@jbrowse/plugin-linear-genome-view 5.0.0-beta.19 → 5.0.0-beta.20

package/esm/LinearGenomeView/model.d.ts

@@ -101,7 +101,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackSelectorType: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showCenterLine: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showCytobands: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"" | "hidden" | "offset" | "overlapping">, [undefined]>;
     axis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly grid: {
             type: "boolean";
@@ -955,6 +955,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * short by the unmeasured bands.
      */
     getTrackYOffset(trackId: string): number | undefined;
+    /**
+     * #getter
+     * `getTrackYOffset` for every shown track, by trackId, from one walk
+     */
+    readonly trackYOffsets: Map<string, number>;
     /**
      * #method
      * the pinned or unpinned sibling list a track renders within; move
@@ -1256,24 +1261,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     toggleTrackSelector(): import("@jbrowse/core/util").Widget;
-    /**
-     * #method
-     * Helper method for the fetchSequence.
-     * Returns the regions the user selected with the
-     * rubberband
-     *
-     * @param leftOffset - `object as {start, end, index, offset}`, offset = start
-     * of user drag
-     * @param rightOffset - `object as {start, end, index, offset}`,
-     * offset = end of user drag
-     * @returns array of Region[]
-     */
-    getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
-        assemblyName: string;
-        refName: string;
-        start: number;
-        end: number;
-    }[];
     /**
      * #action
      */
@@ -1293,6 +1280,25 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setLaunch(launch?: LaunchInput<InitState>): void;
+} & {
+    /**
+     * #method
+     * Helper method for the fetchSequence.
+     * Returns the regions the user selected with the
+     * rubberband
+     *
+     * @param leftOffset - `object as {start, end, index, offset}`, offset = start
+     * of user drag
+     * @param rightOffset - `object as {start, end, index, offset}`,
+     * offset = end of user drag
+     * @returns array of Region[]
+     */
+    getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
+        assemblyName: string;
+        refName: string;
+        start: number;
+        end: number;
+    }[];
 } & {
     slide: (viewWidths: number) => void;
     zoom: (targetBpPerPx: number) => void;
@@ -2054,7 +2060,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackSelectorType: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showCenterLine: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showCytobands: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    trackLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<"" | "hidden" | "offset" | "overlapping">, [undefined]>;
     axis: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         readonly grid: {
             type: "boolean";
@@ -2908,6 +2914,11 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * short by the unmeasured bands.
      */
     getTrackYOffset(trackId: string): number | undefined;
+    /**
+     * #getter
+     * `getTrackYOffset` for every shown track, by trackId, from one walk
+     */
+    readonly trackYOffsets: Map<string, number>;
     /**
      * #method
      * the pinned or unpinned sibling list a track renders within; move
@@ -3209,24 +3220,6 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     toggleTrackSelector(): import("@jbrowse/core/util").Widget;
-    /**
-     * #method
-     * Helper method for the fetchSequence.
-     * Returns the regions the user selected with the
-     * rubberband
-     *
-     * @param leftOffset - `object as {start, end, index, offset}`, offset = start
-     * of user drag
-     * @param rightOffset - `object as {start, end, index, offset}`,
-     * offset = end of user drag
-     * @returns array of Region[]
-     */
-    getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
-        assemblyName: string;
-        refName: string;
-        start: number;
-        end: number;
-    }[];
     /**
      * #action
      */
@@ -3246,6 +3239,25 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
      * #action
      */
     setLaunch(launch?: LaunchInput<InitState>): void;
+} & {
+    /**
+     * #method
+     * Helper method for the fetchSequence.
+     * Returns the regions the user selected with the
+     * rubberband
+     *
+     * @param leftOffset - `object as {start, end, index, offset}`, offset = start
+     * of user drag
+     * @param rightOffset - `object as {start, end, index, offset}`,
+     * offset = end of user drag
+     * @returns array of Region[]
+     */
+    getSelectedRegions(leftOffset?: BpOffset, rightOffset?: BpOffset): {
+        assemblyName: string;
+        refName: string;
+        start: number;
+        end: number;
+    }[];
 } & {
     slide: (viewWidths: number) => void;
     zoom: (targetBpPerPx: number) => void;
@@ -4004,8 +4016,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     hideNoTracksActive: boolean;
     trackSelectorType: string;
     showCytobands: boolean;
-    trackLabels: string;
-    axis: import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, any>>;
+    trackLabels: "" | "hidden" | "offset" | "overlapping";
+    axis: import("@jbrowse/mobx-state-tree").ModelSnapshotType<Record<string, import("@jbrowse/mobx-state-tree").IAnyType>>;
     colorByFrame: boolean;
     showAminoAcids: boolean;
     showTrackOutlines: boolean;

package/esm/LinearGenomeView/model.js

@@ -17,6 +17,7 @@ import { assemblyErrorMessage, computeViewStatus, viewLoading, } from '@jbrowse/
 import { pendingLaunch, withLaunchInput, } from '@jbrowse/core/util/withLaunchInput';
 import { MIN_DISPLAY_HEIGHT } from '@jbrowse/display-kit/const';
 import { contentRightEdgePx } from '@jbrowse/display-kit/regionHost';
+import { VIEW_TRACK_LABEL_MODES } from '@jbrowse/display-kit/types';
 import { cast, getParent, getSnapshot, hasParent, isAlive, types, } from '@jbrowse/mobx-state-tree';
 import { observable, when } from 'mobx';
 import { fetchResults, handleSelectedRegion, isOpenInView, navToOption, } from '../searchUtils.js';
@@ -91,6 +92,11 @@ function canonicalHighlight(self, region) {
 }
 // bpPerPx deltas smaller than this are treated as no zoom change, avoiding
 // pointless offset re-anchoring on micro-steps
+// a stored mode this build does not know reads as unset, the plugin default
+function storedTrackLabels() {
+    const stored = localStorageGetItem('lgv-trackLabels');
+    return VIEW_TRACK_LABEL_MODES.find(mode => mode === stored) ?? '';
+}
 const BP_PER_PX_EPSILON = 0.000001;
 // px of blank space a view may scroll past either end of its regions, enough to
 // read as an edge and too little to lose the content
@@ -165,16 +171,17 @@ function openTrackSelectorWidget(self) {
     throw new Error('session does not support widgets');
 }
 /**
- * Whether the track selector is the drawer widget on screen right now. One
+ * Whether the drawer is showing this view's track selector right now. One
  * spelling for the `isTrackSelectorOpen` getter (which lights up the header
- * button) and for `toggleTrackSelector` (which decides hide-vs-show) — the
- * `!minimized` term is exactly the kind of thing that goes into one of two
- * hand-written copies and not the other.
+ * button) and for `toggleTrackSelector` (which decides hide-vs-show). The
+ * widget id is shared by every view, so the selector's `view` is what says
+ * whose it is.
  */
 function isTrackSelectorVisible(self) {
     const session = getSession(self);
     return (isSessionModelWithWidgets(session) &&
         session.visibleWidget?.id === TRACK_SELECTOR_WIDGET_ID &&
+        session.visibleWidget.view?.id === self.id &&
         !session.minimized);
 }
 /**
@@ -327,7 +334,7 @@ export function stateModelFactory(pluginManager) {
          * https://jbrowse.org/jb2/docs/config/lineargenomeviewconfigschema/ for
          * how the config is used
          */
-        trackLabels: types.optional(types.string, () => localStorageGetItem('lgv-trackLabels') ?? ''),
+        trackLabels: types.optional(types.enumeration('ViewTrackLabels', ['', ...VIEW_TRACK_LABEL_MODES]), () => storedTrackLabels()),
         /**
          * #property
          * The ruler's guide, a [](/docs/config/lineargenomeviewaxis) object:
@@ -919,15 +926,21 @@ export function stateModelFactory(pluginManager) {
          * short by the unmeasured bands.
          */
         getTrackYOffset(trackId) {
+            return this.trackYOffsets.get(trackId);
+        },
+        /**
+         * #getter
+         * `getTrackYOffset` for every shown track, by trackId, from one walk
+         */
+        get trackYOffsets() {
+            const offsets = new Map();
             let y = this.headerHeight + this.scalebarHeight + this.trackLeadingChrome;
             for (const t of [...self.pinnedTracks, ...self.unpinnedTracks]) {
                 y += this.trackLabelBand(t);
-                if (t.configuration.trackId === trackId) {
-                    return y;
-                }
+                offsets.set(t.configuration.trackId, y);
                 y += this.trackHeight(t) + this.trackChromeHeight;
             }
-            return undefined;
+            return offsets;
         },
         /**
          * #method
@@ -1518,8 +1531,9 @@ export function stateModelFactory(pluginManager) {
          * #action
          */
         toggleTrackSelector() {
+            const wasVisible = isTrackSelectorVisible(self);
             const { session, selector } = openTrackSelectorWidget(self);
-            if (isTrackSelectorVisible(self)) {
+            if (wasVisible) {
                 session.hideWidget(selector);
             }
             else {
@@ -1527,40 +1541,6 @@ export function stateModelFactory(pluginManager) {
             }
             return selector;
         },
-        /**
-         * #method
-         * Helper method for the fetchSequence.
-         * Returns the regions the user selected with the
-         * rubberband
-         *
-         * @param leftOffset - `object as {start, end, index, offset}`, offset = start
-         * of user drag
-         * @param rightOffset - `object as {start, end, index, offset}`,
-         * offset = end of user drag
-         * @returns array of Region[]
-         */
-        getSelectedRegions(leftOffset, rightOffset) {
-            if (!leftOffset || !rightOffset) {
-                return [];
-            }
-            const layout = {
-                displayedRegions: self.displayedRegions,
-                bpPerPx: self.bpPerPx,
-                offsetPx: self.offsetPx,
-                width: self.width,
-                minimumBlockWidth: self.minimumBlockWidth,
-            };
-            const { bpPerPx, offsetPx: rawOffsetPx } = computeMoveToLayout(layout, leftOffset, rightOffset);
-            // mirror Base1DView.scrollTo clamping: raw offsetPx can be far outside
-            // the valid range when both offsets are oob on the same side
-            const { min, max } = offsetBounds(self.totalBp / bpPerPx, self.width);
-            const offsetPx = clamp(rawOffsetPx, min, max);
-            return wholeBaseRegions(calculateDynamicBlocks({
-                ...layout,
-                bpPerPx,
-                offsetPx,
-            }).contentBlocks);
-        },
         /**
          * #action
          */
@@ -1605,6 +1585,42 @@ export function stateModelFactory(pluginManager) {
         setLaunch(launch) {
             self.launch = launch;
         },
+    }))
+        .views(self => ({
+        /**
+         * #method
+         * Helper method for the fetchSequence.
+         * Returns the regions the user selected with the
+         * rubberband
+         *
+         * @param leftOffset - `object as {start, end, index, offset}`, offset = start
+         * of user drag
+         * @param rightOffset - `object as {start, end, index, offset}`,
+         * offset = end of user drag
+         * @returns array of Region[]
+         */
+        getSelectedRegions(leftOffset, rightOffset) {
+            if (!leftOffset || !rightOffset) {
+                return [];
+            }
+            const layout = {
+                displayedRegions: self.displayedRegions,
+                bpPerPx: self.bpPerPx,
+                offsetPx: self.offsetPx,
+                width: self.width,
+                minimumBlockWidth: self.minimumBlockWidth,
+            };
+            const { bpPerPx, offsetPx: rawOffsetPx } = computeMoveToLayout(layout, leftOffset, rightOffset);
+            // mirror Base1DView.scrollTo clamping: raw offsetPx can be far outside
+            // the valid range when both offsets are oob on the same side
+            const { min, max } = offsetBounds(self.totalBp / bpPerPx, self.width);
+            const offsetPx = clamp(rawOffsetPx, min, max);
+            return wholeBaseRegions(calculateDynamicBlocks({
+                ...layout,
+                bpPerPx,
+                offsetPx,
+            }).contentBlocks);
+        },
     }))
         .actions(self => {
         let cancelLastSlide = () => { };
@@ -2381,9 +2397,13 @@ export function stateModelFactory(pluginManager) {
             // [minOffset, maxOffset]. scrollTo is called explicitly rather than
             // left to zoomTo's internal scrollTo, which is skipped when bpPerPx
             // is already in range — shrinking the region set would otherwise
-            // strand the view scrolled past the end, on blank space.
-            self.zoomTo(self.bpPerPx);
-            self.scrollTo(self.offsetPx);
+            // strand the view scrolled past the end, on blank space. An unmeasured
+            // view has no bounds to clamp to, and keeps its window as a restored
+            // snapshot does.
+            if (self.bpPerPx > 0) {
+                self.zoomTo(self.bpPerPx);
+                self.scrollTo(self.offsetPx);
+            }
             self.settleCoarseBlocks();
         },
         /**
@@ -2765,10 +2785,11 @@ export function stateModelFactory(pluginManager) {
          */
         nonGenomicTrackBands() {
             const y0 = self.headerHeight + self.scalebarHeight;
+            const { trackYOffsets } = self;
             return [...self.pinnedTracks, ...self.unpinnedTracks].flatMap(track => {
-                const display = track.activeDisplay;
-                const top = self.getTrackYOffset(track.configuration.trackId);
-                return display.drawsGenomicCoordinates === false && top !== undefined
+                const top = trackYOffsets.get(track.configuration.trackId);
+                return track.activeDisplay.drawsGenomicCoordinates === false &&
+                    top !== undefined
                     ? [{ top: top - y0, height: self.trackHeight(track) }]
                     : [];
             });

package/esm/LinearGenomeView/rExport/exportLinearView.d.ts

@@ -1,4 +1,8 @@
 import type { LinearGenomeViewModel } from '../model.ts';
+export declare function recordsDrawnAlone(display: object): {
+    height: number;
+    fits: boolean;
+} | undefined;
 /** The R script that redraws the tracks open in the view, over its visible regions. */
 export declare function exportLinearViewToR(view: LinearGenomeViewModel, out?: string): {
     drawn: number;

package/esm/LinearGenomeView/rExport/exportLinearView.js

@@ -1,4 +1,5 @@
 import { fullConfSnapshot, readConfObject } from '@jbrowse/core/configuration';
+import { svgTrackName } from '@jbrowse/core/svg/trackNames';
 import { getSession } from '@jbrowse/core/util';
 import { getSnapshot } from '@jbrowse/mobx-state-tree';
 import { exportTracksToR } from './rScript.js';
@@ -40,22 +41,41 @@ function assemblyOf(view) {
         ? getSnapshot(configuration)
         : undefined;
 }
+// The variant display drawing no genotype rows (none in the file, or hidden)
+// states, as `recordsAlone`, its records as the feature track R reads them
+// as: the height they draw at, and whether they fit into it whatever the
+// track's `heightMode`.
+export function recordsDrawnAlone(display) {
+    const alone = 'recordsAlone' in display ? display.recordsAlone : undefined;
+    return typeof alone === 'object' &&
+        alone !== null &&
+        'height' in alone &&
+        typeof alone.height === 'number' &&
+        'fits' in alone &&
+        typeof alone.fits === 'boolean'
+        ? { height: alone.height, fits: alone.fits }
+        : undefined;
+}
+// The tracks the screen draws, in the order it draws them, named as the SVG
+// export names them: pinned first, minimized ones left out.
 function tracksOf(view) {
+    const session = getSession(view);
     const tracks = [];
-    for (const track of view.tracks) {
+    for (const track of [...view.pinnedTracks, ...view.unpinnedTracks]) {
         const display = track.displays[0];
-        if (display) {
+        if (display && !track.minimized) {
             const { type, displayId, ...written } = getSnapshot(display.configuration);
             const { heightMode, height } = fullConfSnapshot(display.configuration);
+            const records = recordsDrawnAlone(display);
             tracks.push({
                 trackId: track.configuration.trackId,
-                trackName: readConfObject(track.configuration, 'name') ||
-                    track.configuration.trackId,
+                trackName: svgTrackName(track, session),
                 displayType: display.type,
                 adapter: readConfObject(track.configuration, 'adapter'),
                 display: written,
-                heightMode,
-                height,
+                heightMode: records?.fits ? 'fit' : heightMode,
+                height: records ? records.height : height,
+                recordsOnly: records !== undefined,
             });
         }
     }

package/esm/LinearGenomeView/rExport/rScript.d.ts

@@ -14,21 +14,30 @@ export interface RExportTrack {
     /** The display's resolved sizing, which a feature track exports so the figure drops what the view drops. */
     heightMode?: unknown;
     height?: unknown;
+    /** A variant display drawing its records alone, its genotype rows absent or hidden, which reads as a feature track. */
+    recordsOnly?: boolean;
+}
+interface ReaderAdapter {
+    slot?: string;
+    ext?: RegExp;
+    index?: string;
 }
 /**
  * Each display ggjbrowse reads, by the reader that reads it, and the adapters
- * it opens (the slot holding the file and the extension the reader knows it
- * by).
+ * it opens: the slot holding the file, the extension the reader knows it by,
+ * and the suffix of the index the reader looks for beside it.
  */
 export declare const READERS: Record<string, {
     call: string;
-    adapters: Record<string, {
-        slot?: string;
-        ext?: RegExp;
-    }>;
+    /** The reader for the display drawing no sample rows, its records alone. */
+    recordsOnlyCall?: string;
+    adapters: Record<string, ReaderAdapter>;
 }>;
-/** The ggjbrowse release whose readers and `jbrowse_stack` the script calls. */
-export declare const GGJBROWSE_VERSION = "0.10.0";
+/**
+ * The ggjbrowse release the script is tested against: its floor, and the tag
+ * its install line pins. The R export workflow installs this tag on a push.
+ */
+export declare const GGJBROWSE_VERSION = "0.11.0";
 /**
  * A resolved config writes an unset slot as `''`, `[]` or `{}`, which a reader
  * would take for a setting. Keeps `false` and `0`, which are values.
@@ -81,7 +90,7 @@ export declare function exportTracksToR({ tracks, regions, assembly: assemblySna
     /** The view's assembly config as written, which names its sequence and its contigs' aliases. */
     assembly?: Record<string, unknown>;
     /** The view's zoom, which decides what a feature or quantitative display shows. */
-    bpPerPx?: number;
+    bpPerPx: number;
     /** The view's "CDS reading frame colors", which a feature track takes. */
     colorByFrame?: boolean;
     /** The view's "Amino acids when zoomed in", which a feature track takes. */
@@ -98,3 +107,4 @@ export declare function exportTracksToR({ tracks, regions, assembly: assemblySna
     script: string;
     notes: string[];
 };
+export {};