npm - @jbrowse/plugin-linear-genome-view - Versions diffs - 2.4.2 → 2.5.0 - Mend

@jbrowse/plugin-linear-genome-view 2.4.2 → 2.5.0

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 (180) hide show

package/dist/LinearGenomeView/components/Cytobands.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
 import { ContentBlock } from '@jbrowse/core/util/blockTypes';
 import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
@@ -12,10 +11,10 @@ declare const _default: ({ overview, block, assembly, }: {
         loadingP: Promise<void> | undefined;
         volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         lowerCaseRefNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         cytobands: import("@jbrowse/core/util").Feature[] | undefined;
     } & {
@@ -29,12 +28,12 @@ declare const _default: ({ overview, block, assembly, }: {
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
+        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         readonly refNameColors: string[];
     } & {
         readonly refNames: string[] | undefined;
     } & {
-        getCanonicalRefName(refName: string): string;
+        getCanonicalRefName(refName: string): string | undefined;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -42,21 +41,21 @@ declare const _default: ({ overview, block, assembly, }: {
         setError(e: unknown): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }, lcAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
         setLoadingP(p?: Promise<void> | undefined): void;
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
     } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
         configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
@@ -66,10 +65,10 @@ declare const _default: ({ overview, block, assembly, }: {
         loadingP: Promise<void> | undefined;
         volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
         refNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         lowerCaseRefNameAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         } | undefined;
         cytobands: import("@jbrowse/core/util").Feature[] | undefined;
     } & {
@@ -83,12 +82,12 @@ declare const _default: ({ overview, block, assembly, }: {
         readonly allRefNames: string[] | undefined;
         readonly lowerCaseRefNames: string[] | undefined;
         readonly allRefNamesWithLowerCase: string[] | undefined;
-        readonly rpcManager: any;
+        readonly rpcManager: import("@jbrowse/core/rpc/RpcManager").default;
         readonly refNameColors: string[];
     } & {
         readonly refNames: string[] | undefined;
     } & {
-        getCanonicalRefName(refName: string): string;
+        getCanonicalRefName(refName: string): string | undefined;
         getRefNameColor(refName: string): string | undefined;
         isValidRefName(refName: string): boolean;
     } & {
@@ -96,21 +95,21 @@ declare const _default: ({ overview, block, assembly, }: {
         setError(e: unknown): void;
         setRegions(regions: import("@jbrowse/core/util").Region[]): void;
         setRefNameAliases(aliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }, lcAliases: {
-            [x: string]: string;
+            [x: string]: string | undefined;
         }): void;
         setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
         setLoadingP(p?: Promise<void> | undefined): void;
         load(): Promise<void>;
         loadPre(): Promise<void>;
     } & {
-        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
-        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
-        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
-            [x: string]: string;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/data_adapters/BaseAdapter").BaseOptions): Promise<{
+            [x: string]: string | undefined;
         }>;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
     block: ContentBlock;

package/dist/LinearGenomeView/components/ExportSvgDialog.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { ExportSvgOptions } from '..';
 export default function ExportSvgDlg({ model, handleClose, }: {
     model: {

package/dist/LinearGenomeView/components/GetSequenceDialog.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare function SequenceDialog({ model, handleClose, }: {

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

@@ -84,24 +84,22 @@ function SequenceDialog({ model, handleClose, }) {
     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
-    const regionsSelected = (0, react_1.useMemo)(() => model.getSelectedRegions(leftOffset, rightOffset), [model, leftOffset, rightOffset]);
     (0, react_1.useEffect)(() => {
         let active = true;
         const controller = new AbortController();
         (async () => {
             try {
-                if (regionsSelected.length > 0) {
-                    const chunks = await fetchSequence(model, regionsSelected, controller.signal);
-                    if (active) {
-                        setSequenceChunks(chunks);
-                    }
-                }
-                else {
+                // 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
+                const selection = model.getSelectedRegions(leftOffset, rightOffset);
+                if (selection.length === 0) {
                     throw new Error('Selected region is out of bounds');
                 }
+                const chunks = await fetchSequence(model, selection, controller.signal);
+                if (active) {
+                    setSequenceChunks(chunks);
+                }
             }
             catch (e) {
                 console.error(e);
@@ -114,7 +112,7 @@ function SequenceDialog({ model, handleClose, }) {
             controller.abort();
             active = false;
         };
-    }, [model, session, regionsSelected]);
+    }, [model, session, leftOffset, rightOffset]);
     const sequence = sequenceChunks
         ? (0, formatFastaStrings_1.formatSeqFasta)(sequenceChunks
             .filter(f => !!f)
@@ -123,9 +121,9 @@ function SequenceDialog({ model, handleClose, }) {
             const chunkRefName = chunk.get('refName');
             const chunkStart = chunk.get('start') + 1;
             const chunkEnd = chunk.get('end');
-            const chunkLocstring = `${chunkRefName}:${chunkStart}-${chunkEnd}`;
+            const loc = `${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 ${(chunkEnd - chunkStart).toLocaleString()}`);
+                throw new Error(`${loc} returned ${chunkSeq.length.toLocaleString()} bases, but should have returned ${(chunkEnd - chunkStart).toLocaleString()}`);
             }
             if (rev) {
                 chunkSeq = (0, util_1.reverse)(chunkSeq);
@@ -134,7 +132,7 @@ function SequenceDialog({ model, handleClose, }) {
                 chunkSeq = (0, util_1.complement)(chunkSeq);
             }
             return {
-                header: chunkLocstring + (rev ? '-rev' : '') + (comp ? '-comp' : ''),
+                header: loc + (rev ? '-rev' : '') + (comp ? '-comp' : ''),
                 seq: chunkSeq,
             };
         }))
@@ -142,7 +140,7 @@ function SequenceDialog({ model, handleClose, }) {
     const sequenceTooLarge = sequence ? sequence.length > 1000000 : false;
     return (react_1.default.createElement(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: () => {
             handleClose();
-            model.setOffsets(undefined, undefined);
+            model.setOffsets();
         }, title: "Reference sequence" },
         react_1.default.createElement(material_1.DialogContent, null,
             error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : loading ? (react_1.default.createElement(material_1.Container, null,

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

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package/dist/LinearGenomeView/components/Gridlines.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare function VerticalGuides({ model }: {

package/dist/LinearGenomeView/components/Header.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare const LinearGenomeViewHeader: ({ model }: {

package/dist/LinearGenomeView/components/HelpDialog.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 export default function HelpDialog({ handleClose, }: {
     handleClose: () => void;
 }): JSX.Element;

package/dist/LinearGenomeView/components/ImportForm.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare const _default: ({ model }: {

package/dist/LinearGenomeView/components/ImportForm.js CHANGED Viewed

@@ -37,8 +37,6 @@ const Close_1 = __importDefault(require("@mui/icons-material/Close"));
 // locals
 const RefNameAutocomplete_1 = __importDefault(require("./RefNameAutocomplete"));
 const util_2 = require("./util");
-// lazies
-const SearchResultsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SearchResultsDialog'))));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     importFormContainer: {
         padding: theme.spacing(2),
@@ -55,7 +53,7 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
     const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
     const { assemblyNames, assemblyManager, textSearchManager } = session;
-    const { rankSearchResults, isSearchDialogDisplayed, error } = model;
+    const { rankSearchResults, error } = model;
     const [selectedAsm, setSelectedAsm] = (0, react_1.useState)(assemblyNames[0]);
     const [option, setOption] = (0, react_1.useState)();
     const searchScope = model.searchScope(selectedAsm);
@@ -98,7 +96,7 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
                 await navToOption(option);
             }
             else if ((_a = option === null || option === void 0 ? void 0 : option.results) === null || _a === void 0 ? void 0 : _a.length) {
-                model.setSearchResults(option.results, option.getLabel());
+                model.setSearchResults(option.results, option.getLabel(), selectedAsm);
             }
             else {
                 const [ref, rest] = (0, util_2.splitLast)(input, ':');
@@ -117,7 +115,7 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
                         assembly,
                     });
                     if (results.length > 1) {
-                        model.setSearchResults(results, input.toLowerCase());
+                        model.setSearchResults(results, input.toLowerCase(), selectedAsm);
                     }
                     else if (results.length === 1) {
                         await navToOption(results[0]);
@@ -168,7 +166,6 @@ exports.default = (0, mobx_react_1.observer)(function ({ model }) {
                             react_1.default.createElement(material_1.Button, { disabled: !value, className: classes.button, onClick: () => {
                                     model.setError(undefined);
                                     model.showAllRegionsInAssembly(selectedAsm);
-                                }, variant: "contained", color: "secondary" }, "Show all regions in assembly")))))),
-        isSearchDialogDisplayed ? (react_1.default.createElement(SearchResultsDialog, { model: model, optAssemblyName: selectedAsm, handleClose: () => model.setSearchResults(undefined, undefined) })) : null));
+                                }, variant: "contained", color: "secondary" }, "Show all regions in assembly"))))))));
 });
 //# sourceMappingURL=ImportForm.js.map

package/dist/LinearGenomeView/components/ImportForm.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/LinearGenomeView/components/LinearGenomeView.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 type LGV = LinearGenomeViewModel;
 declare const LinearGenomeView: ({ model }: {

package/dist/LinearGenomeView/components/LinearGenomeView.js CHANGED Viewed

@@ -12,8 +12,6 @@ const mobx_react_1 = require("mobx-react");
 const TrackContainer_1 = __importDefault(require("./TrackContainer"));
 const TracksContainer_1 = __importDefault(require("./TracksContainer"));
 const ImportForm_1 = __importDefault(require("./ImportForm"));
-const GetSequenceDialog_1 = __importDefault(require("./GetSequenceDialog"));
-const SearchResultsDialog_1 = __importDefault(require("./SearchResultsDialog"));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     note: {
         textAlign: 'center',
@@ -33,8 +31,6 @@ const LinearGenomeView = (0, mobx_react_1.observer)(({ model }) => {
     const MiniControlsComponent = model.MiniControlsComponent();
     const HeaderComponent = model.HeaderComponent();
     return (react_1.default.createElement("div", { style: { position: 'relative' } },
-        model.seqDialogDisplayed ? (react_1.default.createElement(GetSequenceDialog_1.default, { model: model, handleClose: () => model.setGetSequenceDialogOpen(false) })) : null,
-        model.isSearchDialogDisplayed ? (react_1.default.createElement(SearchResultsDialog_1.default, { model: model, handleClose: () => model.setSearchResults(undefined, undefined) })) : null,
         react_1.default.createElement(HeaderComponent, { model: model }),
         react_1.default.createElement(MiniControlsComponent, { model: model }),
         react_1.default.createElement(TracksContainer_1.default, { model: model }, !tracks.length ? (react_1.default.createElement(material_1.Paper, { variant: "outlined", className: classes.note }, !model.hideNoTracksActive ? (react_1.default.createElement(react_1.default.Fragment, null,

package/dist/LinearGenomeView/components/LinearGenomeView.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"LinearGenomeView.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/LinearGenomeView.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,4CAAyD;AACzD,uCAA0C;AAC1C,kDAA2E;AAC3E,yCAAkD;AAClD,2CAAqC;AAIrC,sEAA6C;AAC7C,wEAA+C;AAC/C,8DAAqC;~~AACrC~~,~~4EAAmD;AACnD,gFAAuD;AAIvD,~~MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,IAAI,EAAE;QACJ,SAAS,EAAE,QAAQ;QACnB,UAAU,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;QAC5B,aAAa,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC;KAChC;CACF,CAAC,CAAC,CAAA;AAEH,MAAM,gBAAgB,GAAG,IAAA,qBAAQ,EAAC,CAAC,EAAE,KAAK,EAAkB,EAAE,EAAE;IAC9D,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,WAAW,EAAE,mBAAmB,EAAE,GAAG,KAAK,CAAA;IACjE,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAE/B,IAAI,CAAC,WAAW,IAAI,CAAC,KAAK,EAAE;QAC1B,OAAO,8BAAC,oBAAe,IAAC,OAAO,EAAC,IAAI,GAAG,CAAA;KACxC;IACD,IAAI,CAAC,mBAAmB,IAAI,KAAK,EAAE;QACjC,OAAO,8BAAC,oBAAU,IAAC,KAAK,EAAE,KAAK,GAAI,CAAA;KACpC;IAED,MAAM,qBAAqB,GAAG,KAAK,CAAC,qBAAqB,EAAE,CAAA;IAC3D,MAAM,eAAe,GAAG,KAAK,CAAC,eAAe,EAAE,CAAA;IAE/C,OAAO,CACL,uCAAK,KAAK,EAAE,EAAE,QAAQ,EAAE,UAAU,EAAE;~~QACjC~~,~~KAAK,CAAC,kBAAkB,CAAC,CAAC,CAAC,CAC1B,~~8BAAC,2BAAiB,IAChB,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,wBAAwB,CAAC,KAAK,CAAC,GACxD,CACH,CAAC,CAAC,CAAC,IAAI;QACP,KAAK,CAAC,uBAAuB,CAAC,CAAC,CAAC,CAC/B,8BAAC,6BAAmB,IAClB,KAAK,EAAE,KAAK,EACZ,WAAW,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,gBAAgB,CAAC,SAAS,EAAE,SAAS,CAAC,GAC/D,CACH,CAAC,CAAC,CAAC,IAAI;QACR,8BAAC,eAAe,IAAC,KAAK,EAAE,KAAK,GAAI;QACjC,8BAAC,qBAAqB,IAAC,KAAK,EAAE,KAAK,GAAI;QACvC,8BAAC,yBAAe,IAAC,KAAK,EAAE,KAAK,IAC1B,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CAChB,8BAAC,gBAAK,IAAC,OAAO,EAAC,UAAU,EAAC,SAAS,EAAE,OAAO,CAAC,IAAI,IAC9C,CAAC,KAAK,CAAC,kBAAkB,CAAC,CAAC,CAAC,CAC3B;YACE,8BAAC,qBAAU,4BAA+B;YAC1C,8BAAC,iBAAM,IACL,OAAO,EAAC,WAAW,EACnB,KAAK,EAAC,SAAS,EACf,OAAO,EAAE,KAAK,CAAC,qBAAqB,EACpC,KAAK,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,EACvB,SAAS,EAAE,8BAAC,qBAAiB,OAAG,0BAGzB,CACR,CACJ,CAAC,CAAC,CAAC,CACF,uCAAK,KAAK,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,GAAQ,CACvC,CACK,CACT,CAAC,CAAC,CAAC,CACF,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,CAClB,8BAAC,wBAAc,IAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,GAAI,CAC9D,CAAC,CACH,CACe,CACd,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAEF,kBAAe,gBAAgB,CAAA"}
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package/dist/LinearGenomeView/components/MiniControls.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 declare const MiniControls: (props: {
     model: LinearGenomeViewModel;

package/dist/LinearGenomeView/components/OverviewScalebar.js CHANGED Viewed

@@ -66,6 +66,7 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         position: 'relative',
     },
     overviewSvg: {
+        pointerEvents: 'none',
         width: '100%',
         position: 'absolute',
     },
@@ -124,7 +125,7 @@ const OverviewBox = (0, mobx_react_1.observer)(function ({ scale, model, block,
         react_1.default.createElement(material_1.Typography, { style: {
                 left: block.offsetPx + 3,
                 color: canDisplayCytobands
-                    ? theme.palette.primary.contrastText
+                    ? theme.palette.text.primary
                     : refNameColor,
             }, className: classes.scalebarRefName }, refName),
         react_1.default.createElement("div", { className: cx(classes.scalebarContig, canDisplayCytobands

package/dist/LinearGenomeView/components/OverviewScalebar.js.map CHANGED Viewed

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

@@ -68,12 +68,27 @@ function filterOptions(options, searchQuery) {
     return options.filter(({ result }) => result.getLabel().toLowerCase().includes(searchQuery) ||
         result.matchedObject);
 }
+function getFiltered(opts, inputValue) {
+    const filtered = filterOptions(opts, inputValue.toLocaleLowerCase());
+    return [
+        ...filtered.slice(0, 100),
+        ...(filtered.length > 100
+            ? [
+                {
+                    group: 'limitOption',
+                    result: new BaseResults_1.default({
+                        label: 'keep typing for more results',
+                    }),
+                },
+            ]
+            : []),
+    ];
+}
 function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResults, onChange, value, showHelp = true, minWidth = 200, maxWidth = 550, TextFieldProps = {}, }) {
     const session = (0, util_1.getSession)(model);
     const { assemblyManager } = session;
     const [open, setOpen] = (0, react_1.useState)(false);
     const [loaded, setLoaded] = (0, react_1.useState)(true);
-    const [isHelpDialogDisplayed, setHelpDialogDisplayed] = (0, react_1.useState)(false);
     const [currentSearch, setCurrentSearch] = (0, react_1.useState)('');
     const [inputValue, setInputValue] = (0, react_1.useState)('');
     const [searchOptions, setSearchOptions] = (0, react_1.useState)();
@@ -114,9 +129,9 @@ function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResult
         };
     }, [assemblyName, fetchResults, debouncedSearch, session, model]);
     const inputBoxVal = coarseVisibleLocStrings || value || '';
-    // heuristic, text width + icon width + 50 accommodates help icon and search
+    // heuristic, text width + 60 accommodates help icon and search
     // icon
-    const width = Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 16) + 50, minWidth), maxWidth);
+    const width = Math.min(Math.max((0, util_1.measureText)(inputBoxVal, 14) + 100, minWidth), maxWidth);
     // notes on implementation:
     // The selectOnFocus setting helps highlight the field when clicked
     return (react_1.default.createElement(react_1.default.Fragment, null,
@@ -142,41 +157,33 @@ function RefNameAutocomplete({ model, onSelect, assemblyName, style, fetchResult
                     onSelect === null || onSelect === void 0 ? void 0 : onSelect(selectedOption.result);
                 }
                 setInputValue(inputBoxVal);
-            }, options: !(searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length) ? options : searchOptions, getOptionDisabled: option => (option === null || option === void 0 ? void 0 : option.group) === 'limitOption', filterOptions: (options, params) => {
-                const filtered = filterOptions(options, params.inputValue.toLocaleLowerCase());
-                return [
-                    ...filtered.slice(0, 100),
-                    ...(filtered.length > 100
-                        ? [
-                            {
-                                group: 'limitOption',
-                                result: new BaseResults_1.default({
-                                    label: 'keep typing for more results',
-                                }),
-                            },
-                        ]
-                        : []),
-                ];
-            }, renderInput: params => {
-                const { helperText, InputProps = {} } = TextFieldProps;
-                return (react_1.default.createElement(material_1.TextField, { onBlur: () =>
-                    // this is used to restore a refName or the non-user-typed input
-                    // to the box on blurring
-                    setInputValue(inputBoxVal), ...params, ...TextFieldProps, helperText: helperText, InputProps: {
-                        ...params.InputProps,
-                        ...InputProps,
-                        endAdornment: (react_1.default.createElement(react_1.default.Fragment, null,
-                            react_1.default.createElement(material_1.InputAdornment, { position: "end", style: { marginRight: 7 } },
-                                react_1.default.createElement(Search_1.default, { fontSize: "small" }),
-                                showHelp ? (react_1.default.createElement(material_1.IconButton, { onClick: () => setHelpDialogDisplayed(true), size: "small" },
-                                    react_1.default.createElement(Help_1.default, { fontSize: "small" }))) : null),
-                            params.InputProps.endAdornment)),
-                    }, placeholder: "Search for location", onChange: e => setCurrentSearch(e.target.value) }));
-            }, getOptionLabel: option => (typeof option === 'string'
-                ? option
-                : option.result.getDisplayString()) || '' }),
+            }, options: !(searchOptions === null || searchOptions === void 0 ? void 0 : searchOptions.length) ? options : searchOptions, getOptionDisabled: option => option.group === 'limitOption', filterOptions: (opts, { inputValue }) => getFiltered(opts, inputValue), renderInput: params => (react_1.default.createElement(AutocompleteTextField, { showHelp: showHelp, params: params, inputBoxVal: inputBoxVal, TextFieldProps: TextFieldProps, setCurrentSearch: setCurrentSearch, setInputValue: setInputValue })), getOptionLabel: opt => typeof opt === 'string' ? opt : opt.result.getDisplayString() })));
+}
+function AutocompleteTextField({ TextFieldProps, inputBoxVal, params, showHelp, setInputValue, setCurrentSearch, }) {
+    const { helperText, InputProps = {} } = TextFieldProps;
+    return (react_1.default.createElement(material_1.TextField, { onBlur: () =>
+        // this is used to restore a refName or the non-user-typed input
+        // to the box on blurring
+        setInputValue(inputBoxVal), ...params, ...TextFieldProps, size: "small", helperText: helperText, InputProps: {
+            ...params.InputProps,
+            ...InputProps,
+            endAdornment: (react_1.default.createElement(EndAdornment, { showHelp: showHelp, endAdornment: params.InputProps.endAdornment })),
+        }, placeholder: "Search for location", onChange: e => setCurrentSearch(e.target.value) }));
+}
+function HelpAdornment() {
+    const [isHelpDialogDisplayed, setHelpDialogDisplayed] = (0, react_1.useState)(false);
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(material_1.IconButton, { onClick: () => setHelpDialogDisplayed(true), size: "small" },
+            react_1.default.createElement(Help_1.default, { fontSize: "small" })),
         isHelpDialogDisplayed ? (react_1.default.createElement(react_1.Suspense, { fallback: react_1.default.createElement("div", null) },
             react_1.default.createElement(HelpDialog, { handleClose: () => setHelpDialogDisplayed(false) }))) : null));
 }
+function EndAdornment({ showHelp, endAdornment, }) {
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement(material_1.InputAdornment, { position: "end", style: { marginRight: 7 } },
+            react_1.default.createElement(Search_1.default, { fontSize: "small" }),
+            showHelp ? react_1.default.createElement(HelpAdornment, null) : null),
+        endAdornment));
+}
 exports.default = (0, mobx_react_1.observer)(RefNameAutocomplete);
 //# sourceMappingURL=RefNameAutocomplete.js.map

package/dist/LinearGenomeView/components/RefNameAutocomplete.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/LinearGenomeView/components/RubberbandSpan.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 interface Offset {
     coord: number;
     refName?: string;

package/dist/LinearGenomeView/components/SearchBox.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { LinearGenomeViewModel } from '..';
 declare function SearchBox({ model, showHelp, }: {
     showHelp?: boolean;