jbrowse-plugin-msaview 5.3.0 → 5.5.0

package/dist/MsaViewPanel/model.d.ts

@@ -1,6 +1,7 @@
 export type { MSAFormat } from 'msa-parsers';
 import type { BlastDatabase, MsaAlgorithm, PhmmerDatabase } from '../LaunchMsaView/components/BlastQuery/consts';
 import type { UnirefIdentity } from '../utils/unirefHomologs';
+import type { ConnectedDomain } from './connectedDomains';
 import type { MsaDataPayload } from './msaDataStore';
 import type { MafRegion, MsaViewInitState } from './types';
 import type { TranscriptRef } from './util';
@@ -128,7 +129,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
 }, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -497,7 +498,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Clade, import("react-msaview").Clade, import("react-msaview").Clade>>, [undefined]>;
     encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>>, [undefined]>;
     rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>>, [undefined]>;
-}, "init" | "querySeqName" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion"> & {
+}, "init" | "querySeqName" | "launchCompleted" | "embeddedMode" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion" | "domainsOnGenome"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
     connectedTranscript: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -511,6 +512,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     launchCompleted: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
+    embeddedMode: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    domainsOnGenome: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, {
     width: number;
     bodyMounted: boolean;
@@ -549,7 +552,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setCustomColorScheme(map?: Record<string, string>): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
-    setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
+    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
 } & {
     headerHeight: number;
     hideHeader: boolean;
@@ -581,7 +584,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     dismissedWarnings: string[];
     resetCount: number;
     hostCarriesData: boolean;
-    annotations: import("react-msaview").Annotation[];
+    annotations: import("msa-parsers").Annotation[];
 } & {
     drawRelativeTo(id: string | undefined): void;
     setHideGaps(arg: boolean): void;
@@ -632,7 +635,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setGFF(result?: string): void;
 } & {
     readonly hideGapsEffective: boolean;
-    readonly allAnnotations: import("react-msaview").Annotation[];
+    readonly allAnnotations: import("msa-parsers").Annotation[];
     readonly actuallyShowDomains: boolean;
     readonly hostRestoresData: boolean;
     readonly viewInitialized: boolean;
@@ -660,7 +663,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly rowData: Record<string, Record<string, string> | undefined>;
     rowDataOf(name: string): Record<string, string> | undefined;
     readonly rowFields: string[];
-    readonly MSA: import("react-msaview").MSAParserType | null;
+    readonly MSA: import("msa-parsers").MSAParserType | null;
     readonly numColumns: number;
     readonly inputTree: import("react-msaview").NodeWithIds;
     readonly tree: import("react-msaview").NodeWithIds;
@@ -791,9 +794,9 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly topBandHeight: number;
     readonly msaAreaHeight: number;
     readonly totalTrackAreaHeight: number;
-    readonly annotationTypes: Map<string, import("react-msaview").Annotation>;
-    readonly filteredAnnotations: import("react-msaview").Annotation[];
-    readonly annotationsByRow: Record<string, import("react-msaview").Annotation[]>;
+    readonly annotationTypes: Map<string, import("msa-parsers").Annotation>;
+    readonly filteredAnnotations: import("msa-parsers").Annotation[];
+    readonly annotationsByRow: Record<string, import("msa-parsers").Annotation[]>;
 } & {
     readonly showVerticalScrollbar: boolean;
 } & {
@@ -826,7 +829,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     zoomToPos(scaleFactor: number, offsetX: number, offsetY: number, axis?: "both" | "horizontal" | "vertical"): void;
     doScrollY(deltaY: number): void;
     setScrollY(n: number): void;
-    setAnnotations(annotations: import("react-msaview").Annotation[]): void;
+    setAnnotations(annotations: import("msa-parsers").Annotation[]): void;
     applyGFFText(gffText: string): void;
     doScrollX(deltaX: number): void;
     setScrollX(n: number): void;
@@ -845,24 +848,24 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly hoveredCell: import("react-msaview").Cell | undefined;
     readonly clickedCell: import("react-msaview").Cell | undefined;
     readonly viewport: import("react-msaview").Viewport | undefined;
-    readonly segmentDomainTypes: import("react-msaview").Annotation[];
-    readonly categoricalDomainTypes: import("react-msaview").Annotation[];
+    readonly segmentDomainTypes: import("msa-parsers").Annotation[];
+    readonly categoricalDomainTypes: import("msa-parsers").Annotation[];
     readonly fillPalette: {
         [x: string]: string;
     };
     readonly featureFillEncoding: import("react-msaview").ResolvedEncoding | undefined;
-    readonly featureColors: Map<import("react-msaview").Annotation, {
+    readonly featureColors: Map<import("msa-parsers").Annotation, {
         fill: string;
         stroke: string;
     }>;
-    readonly featureLabels: Map<import("react-msaview").Annotation, string> | undefined;
+    readonly featureLabels: Map<import("msa-parsers").Annotation, string> | undefined;
     readonly segmentLabels: Map<string, string>;
-    readonly visibleDomainTypes: import("react-msaview").Annotation[];
+    readonly visibleDomainTypes: import("msa-parsers").Annotation[];
     readonly legends: import("react-msaview").Legend[];
     readonly domainUnderline: boolean;
     readonly domainBands: Map<string, import("react-msaview").DomainBand[]>;
     readonly domainBandsByStart: Map<string, import("react-msaview").DomainBand[]>;
-    readonly mouseOverDomains: import("react-msaview").Annotation[];
+    readonly mouseOverDomains: import("msa-parsers").Annotation[];
     readonly referenceRowIndex: number | undefined;
     readonly hoveredRowIndices: number[];
     readonly highlightedColumnRuns: {
@@ -903,13 +906,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
         x: "column" | "position";
         kind: "features";
         field?: string | undefined;
-        colors: Map<import("react-msaview").Annotation, {
+        colors: Map<import("msa-parsers").Annotation, {
             fill: string;
             stroke: string;
         }>;
         legend: import("react-msaview").LegendEntry[];
         legendTitle?: string | undefined;
-        labels?: Map<import("react-msaview").Annotation, string> | undefined;
+        labels?: Map<import("msa-parsers").Annotation, string> | undefined;
     })[];
     readonly resolvedRowPanels: import("react-msaview").ResolvedRowPanel[];
     readonly featureAlignShifts: Map<string, Map<string, number>>;
@@ -978,6 +981,13 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * to draw the same highlights in its own display
      */
     readonly connectedHighlights: IRegion[];
+    /**
+     * #getter
+     * cross-plugin contract: jbrowse-plugin-protein3d reads this to paint the
+     * domains the alignment shows on the query row onto the structure, in
+     * the alignment's colors
+     */
+    readonly connectedDomains: ConnectedDomain[];
 } & {
     /**
      * #getter
@@ -1088,6 +1098,16 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
      * #action
      */
     setDomainsRequested(arg: boolean): void;
+    /**
+     * #action
+     */
+    setDomainsOnGenome(arg: boolean): void;
+    /**
+     * #action
+     * Add the query row's domains to the connected genome view as a session
+     * track, replacing the one an earlier call added.
+     */
+    showDomainsOnGenome(): void;
     /**
      * #action
      */
@@ -1140,7 +1160,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     customColorScheme: import("@jbrowse/mobx-state-tree").IType<Record<string, string> | undefined, Record<string, string> | undefined, Record<string, string> | undefined>;
     showColumnStats: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("msa-parsers").MSAFormat>>;
 }, "id" | "type" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & {
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     showDomains: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -1509,7 +1529,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     clades: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Clade, import("react-msaview").Clade, import("react-msaview").Clade>>, [undefined]>;
     encodings: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").Encoding, import("react-msaview").Encoding, import("react-msaview").Encoding>>, [undefined]>;
     rowPanels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IType<import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec, import("react-msaview").RowPanelSpec>>, [undefined]>;
-}, "init" | "querySeqName" | "launchCompleted" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion"> & {
+}, "init" | "querySeqName" | "launchCompleted" | "embeddedMode" | "connectedViewId" | "connectedFeature" | "connectedTranscript" | "blastParams" | "orthologParams" | "querySeqOffset" | "uniprotId" | "zoomToBaseLevel" | "dataStoreId" | "mafRegion" | "domainsOnGenome"> & {
     connectedViewId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     connectedFeature: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
     connectedTranscript: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
@@ -1523,12 +1543,14 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     dataStoreId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     launchCompleted: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     mafRegion: import("@jbrowse/mobx-state-tree").IType<MafRegion | undefined, MafRegion | undefined, MafRegion | undefined>;
+    embeddedMode: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    domainsOnGenome: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }>, "id" | "type" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth" | "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats" | "allowedGappyness" | "clades" | "colWidth" | "collapsed" | "columnTracks" | "currentAlignment" | "data" | "drawMsaLetters" | "encodings" | "features" | "gffFilehandle" | "height" | "hideGaps" | "highlightColumns" | "highlights" | "msaFilehandle" | "region" | "relativeTo" | "residueMappings" | "rotated" | "rowHeight" | "rowPanels" | "scrollX" | "scrollY" | "scrollZoom" | "scrollZoomAxis" | "selection" | "showDomainLegend" | "showDomains" | "showOnly" | "subFeatureRows" | "trackHeights" | "treeFilehandle" | "treeMetadataFilehandle" | "treeRoot" | "turnedOffFeatures" | "turnedOffTracks"> & ({
     bgColor: boolean;
     colorSchemeName: string;
     customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
-    msaFormat: import("react-msaview").MSAFormat | undefined;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number | undefined;
@@ -1665,7 +1687,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     colorSchemeName: string;
     customColorScheme: Record<string, string> | undefined;
     showColumnStats: boolean;
-    msaFormat: import("react-msaview").MSAFormat | undefined;
+    msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number | undefined;

package/dist/MsaViewPanel/model.js

@@ -1,9 +1,11 @@
 import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes';
-import { getSession } from '@jbrowse/core/util';
+import { getSession, isSessionWithAddSessionTrack, isSessionWithDeleteTrackConf, isSessionWithSessionTracks, } from '@jbrowse/core/util';
 import { addDisposer, getSnapshot, types } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
 import { MSAModelF } from 'react-msaview';
-import { autoLoadProteinDomains, launchBlastIfNeeded, launchOrthologsIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
+import { autoLoadProteinDomains, launchBlastIfNeeded, launchOrthologsIfNeeded, loadStoredData, observeProteinHighlights, processInit, runCleanup, storeDataToIndexedDB, showDomainsOnGenomeIfAsked, syncGenomeHoverToMsaColumn, } from './afterCreateAutoruns';
+import { connectedDomains } from './connectedDomains';
+import { domainTrackConf } from './domainTrack';
 import { msaCoordToGenomeCoord, msaCoordToGenomeRegions, } from './msaCoordToGenomeCoord';
 import { resolveConnectedTranscriptIfNeeded } from './resolveConnectedTranscript';
 import { transcriptMap } from './transcriptMap';
@@ -99,6 +101,20 @@ export default function stateModelFactory() {
          * #property
          */
         mafRegion: types.frozen(),
+        /**
+         * #property
+         * react-msaview draws the toolbar's menus and Settings as icons, since
+         * a JBrowse view shares its row with other panels. A session spec sets
+         * it false for the labeled toolbar.
+         */
+        embeddedMode: true,
+        /**
+         * #property
+         * a launch asking for the domains on the genome: once the connected
+         * view and the query row's domains are both there, the view adds the
+         * domain track and clears this
+         */
+        domainsOnGenome: types.stripDefault(types.boolean, false),
     }))
         .volatile(() => ({
         /**
@@ -198,6 +214,15 @@ export default function stateModelFactory() {
                 ...this.connectedClickHighlights,
             ];
         },
+        /**
+         * #getter
+         * cross-plugin contract: jbrowse-plugin-protein3d reads this to paint the
+         * domains the alignment shows on the query row onto the structure, in
+         * the alignment's colors
+         */
+        get connectedDomains() {
+            return connectedDomains(self);
+        },
     }))
         .views(self => ({
         /**
@@ -389,6 +414,46 @@ export default function stateModelFactory() {
         setDomainsRequested(arg) {
             self.domainsRequested = arg;
         },
+        /**
+         * #action
+         */
+        setDomainsOnGenome(arg) {
+            self.domainsOnGenome = arg;
+        },
+        /**
+         * #action
+         * Add the query row's domains to the connected genome view as a session
+         * track, replacing the one an earlier call added.
+         */
+        showDomainsOnGenome() {
+            const session = getSession(self);
+            const { connectedView, connectedDomains, connectedFeature } = self;
+            const assemblyName = connectedView?.assemblyNames[0];
+            if (!connectedView ||
+                !assemblyName ||
+                connectedDomains.length === 0 ||
+                !isSessionWithAddSessionTrack(session)) {
+                return;
+            }
+            const feature = connectedFeature;
+            const label = [feature?.gene_name, feature?.gene, feature?.name].find((v) => typeof v === 'string' && v !== '');
+            const conf = domainTrackConf({
+                viewId: self.id,
+                assemblyName,
+                name: `${label ?? self.querySeqName} domains (from the alignment)`,
+                strand: self.mafRegion ? undefined : self.transcriptToMsaMap?.strand,
+                domains: connectedDomains,
+            });
+            const existing = isSessionWithSessionTracks(session)
+                ? session.sessionTracks.find(t => t.trackId === conf.trackId)
+                : undefined;
+            if (existing && isSessionWithDeleteTrackConf(session)) {
+                session.deleteTrackConf(existing);
+            }
+            if (session.addSessionTrackConf(conf)) {
+                void connectedView.launchTrack(conf.trackId);
+            }
+        },
         /**
          * #action
          */
@@ -470,6 +535,16 @@ export default function stateModelFactory() {
                             self.setZoomToBaseLevel(!self.zoomToBaseLevel);
                         },
                     },
+                    ...(self.connectedView && self.connectedDomains.length > 0
+                        ? [
+                            {
+                                label: 'Show domains on the genome',
+                                onClick: () => {
+                                    self.showDomainsOnGenome();
+                                },
+                            },
+                        ]
+                        : []),
                 ];
             },
         };
@@ -491,6 +566,7 @@ export default function stateModelFactory() {
                 launchOrthologsIfNeeded,
                 processInit,
                 autoLoadProteinDomains,
+                showDomainsOnGenomeIfAsked,
             ]) {
                 addDisposer(self, autorun(() => {
                     fn(self);

package/dist/MsaViewPanel/model.test.js

@@ -163,3 +163,88 @@ describe('returning to the import form', () => {
         expect(model.dataStoreId).toBeUndefined();
     });
 });
+test('the view asks react-msaview for its icon toolbar', () => {
+    expect(view().embeddedMode).toBe(true);
+});
+// two CDS on the reverse strand, so residue 3's codon straddles the intron
+const reverseTranscript = {
+    refName: 'chr1',
+    strand: -1,
+    start: 100,
+    end: 208,
+    subfeatures: [
+        { type: 'CDS', start: 100, end: 107, phase: 0 },
+        { type: 'CDS', start: 200, end: 208, phase: 0 },
+    ],
+};
+describe('connectedDomains', () => {
+    function domainView() {
+        const model = stateModelFactory().create({
+            type: 'MsaView',
+            id: 'msaview1',
+            data: { msa: '>QUERY\nMKV-LA\n>Mouse\nMKVQLA' },
+            connectedFeature: reverseTranscript,
+        });
+        model.setAnnotations([
+            {
+                id: 'QUERY',
+                accession: 'cd1',
+                name: 'Hb beta-like',
+                description: '',
+                start: 1,
+                end: 5,
+            },
+            {
+                id: 'QUERY',
+                accession: 'cd2',
+                name: 'heme binding site',
+                description: '',
+                start: 2,
+                end: 4,
+            },
+            {
+                id: 'Mouse',
+                accession: 'cd1',
+                name: 'Hb beta-like',
+                description: '',
+                start: 1,
+                end: 6,
+            },
+        ]);
+        return model;
+    }
+    test('carries the query row domains in the colors the alignment draws', () => {
+        const model = domainView();
+        const fills = new Map([...model.featureColors].map(([a, c]) => [
+            `${a.id}:${a.accession}`,
+            c.fill,
+        ]));
+        expect(model.connectedDomains).toEqual([
+            {
+                name: 'Hb beta-like',
+                accession: 'cd1',
+                color: fills.get('QUERY:cd1'),
+                regions: [
+                    { refName: 'chr1', start: 100, end: 107 },
+                    { refName: 'chr1', start: 200, end: 208 },
+                ],
+            },
+            {
+                name: 'heme binding site',
+                accession: 'cd2',
+                color: fills.get('QUERY:cd2'),
+                regions: [
+                    { refName: 'chr1', start: 103, end: 107 },
+                    { refName: 'chr1', start: 200, end: 205 },
+                ],
+            },
+        ]);
+    });
+    test('follows the overlay and the legend filter', () => {
+        const model = domainView();
+        model.setFilter('cd2', false);
+        expect(model.connectedDomains.map(d => d.accession)).toEqual(['cd1']);
+        model.setShowDomains(false);
+        expect(model.connectedDomains).toEqual([]);
+    });
+});

package/dist/MsaViewPanel/msaCoordToGenomeCoord.d.ts

@@ -1,11 +1,10 @@
 import type { MafRegion } from './types';
-interface GenomeRegion {
+export interface GenomeRegion {
     refName: string;
     start: number;
     end: number;
 }
-interface CoordModel {
-    querySeqName: string;
+export interface SeqPosModel {
     transcriptToMsaMap: {
         refName: string;
         p2gCodon: Record<number, number[]>;
@@ -13,6 +12,9 @@ interface CoordModel {
     mafRegion?: MafRegion;
     /** transcript residues before the query row's first residue */
     querySeqOffset?: number;
+}
+interface CoordModel extends SeqPosModel {
+    querySeqName: string;
     /**
      * react-msaview's converter, which is the only thing that knows which columns
      * are on screen. `rows` carries the whole gapped alignment, so counting
@@ -22,6 +24,12 @@ interface CoordModel {
      */
     visibleColToSeqPos: (rowName: string, visibleCol: number) => number | undefined;
 }
+/**
+ * The genome regions under residue `ungappedPos` (0-based) of the query row,
+ * 0-based half-open: the codon, one region per contiguous piece, or one base
+ * in a MAF alignment.
+ */
+export declare function seqPosToGenomeRegions(model: SeqPosModel, ungappedPos: number): GenomeRegion[];
 /**
  * The genome regions covered by MSA column `coord` of the query row, in 0-based
  * half-open coordinates (what bpToPx and navTo take).

package/dist/MsaViewPanel/msaCoordToGenomeCoord.js

@@ -1,20 +1,11 @@
 import { getCodonRanges } from 'g2p_mapper';
 /**
- * The genome regions covered by MSA column `coord` of the query row, in 0-based
- * half-open coordinates (what bpToPx and navTo take).
- *
- * `coord` is a VISIBLE column -- what mouseCol and mouseClickCol carry.
- *
- * Usually one region -- one codon, or one base in a MAF alignment -- but a
- * codon split across an exon boundary yields one region per contiguous piece,
- * which is why this returns a list.
+ * The genome regions under residue `ungappedPos` (0-based) of the query row,
+ * 0-based half-open: the codon, one region per contiguous piece, or one base
+ * in a MAF alignment.
  */
-export function msaCoordToGenomeRegions({ model, coord: mouseCol, }) {
-    const { querySeqName, transcriptToMsaMap, mafRegion } = model;
-    const ungappedPos = model.visibleColToSeqPos(querySeqName, mouseCol);
-    if (ungappedPos === undefined) {
-        return [];
-    }
+export function seqPosToGenomeRegions(model, ungappedPos) {
+    const { transcriptToMsaMap, mafRegion } = model;
     if (mafRegion) {
         const genomePos = mafRegion.start + ungappedPos;
         return genomePos < mafRegion.end
@@ -40,6 +31,22 @@ export function msaCoordToGenomeRegions({ model, coord: mouseCol, }) {
     }
     return [];
 }
+/**
+ * The genome regions covered by MSA column `coord` of the query row, in 0-based
+ * half-open coordinates (what bpToPx and navTo take).
+ *
+ * `coord` is a VISIBLE column -- what mouseCol and mouseClickCol carry.
+ *
+ * Usually one region -- one codon, or one base in a MAF alignment -- but a
+ * codon split across an exon boundary yields one region per contiguous piece,
+ * which is why this returns a list.
+ */
+export function msaCoordToGenomeRegions({ model, coord: mouseCol, }) {
+    const ungappedPos = model.visibleColToSeqPos(model.querySeqName, mouseCol);
+    return ungappedPos === undefined
+        ? []
+        : seqPosToGenomeRegions(model, ungappedPos);
+}
 /**
  * A single region spanning the codon at MSA column `coord`, for navigation. For
  * a codon split across an exon boundary this spans the intervening intron.

package/dist/chunks/{AboutDialog-447TIFAW.js → AboutDialog-HCCCEJ6V.js}

@@ -1,2 +1,2 @@
-import{a as l}from"./chunk-6EOYBBT4.js";import{a as i}from"./chunk-DNFD5II2.js";import{a as m}from"./chunk-BX4Z274Q.js";import{a}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(a(),1),o=r(i(),1),t=r(m(),1);function c({onClose:n}){return e.default.createElement(o.Dialog,{open:!0,title:"About",onClose:()=>{n()}},e.default.createElement(t.DialogContent,null,e.default.createElement(t.Typography,null,"MSAView ",l," (",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/gmod/react-msaview"},"Github"),")"),e.default.createElement("ul",null,e.default.createElement("li",null,e.default.createElement(t.Typography,null,"We use some color schemes from the"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite"},"biotite")," ","project, and their license is reproduced"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some information on jalview colorings"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.jalview.org/help/html/colourSchemes/"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some info on the clustal, cinema, maeditor, and lesk color schemes"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"http://www.bioinformatics.nl/~berndb/aacolour.html"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this paper about the flower color scheme"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/"},"here"))))))}export{c as default};
-//# sourceMappingURL=AboutDialog-447TIFAW.js.map
+import{a as l}from"./chunk-XTQQNBQ5.js";import{a as i}from"./chunk-DNFD5II2.js";import{a as m}from"./chunk-BX4Z274Q.js";import{a}from"./chunk-J6KYLXRD.js";import{b as r}from"./chunk-FY3BTKY4.js";var e=r(a(),1),o=r(i(),1),t=r(m(),1);function c({onClose:n}){return e.default.createElement(o.Dialog,{open:!0,title:"About",onClose:()=>{n()}},e.default.createElement(t.DialogContent,null,e.default.createElement(t.Typography,null,"MSAView ",l," (",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/gmod/react-msaview"},"Github"),")"),e.default.createElement("ul",null,e.default.createElement("li",null,e.default.createElement(t.Typography,null,"We use some color schemes from the"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite"},"biotite")," ","project, and their license is reproduced"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some information on jalview colorings"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.jalview.org/help/html/colourSchemes/"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this page for some info on the clustal, cinema, maeditor, and lesk color schemes"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"http://www.bioinformatics.nl/~berndb/aacolour.html"},"here"))),e.default.createElement("li",null,e.default.createElement(t.Typography,null,"See this paper about the flower color scheme"," ",e.default.createElement(t.Link,{target:"_blank",rel:"noopener",href:"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/"},"here"))))))}export{c as default};
+//# sourceMappingURL=AboutDialog-HCCCEJ6V.js.map

package/dist/chunks/{AboutDialog-447TIFAW.js.map → AboutDialog-HCCCEJ6V.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx"],
   "sourcesContent": ["import React from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport { DialogContent, Link, Typography } from '@mui/material'\n\nimport { version } from '../../version.ts'\n\nexport default function AboutDialog({ onClose }: { onClose: () => void }) {\n  return (\n    <Dialog\n      open\n      title=\"About\"\n      onClose={() => {\n        onClose()\n      }}\n    >\n      <DialogContent>\n        <Typography>\n          MSAView {version} (\n          <Link\n            target=\"_blank\"\n            rel=\"noopener\"\n            href=\"https://github.com/gmod/react-msaview\"\n          >\n            Github\n          </Link>\n          )\n        </Typography>\n\n        <ul>\n          <li>\n            <Typography>\n              We use some color schemes from the{' '}\n              <Link\n                target=\"_blank\"\n                rel=\"noopener\"\n                href=\"https://github.com/biotite-dev/biotite\"\n              >\n                biotite\n              </Link>{' '}\n              project, and their license is reproduced{' '}\n              <Link\n                target=\"_blank\"\n                rel=\"noopener\"\n                href=\"https://github.com/biotite-dev/biotite/blob/master/LICENSE.rst\"\n              >\n                here\n              </Link>\n            </Typography>\n          </li>\n          <li>\n            <Typography>\n              See this page for some information on jalview colorings{' '}\n              <Link\n                target=\"_blank\"\n                rel=\"noopener\"\n                href=\"https://www.jalview.org/help/html/colourSchemes/\"\n              >\n                here\n              </Link>\n            </Typography>\n          </li>\n          <li>\n            <Typography>\n              See this page for some info on the clustal, cinema, maeditor, and\n              lesk color schemes{' '}\n              <Link\n                target=\"_blank\"\n                rel=\"noopener\"\n                href=\"http://www.bioinformatics.nl/~berndb/aacolour.html\"\n              >\n                here\n              </Link>\n            </Typography>\n          </li>\n          <li>\n            <Typography>\n              See this paper about the flower color scheme{' '}\n              <Link\n                target=\"_blank\"\n                rel=\"noopener\"\n                href=\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7245768/\"\n              >\n                here\n              </Link>\n            </Typography>\n          </li>\n        </ul>\n      </DialogContent>\n    </Dialog>\n  )\n}\n"],
   "mappings": "mMAAA,IAAAA,EAAkB,SAElBC,EAAuB,SACvBC,EAAgD,SAIlC,SAAPC,EAA6B,CAAE,QAAAC,CAAO,EAA2B,CACtE,OACE,EAAAC,QAAA,cAAC,SAAM,CACL,KAAI,GACJ,MAAM,QACN,QAAS,IAAK,CACZD,EAAO,CACT,CAAC,EAED,EAAAC,QAAA,cAAC,gBAAa,KACZ,EAAAA,QAAA,cAAC,aAAU,gBACAC,OACT,EAAAD,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,uCAAuC,EAAA,QAAA,OAOhD,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,0CAC0B,IACnC,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,wCAAwC,EAAA,SAAA,EAGvC,+CACiC,IACzC,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,gEAAgE,EAAA,MAAA,CAGhE,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,+DAC+C,IACxD,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,kDAAkD,EAAA,MAAA,CAGlD,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,4FAEU,IACnB,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,oDAAoD,EAAA,MAAA,CAGpD,CACI,EAEf,EAAAA,QAAA,cAAA,KAAA,KACE,EAAAA,QAAA,cAAC,aAAU,oDACoC,IAC7C,EAAAA,QAAA,cAAC,OAAI,CACH,OAAO,SACP,IAAI,WACJ,KAAK,uDAAuD,EAAA,MAAA,CAGvD,CACI,CACV,CACF,CACS,CAGtB",
   "names": ["import_react", "import_ui", "import_material", "AboutDialog", "onClose", "React", "version"]

package/dist/chunks/AnnotationFileDialog-CPJ4X7XW.js

@@ -0,0 +1,2 @@
+import{i as E}from"./chunk-XXCNVFGP.js";import"./chunk-73KAPCJ2.js";import{a as x}from"./chunk-CVLB4VFP.js";import{a as C}from"./chunk-DNFD5II2.js";import{a as w}from"./chunk-BX4Z274Q.js";import{a as y}from"./chunk-J6KYLXRD.js";import{b as i}from"./chunk-FY3BTKY4.js";var e=i(y(),1),c=i(C(),1),t=i(w(),1),d=i(x(),1);async function T(o){let l=await fetch(o);if(!l.ok)throw new Error(`HTTP ${l.status} fetching ${o} ${await l.text()}`);return l.text()}var b=(0,d.observer)(function({handleClose:o,model:l}){let[a,h]=(0,e.useState)(),[r,g]=(0,e.useState)("file"),[s,F]=(0,e.useState)(""),[m,u]=(0,e.useState)(),[v,f]=(0,e.useState)(!1);return e.default.createElement(c.Dialog,{maxWidth:"xl",title:"Open annotation file",onClose:()=>{o()},open:!0},e.default.createElement(t.DialogContent,null,m?e.default.createElement(c.ErrorMessage,{error:m}):null,e.default.createElement(t.Typography,null,"Open a GFF3 file of annotations, such as the one `react-msaview-cli interpro` writes, or the JSON an InterProScan run returns."),e.default.createElement("div",{style:{display:"flex",margin:30}},e.default.createElement(t.FormControl,{component:"fieldset"},e.default.createElement(t.RadioGroup,{value:r,onChange:n=>{g(n.target.value)}},e.default.createElement(t.FormControlLabel,{value:"url",control:e.default.createElement(t.Radio,null),label:"URL"}),e.default.createElement(t.FormControlLabel,{value:"file",control:e.default.createElement(t.Radio,null),label:"File"}))),r==="url"?e.default.createElement("div",null,e.default.createElement(t.Typography,null,"Open an annotation file from a URL"),e.default.createElement(t.TextField,{label:"URL",value:s,onChange:n=>{F(n.target.value)}})):e.default.createElement("div",{style:{paddingTop:20}},e.default.createElement(t.Typography,null,"Open an annotation file from your local drive"),e.default.createElement(t.Button,{variant:"outlined",component:"label"},"Choose File",e.default.createElement("input",{type:"file",hidden:!0,onChange:({target:n})=>{let p=n.files?.[0];p&&h(p)}})),a?e.default.createElement(t.Typography,null,a.name):null))),e.default.createElement(t.DialogActions,null,e.default.createElement(t.Button,{variant:"contained",color:"primary",disabled:v||(r==="file"?!a:!s.trim()),onClick:()=>{(async()=>{f(!0),u(void 0);try{let n=await(r==="file"&&a?a.text():T(s));l.setGFFFilehandle(void 0),l.setGFF(E(n)),l.setShowDomains(!0),o()}catch(n){console.error(n),u(n)}finally{f(!1)}})()}},"Open annotations"),e.default.createElement(t.Button,{variant:"contained",color:"secondary",onClick:()=>{o()}},"Cancel")))}),R=b;export{R as default};
+//# sourceMappingURL=AnnotationFileDialog-CPJ4X7XW.js.map

package/dist/chunks/{AnnotationFileDialog-S3N5EHHE.js.map → AnnotationFileDialog-CPJ4X7XW.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/AnnotationFileDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.1.0_a4121c98828e538e8b3708814bbfe622/node_modules/react-msaview/src/components/dialogs/AnnotationFileDialog.tsx"],
   "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog, ErrorMessage } from '@jbrowse/core/ui'\nimport {\n  Button,\n  DialogActions,\n  DialogContent,\n  FormControl,\n  FormControlLabel,\n  Radio,\n  RadioGroup,\n  TextField,\n  Typography,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\nimport { annotationTextToGFF } from 'msa-parsers'\n\nimport type { MsaViewModel } from '../../model.ts'\n\nasync function fetchText(url: string) {\n  const response = await fetch(url)\n  if (!response.ok) {\n    throw new Error(\n      `HTTP ${response.status} fetching ${url} ${await response.text()}`,\n    )\n  }\n  return response.text()\n}\n\nconst AnnotationFileDialog = observer(function ({\n  handleClose,\n  model,\n}: {\n  handleClose: () => void\n  model: MsaViewModel\n}) {\n  const [file, setFile] = useState<File>()\n  const [choice, setChoice] = useState('file')\n  const [url, setUrl] = useState('')\n  const [error, setError] = useState<unknown>()\n  const [loading, setLoading] = useState(false)\n\n  // the error is shown here rather than notified: the standalone app and the\n  // MSAViewer component have no jbrowse session to notify, and asking one for\n  // its notify() threw out of the success path into the catch, which threw\n  // again on the same missing session\n  return (\n    <Dialog\n      maxWidth=\"xl\"\n      title=\"Open annotation file\"\n      onClose={() => {\n        handleClose()\n      }}\n      open\n    >\n      <DialogContent>\n        {error ? <ErrorMessage error={error} /> : null}\n        <Typography>\n          Open a GFF3 file of annotations, such as the one `react-msaview-cli\n          interpro` writes, or the JSON an InterProScan run returns.\n        </Typography>\n\n        <div style={{ display: 'flex', margin: 30 }}>\n          <FormControl component=\"fieldset\">\n            <RadioGroup\n              value={choice}\n              onChange={event => {\n                setChoice(event.target.value)\n              }}\n            >\n              <FormControlLabel value=\"url\" control={<Radio />} label=\"URL\" />\n              <FormControlLabel value=\"file\" control={<Radio />} label=\"File\" />\n            </RadioGroup>\n          </FormControl>\n          {choice === 'url' ? (\n            <div>\n              <Typography>Open an annotation file from a URL</Typography>\n              <TextField\n                label=\"URL\"\n                value={url}\n                onChange={event => {\n                  setUrl(event.target.value)\n                }}\n              />\n            </div>\n          ) : (\n            <div style={{ paddingTop: 20 }}>\n              <Typography>\n                Open an annotation file from your local drive\n              </Typography>\n              <Button variant=\"outlined\" component=\"label\">\n                Choose File\n                <input\n                  type=\"file\"\n                  hidden\n                  onChange={({ target }) => {\n                    const chosen = target.files?.[0]\n                    if (chosen) {\n                      setFile(chosen)\n                    }\n                  }}\n                />\n              </Button>\n              {file ? <Typography>{file.name}</Typography> : null}\n            </div>\n          )}\n        </div>\n      </DialogContent>\n      <DialogActions>\n        <Button\n          variant=\"contained\"\n          color=\"primary\"\n          disabled={loading || (choice === 'file' ? !file : !url.trim())}\n          onClick={() => {\n            // eslint-disable-next-line @typescript-eslint/no-floating-promises\n            ;(async () => {\n              setLoading(true)\n              setError(undefined)\n              try {\n                const text = await (choice === 'file' && file\n                  ? file.text()\n                  : fetchText(url))\n                // through the model's own GFF text, so the annotations travel\n                // in the snapshot and the shared URL like every other layer. A\n                // filehandle left set would make the snapshot drop that text\n                model.setGFFFilehandle(undefined)\n                model.setGFF(annotationTextToGFF(text))\n                model.setShowDomains(true)\n                handleClose()\n              } catch (e) {\n                console.error(e)\n                setError(e)\n              } finally {\n                setLoading(false)\n              }\n            })()\n          }}\n        >\n          Open annotations\n        </Button>\n        <Button\n          variant=\"contained\"\n          color=\"secondary\"\n          onClick={() => {\n            handleClose()\n          }}\n        >\n          Cancel\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default AnnotationFileDialog\n"],
-  "mappings": "wSAAA,IAAAA,EAAgC,SAEhCC,EAAqC,SACrCC,EAUO,SACPC,EAAyB,SAKzB,eAAeC,EAAUC,EAAW,CAClC,IAAMC,EAAW,MAAM,MAAMD,CAAG,EAChC,GAAI,CAACC,EAAS,GACZ,MAAM,IAAI,MACR,QAAQA,EAAS,MAAM,aAAaD,CAAG,IAAI,MAAMC,EAAS,KAAI,CAAE,EAAE,EAGtE,OAAOA,EAAS,KAAI,CACtB,CAEA,IAAMC,KAAuB,YAAS,SAAU,CAC9C,YAAAC,EACA,MAAAC,CAAK,EAIN,CACC,GAAM,CAACC,EAAMC,CAAO,KAAI,YAAQ,EAC1B,CAACC,EAAQC,CAAS,KAAI,YAAS,MAAM,EACrC,CAACR,EAAKS,CAAM,KAAI,YAAS,EAAE,EAC3B,CAACC,EAAOC,CAAQ,KAAI,YAAQ,EAC5B,CAACC,EAASC,CAAU,KAAI,YAAS,EAAK,EAM5C,OACE,EAAAC,QAAA,cAAC,SAAM,CACL,SAAS,KACT,MAAM,uBACN,QAAS,IAAK,CACZX,EAAW,CACb,EACA,KAAI,EAAA,EAEJ,EAAAW,QAAA,cAAC,gBAAa,KACXJ,EAAQ,EAAAI,QAAA,cAAC,eAAY,CAAC,MAAOJ,CAAK,CAAA,EAAO,KAC1C,EAAAI,QAAA,cAAC,aAAU,KAAA,gIAAA,EAKX,EAAAA,QAAA,cAAA,MAAA,CAAK,MAAO,CAAE,QAAS,OAAQ,OAAQ,EAAE,CAAE,EACzC,EAAAA,QAAA,cAAC,cAAW,CAAC,UAAU,UAAU,EAC/B,EAAAA,QAAA,cAAC,aAAU,CACT,MAAOP,EACP,SAAUQ,GAAQ,CAChBP,EAAUO,EAAM,OAAO,KAAK,CAC9B,CAAC,EAED,EAAAD,QAAA,cAAC,mBAAgB,CAAC,MAAM,MAAM,QAAS,EAAAA,QAAA,cAAC,QAAK,IAAA,EAAK,MAAM,KAAK,CAAA,EAC7D,EAAAA,QAAA,cAAC,mBAAgB,CAAC,MAAM,OAAO,QAAS,EAAAA,QAAA,cAAC,QAAK,IAAA,EAAK,MAAM,MAAM,CAAA,CAAG,CACvD,EAEdP,IAAW,MACV,EAAAO,QAAA,cAAA,MAAA,KACE,EAAAA,QAAA,cAAC,aAAU,KAAA,oCAAA,EACX,EAAAA,QAAA,cAAC,YAAS,CACR,MAAM,MACN,MAAOd,EACP,SAAUe,GAAQ,CAChBN,EAAOM,EAAM,OAAO,KAAK,CAC3B,CAAC,CAAA,CACD,EAGJ,EAAAD,QAAA,cAAA,MAAA,CAAK,MAAO,CAAE,WAAY,EAAE,CAAE,EAC5B,EAAAA,QAAA,cAAC,aAAU,KAAA,+CAAA,EAGX,EAAAA,QAAA,cAAC,SAAM,CAAC,QAAQ,WAAW,UAAU,OAAO,gBAE1C,EAAAA,QAAA,cAAA,QAAA,CACE,KAAK,OACL,OAAM,GACN,SAAU,CAAC,CAAE,OAAAE,CAAM,IAAM,CACvB,IAAMC,EAASD,EAAO,QAAQ,CAAC,EAC3BC,GACFX,EAAQW,CAAM,CAElB,CAAC,CAAA,CACD,EAEHZ,EAAO,EAAAS,QAAA,cAAC,aAAU,KAAET,EAAK,IAAI,EAAiB,IAAI,CAEtD,CACG,EAER,EAAAS,QAAA,cAAC,gBAAa,KACZ,EAAAA,QAAA,cAAC,SAAM,CACL,QAAQ,YACR,MAAM,UACN,SAAUF,IAAYL,IAAW,OAAS,CAACF,EAAO,CAACL,EAAI,KAAI,GAC3D,QAAS,IAAK,EAEV,SAAW,CACXa,EAAW,EAAI,EACfF,EAAS,MAAS,EAClB,GAAI,CACF,IAAMO,EAAO,MAAOX,IAAW,QAAUF,EACrCA,EAAK,KAAI,EACTN,EAAUC,CAAG,GAIjBI,EAAM,iBAAiB,MAAS,EAChCA,EAAM,OAAOe,EAAoBD,CAAI,CAAC,EACtCd,EAAM,eAAe,EAAI,EACzBD,EAAW,CACb,OAASiB,EAAG,CACV,QAAQ,MAAMA,CAAC,EACfT,EAASS,CAAC,CACZ,SACEP,EAAW,EAAK,CAClB,CACF,GAAE,CACJ,CAAC,EAAA,kBAAA,EAIH,EAAAC,QAAA,cAAC,SAAM,CACL,QAAQ,YACR,MAAM,YACN,QAAS,IAAK,CACZX,EAAW,CACb,CAAC,EAAA,QAAA,CAGM,CACK,CAGtB,CAAC,EAEDkB,EAAenB",
+  "mappings": "4QAAA,IAAAA,EAAgC,SAEhCC,EAAqC,SACrCC,EAUO,SACPC,EAAyB,SAKzB,eAAeC,EAAUC,EAAW,CAClC,IAAMC,EAAW,MAAM,MAAMD,CAAG,EAChC,GAAI,CAACC,EAAS,GACZ,MAAM,IAAI,MACR,QAAQA,EAAS,MAAM,aAAaD,CAAG,IAAI,MAAMC,EAAS,KAAI,CAAE,EAAE,EAGtE,OAAOA,EAAS,KAAI,CACtB,CAEA,IAAMC,KAAuB,YAAS,SAAU,CAC9C,YAAAC,EACA,MAAAC,CAAK,EAIN,CACC,GAAM,CAACC,EAAMC,CAAO,KAAI,YAAQ,EAC1B,CAACC,EAAQC,CAAS,KAAI,YAAS,MAAM,EACrC,CAACR,EAAKS,CAAM,KAAI,YAAS,EAAE,EAC3B,CAACC,EAAOC,CAAQ,KAAI,YAAQ,EAC5B,CAACC,EAASC,CAAU,KAAI,YAAS,EAAK,EAM5C,OACE,EAAAC,QAAA,cAAC,SAAM,CACL,SAAS,KACT,MAAM,uBACN,QAAS,IAAK,CACZX,EAAW,CACb,EACA,KAAI,EAAA,EAEJ,EAAAW,QAAA,cAAC,gBAAa,KACXJ,EAAQ,EAAAI,QAAA,cAAC,eAAY,CAAC,MAAOJ,CAAK,CAAA,EAAO,KAC1C,EAAAI,QAAA,cAAC,aAAU,KAAA,gIAAA,EAKX,EAAAA,QAAA,cAAA,MAAA,CAAK,MAAO,CAAE,QAAS,OAAQ,OAAQ,EAAE,CAAE,EACzC,EAAAA,QAAA,cAAC,cAAW,CAAC,UAAU,UAAU,EAC/B,EAAAA,QAAA,cAAC,aAAU,CACT,MAAOP,EACP,SAAUQ,GAAQ,CAChBP,EAAUO,EAAM,OAAO,KAAK,CAC9B,CAAC,EAED,EAAAD,QAAA,cAAC,mBAAgB,CAAC,MAAM,MAAM,QAAS,EAAAA,QAAA,cAAC,QAAK,IAAA,EAAK,MAAM,KAAK,CAAA,EAC7D,EAAAA,QAAA,cAAC,mBAAgB,CAAC,MAAM,OAAO,QAAS,EAAAA,QAAA,cAAC,QAAK,IAAA,EAAK,MAAM,MAAM,CAAA,CAAG,CACvD,EAEdP,IAAW,MACV,EAAAO,QAAA,cAAA,MAAA,KACE,EAAAA,QAAA,cAAC,aAAU,KAAA,oCAAA,EACX,EAAAA,QAAA,cAAC,YAAS,CACR,MAAM,MACN,MAAOd,EACP,SAAUe,GAAQ,CAChBN,EAAOM,EAAM,OAAO,KAAK,CAC3B,CAAC,CAAA,CACD,EAGJ,EAAAD,QAAA,cAAA,MAAA,CAAK,MAAO,CAAE,WAAY,EAAE,CAAE,EAC5B,EAAAA,QAAA,cAAC,aAAU,KAAA,+CAAA,EAGX,EAAAA,QAAA,cAAC,SAAM,CAAC,QAAQ,WAAW,UAAU,OAAO,gBAE1C,EAAAA,QAAA,cAAA,QAAA,CACE,KAAK,OACL,OAAM,GACN,SAAU,CAAC,CAAE,OAAAE,CAAM,IAAM,CACvB,IAAMC,EAASD,EAAO,QAAQ,CAAC,EAC3BC,GACFX,EAAQW,CAAM,CAElB,CAAC,CAAA,CACD,EAEHZ,EAAO,EAAAS,QAAA,cAAC,aAAU,KAAET,EAAK,IAAI,EAAiB,IAAI,CAEtD,CACG,EAER,EAAAS,QAAA,cAAC,gBAAa,KACZ,EAAAA,QAAA,cAAC,SAAM,CACL,QAAQ,YACR,MAAM,UACN,SAAUF,IAAYL,IAAW,OAAS,CAACF,EAAO,CAACL,EAAI,KAAI,GAC3D,QAAS,IAAK,EAEV,SAAW,CACXa,EAAW,EAAI,EACfF,EAAS,MAAS,EAClB,GAAI,CACF,IAAMO,EAAO,MAAOX,IAAW,QAAUF,EACrCA,EAAK,KAAI,EACTN,EAAUC,CAAG,GAIjBI,EAAM,iBAAiB,MAAS,EAChCA,EAAM,OAAOe,EAAoBD,CAAI,CAAC,EACtCd,EAAM,eAAe,EAAI,EACzBD,EAAW,CACb,OAASiB,EAAG,CACV,QAAQ,MAAMA,CAAC,EACfT,EAASS,CAAC,CACZ,SACEP,EAAW,EAAK,CAClB,CACF,GAAE,CACJ,CAAC,EAAA,kBAAA,EAIH,EAAAC,QAAA,cAAC,SAAM,CACL,QAAQ,YACR,MAAM,YACN,QAAS,IAAK,CACZX,EAAW,CACb,CAAC,EAAA,QAAA,CAGM,CACK,CAGtB,CAAC,EAEDkB,EAAenB",
   "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "fetchText", "url", "response", "AnnotationFileDialog", "handleClose", "model", "file", "setFile", "choice", "setChoice", "setUrl", "error", "setError", "loading", "setLoading", "React", "event", "target", "chosen", "text", "annotationTextToGFF", "e", "AnnotationFileDialog_default"]
 }

package/dist/chunks/{ExportSVGDialog-7ZHKKQ7W.js → ExportSVGDialog-YUFLYBYW.js}

@@ -1,2 +1,2 @@
-import{a as p}from"./chunk-ERCMNTEQ.js";import{X as v,Y as y}from"./chunk-OVAXNTPN.js";import{a as L}from"./chunk-CVLB4VFP.js";import{a as D}from"./chunk-DNFD5II2.js";import{a as V}from"./chunk-BX4Z274Q.js";import{a as I}from"./chunk-J6KYLXRD.js";import{b as l}from"./chunk-FY3BTKY4.js";var t=l(I(),1),i=l(D(),1),e=l(V(),1),k=l(L(),1);function z(r){requestAnimationFrame(()=>{requestAnimationFrame(r)})}var P=(0,k.observer)(function({model:r,onClose:c}){let[s,C]=(0,t.useState)(!0),[n,T]=(0,t.useState)(!0),[o,b]=(0,t.useState)("viewport"),[E,w]=(0,t.useState)(),[m,h]=(0,t.useState)(!1),d=(0,e.useTheme)(),{turnedOnTracks:M,numColumns:S,leaves:A,showMsaLetters:F}=r,g=M.length>0,x=y(r,v(r,{theme:d,exportType:"entire",includeTracks:n})),f=F&&o==="entire"?S*A.length:0,G=f>1e5;return t.default.createElement(i.Dialog,{onClose:()=>{c()},open:!0,title:"Export SVG"},t.default.createElement(e.DialogContent,null,E?t.default.createElement(i.ErrorMessage,{error:E}):null,t.default.createElement(e.Typography,null,"Settings:"),t.default.createElement(p,{label:"Include minimap?",disabled:o==="entire",checked:s,onChange:()=>{C(!s)}}),g?t.default.createElement(p,{label:"Include tracks?",checked:n,onChange:()=>{T(!n)}}):null,t.default.createElement("div",null,t.default.createElement(e.FormControl,null,t.default.createElement(e.FormLabel,null,"Export type"),t.default.createElement(e.RadioGroup,{value:o,onChange:a=>{let{value:u}=a.target;(u==="entire"||u==="viewport")&&b(u)}},t.default.createElement(e.FormControlLabel,{value:"entire",control:t.default.createElement(e.Radio,null),label:"Entire MSA"}),t.default.createElement(e.FormControlLabel,{value:"viewport",control:t.default.createElement(e.Radio,null),label:"Current viewport only"})))),G?t.default.createElement(e.Alert,{severity:"warning",style:{marginTop:8}},"The entire MSA is ",Math.round(x.width),"x",Math.round(x.height)," pixels and draws"," ",Math.round(f/1e3),"k residue letters, each its own SVG element. Export may be slow or fail \u2014 zooming out far enough to hide the letters exports the same alignment as an image instead."):null),t.default.createElement(e.DialogActions,null,t.default.createElement(e.Button,{variant:"contained",color:"primary",disabled:m,startIcon:m?t.default.createElement(e.CircularProgress,{size:16,color:"inherit"}):null,onClick:()=>{h(!0),z(()=>{r.exportSVG({theme:d,includeMinimap:s,includeTracks:g&&n,exportType:o}).then(()=>{c()}).catch(a=>{console.error(a),w(a)}).finally(()=>{h(!1)})})}},m?"Exporting\u2026":"Export"),t.default.createElement(e.Button,{variant:"contained",color:"secondary",onClick:()=>{c()}},"Cancel")))}),B=P;export{B as default};
-//# sourceMappingURL=ExportSVGDialog-7ZHKKQ7W.js.map
+import{a as p}from"./chunk-GAY2PLS6.js";import{X as v,Y as y}from"./chunk-ZQSWX57C.js";import{a as L}from"./chunk-CVLB4VFP.js";import{a as D}from"./chunk-DNFD5II2.js";import{a as V}from"./chunk-BX4Z274Q.js";import{a as I}from"./chunk-J6KYLXRD.js";import{b as l}from"./chunk-FY3BTKY4.js";var t=l(I(),1),i=l(D(),1),e=l(V(),1),k=l(L(),1);function z(r){requestAnimationFrame(()=>{requestAnimationFrame(r)})}var P=(0,k.observer)(function({model:r,onClose:c}){let[s,C]=(0,t.useState)(!0),[n,T]=(0,t.useState)(!0),[o,b]=(0,t.useState)("viewport"),[E,w]=(0,t.useState)(),[m,h]=(0,t.useState)(!1),d=(0,e.useTheme)(),{turnedOnTracks:M,numColumns:S,leaves:A,showMsaLetters:F}=r,g=M.length>0,x=y(r,v(r,{theme:d,exportType:"entire",includeTracks:n})),f=F&&o==="entire"?S*A.length:0,G=f>1e5;return t.default.createElement(i.Dialog,{onClose:()=>{c()},open:!0,title:"Export SVG"},t.default.createElement(e.DialogContent,null,E?t.default.createElement(i.ErrorMessage,{error:E}):null,t.default.createElement(e.Typography,null,"Settings:"),t.default.createElement(p,{label:"Include minimap?",disabled:o==="entire",checked:s,onChange:()=>{C(!s)}}),g?t.default.createElement(p,{label:"Include tracks?",checked:n,onChange:()=>{T(!n)}}):null,t.default.createElement("div",null,t.default.createElement(e.FormControl,null,t.default.createElement(e.FormLabel,null,"Export type"),t.default.createElement(e.RadioGroup,{value:o,onChange:a=>{let{value:u}=a.target;(u==="entire"||u==="viewport")&&b(u)}},t.default.createElement(e.FormControlLabel,{value:"entire",control:t.default.createElement(e.Radio,null),label:"Entire MSA"}),t.default.createElement(e.FormControlLabel,{value:"viewport",control:t.default.createElement(e.Radio,null),label:"Current viewport only"})))),G?t.default.createElement(e.Alert,{severity:"warning",style:{marginTop:8}},"The entire MSA is ",Math.round(x.width),"x",Math.round(x.height)," pixels and draws"," ",Math.round(f/1e3),"k residue letters, each its own SVG element. Export may be slow or fail \u2014 zooming out far enough to hide the letters exports the same alignment as an image instead."):null),t.default.createElement(e.DialogActions,null,t.default.createElement(e.Button,{variant:"contained",color:"primary",disabled:m,startIcon:m?t.default.createElement(e.CircularProgress,{size:16,color:"inherit"}):null,onClick:()=>{h(!0),z(()=>{r.exportSVG({theme:d,includeMinimap:s,includeTracks:g&&n,exportType:o}).then(()=>{c()}).catch(a=>{console.error(a),w(a)}).finally(()=>{h(!1)})})}},m?"Exporting\u2026":"Export"),t.default.createElement(e.Button,{variant:"contained",color:"secondary",onClick:()=>{c()}},"Cancel")))}),B=P;export{B as default};
+//# sourceMappingURL=ExportSVGDialog-YUFLYBYW.js.map