npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.3.1 → 2.3.3 - Mend

@jbrowse/plugin-linear-genome-view 2.3.1 → 2.3.3

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 (29) hide show

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js CHANGED Viewed

@@ -1,4 +1,4 @@
-import { types, getParent, isAlive, cast } from 'mobx-state-tree';
+import { types, getParent, isAlive, cast, getSnapshot, } from 'mobx-state-tree';
 import { readConfObject } from '@jbrowse/core/configuration';
 import { assembleLocString, getSession, getContainingDisplay, getContainingView, getViewParams, makeAbortableReaction, } from '@jbrowse/core/util';
 import { Region } from '@jbrowse/core/util/types/mst';
@@ -178,7 +178,7 @@ export function renderBlockData(self, optDisplay) {
                     }
                 },
                 assemblyName: self.region.assemblyName,
-                regions: [self.region],
+                regions: [getSnapshot(self.region)],
                 adapterConfig,
                 rendererType: rendererType.name,
                 sessionId,

package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"serverSideRenderedBlock.js","sourceRoot":"","sources":["../../../src/BaseLinearDisplay/models/serverSideRenderedBlock.ts"],"names":[],"mappings":"AAEA,OAAO,EACL,KAAK,EACL,SAAS,EACT,OAAO,EACP,IAAI,EAEJ,WAAW,GACZ,MAAM,iBAAiB,CAAA;AACxB,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EACL,iBAAiB,EACjB,UAAU,EACV,oBAAoB,EACpB,iBAAiB,EACjB,aAAa,EACb,qBAAqB,GAEtB,MAAM,oBAAoB,CAAA;AAC3B,OAAO,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAA;AACrD,OAAO,EAEL,gBAAgB,GACjB,MAAM,0BAA0B,CAAA;AAEjC,OAAO,EACL,qBAAqB,EACrB,eAAe,GAChB,MAAM,2BAA2B,CAAA;AAElC,OAAO,8BAA8B,MAAM,8CAA8C,CAAA;AAEzF,oEAAoE;AACpE,MAAM,UAAU,GAAG,KAAK;KACrB,KAAK,CAAC,YAAY,EAAE;IACnB,GAAG,EAAE,KAAK,CAAC,MAAM;IACjB,MAAM,EAAE,MAAM;IACd,UAAU,EAAE,CAAC;IACb,0BAA0B,EAAE,KAAK;IACjC,2BAA2B,EAAE,KAAK;CACnC,CAAC;IACF,yFAAyF;KACxF,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;IACf,gBAAgB,EAAE,SAAwC;IAC1D,MAAM,EAAE,KAAK;IACb,YAAY,EAAE,SAA2C;IACzD,QAAQ,EAAE,SAA6C;IACvD,MAAM,EAAE,SAAgB;IACxB,MAAM,EAAE,EAAE;IACV,KAAK,EAAE,SAAoB;IAC3B,OAAO,EAAE,SAA+B;IACxC,gBAAgB,EAAE,KAAK;IACvB,cAAc,EAAE,8BAA8B;IAC9C,WAAW,EAAE,SAAgB;CAC9B,CAAC,CAAC;KACF,OAAO,CAAC,IAAI,CAAC,EAAE;IACd,IAAI,gBAA6C,CAAA;IACjD,OAAO;QACL,QAAQ;YACN,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;QACvC,CAAC;QACD,WAAW;YACT,MAAM,OAAO,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAA;YAC1C,qBAAqB,CACnB,IAAW,EACX,eAAe,EACf,iBAAwB,EAAE,qCAAqC;YAC/D;gBACE,IAAI,EAAE,GAAG,OAAO,CAAC,EAAE,IAAI,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY;gBACjE,KAAK,EAAE,OAAO,CAAC,WAAW;gBAC1B,eAAe,EAAE,IAAI;aACtB,EACD,IAAI,CAAC,UAAU,EACf,IAAI,CAAC,WAAW,EAChB,IAAI,CAAC,QAAQ,CACd,CAAA;QACH,CAAC;QACD,SAAS,CAAC,OAAe;YACvB,IAAI,CAAC,MAAM,GAAG,OAAO,CAAA;QACvB,CAAC;QACD,UAAU,CAAC,eAAgC;YACzC,IAAI,gBAAgB,KAAK,SAAS,EAAE;gBAClC,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;oBACpC,gBAAgB,CAAC,KAAK,EAAE,CAAA;iBACzB;aACF;YACD,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,eAAe,CAAA;QACpC,CAAC;QACD,UAAU,CAAC,WAAmB;YAC5B,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,WAAW,CAAA;YAC1B,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,SAAS,CAAA;QAC9B,CAAC;QACD,WAAW,CACT,KAQa;YAEb,IAAI,CAAC,KAAK,EAAE;gBACV,OAAM;aACP;YACD,MAAM,EACJ,YAAY,EACZ,QAAQ,EACR,MAAM,EACN,gBAAgB,EAChB,WAAW,GACZ,GAAG,KAAK,CAAA;YACT,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;YAClB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;YAChC,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;YACxB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;YACpB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;YACxC,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;YAC9B,gBAAgB,GAAG,SAAS,CAAA;QAC9B,CAAC;QACD,QAAQ,CAAC,KAAsB;YAC7B,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;YACpB,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,uCAAuC;YACvC,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,KAAK,GAAG,KAAK,CAAA;YAClB,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,gBAAgB,GAAG,SAAS,CAAA;YAC5B,IAAI,gBAAgB,CAAC,KAAc,CAAC,EAAE;gBACpC,IAAI,CAAC,MAAM,EAAE,CAAA;aACd;QACH,CAAC;QACD,MAAM;YACJ,IAAI,CAAC,gBAAgB,GAAG,SAAS,CAAA;YACjC,IAAI,CAAC,MAAM,GAAG,KAAK,CAAA;YACnB,IAAI,CAAC,YAAY,GAAG,SAAS,CAAA;YAC7B,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAA;YACzB,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;YACtB,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;YACxB,IAAI,CAAC,gBAAgB,GAAG,KAAK,CAAA;YAC7B,IAAI,CAAC,cAAc,GAAG,8BAA8B,CAAA;YACpD,IAAI,CAAC,WAAW,GAAG,SAAS,CAAA;YAC5B,SAAS,CAAM,IAAI,EAAE,CAAC,CAAC,CAAC,MAAM,EAAE,CAAA;QAClC,CAAC;QACD,aAAa;YACX,IAAI,gBAAgB,IAAI,CAAC,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;gBACxD,gBAAgB,CAAC,KAAK,EAAE,CAAA;aACzB;YACD,MAAM,OAAO,GAAG,oBAAoB,CAAC,IAAI,CAAC,CAAA;YAC1C,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,IAAI,CAAC,CAAA;YACvC,MAAM,EAAE,YAAY,EAAE,GAAG,OAAO,CAAA;YAChC,MAAM,EAAE,UAAU,EAAE,GAAG,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;YAClD,iEAAiE;YACjE,IAAI,UAAU,EAAE;gBACd,YAAY;qBACT,qBAAqB,CACpB,UAAU,EACV,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,CAAC,CACvC;qBACA,KAAK,CAAC,CAAC,CAAQ,EAAE,EAAE;oBAClB,kEAAkE;oBAClE,OAAO,CAAC,IAAI,CAAC,8BAA8B,EAAE,CAAC,CAAC,CAAA;gBACjD,CAAC,CAAC,CAAA;aACL;QACH,CAAC;KACF,CAAA;AACH,CAAC,CAAC,CAAA;AAEJ,eAAe,UAAU,CAAA;AAIzB,2EAA2E;AAC3E,mDAAmD;AACnD,MAAM,UAAU,eAAe,CAC7B,IAAgB,EAChB,UAAiC;IAEjC,IAAI;QACF,MAAM,OAAO,GAAG,UAAU,IAAK,oBAAoB,CAAC,IAAI,CAAS,CAAA;QACjE,MAAM,EAAE,eAAe,EAAE,UAAU,EAAE,GAAG,UAAU,CAAC,OAAO,CAAC,CAAA;QAC3D,MAAM,EAAE,aAAa,EAAE,YAAY,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,OAAO,CAAA;QACnE,MAAM,aAAa,GAAG,qBAAqB,CAAC,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package/esm/LinearBasicDisplay/model.d.ts CHANGED Viewed

@@ -38,30 +38,29 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         layout: any;
         status: string;
         error: unknown;
-        message: string | undefined;
-        maxHeightReached: boolean; /**
+        message: string | undefined; /**
          * #getter
          */
+        maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
         renderProps: any;
     } & {
-        doReload(): void;
+        doReload(): void; /**
+         * #getter
+         */
         afterAttach(): void;
         setStatus(message: string): void;
-        /**
-         * #getter
+        setLoading(abortController: AbortController): void; /**
+         * #action
          */
-        setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
-            maxHeightReached: boolean; /**
-             * #method
-             */
+            maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
         setError(error: unknown): void;

package/esm/LinearGenomeView/components/GetSequenceDialog.js CHANGED Viewed

@@ -1,12 +1,12 @@
 import React, { useEffect, useMemo, useState } from 'react';
 import { makeStyles } from 'tss-react/mui';
-import { Button, CircularProgress, Container, DialogActions, DialogContent, TextField, Typography, } from '@mui/material';
+import { Button, Checkbox, CircularProgress, Container, DialogActions, DialogContent, FormGroup, FormControlLabel, TextField, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
 import { saveAs } from 'file-saver';
 import { getConf } from '@jbrowse/core/configuration';
 import copy from 'copy-to-clipboard';
 import { Dialog } from '@jbrowse/core/ui';
-import { getSession } from '@jbrowse/core/util';
+import { getSession, reverse, complement, } from '@jbrowse/core/util';
 import { formatSeqFasta } from '@jbrowse/core/util/formatFastaStrings';
 // icons
 import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
@@ -50,9 +50,12 @@ function SequenceDialog({ model, handleClose, }) {
     const { classes } = useStyles();
     const session = getSession(model);
     const [error, setError] = useState();
-    const [sequence, setSequence] = useState();
-    const loading = Boolean(sequence === undefined);
+    const [sequenceChunks, setSequenceChunks] = useState();
+    const [rev, setReverse] = useState(false);
+    const [copied, setCopied] = useState(false);
+    const [comp, setComplement] = useState(false);
     const { leftOffset, rightOffset } = model;
+    const loading = Boolean(sequenceChunks === undefined);
     // avoid infinite looping of useEffect
     // random note: the current selected region can't be a computed because it
     // uses action on base1dview even though it's on the ephemeral base1dview
@@ -65,19 +68,7 @@ function SequenceDialog({ model, handleClose, }) {
                 if (regionsSelected.length > 0) {
                     const chunks = await fetchSequence(model, regionsSelected, controller.signal);
                     if (active) {
-                        setSequence(formatSeqFasta(chunks
-                            .filter(f => !!f)
-                            .map(chunk => {
-                            const chunkSeq = chunk.get('seq');
-                            const chunkRefName = chunk.get('refName');
-                            const chunkStart = chunk.get('start') + 1;
-                            const chunkEnd = chunk.get('end');
-                            const chunkLocstring = `${chunkRefName}:${chunkStart}-${chunkEnd}`;
-                            if ((chunkSeq === null || chunkSeq === void 0 ? void 0 : chunkSeq.length) !== chunkEnd - chunkStart + 1) {
-                                throw new Error(`${chunkLocstring} returned ${chunkSeq.length.toLocaleString()} bases, but should have returned ${(chunkEnd - chunkStart).toLocaleString()}`);
-                            }
-                            return { header: chunkLocstring, seq: chunkSeq };
-                        })));
+                        setSequenceChunks(chunks);
                     }
                 }
                 else {
@@ -95,37 +86,59 @@ function SequenceDialog({ model, handleClose, }) {
             controller.abort();
             active = false;
         };
-    }, [model, session, regionsSelected, setSequence]);
+    }, [model, session, regionsSelected]);
+    const sequence = sequenceChunks
+        ? formatSeqFasta(sequenceChunks
+            .filter(f => !!f)
+            .map(chunk => {
+            let chunkSeq = chunk.get('seq');
+            const chunkRefName = chunk.get('refName');
+            const chunkStart = chunk.get('start') + 1;
+            const chunkEnd = chunk.get('end');
+            const chunkLocstring = `${chunkRefName}:${chunkStart}-${chunkEnd}`;
+            if ((chunkSeq === null || chunkSeq === void 0 ? void 0 : chunkSeq.length) !== chunkEnd - chunkStart + 1) {
+                throw new Error(`${chunkLocstring} returned ${chunkSeq.length.toLocaleString()} bases, but should have returned ${(chunkEnd - chunkStart).toLocaleString()}`);
+            }
+            if (rev) {
+                chunkSeq = reverse(chunkSeq);
+            }
+            if (comp) {
+                chunkSeq = complement(chunkSeq);
+            }
+            return { header: chunkLocstring, seq: chunkSeq };
+        }))
+        : '';
     const sequenceTooLarge = sequence ? sequence.length > 1000000 : false;
     return (React.createElement(Dialog, { maxWidth: "xl", open: true, onClose: () => {
             handleClose();
             model.setOffsets(undefined, undefined);
         }, title: "Reference sequence" },
         React.createElement(DialogContent, null,
-            error ? React.createElement(Typography, { color: "error" }, `${error}`) : null,
-            loading && !error ? (React.createElement(Container, null,
+            error ? (React.createElement(Typography, { color: "error" }, `${error}`)) : loading ? (React.createElement(Container, null,
                 "Retrieving reference sequence...",
-                React.createElement(CircularProgress, { style: {
-                        marginLeft: 10,
-                    }, size: 20, disableShrink: true }))) : null,
-            React.createElement(TextField, { "data-testid": "rubberband-sequence", variant: "outlined", multiline: true, minRows: 5, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: sequenceTooLarge
+                React.createElement(CircularProgress, { style: { marginLeft: 10 }, size: 20, disableShrink: true }))) : null,
+            React.createElement(TextField, { "data-testid": "rubberband-sequence", variant: "outlined", multiline: true, minRows: 5, maxRows: 10, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: sequenceTooLarge
                     ? 'Reference sequence too large to display, use the download FASTA button'
                     : sequence, InputProps: {
                     readOnly: true,
                     classes: {
                         input: classes.textAreaFont,
                     },
-                } })),
+                } }),
+            React.createElement(FormGroup, null,
+                React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { value: rev, onChange: event => setReverse(event.target.checked) }), label: "Reverse sequence" }),
+                React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { value: comp, onChange: event => setComplement(event.target.checked) }), label: "Complement sequence" })),
+            React.createElement(Typography, { style: { margin: 10 } }, "Note: Check both boxes for the \"reverse complement\"")),
         React.createElement(DialogActions, null,
             React.createElement(Button, { onClick: () => {
-                    copy(sequence || '');
-                    session.notify('Copied to clipboard', 'success');
-                }, disabled: loading || !!error || sequenceTooLarge, color: "primary", startIcon: React.createElement(ContentCopyIcon, null) }, "Copy to clipboard"),
+                    copy(sequence);
+                    setCopied(true);
+                    setTimeout(() => setCopied(false), 500);
+                }, disabled: loading || !!error || sequenceTooLarge, color: "primary", startIcon: React.createElement(ContentCopyIcon, null) }, copied ? 'Copied' : 'Copy to clipboard'),
             React.createElement(Button, { onClick: () => {
-                    const seqFastaFile = new Blob([sequence || ''], {
+                    saveAs(new Blob([sequence || ''], {
                         type: 'text/x-fasta;charset=utf-8',
-                    });
-                    saveAs(seqFastaFile, 'jbrowse_ref_seq.fa');
+                    }), 'jbrowse_ref_seq.fa');
                 }, disabled: loading || !!error, color: "primary", startIcon: React.createElement(GetAppIcon, null) }, "Download FASTA"),
             React.createElement(Button, { onClick: handleClose, variant: "contained" }, "Close"))));
 }

package/esm/LinearGenomeView/components/GetSequenceDialog.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/esm/LinearGenomeView/components/RefNameAutocomplete.js CHANGED Viewed

@@ -90,7 +90,7 @@ function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResult
     const inputBoxVal = coarseVisibleLocStrings || value || '';
     // heuristic, text width + icon width
     // + 45 accommodates help icon and search icon
-    const width = Math.min(Math.max(measureText(inputBoxVal, 16) + 45, minWidth), 550);
+    const width = Math.min(Math.max(measureText(inputBoxVal, 16) + 50, minWidth), 550);
     // notes on implementation:
     // The selectOnFocus setting helps highlight the field when clicked
     return (React.createElement(React.Fragment, null,

package/esm/LinearGenomeView/model.js CHANGED Viewed

@@ -3,7 +3,7 @@ import { getConf } from '@jbrowse/core/configuration';
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models';
 import { ElementId, Region as MUIRegion } from '@jbrowse/core/util/types/mst';
 import { ReturnToImportFormDialog } from '@jbrowse/core/ui';
-import { assembleLocString, clamp, findLastIndex, getContainingView, getSession, isViewContainer, isSessionModelWithWidgets, measureText, parseLocString, springAnimate, isSessionWithAddTracks, } from '@jbrowse/core/util';
+import { assembleLocString, clamp, findLastIndex, getContainingView, getSession, isViewContainer, isSessionModelWithWidgets, isSessionWithAddTracks, localStorageGetItem, measureText, parseLocString, springAnimate, } from '@jbrowse/core/util';
 import calculateDynamicBlocks from '@jbrowse/core/util/calculateDynamicBlocks';
 import calculateStaticBlocks from '@jbrowse/core/util/calculateStaticBlocks';
 import { getParentRenderProps } from '@jbrowse/core/util/tracks';
@@ -53,11 +53,6 @@ export const RESIZE_HANDLE_HEIGHT = 3;
 export const INTER_REGION_PADDING_WIDTH = 2;
 export const SPACING = 7;
 export const WIDGET_HEIGHT = 32;
-function localStorageGetItem(item) {
-    return typeof localStorage !== 'undefined'
-        ? localStorage.getItem(item)
-        : undefined;
-}
 /**
  * #stateModel LinearGenomeView
  */
@@ -70,9 +65,9 @@ export function stateModelFactory(pluginManager) {
         id: ElementId,
         /**
          * #property
-         * this is a string instead of the const literal 'LinearGenomeView' to reduce some
-         * typescripting strictness, but you should pass the string 'LinearGenomeView' to
-         * the model explicitly
+         * this is a string instead of the const literal 'LinearGenomeView' to
+         * reduce some typescripting strictness, but you should pass the string
+         * 'LinearGenomeView' to the model explicitly
          */
         type: types.literal('LinearGenomeView'),
         /**
@@ -87,9 +82,10 @@ export function stateModelFactory(pluginManager) {
         bpPerPx: 1,
         /**
          * #property
-         * currently displayed regions, can be a single chromosome, arbitrary subsections,
-         * or the entire  set of chromosomes in the genome, but it not advised to use the
-         * entire set of chromosomes if your assembly is very fragmented
+         * currently displayed regions, can be a single chromosome, arbitrary
+         * subsections, or the entire  set of chromosomes in the genome, but it not
+         * advised to use the entire set of chromosomes if your assembly is very
+         * fragmented
          */
         displayedRegions: types.array(MUIRegion),
         /**
@@ -123,18 +119,12 @@ export function stateModelFactory(pluginManager) {
          * #property
          * show the "center line"
          */
-        showCenterLine: types.optional(types.boolean, () => {
-            const setting = localStorageGetItem('lgv-showCenterLine');
-            return setting !== undefined && setting !== null ? !!+setting : false;
-        }),
+        showCenterLine: types.optional(types.boolean, () => JSON.parse(localStorageGetItem('lgv-showCenterLine') || 'false')),
         /**
          * #property
          * show the "cytobands" in the overview scale bar
          */
-        showCytobandsSetting: types.optional(types.boolean, () => {
-            const setting = localStorageGetItem('lgv-showCytobands');
-            return setting !== undefined && setting !== null ? !!+setting : true;
-        }),
+        showCytobandsSetting: types.optional(types.boolean, () => JSON.parse(localStorageGetItem('lgv-showCytobands') || 'true')),
         /**
          * #property
          * show the "gridlines" in the track area
@@ -406,7 +396,6 @@ export function stateModelFactory(pluginManager) {
          */
         setShowCytobands(flag) {
             self.showCytobandsSetting = flag;
-            localStorage.setItem('lgv-showCytobands', `${+flag}`);
         },
         /**
          * #action
@@ -608,14 +597,12 @@ export function stateModelFactory(pluginManager) {
          */
         setTrackLabels(setting) {
             self.trackLabels = setting;
-            localStorage.setItem('lgv-trackLabels', setting);
         },
         /**
          * #action
          */
         toggleCenterLine() {
             self.showCenterLine = !self.showCenterLine;
-            localStorage.setItem('lgv-showCenterLine', `${+self.showCenterLine}`);
         },
         /**
          * #action
@@ -1039,6 +1026,15 @@ export function stateModelFactory(pluginManager) {
                     this.setCoarseDynamicBlocks(self.dynamicBlocks);
                 }
             }, { delay: 150 }));
+            addDisposer(self, autorun(() => {
+                const s = (s) => JSON.stringify(s);
+                const { trackLabels, showCytobandsSetting, showCenterLine } = self;
+                if (typeof localStorage !== 'undefined') {
+                    localStorage.setItem('lgv-trackLabels', trackLabels);
+                    localStorage.setItem('lgv-showCytobands', s(showCytobandsSetting));
+                    localStorage.setItem('lgv-showCenterLine', s(showCenterLine));
+                }
+            }));
         },
     }))
         .actions(self => ({

package/esm/LinearGenomeView/model.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.3.1",
+  "version": "2.3.3",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -41,6 +41,8 @@
   "dependencies": {
     "@mui/icons-material": "^5.0.1",
     "@popperjs/core": "^2.11.0",
+    "@types/file-saver": "^2.0.1",
+    "@types/normalize-wheel": "^1.0.0",
     "clone": "^2.1.2",
     "clsx": "^1.0.4",
     "copy-to-clipboard": "^3.3.1",
@@ -64,5 +66,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "75c4cba2f50c626c62881abd5851dbf2435c2401"
+  "gitHead": "283e0387ccd5acc9f092cf00804d1fcac212e68d"
 }

package/src/BaseLinearDisplay/components/ServerSideRenderedBlockContent.tsx CHANGED Viewed

@@ -3,8 +3,11 @@ import { makeStyles } from 'tss-react/mui'
 import { observer } from 'mobx-react'
 import { getParent } from 'mobx-state-tree'
 import { LoadingEllipses } from '@jbrowse/core/ui'
+// icons
 import RefreshIcon from '@mui/icons-material/Refresh'
+// locals
 import BlockMsg from './BlockMsg'
 const useStyles = makeStyles()(theme => ({
@@ -53,37 +56,35 @@ const LoadingMessage = observer(({ model }: { model: any }) => {
   )
 })
-const ServerSideRenderedBlockContent = observer(
-  ({
-    model,
-  }: {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    model: any
-  }) => {
-    if (model.error) {
-      return (
-        <BlockMsg
-          message={`${model.error}`}
-          severity="error"
-          buttonText="reload"
-          icon={<RefreshIcon />}
-          action={model.reload}
-        />
-      )
-    }
-    if (model.message) {
-      // the message can be a fully rendered react component, e.g. the region too large message
-      return React.isValidElement(model.message) ? (
-        model.message
-      ) : (
-        <BlockMsg message={`${model.message}`} severity="info" />
-      )
-    }
-    if (!model.filled) {
-      return <LoadingMessage model={model} />
-    }
-    return model.reactElement
-  },
-)
+const ServerSideRenderedBlockContent = observer(function ({
+  model,
+}: {
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  model: any
+}) {
+  if (model.error) {
+    return (
+      <BlockMsg
+        message={`${model.error}`}
+        severity="error"
+        buttonText="reload"
+        icon={<RefreshIcon />}
+        action={model.reload}
+      />
+    )
+  }
+  if (model.message) {
+    // the message can be a fully rendered react component, e.g. the region too large message
+    return React.isValidElement(model.message) ? (
+      model.message
+    ) : (
+      <BlockMsg message={`${model.message}`} severity="info" />
+    )
+  }
+  if (!model.filled) {
+    return <LoadingMessage model={model} />
+  }
+  return model.reactElement
+})
 export default ServerSideRenderedBlockContent