequence(model, regions, {
-            stopToken,
+            signal,
             statusCallback,
         });
         // validate here (in the async path) so a length mismatch surfaces via the