@jbrowse/plugin-alignments 4.0.4 → 4.1.3

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -87,8 +87,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
     descriptions: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 }>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & import("@jbrowse/mobx-state-tree")._NotCustomized, {
-    id: string;
     type: "BaseFeatureWidget";
+    id: string;
     track: import("@jbrowse/mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("@jbrowse/mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;

package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts

@@ -14,7 +14,7 @@ export default class CramSlightlyLazyFeature implements Feature {
     get flags(): number;
     get strand(): 1 | -1;
     get qual(): string;
-    get qualRaw(): number[] | null | undefined;
+    get qualRaw(): Uint8Array<ArrayBufferLike> | null | undefined;
     get refName(): string;
     get pair_orientation(): string | null | undefined;
     get template_length(): number | undefined;

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -5,7 +5,7 @@ import { SimpleFeature, getContainingTrack, getContainingView, getSession, isSes
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { cast, isAlive, types } from '@jbrowse/mobx-state-tree';
 import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
-import FilterListIcon from '@mui/icons-material/ClearAll';
+import ClearAllIcon from '@mui/icons-material/ClearAll';
 import ContentCopyIcon from '@mui/icons-material/ContentCopy';
 import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 import VisibilityIcon from '@mui/icons-material/Visibility';
@@ -459,7 +459,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                     },
                     {
                         label: 'Filter by...',
-                        icon: FilterListIcon,
+                        icon: ClearAllIcon,
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
                                 FilterByTagDialog,

package/esm/LinearPileupDisplay/components/GroupByDialog.js

@@ -1,27 +1,115 @@
-import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { jsxs as _jsxs, jsx as _jsx, Fragment as _Fragment } from "react/jsx-runtime";
 import { useEffect, useState } from 'react';
 import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
 import { getContainingTrack, getContainingView, getSession, useDebounce, } from '@jbrowse/core/util';
-import { getSnapshot } from '@jbrowse/mobx-state-tree';
+import { getSnapshot, isStateTreeNode } from '@jbrowse/mobx-state-tree';
 import { Button, DialogActions, DialogContent, MenuItem, TextField, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { getUniqueTags } from "../../shared/getUniqueTags.js";
 import { defaultFilterFlags, negFlags, posFlags } from "../../shared/util.js";
+const TAG_REGEX = /^[A-Za-z][A-Za-z0-9]$/;
+function TagResults({ tag, tagSet }) {
+    if (tagSet.length === 0) {
+        return (_jsxs(Typography, { color: "warning.main", children: ["No values found for tag ", tag, " in the current region"] }));
+    }
+    return (_jsxs("div", { children: [_jsxs("div", { children: ["Found unique ", tag, " values:"] }), _jsx("div", { children: tagSet.join(', ') })] }));
+}
+function createTrackId(baseId, suffix) {
+    return `${baseId}-${suffix}-${Date.now()}-sessionTrack`;
+}
+function createTagBasedTracks({ trackConf, tag, tagSet, session, view, }) {
+    const values = [...tagSet, undefined];
+    for (const tagValue of values) {
+        const trackId = createTrackId(trackConf.trackId, `${tag}:${tagValue}`);
+        session.addTrackConf({
+            ...trackConf,
+            trackId,
+            name: `${trackConf.name} (${tag}:${tagValue})`,
+            displays: [
+                {
+                    displayId: `${trackId}-LinearAlignmentsDisplay`,
+                    type: 'LinearAlignmentsDisplay',
+                    pileupDisplay: {
+                        displayId: `${trackId}-LinearAlignmentsDisplay-LinearPileupDisplay`,
+                        type: 'LinearPileupDisplay',
+                        filterBy: {
+                            ...defaultFilterFlags,
+                            tagFilter: {
+                                tag,
+                                value: tagValue,
+                            },
+                        },
+                    },
+                },
+            ],
+        });
+        view.showTrack(trackId);
+    }
+}
+function createStrandBasedTracks({ trackConf, session, view, }) {
+    const negTrackId = createTrackId(trackConf.trackId, 'strand:(-)');
+    const posTrackId = createTrackId(trackConf.trackId, 'strand:(+)');
+    session.addTrackConf({
+        ...trackConf,
+        trackId: negTrackId,
+        name: `${trackConf.name} (-)`,
+        displays: [
+            {
+                displayId: `${negTrackId}-LinearAlignmentsDisplay`,
+                type: 'LinearAlignmentsDisplay',
+                pileupDisplay: {
+                    displayId: `${negTrackId}-LinearAlignmentsDisplay-LinearPileupDisplay`,
+                    type: 'LinearPileupDisplay',
+                    filterBy: negFlags,
+                },
+            },
+            {
+                displayId: `${negTrackId}-LinearSNPCoverageDisplay`,
+                type: 'LinearSNPCoverageDisplay',
+                filterBy: negFlags,
+            },
+        ],
+    });
+    session.addTrackConf({
+        ...trackConf,
+        trackId: posTrackId,
+        name: `${trackConf.name} (+)`,
+        displays: [
+            {
+                displayId: `${posTrackId}-LinearAlignmentsDisplay`,
+                type: 'LinearAlignmentsDisplay',
+                pileupDisplay: {
+                    displayId: `${posTrackId}-LinearAlignmentsDisplay-LinearPileupDisplay`,
+                    type: 'LinearPileupDisplay',
+                    filterBy: posFlags,
+                },
+            },
+            {
+                displayId: `${posTrackId}-LinearSNPCoverageDisplay`,
+                type: 'LinearSNPCoverageDisplay',
+                filterBy: posFlags,
+            },
+        ],
+    });
+    view.showTrack(negTrackId);
+    view.showTrack(posTrackId);
+}
 const GroupByTagDialog = observer(function GroupByTagDialog(props) {
     const { model, handleClose } = props;
     const [tag, setGroupByTag] = useState('');
     const [tagSet, setGroupByTagSet] = useState();
     const [loading, setLoading] = useState(false);
     const [error, setError] = useState();
-    const validTag = /^[A-Za-z][A-Za-z0-9]$/.exec(tag);
+    const validTag = TAG_REGEX.exec(tag);
     const isInvalid = tag.length === 2 && !validTag;
     const debouncedTag = useDebounce(tag, 1000);
     const [type, setType] = useState('');
     useEffect(() => {
         ;
         (async () => {
-            try {
-                if (!isInvalid) {
+            const isValidTag = TAG_REGEX.test(debouncedTag);
+            if (type === 'tag' && isValidTag) {
+                try {
                     setError(undefined);
                     setLoading(true);
                     const vals = await getUniqueTags({
@@ -32,16 +120,23 @@ const GroupByTagDialog = observer(function GroupByTagDialog(props) {
                     });
                     setGroupByTagSet(vals);
                 }
-            }
-            catch (e) {
-                console.error(e);
-                setError(e);
-            }
-            finally {
-                setLoading(false);
+                catch (e) {
+                    console.error(e);
+                    setError(e);
+                }
+                finally {
+                    setLoading(false);
+                }
             }
         })();
-    }, [model, isInvalid, debouncedTag]);
+    }, [model, type, debouncedTag]);
+    useEffect(() => {
+        if (type !== 'tag') {
+            setGroupByTagSet(undefined);
+            setError(undefined);
+            setLoading(false);
+        }
+    }, [type]);
     return (_jsxs(Dialog, { open: true, onClose: handleClose, title: "Group by", children: [_jsxs(DialogContent, { children: [_jsx(Typography, { children: "NOTE: this will create new session tracks with the \"filter by\" set to the values chosen here rather than affecting the current track state" }), _jsxs(TextField, { fullWidth: true, value: type, onChange: event => {
                             setType(event.target.value);
                         }, label: "Group by...", select: true, children: [_jsx(MenuItem, { value: "strand", children: "Strand" }), _jsx(MenuItem, { value: "tag", children: "Tag" })] }), type === 'tag' ? (_jsxs(_Fragment, { children: [_jsx(Typography, { color: "textSecondary", children: "Examples: HP for haplotype, RG for read group, etc." }), _jsx(TextField, { value: tag, onChange: event => {
@@ -51,93 +146,32 @@ const GroupByTagDialog = observer(function GroupByTagDialog(props) {
                                         maxLength: 2,
                                         'data-testid': 'group-tag-name-input',
                                     },
-                                } }), error ? (_jsx(ErrorMessage, { error: error })) : loading ? (_jsx(LoadingEllipses, { message: "Loading unique tags" })) : tagSet ? (_jsxs("div", { children: [_jsxs("div", { children: ["Found unique ", tag, " values:"] }), _jsx("div", { children: tagSet.join(', ') })] })) : null] })) : null] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "primary", type: "submit", disabled: !tagSet, autoFocus: true, onClick: () => {
+                                } }), error ? (_jsx(ErrorMessage, { error: error })) : loading ? (_jsx(LoadingEllipses, { message: "Loading unique tags" })) : tagSet ? (_jsx(TagResults, { tag: tag, tagSet: tagSet })) : null] })) : null] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "primary", type: "submit", disabled: !type ||
+                            loading ||
+                            (type === 'tag' && (!tagSet || tagSet.length === 0)), autoFocus: true, onClick: () => {
                             const track = getContainingTrack(model);
-                            const trackConf = structuredClone(getSnapshot(track.configuration));
+                            const trackConf = isStateTreeNode(track.configuration)
+                                ? structuredClone(getSnapshot(track.configuration))
+                                : track.configuration;
                             const session = getSession(model);
                             const view = getContainingView(model);
-                            if (type === 'tag') {
-                                if (tagSet) {
-                                    const ret = [...tagSet, undefined];
-                                    for (const tagValue of ret) {
-                                        const t1 = `${trackConf.trackId}-${tag}:${tagValue}-${Date.now()}-sessionTrack`;
-                                        session.addTrackConf({
-                                            ...trackConf,
-                                            trackId: t1,
-                                            name: `${trackConf.name} (${tag}:${tagValue})`,
-                                            displays: [
-                                                {
-                                                    displayId: `${t1}-LinearAlignmentsDisplay`,
-                                                    type: 'LinearAlignmentsDisplay',
-                                                    pileupDisplay: {
-                                                        displayId: `${t1}-LinearAlignmentsDisplay-LinearPileupDisplay`,
-                                                        type: 'LinearPileupDisplay',
-                                                        filterBy: {
-                                                            ...defaultFilterFlags,
-                                                            tagFilter: {
-                                                                tag,
-                                                                value: tagValue,
-                                                            },
-                                                        },
-                                                    },
-                                                },
-                                            ],
-                                        });
-                                        view.showTrack(t1);
-                                    }
-                                }
+                            if (type === 'tag' && tagSet) {
+                                createTagBasedTracks({
+                                    trackConf,
+                                    tag,
+                                    tagSet,
+                                    session,
+                                    view,
+                                });
                             }
                             else if (type === 'strand') {
-                                const t1 = `${trackConf.trackId}-${tag}:(-)-${Date.now()}-sessionTrack`;
-                                const t2 = `${trackConf.trackId}-${tag}:(+)-${Date.now()}-sessionTrack`;
-                                session.addTrackConf({
-                                    ...trackConf,
-                                    trackId: t1,
-                                    name: `${trackConf.name} (-)`,
-                                    displays: [
-                                        {
-                                            displayId: `${t1}-LinearAlignmentsDisplay`,
-                                            type: 'LinearAlignmentsDisplay',
-                                            pileupDisplay: {
-                                                displayId: `${t1}-LinearAlignmentsDisplay-LinearPileupDisplay`,
-                                                type: 'LinearPileupDisplay',
-                                                filterBy: negFlags,
-                                            },
-                                        },
-                                        {
-                                            displayId: `${t1}-LinearSNPCoverageDisplay`,
-                                            type: 'LinearSNPCoverageDisplay',
-                                            filterBy: negFlags,
-                                        },
-                                    ],
+                                createStrandBasedTracks({
+                                    trackConf,
+                                    session,
+                                    view,
                                 });
-                                session.addTrackConf({
-                                    ...trackConf,
-                                    trackId: t2,
-                                    name: `${trackConf.name} (+)`,
-                                    displays: [
-                                        {
-                                            displayId: `${t2}-LinearAlignmentsDisplay`,
-                                            type: 'LinearAlignmentsDisplay',
-                                            pileupDisplay: {
-                                                displayId: `${t2}-LinearAlignmentsDisplay-LinearPileupDisplay`,
-                                                type: 'LinearPileupDisplay',
-                                                filterBy: posFlags,
-                                            },
-                                        },
-                                        {
-                                            displayId: `${t2}-LinearSNPCoverageDisplay`,
-                                            type: 'LinearSNPCoverageDisplay',
-                                            filterBy: posFlags,
-                                        },
-                                    ],
-                                });
-                                view.showTrack(t1);
-                                view.showTrack(t2);
                             }
                             handleClose();
-                        }, children: "Submit" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
+                        }, children: "Submit" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: handleClose, children: "Cancel" })] })] }));
 });
 export default GroupByTagDialog;

package/esm/LinearReadArcsDisplay/model.d.ts

@@ -233,19 +233,24 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     loading: boolean;
     lastDrawnOffsetPx: number | undefined;
+    lastDrawnBpPerPx: number | undefined;
     ref: HTMLCanvasElement | null;
     renderingImageData: ImageBitmap | undefined;
     renderingStopToken: import("@jbrowse/core/util").StopToken | undefined;
     statusMessage: string | undefined;
+    canvasDrawn: boolean;
 } & {
     readonly drawn: boolean;
+    readonly fullyDrawn: boolean;
 } & {
     setLastDrawnOffsetPx(n: number): void;
+    setLastDrawnBpPerPx(n: number): void;
     setLoading(f: boolean): void;
     setRef(ref: HTMLCanvasElement | null): void;
     setRenderingImageData(imageData: ImageBitmap | undefined): void;
     setRenderingStopToken(token?: import("@jbrowse/core/util").StopToken): void;
     setStatusMessage(msg?: string): void;
+    setCanvasDrawn(drawn: boolean): void;
 } & {
     beforeDestroy(): void;
 } & {

package/esm/LinearReadCloudDisplay/components/LinearReadCloudReactComponent.js

@@ -236,17 +236,16 @@ const Cloud = observer(function Cloud({ model, }) {
             width,
             height,
             cursor: hasHover ? 'pointer' : undefined,
-        }, onMouseMove: onMouseMove, onMouseLeave: onMouseLeave, onClick: onClick, children: [_jsx(CloudCanvases, { model: model, width: width, height: height }), _jsx(FeatureHighlights, { selectedFeatureBounds: selectedFeatureBounds, hoveredFeature: hoveredFeature }), model.drawCloud && model.cloudTicks ? (_jsx("svg", { style: {
+        }, onMouseMove: onMouseMove, onMouseLeave: onMouseLeave, onClick: onClick, children: [_jsx(CloudCanvases, { model: model, width: width, height: height }), _jsx(FeatureHighlights, { selectedFeatureBounds: selectedFeatureBounds, hoveredFeature: hoveredFeature }), hoveredMismatchData && mousePosition ? (_jsx(MismatchTooltip, { mismatchData: hoveredMismatchData, mousePosition: mousePosition })) : hoveredFeatureData && mousePosition ? (_jsx(FeatureTooltip, { hoveredFeatureData: hoveredFeatureData, hasSupplementary: hoveredHasSupplementary, mousePosition: mousePosition })) : null] }));
+});
+const LinearReadCloudReactComponent = observer(function LinearReadCloudReactComponent({ model, }) {
+    return (_jsxs("div", { children: [_jsx(BaseDisplayComponent, { model: model, children: _jsx(Cloud, { model: model }) }), model.drawCloud && model.cloudTicks ? (_jsx("svg", { style: {
                     position: 'absolute',
                     top: 0,
                     left: 50,
                     pointerEvents: 'none',
                     height: model.cloudTicks.height,
-                    width: 60,
-                    zIndex: 100,
-                }, children: _jsx("g", { transform: "translate(55, 0)", children: _jsx(CloudYScaleBar, { model: model, orientation: "left" }) }) })) : null, hoveredMismatchData && mousePosition ? (_jsx(MismatchTooltip, { mismatchData: hoveredMismatchData, mousePosition: mousePosition })) : hoveredFeatureData && mousePosition ? (_jsx(FeatureTooltip, { hoveredFeatureData: hoveredFeatureData, hasSupplementary: hoveredHasSupplementary, mousePosition: mousePosition })) : null] }));
-});
-const LinearReadCloudReactComponent = observer(function LinearReadCloudReactComponent({ model, }) {
-    return (_jsx(BaseDisplayComponent, { model: model, children: _jsx(Cloud, { model: model }) }));
+                    width: 50,
+                }, children: _jsx("g", { transform: "translate(45, 0)", children: _jsx(CloudYScaleBar, { model: model, orientation: "left" }) }) })) : null] }));
 });
 export default LinearReadCloudReactComponent;

package/esm/LinearReadCloudDisplay/model.d.ts

@@ -242,19 +242,24 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     loading: boolean;
     lastDrawnOffsetPx: number | undefined;
+    lastDrawnBpPerPx: number | undefined;
     ref: HTMLCanvasElement | null;
     renderingImageData: ImageBitmap | undefined;
     renderingStopToken: import("@jbrowse/core/util").StopToken | undefined;
     statusMessage: string | undefined;
+    canvasDrawn: boolean;
 } & {
     readonly drawn: boolean;
+    readonly fullyDrawn: boolean;
 } & {
     setLastDrawnOffsetPx(n: number): void;
+    setLastDrawnBpPerPx(n: number): void;
     setLoading(f: boolean): void;
     setRef(ref: HTMLCanvasElement | null): void;
     setRenderingImageData(imageData: ImageBitmap | undefined): void;
     setRenderingStopToken(token?: import("@jbrowse/core/util").StopToken): void;
     setStatusMessage(msg?: string): void;
+    setCanvasDrawn(drawn: boolean): void;
 } & {
     beforeDestroy(): void;
 } & {
@@ -311,8 +316,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly hideLargeIndels: any;
 } & {
     readonly modificationThreshold: any;
-    readonly cloudDomain: [number, number] | undefined;
-} & {
     readonly cloudTicks: import("../RenderLinearReadCloudDisplayRPC/drawFeatsCloud.ts").CloudTicks | undefined;
 } & {
     setNoSpacing(flag?: boolean): void;

package/esm/LinearReadCloudDisplay/model.js

@@ -68,19 +68,13 @@ function stateModelFactory(configSchema) {
         get modificationThreshold() {
             return self.colorBy?.modifications?.threshold ?? 10;
         },
-        get cloudDomain() {
-            if (self.cloudMaxDistance === undefined) {
-                return undefined;
-            }
-            return [1, self.cloudMaxDistance];
-        },
-    }))
-        .views(self => ({
         get cloudTicks() {
-            if (!self.drawCloud || !self.cloudDomain || !self.showYScalebar) {
+            if (!self.drawCloud ||
+                self.cloudMaxDistance === undefined ||
+                !self.showYScalebar) {
                 return undefined;
             }
-            return calculateCloudTicks(self.cloudDomain, self.height);
+            return calculateCloudTicks(self.cloudMaxDistance, self.height);
         },
     }))
         .actions(self => ({
@@ -166,7 +160,6 @@ function stateModelFactory(configSchema) {
                     hideMismatches: self.hideMismatches,
                     hideLargeIndels: self.hideLargeIndels,
                     showOutline: self.showOutline,
-                    cloudDomain: self.cloudDomain,
                     visibleModifications: Object.fromEntries(self.visibleModifications.toJSON()),
                 };
             },

package/esm/LinearReadCloudDisplay/renderSvg.js

@@ -37,11 +37,10 @@ export async function renderSvg(self, opts) {
     const visibleWidth = view.width;
     const clipId = `clip-${self.id}-svg`;
     const legendItems = self.showLegend ? self.legendItems() : [];
-    const cloudDomain = rendering.cloudMaxDistance !== undefined && self.drawCloud
-        ? [1, rendering.cloudMaxDistance]
-        : null;
-    const cloudTicks = cloudDomain && self.showYScalebar
-        ? calculateCloudTicks(cloudDomain, height)
+    const cloudTicks = rendering.cloudMaxDistance !== undefined &&
+        self.drawCloud &&
+        self.showYScalebar
+        ? calculateCloudTicks(rendering.cloudMaxDistance, height)
         : null;
     return (_jsxs(_Fragment, { children: [_jsx("defs", { children: _jsx("clipPath", { id: clipId, children: _jsx("rect", { x: 0, y: 0, width: visibleWidth, height: height }) }) }), _jsx("g", { clipPath: `url(#${clipId})`, children: _jsx("g", { transform: `translate(${Math.max(0, -view.offsetPx)} 0)`, children: _jsx(ReactRendering, { rendering: finalRendering }) }) }), cloudTicks ? (_jsx("g", { transform: `translate(${Math.max(-view.offsetPx, 0)})`, children: _jsx(CloudYScaleBar, { model: { cloudTicks }, orientation: "left" }) })) : null, legendItems.length > 0 ? (_jsx(SVGLegend, { items: legendItems, width: visibleWidth, legendAreaWidth: opts.legendWidth })) : null] }));
 }

package/esm/LinearSNPCoverageDisplay/model.js

@@ -4,7 +4,7 @@ import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/rendere
 import { getContainingView, getSession } from '@jbrowse/core/util';
 import { cast, getSnapshot, isAlive, types } from '@jbrowse/mobx-state-tree';
 import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle';
-import FilterListIcon from '@mui/icons-material/FilterList';
+import ClearAllIcon from '@mui/icons-material/ClearAll';
 import VisibilityIcon from '@mui/icons-material/Visibility';
 import { SharedModificationsMixin } from "../shared/SharedModificationsMixin.js";
 import { getUniqueModifications } from "../shared/getUniqueModifications.js";
@@ -268,7 +268,7 @@ function stateModelFactory(pluginManager, configSchema) {
                     },
                     {
                         label: 'Filter arcs by score...',
-                        icon: FilterListIcon,
+                        icon: ClearAllIcon,
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
                                 FilterArcsByScoreDialog,

package/esm/PileupRenderer/makeImageData.js

@@ -3,7 +3,7 @@ import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { createJBrowseTheme } from '@jbrowse/core/ui';
 import { renderToAbstractCanvas } from '@jbrowse/core/util';
 import Flatbush from '@jbrowse/core/util/flatbush';
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { layoutFeats } from "./layoutFeatures.js";
 import { renderAlignment } from "./renderers/renderAlignment.js";
 import { renderMismatchesCallback } from "./renderers/renderMismatchesCallback.js";
@@ -29,7 +29,7 @@ async function fetchRegionSequence(renderArgs, pluginManager) {
     });
 }
 function renderFeatures({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
-    const { stopToken, config, showSoftClip, colorBy, theme: configTheme, } = renderArgs;
+    const { stopTokenCheck, config, showSoftClip, colorBy, theme: configTheme, } = renderArgs;
     const mismatchAlpha = readConfObject(config, 'mismatchAlpha');
     const minSubfeatureWidth = readConfObject(config, 'minSubfeatureWidth');
     const largeInsertionIndicatorScale = readConfObject(config, 'largeInsertionIndicatorScale');
@@ -46,7 +46,6 @@ function renderFeatures({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
     const drawIndels = shouldDrawIndels();
     const coords = [];
     const items = [];
-    const lastCheck = createStopTokenChecker(stopToken);
     for (const feat of layoutRecords) {
         const alignmentRet = renderAlignment({
             ctx,
@@ -101,7 +100,7 @@ function renderFeatures({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
                 canvasWidth,
             });
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
     const flatbush = new Flatbush(Math.max(items.length, 1));
     if (coords.length) {

package/esm/RenderLinearReadArcsDisplayRPC/drawFeatsRPC.d.ts

@@ -1,4 +1,5 @@
 import type { ChainData, ColorBy } from '../shared/types.ts';
+import type { LastStopTokenCheck } from '@jbrowse/core/util';
 interface DrawFeatsRPCParams {
     ctx: CanvasRenderingContext2D;
     width: number;
@@ -18,7 +19,7 @@ interface DrawFeatsRPCParams {
         } | undefined;
     };
     offsetPx: number;
-    stopToken?: string;
+    stopTokenCheck?: LastStopTokenCheck;
 }
 export declare function drawFeatsRPC(params: DrawFeatsRPCParams): void;
 export {};

package/esm/RenderLinearReadArcsDisplayRPC/drawFeatsRPC.js

@@ -1,4 +1,4 @@
-import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
 import { featurizeSA, getTag } from "../MismatchParser/index.js";
 import { drawVerticalLine, extractCoreFeat, extractCoreFeatBasic, filterAndSortLongReadChain, filterPairedChain, getMateInfo, getStrandRelativeFirstClipLength, jitter, toCoreFeat, toCoreFeatBasic, } from "../shared/arcUtils.js";
 import { getPairedInsertSizeAndOrientationColor, getPairedInsertSizeColor, getPairedOrientationColor, } from "../shared/color.js";
@@ -63,7 +63,7 @@ function drawBezierArc(ctx, startX, endX, destY, jitterVal) {
     ctx.stroke();
 }
 export function drawFeatsRPC(params) {
-    const { ctx, height, chainData, colorBy, drawInter, drawLongRange, lineWidth, jitter: jitterVal, view, offsetPx, stopToken, } = params;
+    const { ctx, height, chainData, colorBy, drawInter, drawLongRange, lineWidth, jitter: jitterVal, view, offsetPx, stopTokenCheck, } = params;
     const { chains, stats } = chainData;
     const colorByType = colorBy.type;
     const hasPaired = hasPairedReads(chainData);
@@ -136,7 +136,6 @@ export function drawFeatsRPC(params) {
             draw(extractCoreFeat(filtered[i]), extractCoreFeatBasic(filtered[i + 1]), false);
         }
     }
-    const lastCheck = createStopTokenChecker(stopToken);
     for (const chain of chains) {
         if (chain.length === 1 && drawLongRange) {
             const f = chain[0];
@@ -151,6 +150,6 @@ export function drawFeatsRPC(params) {
         else {
             drawMultiFeatureChain(chain);
         }
-        checkStopToken2(lastCheck);
+        checkStopToken2(stopTokenCheck);
     }
 }

package/esm/RenderLinearReadArcsDisplayRPC/executeRenderLinearReadArcsDisplay.js

@@ -3,7 +3,7 @@ import { collectTransferables, dedupe, groupBy, max, min, renderToAbstractCanvas
 import { bpToPx } from '@jbrowse/core/util/Base1DUtils';
 import Base1DView from '@jbrowse/core/util/Base1DViewModel';
 import { rpcResult } from '@jbrowse/core/util/librpc';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { checkStopToken2, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
 import { getSnapshot } from '@jbrowse/mobx-state-tree';
 import { firstValueFrom } from 'rxjs';
 import { toArray } from 'rxjs/operators';
@@ -11,6 +11,7 @@ import { drawFeatsRPC } from "./drawFeatsRPC.js";
 import { getInsertSizeStats } from "../shared/insertSizeStats.js";
 export async function executeRenderLinearReadArcsDisplay({ pluginManager, args, }) {
     const { sessionId, view: viewSnapshot, adapterConfig, sequenceAdapter, colorBy, drawInter, drawLongRange, lineWidth, jitter, height, highResolutionScaling, exportSVG, statusCallback = () => { }, stopToken, } = args;
+    const stopTokenCheck = createStopTokenChecker(stopToken);
     const view = Base1DView.create(viewSnapshot);
     if (viewSnapshot.width) {
         view.setVolatileWidth(viewSnapshot.width);
@@ -39,7 +40,7 @@ export async function executeRenderLinearReadArcsDisplay({ pluginManager, args,
         dataAdapter.setSequenceAdapterConfig(sequenceAdapter);
     }
     const featuresArray = await updateStatus('Fetching alignments', statusCallback, () => firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe(toArray())));
-    checkStopToken(stopToken);
+    checkStopToken2(stopTokenCheck);
     const { chains, stats } = await updateStatus('Processing alignments', statusCallback, async () => {
         const deduped = dedupe(featuresArray, f => f.id());
         const filtered = deduped.filter(f => {
@@ -78,7 +79,7 @@ export async function executeRenderLinearReadArcsDisplay({ pluginManager, args,
         chains,
         stats,
     };
-    checkStopToken(stopToken);
+    checkStopToken2(stopTokenCheck);
     const renderOpts = {
         highResolutionScaling,
         exportSVG,
@@ -96,7 +97,7 @@ export async function executeRenderLinearReadArcsDisplay({ pluginManager, args,
             jitter,
             view: viewSnap,
             offsetPx,
-            stopToken,
+            stopTokenCheck,
         });
         return undefined;
     }));

package/esm/RenderLinearReadCloudDisplayRPC/RenderLinearReadCloudDisplay.d.ts

@@ -20,7 +20,6 @@ export interface RenderLinearReadCloudDisplayArgs {
     flipStrandLongReadChains: boolean;
     trackMaxHeight?: number;
     cloudModeHeight?: number;
-    cloudDomain?: [number, number];
     highResolutionScaling?: number;
     exportSVG?: {
         rasterizeLayers?: boolean;

package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCloud.d.ts

@@ -6,12 +6,11 @@ export interface CloudTicks {
         y: number;
     }[];
     height: number;
-    minDistance: number;
     maxDistance: number;
 }
-export declare function createCloudScale(minDistance: number, maxDistance: number, height: number): import("d3-scale").ScaleLogarithmic<number, number, never>;
-export declare function calculateCloudTicks(domain: [number, number], height: number): CloudTicks;
-export declare function calculateCloudYOffsetsUtil(computedChains: ComputedChain[], height: number, cloudDomain?: [number, number]): {
+export declare function createCloudScale(maxDistance: number, height: number): import("d3-scale").ScaleLogarithmic<number, number, never>;
+export declare function calculateCloudTicks(maxDistance: number, height: number): CloudTicks;
+export declare function calculateCloudYOffsetsUtil(computedChains: ComputedChain[], height: number): {
     chainYOffsets: Map<string, number>;
     cloudMaxDistance: number;
 };