npm - @jbrowse/plugin-alignments - Versions diffs - 4.0.3 → 4.1.1 - Mend

@jbrowse/plugin-alignments 4.0.3 → 4.1.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (27) hide show

package/esm/CramAdapter/CramSlightlyLazyFeature.d.ts CHANGED Viewed

@@ -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/LinearAlignmentsDisplay/model.d.ts CHANGED Viewed

@@ -64,6 +64,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -120,6 +121,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -173,6 +175,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts CHANGED Viewed

@@ -148,6 +148,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -204,6 +205,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -257,6 +259,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -538,6 +541,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -594,6 +598,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -647,6 +652,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -873,6 +879,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -929,6 +936,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -982,6 +990,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1114,10 +1123,18 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     setHideLargeIndels(arg: boolean): void;
 } & {
     copyFeatureToClipboard(feature: Feature): Promise<void>;
-    readonly rendererConfig: any;
+    readonly rendererConfig: {
+        height: any;
+        noSpacing: any;
+        maxHeight: any;
+        hideSmallIndels: any;
+        hideMismatches: any;
+        hideLargeIndels: any;
+    };
 } & {
     readonly maxHeight: any;
     readonly featureHeightSetting: any;
+    readonly noSpacingSetting: any;
     readonly featureUnderMouse: Feature | undefined;
     renderReady(): boolean;
     readonly filters: SerializableFilterChain;
@@ -1207,6 +1224,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1260,6 +1278,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js CHANGED Viewed

@@ -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';
@@ -52,6 +52,9 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
     }))
         .views(self => ({
         get autorunReady() {
+            if (self.isMinimized) {
+                return false;
+            }
             const view = getContainingView(self);
             return (view.initialized && self.featureDensityStatsReadyAndRegionNotTooLarge);
         },
@@ -152,25 +155,27 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
             session.notify('Copied to clipboard', 'success');
         },
         get rendererConfig() {
-            const { featureHeight: height, noSpacing, hideSmallIndels, hideMismatches, hideLargeIndels, trackMaxHeight: maxHeight, rendererTypeName, } = self;
-            const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};
+            const { featureHeight, noSpacing, hideSmallIndels, hideMismatches, hideLargeIndels, trackMaxHeight, rendererTypeName, } = self;
+            const conf = self.configuration.renderers?.[rendererTypeName];
             return {
-                ...configBlob,
-                ...(hideSmallIndels !== undefined ? { hideSmallIndels } : {}),
-                ...(hideMismatches !== undefined ? { hideMismatches } : {}),
-                ...(hideLargeIndels !== undefined ? { hideLargeIndels } : {}),
-                ...(height !== undefined ? { height } : {}),
-                ...(noSpacing !== undefined ? { noSpacing } : {}),
-                ...(maxHeight !== undefined ? { maxHeight } : {}),
+                height: featureHeight ?? readConfObject(conf, 'height'),
+                noSpacing: noSpacing ?? readConfObject(conf, 'noSpacing'),
+                maxHeight: trackMaxHeight ?? readConfObject(conf, 'maxHeight'),
+                hideSmallIndels: hideSmallIndels ?? readConfObject(conf, 'hideSmallIndels'),
+                hideMismatches: hideMismatches ?? readConfObject(conf, 'hideMismatches'),
+                hideLargeIndels: hideLargeIndels ?? readConfObject(conf, 'hideLargeIndels'),
             };
         },
     }))
         .views(self => ({
         get maxHeight() {
-            return readConfObject(self.rendererConfig, 'maxHeight');
+            return self.rendererConfig.maxHeight;
         },
         get featureHeightSetting() {
-            return readConfObject(self.rendererConfig, 'height');
+            return self.rendererConfig.height;
+        },
+        get noSpacingSetting() {
+            return self.rendererConfig.noSpacing;
         },
         get featureUnderMouse() {
             return self.featureUnderMouseVolatile;
@@ -391,7 +396,8 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                             {
                                 label: 'Normal',
                                 type: 'radio',
-                                checked: self.featureHeight === 7 && self.noSpacing === false,
+                                checked: self.featureHeightSetting === 7 &&
+                                    self.noSpacingSetting === false,
                                 onClick: () => {
                                     self.setFeatureHeight(7);
                                     self.setNoSpacing(false);
@@ -400,7 +406,8 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                             {
                                 label: 'Compact',
                                 type: 'radio',
-                                checked: self.featureHeight === 2 && self.noSpacing === true,
+                                checked: self.featureHeightSetting === 2 &&
+                                    self.noSpacingSetting === true,
                                 onClick: () => {
                                     self.setFeatureHeight(2);
                                     self.setNoSpacing(true);
@@ -409,7 +416,8 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                             {
                                 label: 'Super-compact',
                                 type: 'radio',
-                                checked: self.featureHeight === 1 && self.noSpacing === true,
+                                checked: self.featureHeightSetting === 1 &&
+                                    self.noSpacingSetting === true,
                                 onClick: () => {
                                     self.setFeatureHeight(1);
                                     self.setNoSpacing(true);
@@ -451,7 +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 CHANGED Viewed

@@ -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/LinearPileupDisplay/doAfterAttach.js CHANGED Viewed

@@ -5,21 +5,21 @@ import { setupModificationsAutorun } from "../shared/setupModificationsAutorun.j
 import { createAutorun } from "../util.js";
 export function doAfterAttach(model) {
     createAutorun(model, async () => {
-        const view = getContainingView(model);
         if (!model.autorunReady) {
             return;
         }
+        const view = getContainingView(model);
         model.setCurrSortBpPerPx(view.bpPerPx);
     }, {
         delay: 1000,
         name: 'CurrBpPerPx',
     });
     createAutorun(model, async () => {
-        const { rpcManager } = getSession(model);
-        const view = getContainingView(model);
         if (!model.autorunReady) {
             return;
         }
+        const { rpcManager } = getSession(model);
+        const view = getContainingView(model);
         const { sortedBy, adapterConfig, rendererType, sortReady } = model;
         const { bpPerPx } = view;
         if (sortedBy && (!sortReady || model.currSortBpPerPx === view.bpPerPx)) {

package/esm/LinearPileupDisplay/model.d.ts CHANGED Viewed

@@ -151,6 +151,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -207,6 +208,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -260,6 +262,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -541,6 +544,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -597,6 +601,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -650,6 +655,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -876,6 +882,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & {
@@ -932,6 +939,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -985,6 +993,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
                     }> | null;
                     readonly adapterConfig: any;
                     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+                    readonly isMinimized: boolean;
                     readonly parentDisplay: any;
                     readonly effectiveRpcDriverName: any;
                 }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1117,10 +1126,18 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     setHideLargeIndels(arg: boolean): void;
 } & {
     copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): Promise<void>;
-    readonly rendererConfig: any;
+    readonly rendererConfig: {
+        height: any;
+        noSpacing: any;
+        maxHeight: any;
+        hideSmallIndels: any;
+        hideMismatches: any;
+        hideLargeIndels: any;
+    };
 } & {
     readonly maxHeight: any;
     readonly featureHeightSetting: any;
+    readonly noSpacingSetting: any;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
     renderReady(): boolean;
     readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
@@ -1210,6 +1227,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -1263,6 +1281,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -1351,7 +1370,15 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     reload(): void;
 } & {
     readonly modificationThreshold: any;
-    readonly rendererConfig: any;
+    readonly rendererConfig: {
+        height: any;
+        noSpacing: any;
+        maxHeight: any;
+        mismatchAlpha: any;
+        hideSmallIndels: any;
+        hideMismatches: any;
+        hideLargeIndels: any;
+    };
 } & {
     readonly mismatchAlphaSetting: any;
     renderReady(): boolean;

package/esm/LinearPileupDisplay/model.js CHANGED Viewed

@@ -1,5 +1,5 @@
 import { lazy } from 'react';
-import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
+import { ConfigurationReference, readConfObject, } from '@jbrowse/core/configuration';
 import { getContainingView, getSession } from '@jbrowse/core/util';
 import { types } from '@jbrowse/mobx-state-tree';
 import ColorLensIcon from '@mui/icons-material/ColorLens';
@@ -91,18 +91,16 @@ function stateModelFactory(configSchema) {
             return self.colorBy?.modifications?.threshold ?? 10;
         },
         get rendererConfig() {
-            const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, rendererTypeName, hideSmallIndels, hideMismatches, } = self;
-            const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};
+            const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, hideSmallIndels, hideMismatches, hideLargeIndels, } = self;
+            const conf = self.configuration.renderers?.PileupRenderer;
             return {
-                ...configBlob,
-                ...(featureHeight !== undefined ? { height: featureHeight } : {}),
-                ...(hideSmallIndels !== undefined ? { hideSmallIndels } : {}),
-                ...(hideMismatches !== undefined ? { hideMismatches } : {}),
-                ...(noSpacing !== undefined ? { noSpacing } : {}),
-                ...(mismatchAlpha !== undefined ? { mismatchAlpha } : {}),
-                ...(trackMaxHeight !== undefined
-                    ? { maxHeight: trackMaxHeight }
-                    : {}),
+                height: featureHeight ?? readConfObject(conf, 'height'),
+                noSpacing: noSpacing ?? readConfObject(conf, 'noSpacing'),
+                maxHeight: trackMaxHeight ?? readConfObject(conf, 'maxHeight'),
+                mismatchAlpha: mismatchAlpha ?? readConfObject(conf, 'mismatchAlpha'),
+                hideSmallIndels: hideSmallIndels ?? readConfObject(conf, 'hideSmallIndels'),
+                hideMismatches: hideMismatches ?? readConfObject(conf, 'hideMismatches'),
+                hideLargeIndels: hideLargeIndels ?? readConfObject(conf, 'hideLargeIndels'),
             };
         },
     }))
@@ -110,7 +108,7 @@ function stateModelFactory(configSchema) {
         const { renderReady: superRenderReady } = self;
         return {
             get mismatchAlphaSetting() {
-                return readConfObject(self.rendererConfig, 'mismatchAlpha');
+                return self.rendererConfig.mismatchAlpha;
             },
             renderReady() {
                 const view = getContainingView(self);

package/esm/LinearPileupDisplay/sharedDoAfterAttach.js CHANGED Viewed

@@ -4,10 +4,10 @@ import { getUniqueTags } from "../shared/getUniqueTags.js";
 import { createAutorun } from "../util.js";
 export function sharedDoAfterAttach(self) {
     createAutorun(self, async () => {
-        const view = getContainingView(self);
         if (!self.autorunReady) {
             return;
         }
+        const view = getContainingView(self);
         const { colorBy, tagsReady } = self;
         const { staticBlocks } = view;
         if (colorBy?.tag && !tagsReady) {

package/esm/LinearReadArcsDisplay/model.d.ts CHANGED Viewed

@@ -70,6 +70,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -126,6 +127,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -179,6 +181,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -230,19 +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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -79,6 +79,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+    readonly isMinimized: boolean;
     readonly parentDisplay: any;
     readonly effectiveRpcDriverName: any;
 } & {
@@ -135,6 +136,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/mobx-state-tree").IModelType<{
@@ -188,6 +190,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             }> | null;
             readonly adapterConfig: any;
             readonly parentTrack: import("@jbrowse/core/util").AbstractTrackModel;
+            readonly isMinimized: boolean;
             readonly parentDisplay: any;
             readonly effectiveRpcDriverName: any;
         }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>>;
@@ -239,19 +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;
 } & {
@@ -308,8 +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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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";
@@ -61,17 +61,18 @@ function stateModelFactory(pluginManager, configSchema) {
                 return self.colorBy?.modifications?.threshold ?? 10;
             },
             get rendererConfig() {
-                const configBlob = getConf(self, ['renderers', self.rendererTypeName]) || {};
                 const { showArcs, showInterbaseCounts, showInterbaseIndicators } = self;
+                const conf = self.configuration.renderers?.[self.rendererTypeName];
                 return {
-                    ...configBlob,
-                    showInterbaseCounts: showInterbaseCounts ?? configBlob.showInterbaseCounts,
-                    showInterbaseIndicators: showInterbaseIndicators ?? configBlob.showInterbaseIndicators,
-                    showArcs: showArcs ?? configBlob.showArcs,
+                    showInterbaseCounts: showInterbaseCounts ??
+                        readConfObject(conf, 'showInterbaseCounts'),
+                    showInterbaseIndicators: showInterbaseIndicators ??
+                        readConfObject(conf, 'showInterbaseIndicators'),
+                    showArcs: showArcs ?? readConfObject(conf, 'showArcs'),
                 };
             },
             get showArcsSetting() {
-                return (self.showArcs ?? readConfObject(this.rendererConfig, 'showArcs'));
+                return this.rendererConfig.showArcs;
             },
             get skipFeatures() {
                 if (!this.showArcsSetting) {
@@ -92,12 +93,10 @@ function stateModelFactory(pluginManager, configSchema) {
                 return [...skipFeaturesMap.values()];
             },
             get showInterbaseCountsSetting() {
-                return (self.showInterbaseCounts ??
-                    readConfObject(this.rendererConfig, 'showInterbaseCounts'));
+                return this.rendererConfig.showInterbaseCounts;
             },
             get showInterbaseIndicatorsSetting() {
-                return (self.showInterbaseIndicators ??
-                    readConfObject(this.rendererConfig, 'showInterbaseIndicators'));
+                return this.rendererConfig.showInterbaseIndicators;
             },
             get autorunReady() {
                 const view = getContainingView(self);
@@ -269,7 +268,7 @@ function stateModelFactory(pluginManager, configSchema) {
                     },
                     {
                         label: 'Filter arcs by score...',
-                        icon: FilterListIcon,
+                        icon: ClearAllIcon,
                         onClick: () => {
                             getSession(self).queueDialog(handleClose => [
                                 FilterArcsByScoreDialog,

package/esm/RenderLinearReadCloudDisplayRPC/RenderLinearReadCloudDisplay.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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;
 };

package/esm/RenderLinearReadCloudDisplayRPC/drawFeatsCloud.js CHANGED Viewed

@@ -1,37 +1,24 @@
 import { scaleLog } from '@mui/x-charts-vendor/d3-scale';
 export const CLOUD_HEIGHT_PADDING = 20;
 const DEFAULT_MAX_DISTANCE = 1000;
-export function createCloudScale(minDistance, maxDistance, height) {
+export function createCloudScale(maxDistance, height) {
     return scaleLog()
         .base(2)
-        .domain([Math.max(1, minDistance), Math.max(2, maxDistance)])
+        .domain([1, Math.max(2, maxDistance)])
         .range([0, height - CLOUD_HEIGHT_PADDING])
         .clamp(true);
 }
-export function calculateCloudTicks(domain, height) {
-    const [minDistance, maxDistance] = domain;
-    const scale = createCloudScale(minDistance, maxDistance, height);
+export function calculateCloudTicks(maxDistance, height) {
+    const scale = createCloudScale(maxDistance, height);
     const tickValues = scale.ticks(6);
     const ticks = tickValues.map(value => ({
         value,
         y: scale(value),
     }));
-    return { ticks, height, minDistance, maxDistance };
+    return { ticks, height, maxDistance };
 }
-export function calculateCloudYOffsetsUtil(computedChains, height, cloudDomain) {
+export function calculateCloudYOffsetsUtil(computedChains, height) {
     const chainYOffsets = new Map();
-    if (cloudDomain) {
-        const [, maxDistance] = cloudDomain;
-        const scale = createCloudScale(1, maxDistance, height);
-        for (const { id, distance } of computedChains) {
-            const top = distance > 0 ? scale(distance) : 0;
-            chainYOffsets.set(id, top);
-        }
-        return {
-            chainYOffsets,
-            cloudMaxDistance: maxDistance,
-        };
-    }
     let maxDistance = Number.MIN_VALUE;
     for (const { distance } of computedChains) {
         if (distance > 0) {
@@ -41,7 +28,7 @@ export function calculateCloudYOffsetsUtil(computedChains, height, cloudDomain)
     if (maxDistance === Number.MIN_VALUE) {
         maxDistance = DEFAULT_MAX_DISTANCE;
     }
-    const scale = createCloudScale(1, maxDistance, height);
+    const scale = createCloudScale(maxDistance, height);
     for (const { id, distance } of computedChains) {
         const top = distance > 0 ? scale(distance) : 0;
         chainYOffsets.set(id, top);

package/esm/RenderLinearReadCloudDisplayRPC/executeRenderLinearReadCloudDisplay.js CHANGED Viewed

@@ -12,7 +12,7 @@ import { computeChainBounds, drawFeatsCore, filterChains, sortComputedChains, }
 import { calculateStackYOffsetsUtil } from "./drawFeatsStack.js";
 import { getInsertSizeStats } from "../shared/insertSizeStats.js";
 export async function executeRenderLinearReadCloudDisplay({ pluginManager, args, }) {
-    const { sessionId, view: viewSnapshot, adapterConfig, sequenceAdapter, config, theme, featureHeight, noSpacing, drawCloud, colorBy, drawSingletons, drawProperPairs, flipStrandLongReadChains, trackMaxHeight, cloudModeHeight, cloudDomain, highResolutionScaling, exportSVG, statusCallback = () => { }, stopToken, visibleModifications, hideSmallIndels, hideMismatches, hideLargeIndels, showOutline, } = args;
+    const { sessionId, view: viewSnapshot, adapterConfig, sequenceAdapter, config, theme, featureHeight, noSpacing, drawCloud, colorBy, drawSingletons, drawProperPairs, flipStrandLongReadChains, trackMaxHeight, cloudModeHeight, highResolutionScaling, exportSVG, statusCallback = () => { }, stopToken, visibleModifications, hideSmallIndels, hideMismatches, hideLargeIndels, showOutline, } = args;
     const view = Base1DView.create(viewSnapshot);
     if (viewSnapshot.width) {
         view.setVolatileWidth(viewSnapshot.width);
@@ -125,7 +125,7 @@ export async function executeRenderLinearReadCloudDisplay({ pluginManager, args,
             view: viewSnap,
             calculateYOffsets: (chains) => {
                 return drawCloud
-                    ? calculateCloudYOffsetsUtil(chains, actualHeight, cloudDomain)
+                    ? calculateCloudYOffsetsUtil(chains, actualHeight)
                     : calculateStackYOffsetsUtil(chains, featureHeight, noSpacing, trackMaxHeight ?? 1200);
             },
         });

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js CHANGED Viewed

@@ -156,10 +156,14 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     }
     async getCoverageBins(region, opts = {}) {
         const { bpPerPx, statsEstimationMode } = opts;
-        if (this.lastBpPerPx !== undefined && this.lastBpPerPx !== bpPerPx) {
+        if (bpPerPx !== undefined &&
+            this.lastBpPerPx !== undefined &&
+            this.lastBpPerPx !== bpPerPx) {
             this.cache.clear();
         }
-        this.lastBpPerPx = bpPerPx;
+        if (bpPerPx !== undefined) {
+            this.lastBpPerPx = bpPerPx;
+        }
         if (statsEstimationMode) {
             const regionFilterKey = makeRegionFilterKey(region, opts);
             for (const key of this.cache.keys()) {

package/esm/SNPCoverageAdapter/generateCoverageBinsPrefixSum.js CHANGED Viewed

@@ -79,6 +79,7 @@ export async function generateCoverageBinsPrefixSum({ fetchSequence, features, r
     for (let i = 0, l = features.length; i < l; i++) {
         processFeature(region, features[i], skipmap, noncovEvents, snpEvents);
     }
+    featureCtx.feature = undefined;
     const deletionDepth = new Int32Array(regionSize);
     let dd = 0;
     for (let i = 0; i < regionSize; i++) {
@@ -346,7 +347,6 @@ function mismatchHandler(type, start, refLen, base, _qual, altbase, interbaseLen
             const hash = `${mstart}_${mend}_${effectiveStrand}`;
             if (skipmap[hash] === undefined) {
                 skipmap[hash] = {
-                    feature: feature,
                     start: mstart,
                     end: mend,
                     strand: fstrand,

package/esm/shared/LinearReadDisplayBaseMixin.d.ts CHANGED Viewed

@@ -5,19 +5,24 @@ export declare function LinearReadDisplayBaseMixin(): import("@jbrowse/mobx-stat
 }, {
     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/shared/createRPCRenderingSetup.d.ts CHANGED Viewed

@@ -20,6 +20,7 @@ export interface RPCRenderableModel {
     ref: HTMLCanvasElement | null;
     renderingImageData?: ImageBitmap;
     setStatusMessage?: (msg: string) => void;
+    setCanvasDrawn?: (drawn: boolean) => void;
 }
 export interface RPCRenderSetupParams<T extends RPCRenderableModel, R = Record<string, unknown>> {
     self: T;

package/esm/shared/createRPCRenderingSetup.js CHANGED Viewed

@@ -33,18 +33,24 @@ export function createRPCRenderFunction({ self, rpcMethodName, getRPCParams, onR
             const stopToken = createStopToken();
             self.setRenderingStopToken(stopToken);
             self.setLoading(true);
-            const viewSnapshot = structuredClone({
-                ...getSnapshot(view),
-                staticBlocks: view.staticBlocks,
+            self.setCanvasDrawn?.(false);
+            const viewSnapshot = {
+                displayedRegions: structuredClone(view.displayedRegions),
+                bpPerPx: view.bpPerPx,
+                offsetPx: view.offsetPx,
+                interRegionPaddingWidth: view.interRegionPaddingWidth,
+                minimumBlockWidth: view.minimumBlockWidth,
                 width: view.width,
-            });
+            };
             const sessionId = getRpcSessionId(self);
+            const adapterConfig = self.adapterConfig;
+            const config = getSnapshot(self.configuration);
             const result = (await rpcManager.call(sessionId, rpcMethodName, {
                 sessionId,
                 view: viewSnapshot,
-                adapterConfig: self.adapterConfig,
+                adapterConfig,
                 sequenceAdapter,
-                config: getSnapshot(self.configuration),
+                config,
                 statusCallback: (msg) => {
                     if (isAlive(self)) {
                         self.setStatusMessage?.(msg);
@@ -64,6 +70,7 @@ export function createRPCRenderFunction({ self, rpcMethodName, getRPCParams, onR
         }
         catch (error) {
             if (!isAbortException(error)) {
+                console.error(error);
                 self.setError(error);
             }
         }
@@ -75,7 +82,10 @@ export function createRPCRenderFunction({ self, rpcMethodName, getRPCParams, onR
 }
 export function setupCanvasRenderingAutorun(self) {
     createAutorun(self, async () => {
-        drawCanvasImageData(self.ref, self.renderingImageData);
+        const success = drawCanvasImageData(self.ref, self.renderingImageData);
+        if (isAlive(self)) {
+            self.setCanvasDrawn?.(success);
+        }
     }, {
         name: 'CanvasRenderAutorun',
     });

package/esm/shared/menuItems.js CHANGED Viewed

@@ -1,6 +1,6 @@
 import { lazy } from 'react';
 import { getSession } from '@jbrowse/core/util';
-import FilterListIcon from '@mui/icons-material/ClearAll';
+import ClearAllIcon from '@mui/icons-material/ClearAll';
 import PaletteIcon from '@mui/icons-material/Palette';
 import { modificationData } from "./modificationData.js";
 const FilterByTagDialog = lazy(() => import("./components/FilterByTagDialog.js"));
@@ -150,7 +150,7 @@ export function getColorSchemeMenuItem(model) {
 export function getFilterByMenuItem(model) {
     return {
         label: 'Filter by',
-        icon: FilterListIcon,
+        icon: ClearAllIcon,
         onClick: () => {
             getSession(model).queueDialog((handleClose) => [
                 FilterByTagDialog,
@@ -162,7 +162,7 @@ export function getFilterByMenuItem(model) {
 export function getEditFiltersMenuItem(model) {
     return {
         label: 'Edit filters',
-        icon: FilterListIcon,
+        icon: ClearAllIcon,
         type: 'subMenu',
         subMenu: [
             {

package/esm/shared/types.d.ts CHANGED Viewed

@@ -2,7 +2,6 @@ import type { MismatchCallback } from './forEachMismatchTypes.ts';
 import type { Feature } from '@jbrowse/core/util';
 export type SkipMap = Record<string, {
     score: number;
-    feature: unknown;
     start: number;
     end: number;
     strand: number;

package/package.json CHANGED Viewed

@@ -1,6 +1,7 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "4.0.3",
+  "version": "4.1.1",
+  "type": "module",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -21,11 +22,11 @@
   ],
   "dependencies": {
     "@gmod/bam": "^7.1.15",
-    "@gmod/cram": "^7.0.3",
+    "@gmod/cram": "^8.0.0",
     "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/icons-material": "^7.3.6",
-    "@mui/material": "^7.3.6",
-    "@mui/x-charts-vendor": "^8.23.0",
+    "@mui/icons-material": "^7.3.7",
+    "@mui/material": "^7.3.7",
+    "@mui/x-charts-vendor": "^8.26.0",
     "canvas2svg": "^1.0.16",
     "copy-to-clipboard": "^3.3.3",
     "fast-deep-equal": "^3.1.3",
@@ -33,10 +34,10 @@
     "mobx": "^6.15.0",
     "mobx-react": "^9.2.1",
     "rxjs": "^7.8.2",
-    "@jbrowse/sv-core": "^4.0.3",
-    "@jbrowse/plugin-linear-genome-view": "^4.0.3",
-    "@jbrowse/core": "^4.0.3",
-    "@jbrowse/plugin-wiggle": "^4.0.3"
+    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/plugin-linear-genome-view": "^4.1.1",
+    "@jbrowse/plugin-wiggle": "^4.1.1",
+    "@jbrowse/sv-core": "^4.1.1"
   },
   "peerDependencies": {
     "react": ">=18.0.0"