@jbrowse/plugin-linear-genome-view 2.3.1 → 2.3.2

package/dist/LinearGenomeView/components/GetSequenceDialog.js

@@ -78,9 +78,12 @@ function SequenceDialog({ model, handleClose, }) {
     const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
     const [error, setError] = (0, react_1.useState)();
-    const [sequence, setSequence] = (0, react_1.useState)();
-    const loading = Boolean(sequence === undefined);
+    const [sequenceChunks, setSequenceChunks] = (0, react_1.useState)();
+    const [rev, setReverse] = (0, react_1.useState)(false);
+    const [copied, setCopied] = (0, react_1.useState)(false);
+    const [comp, setComplement] = (0, react_1.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
@@ -93,19 +96,7 @@ function SequenceDialog({ model, handleClose, }) {
                 if (regionsSelected.length > 0) {
                     const chunks = await fetchSequence(model, regionsSelected, controller.signal);
                     if (active) {
-                        setSequence((0, formatFastaStrings_1.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 ${(chunkEnd - chunkStart).toLocaleString()}`);
-                            }
-                            return { header: chunkLocstring, seq: chunkSeq };
-                        })));
+                        setSequenceChunks(chunks);
                     }
                 }
                 else {
@@ -123,37 +114,59 @@ function SequenceDialog({ model, handleClose, }) {
             controller.abort();
             active = false;
         };
-    }, [model, session, regionsSelected, setSequence]);
+    }, [model, session, regionsSelected]);
+    const sequence = sequenceChunks
+        ? (0, formatFastaStrings_1.formatSeqFasta)(sequenceChunks
+            .filter(f => !!f)
+            .map(chunk => {
+            let chunkSeq = chunk.get('seq');
+            const chunkRefName = chunk.get('refName');
+            const chunkStart = chunk.get('start') + 1;
+            const chunkEnd = chunk.get('end');
+            const chunkLocstring = `${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 ${(chunkEnd - chunkStart).toLocaleString()}`);
+            }
+            if (rev) {
+                chunkSeq = (0, util_1.reverse)(chunkSeq);
+            }
+            if (comp) {
+                chunkSeq = (0, util_1.complement)(chunkSeq);
+            }
+            return { header: chunkLocstring, seq: chunkSeq };
+        }))
+        : '';
     const sequenceTooLarge = sequence ? sequence.length > 1000000 : false;
     return (react_1.default.createElement(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => {
             handleClose();
             model.setOffsets(undefined, undefined);
         }, title: "Reference sequence" },
         react_1.default.createElement(material_1.DialogContent, null,
-            error ? react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`) : null,
-            loading && !error ? (react_1.default.createElement(material_1.Container, null,
+            error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : loading ? (react_1.default.createElement(material_1.Container, null,
                 "Retrieving reference sequence...",
-                react_1.default.createElement(material_1.CircularProgress, { style: {
-                        marginLeft: 10,
-                    }, size: 20, disableShrink: true }))) : null,
-            react_1.default.createElement(material_1.TextField, { "data-testid": "rubberband-sequence", variant: "outlined", multiline: true, minRows: 5, disabled: sequenceTooLarge, className: classes.dialogContent, fullWidth: true, value: sequenceTooLarge
+                react_1.default.createElement(material_1.CircularProgress, { style: { marginLeft: 10 }, size: 20, disableShrink: true }))) : null,
+            react_1.default.createElement(material_1.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_1.default.createElement(material_1.FormGroup, null,
+                react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { value: rev, onChange: event => setReverse(event.target.checked) }), label: "Reverse sequence" }),
+                react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { value: comp, onChange: event => setComplement(event.target.checked) }), label: "Complement sequence" })),
+            react_1.default.createElement(material_1.Typography, { style: { margin: 10 } }, "Note: Check both boxes for the \"reverse complement\"")),
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { onClick: () => {
-                    (0, copy_to_clipboard_1.default)(sequence || '');
-                    session.notify('Copied to clipboard', 'success');
-                }, disabled: loading || !!error || sequenceTooLarge, color: "primary", startIcon: react_1.default.createElement(Icons_1.ContentCopy, null) }, "Copy to clipboard"),
+                    (0, copy_to_clipboard_1.default)(sequence);
+                    setCopied(true);
+                    setTimeout(() => setCopied(false), 500);
+                }, disabled: loading || !!error || sequenceTooLarge, color: "primary", startIcon: react_1.default.createElement(Icons_1.ContentCopy, null) }, copied ? 'Copied' : 'Copy to clipboard'),
             react_1.default.createElement(material_1.Button, { onClick: () => {
-                    const seqFastaFile = new Blob([sequence || ''], {
+                    (0, file_saver_1.saveAs)(new Blob([sequence || ''], {
                         type: 'text/x-fasta;charset=utf-8',
-                    });
-                    (0, file_saver_1.saveAs)(seqFastaFile, 'jbrowse_ref_seq.fa');
+                    }), 'jbrowse_ref_seq.fa');
                 }, disabled: loading || !!error, color: "primary", startIcon: react_1.default.createElement(GetApp_1.default, null) }, "Download FASTA"),
             react_1.default.createElement(material_1.Button, { onClick: handleClose, variant: "contained" }, "Close"))));
 }

package/dist/LinearGenomeView/components/GetSequenceDialog.js.map

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+{"version":3,"file":"GetSequenceDialog.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/GetSequenceDialog.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAA2D;AAC3D,uCAA0C;AAC1C,4CAWsB;AACtB,2CAAqC;AACrC,2CAAmC;AACnC,+DAAqD;AACrD,0EAAoC;AACpC,yCAAyC;AACzC,6CAM2B;AAC3B,8EAAsE;AAEtE,QAAQ;AACR,kDAAuE;AACvE,wEAAmD;AAKnD,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC;IAC7B,aAAa,EAAE;QACb,KAAK,EAAE,MAAM;KACd;IACD,YAAY,EAAE;QACZ,UAAU,EAAE,aAAa;KAC1B;CACF,CAAC,CAAA;AAIF;;GAEG;AACH,KAAK,UAAU,aAAa,CAC1B,KAAU,EACV,OAAiB,EACjB,MAAoB;IAEpB,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IAEzC,IAAI,CAAC,UAAU,IAAI,CAAC,WAAW,EAAE;QAC/B,MAAM,IAAI,KAAK,CAAC,sCAAsC,CAAC,CAAA;KACxD;IAED,IAAI,UAAU,CAAC,YAAY,KAAK,WAAW,CAAC,YAAY,EAAE;QACxD,MAAM,IAAI,KAAK,CAAC,sDAAsD,CAAC,CAAA;KACxE;IACD,MAAM,EAAE,UAAU,EAAE,eAAe,EAAE,GAAG,OAAO,CAAA;IAC/C,MAAM,YAAY,GAAG,UAAU,CAAC,YAAY,IAAI,WAAW,CAAC,YAAY,IAAI,EAAE,CAAA;IAC9E,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAClD,IAAI,CAAC,QAAQ,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,YAAY,YAAY,YAAY,CAAC,CAAA;KACtD;IACD,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,QAAQ,EAAE,CAAC,UAAU,EAAE,SAAS,CAAC,CAAC,CAAA;IAEhE,MAAM,SAAS,GAAG,aAAa,CAAA;IAC/B,OAAO,UAAU,CAAC,IAAI,CAAC,SAAS,EAAE,iBAAiB,EAAE;QACnD,aAAa;QACb,OAAO;QACP,SAAS;QACT,MAAM;KACP,CAAuB,CAAA;AAC1B,CAAC;AAED,SAAS,cAAc,CAAC,EACtB,KAAK,EACL,WAAW,GAIZ;IACC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,KAAK,CAAC,CAAA;IACjC,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,GAAG,IAAA,gBAAQ,GAAW,CAAA;IAC7C,MAAM,CAAC,cAAc,EAAE,iBAAiB,CAAC,GAAG,IAAA,gBAAQ,GAAa,CAAA;IACjE,MAAM,CAAC,GAAG,EAAE,UAAU,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IACzC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,CAAC,IAAI,EAAE,aAAa,CAAC,GAAG,IAAA,gBAAQ,EAAC,KAAK,CAAC,CAAA;IAC7C,MAAM,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,KAAK,CAAA;IACzC,MAAM,OAAO,GAAG,OAAO,CAAC,cAAc,KAAK,SAAS,CAAC,CAAA;IAErD,sCAAsC;IACtC,0EAA0E;IAC1E,yEAAyE;IACzE,MAAM,eAAe,GAAG,IAAA,eAAO,EAC7B,GAAG,EAAE,CAAC,KAAK,CAAC,kBAAkB,CAAC,UAAU,EAAE,WAAW,CAAC,EACvD,CAAC,KAAK,EAAE,UAAU,EAAE,WAAW,CAAC,CACjC,CAAA;IAED,IAAA,iBAAS,EAAC,GAAG,EAAE;QACb,IAAI,MAAM,GAAG,IAAI,CAAA;QACjB,MAAM,UAAU,GAAG,IAAI,eAAe,EAAE,CAGvC;QAAA,CAAC,KAAK,IAAI,EAAE;YACX,IAAI;gBACF,IAAI,eAAe,CAAC,MAAM,GAAG,CAAC,EAAE;oBAC9B,MAAM,MAAM,GAAG,MAAM,aAAa,CAChC,KAAK,EACL,eAAe,EACf,UAAU,CAAC,MAAM,CAClB,CAAA;oBACD,IAAI,MAAM,EAAE;wBACV,iBAAiB,CAAC,MAAM,CAAC,CAAA;qBAC1B;iBACF;qBAAM;oBACL,MAAM,IAAI,KAAK,CAAC,kCAAkC,CAAC,CAAA;iBACpD;aACF;YAAC,OAAO,CAAC,EAAE;gBACV,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;gBAChB,IAAI,MAAM,EAAE;oBACV,QAAQ,CAAC,CAAC,CAAC,CAAA;iBACZ;aACF;QACH,CAAC,CAAC,EAAE,CAAA;QAEJ,OAAO,GAAG,EAAE;YACV,UAAU,CAAC,KAAK,EAAE,CAAA;YAClB,MAAM,GAAG,KAAK,CAAA;QAChB,CAAC,CAAA;IACH,CAAC,EAAE,CAAC,KAAK,EAAE,OAAO,EAAE,eAAe,CAAC,CAAC,CAAA;IAErC,MAAM,QAAQ,GAAG,cAAc;QAC7B,CAAC,CAAC,IAAA,mCAAc,EACZ,cAAc;aACX,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;aAChB,GAAG,CAAC,KAAK,CAAC,EAAE;YACX,IAAI,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAC/B,MAAM,YAAY,GAAG,KAAK,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;YACzC,MAAM,UAAU,GAAG,KAAK,CAAC,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;YACzC,MAAM,QAAQ,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YACjC,MAAM,cAAc,GAAG,GAAG,YAAY,IAAI,UAAU,IAAI,QAAQ,EAAE,CAAA;YAClE,IAAI,CAAA,QAAQ,aAAR,QAAQ,uBAAR,QAAQ,CAAE,MAAM,MAAK,QAAQ,GAAG,UAAU,GAAG,CAAC,EAAE;gBAClD,MAAM,IAAI,KAAK,CACb,GAAG,cAAc,aAAa,QAAQ,CAAC,MAAM,CAAC,cAAc,EAAE,oCAAoC,CAChG,QAAQ,GAAG,UAAU,CACtB,CAAC,cAAc,EAAE,EAAE,CACrB,CAAA;aACF;YAED,IAAI,GAAG,EAAE;gBACP,QAAQ,GAAG,IAAA,cAAO,EAAC,QAAQ,CAAC,CAAA;aAC7B;YACD,IAAI,IAAI,EAAE;gBACR,QAAQ,GAAG,IAAA,iBAAU,EAAC,QAAQ,CAAC,CAAA;aAChC;YACD,OAAO,EAAE,MAAM,EAAE,cAAc,EAAE,GAAG,EAAE,QAAQ,EAAE,CAAA;QAClD,CAAC,CAAC,CACL;QACH,CAAC,CAAC,EAAE,CAAA;IAEN,MAAM,gBAAgB,GAAG,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,GAAG,OAAS,CAAC,CAAC,CAAC,KAAK,CAAA;IAEvE,OAAO,CACL,8BAAC,WAAM,IACL,QAAQ,EAAC,IAAI,EACb,IAAI,QACJ,OAAO,EAAE,GAAG,EAAE;YACZ,WAAW,EAAE,CAAA;YACb,KAAK,CAAC,UAAU,CAAC,SAAS,EAAE,SAAS,CAAC,CAAA;QACxC,CAAC,EACD,KAAK,EAAC,oBAAoB;QAE1B,8BAAC,wBAAa;YACX,KAAK,CAAC,CAAC,CAAC,CACP,8BAAC,qBAAU,IAAC,KAAK,EAAC,OAAO,IAAE,GAAG,KAAK,EAAE,CAAc,CACpD,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CACZ,8BAAC,oBAAS;;gBAER,8BAAC,2BAAgB,IACf,KAAK,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE,EACzB,IAAI,EAAE,EAAE,EACR,aAAa,SACb,CACQ,CACb,CAAC,CAAC,CAAC,IAAI;YACR,8BAAC,oBAAS,mBACI,qBAAqB,EACjC,OAAO,EAAC,UAAU,EAClB,SAAS,QACT,OAAO,EAAE,CAAC,EACV,OAAO,EAAE,EAAE,EACX,QAAQ,EAAE,gBAAgB,EAC1B,SAAS,EAAE,OAAO,CAAC,aAAa,EAChC,SAAS,QACT,KAAK,EACH,gBAAgB;oBACd,CAAC,CAAC,wEAAwE;oBAC1E,CAAC,CAAC,QAAQ,EAEd,UAAU,EAAE;oBACV,QAAQ,EAAE,IAAI;oBACd,OAAO,EAAE;wBACP,KAAK,EAAE,OAAO,CAAC,YAAY;qBAC5B;iBACF,GACD;YACF,8BAAC,oBAAS;gBACR,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,KAAK,EAAE,GAAG,EACV,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,GACnD,EAEJ,KAAK,EAAC,kBAAkB,GACxB;gBACF,8BAAC,2BAAgB,IACf,OAAO,EACL,8BAAC,mBAAQ,IACP,KAAK,EAAE,IAAI,EACX,QAAQ,EAAE,KAAK,CAAC,EAAE,CAAC,aAAa,CAAC,KAAK,CAAC,MAAM,CAAC,OAAO,CAAC,GACtD,EAEJ,KAAK,EAAC,qBAAqB,GAC3B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package/dist/LinearGenomeView/components/RefNameAutocomplete.js

@@ -118,7 +118,7 @@ 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((0, util_1.measureText)(inputBoxVal, 16) + 45, minWidth), 550);
+    const width = Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 16) + 50, minWidth), 550);
     // notes on implementation:
     // The selectOnFocus setting helps highlight the field when clicked
     return (react_1.default.createElement(react_1.default.Fragment, null,

package/dist/LinearGenomeView/model.js

@@ -87,11 +87,6 @@ exports.RESIZE_HANDLE_HEIGHT = 3;
 exports.INTER_REGION_PADDING_WIDTH = 2;
 exports.SPACING = 7;
 exports.WIDGET_HEIGHT = 32;
-function localStorageGetItem(item) {
-    return typeof localStorage !== 'undefined'
-        ? localStorage.getItem(item)
-        : undefined;
-}
 /**
  * #stateModel LinearGenomeView
  */
@@ -104,9 +99,9 @@ function stateModelFactory(pluginManager) {
         id: mst_1.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: mobx_state_tree_1.types.literal('LinearGenomeView'),
         /**
@@ -121,9 +116,10 @@ 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: mobx_state_tree_1.types.array(mst_1.Region),
         /**
@@ -152,23 +148,17 @@ function stateModelFactory(pluginManager) {
          * #property
          * how to display the track labels, can be "overlapping", "offset", or "hidden"
          */
-        trackLabels: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, () => localStorageGetItem('lgv-trackLabels') || 'overlapping'),
+        trackLabels: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, () => (0, util_1.localStorageGetItem)('lgv-trackLabels') || 'overlapping'),
         /**
          * #property
          * show the "center line"
          */
-        showCenterLine: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => {
-            const setting = localStorageGetItem('lgv-showCenterLine');
-            return setting !== undefined && setting !== null ? !!+setting : false;
-        }),
+        showCenterLine: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => JSON.parse((0, util_1.localStorageGetItem)('lgv-showCenterLine') || 'false')),
         /**
          * #property
          * show the "cytobands" in the overview scale bar
          */
-        showCytobandsSetting: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => {
-            const setting = localStorageGetItem('lgv-showCytobands');
-            return setting !== undefined && setting !== null ? !!+setting : true;
-        }),
+        showCytobandsSetting: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => JSON.parse((0, util_1.localStorageGetItem)('lgv-showCytobands') || 'true')),
         /**
          * #property
          * show the "gridlines" in the track area
@@ -440,7 +430,6 @@ function stateModelFactory(pluginManager) {
          */
         setShowCytobands(flag) {
             self.showCytobandsSetting = flag;
-            localStorage.setItem('lgv-showCytobands', `${+flag}`);
         },
         /**
          * #action
@@ -642,14 +631,12 @@ function stateModelFactory(pluginManager) {
          */
         setTrackLabels(setting) {
             self.trackLabels = setting;
-            localStorage.setItem('lgv-trackLabels', setting);
         },
         /**
          * #action
          */
         toggleCenterLine() {
             self.showCenterLine = !self.showCenterLine;
-            localStorage.setItem('lgv-showCenterLine', `${+self.showCenterLine}`);
         },
         /**
          * #action
@@ -1073,6 +1060,13 @@ function stateModelFactory(pluginManager) {
                     this.setCoarseDynamicBlocks(self.dynamicBlocks);
                 }
             }, { delay: 150 }));
+            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
+                const s = (s) => JSON.stringify(s);
+                const { trackLabels, showCytobandsSetting, showCenterLine } = self;
+                localStorage.setItem('lgv-trackLabels', trackLabels);
+                localStorage.setItem('lgv-showCytobands', s(showCytobandsSetting));
+                localStorage.setItem('lgv-showCenterLine', s(showCenterLine));
+            }));
         },
     }))
         .actions(self => ({

package/dist/LinearGenomeView/model.js.map

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package/esm/LinearGenomeView/components/GetSequenceDialog.js

@@ -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

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

@@ -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

@@ -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 +1026,13 @@ export function stateModelFactory(pluginManager) {
                     this.setCoarseDynamicBlocks(self.dynamicBlocks);
                 }
             }, { delay: 150 }));
+            addDisposer(self, autorun(() => {
+                const s = (s) => JSON.stringify(s);
+                const { trackLabels, showCytobandsSetting, showCenterLine } = self;
+                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

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-genome-view",
-  "version": "2.3.1",
+  "version": "2.3.2",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -64,5 +64,5 @@
     "access": "public"
   },
   "module": "esm/index.js",
-  "gitHead": "75c4cba2f50c626c62881abd5851dbf2435c2401"
+  "gitHead": "467d973535bb7b2664e9f66311fb0dc21c1ce5ba"
 }

package/src/LinearGenomeView/components/GetSequenceDialog.tsx

@@ -2,10 +2,13 @@ import React, { useEffect, useMemo, useState } from 'react'
 import { makeStyles } from 'tss-react/mui'
 import {
   Button,
+  Checkbox,
   CircularProgress,
   Container,
   DialogActions,
   DialogContent,
+  FormGroup,
+  FormControlLabel,
   TextField,
   Typography,
 } from '@mui/material'
@@ -14,7 +17,13 @@ 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, Feature, Region } from '@jbrowse/core/util'
+import {
+  getSession,
+  reverse,
+  complement,
+  Feature,
+  Region,
+} from '@jbrowse/core/util'
 import { formatSeqFasta } from '@jbrowse/core/util/formatFastaStrings'
 
 // icons
@@ -80,9 +89,12 @@ function SequenceDialog({
   const { classes } = useStyles()
   const session = getSession(model)
   const [error, setError] = useState<unknown>()
-  const [sequence, setSequence] = useState<string>()
-  const loading = Boolean(sequence === undefined)
+  const [sequenceChunks, setSequenceChunks] = useState<Feature[]>()
+  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
@@ -106,27 +118,7 @@ function SequenceDialog({
             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}-${chunkEnd}`
-                    if (chunkSeq?.length !== chunkEnd - chunkStart + 1) {
-                      throw new Error(
-                        `${chunkLocstring} returned ${chunkSeq.length.toLocaleString()} bases, but should have returned ${(
-                          chunkEnd - chunkStart
-                        ).toLocaleString()}`,
-                      )
-                    }
-                    return { header: chunkLocstring, seq: chunkSeq }
-                  }),
-              ),
-            )
+            setSequenceChunks(chunks)
           }
         } else {
           throw new Error('Selected region is out of bounds')
@@ -143,7 +135,36 @@ function SequenceDialog({
       controller.abort()
       active = false
     }
-  }, [model, session, regionsSelected, setSequence])
+  }, [model, session, regionsSelected])
+
+  const sequence = sequenceChunks
+    ? formatSeqFasta(
+        sequenceChunks
+          .filter(f => !!f)
+          .map(chunk => {
+            let chunkSeq = chunk.get('seq')
+            const chunkRefName = chunk.get('refName')
+            const chunkStart = chunk.get('start') + 1
+            const chunkEnd = chunk.get('end')
+            const chunkLocstring = `${chunkRefName}:${chunkStart}-${chunkEnd}`
+            if (chunkSeq?.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 > 1_000_000 : false
 
@@ -158,14 +179,13 @@ function SequenceDialog({
       title="Reference sequence"
     >
       <DialogContent>
-        {error ? <Typography color="error">{`${error}`}</Typography> : null}
-        {loading && !error ? (
+        {error ? (
+          <Typography color="error">{`${error}`}</Typography>
+        ) : loading ? (
           <Container>
             Retrieving reference sequence...
             <CircularProgress
-              style={{
-                marginLeft: 10,
-              }}
+              style={{ marginLeft: 10 }}
               size={20}
               disableShrink
             />
@@ -176,6 +196,7 @@ function SequenceDialog({
           variant="outlined"
           multiline
           minRows={5}
+          maxRows={10}
           disabled={sequenceTooLarge}
           className={classes.dialogContent}
           fullWidth
@@ -191,25 +212,51 @@ function SequenceDialog({
             },
           }}
         />
+        <FormGroup>
+          <FormControlLabel
+            control={
+              <Checkbox
+                value={rev}
+                onChange={event => setReverse(event.target.checked)}
+              />
+            }
+            label="Reverse sequence"
+          />
+          <FormControlLabel
+            control={
+              <Checkbox
+                value={comp}
+                onChange={event => setComplement(event.target.checked)}
+              />
+            }
+            label="Complement sequence"
+          />
+        </FormGroup>
+        <Typography style={{ margin: 10 }}>
+          Note: Check both boxes for the "reverse complement"
+        </Typography>
       </DialogContent>
       <DialogActions>
         <Button
           onClick={() => {
-            copy(sequence || '')
-            session.notify('Copied to clipboard', 'success')
+            copy(sequence)
+            setCopied(true)
+            setTimeout(() => setCopied(false), 500)
           }}
           disabled={loading || !!error || sequenceTooLarge}
           color="primary"
           startIcon={<ContentCopyIcon />}
         >
-          Copy to clipboard
+          {copied ? 'Copied' : 'Copy to clipboard'}
         </Button>
         <Button
           onClick={() => {
-            const seqFastaFile = new Blob([sequence || ''], {
-              type: 'text/x-fasta;charset=utf-8',
-            })
-            saveAs(seqFastaFile, 'jbrowse_ref_seq.fa')
+            saveAs(
+              new Blob([sequence || ''], {
+                type: 'text/x-fasta;charset=utf-8',
+              }),
+              'jbrowse_ref_seq.fa',
+            )
           }}
           disabled={loading || !!error}
           color="primary"

package/src/LinearGenomeView/components/RefNameAutocomplete.tsx

@@ -149,7 +149,7 @@ function RefNameAutocomplete({
   // heuristic, text width + icon width
   // + 45 accommodates help icon and search icon
   const width = Math.min(
-    Math.max(measureText(inputBoxVal, 16) + 45, minWidth),
+    Math.max(measureText(inputBoxVal, 16) + 50, minWidth),
     550,
   )
 

package/src/LinearGenomeView/components/__snapshots__/LinearGenomeView.test.tsx.snap

@@ -718,7 +718,7 @@ exports[`renders two tracks, two regions 1`] = `
           <div
             class="MuiAutocomplete-root css-1qqsdnr-MuiAutocomplete-root"
             data-testid="autocomplete"
-            style="width: 255.27500000000003px;"
+            style="width: 260.27500000000003px;"
           >
             <div
               class="MuiFormControl-root MuiFormControl-fullWidth MuiTextField-root css-1efd6m0-MuiFormControl-root-MuiTextField-root-headerRefName"

package/src/LinearGenomeView/model.ts

@@ -12,10 +12,11 @@ import {
   getSession,
   isViewContainer,
   isSessionModelWithWidgets,
+  isSessionWithAddTracks,
+  localStorageGetItem,
   measureText,
   parseLocString,
   springAnimate,
-  isSessionWithAddTracks,
 } from '@jbrowse/core/util'
 import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
 import { BlockSet, BaseBlock } from '@jbrowse/core/util/blockTypes'
@@ -116,12 +117,6 @@ export const INTER_REGION_PADDING_WIDTH = 2
 export const SPACING = 7
 export const WIDGET_HEIGHT = 32
 
-function localStorageGetItem(item: string) {
-  return typeof localStorage !== 'undefined'
-    ? localStorage.getItem(item)
-    : undefined
-}
-
 /**
  * #stateModel LinearGenomeView
  */
@@ -137,9 +132,9 @@ export function stateModelFactory(pluginManager: PluginManager) {
 
         /**
          * #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') as unknown as string,
 
@@ -157,9 +152,10 @@ export function stateModelFactory(pluginManager: PluginManager) {
 
         /**
          * #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),
 
@@ -208,19 +204,17 @@ export function stateModelFactory(pluginManager: 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
@@ -529,7 +523,6 @@ export function stateModelFactory(pluginManager: PluginManager) {
        */
       setShowCytobands(flag: boolean) {
         self.showCytobandsSetting = flag
-        localStorage.setItem('lgv-showCytobands', `${+flag}`)
       },
       /**
        * #action
@@ -757,7 +750,6 @@ export function stateModelFactory(pluginManager: PluginManager) {
        */
       setTrackLabels(setting: 'overlapping' | 'offset' | 'hidden') {
         self.trackLabels = setting
-        localStorage.setItem('lgv-trackLabels', setting)
       },
 
       /**
@@ -765,7 +757,6 @@ export function stateModelFactory(pluginManager: PluginManager) {
        */
       toggleCenterLine() {
         self.showCenterLine = !self.showCenterLine
-        localStorage.setItem('lgv-showCenterLine', `${+self.showCenterLine}`)
       },
 
       /**
@@ -1241,6 +1232,17 @@ export function stateModelFactory(pluginManager: PluginManager) {
             { delay: 150 },
           ),
         )
+
+        addDisposer(
+          self,
+          autorun(() => {
+            const s = (s: unknown) => JSON.stringify(s)
+            const { trackLabels, showCytobandsSetting, showCenterLine } = self
+            localStorage.setItem('lgv-trackLabels', trackLabels)
+            localStorage.setItem('lgv-showCytobands', s(showCytobandsSetting))
+            localStorage.setItem('lgv-showCenterLine', s(showCenterLine))
+          }),
+        )
       },
     }))
     .actions(self => ({