jbrowse-plugin-msaview 5.1.1 → 5.2.0

package/dist/LaunchMsaView/components/PreLoadedMSA/PreLoadedMSADataPanel.js

@@ -92,8 +92,6 @@ const PreLoadedMSA = observer(function ({ model, feature, handleClose, preferred
                         feature: selectedTranscript,
                         placement,
                         displayName: getGeneDisplayName(selectedTranscript),
-                        treeAreaWidth: 200,
-                        treeWidth: 100,
                         drawNodeBubbles: false,
                         labelsAlignRight: true,
                         showBranchLen: false,

package/dist/MsaViewPanel/model.d.ts

@@ -111,11 +111,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "id" | "type" | "autoTreeAreaWidth" | "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"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+}, "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"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").TreeOrder>, [undefined]>;
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -123,7 +123,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -535,11 +534,10 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     removeActiveDialog(): void;
     queueDialog(cb: (doneCallback: () => void) => [import("@jbrowse/core/util").DialogComponentType, unknown]): void;
 } & {
-    setTreeAreaWidth(n: number): void;
-    setTreeWidth(n: number): void;
+    setTreeAreaWidth(n: number | undefined): void;
+    setTreeWidth(n: number | undefined): void;
     setLabelsAlignRight(arg: boolean): void;
     setDrawTree(arg: boolean): void;
-    setAutoTreeAreaWidth(arg: boolean): void;
     setShowBranchLen(arg: boolean): void;
     setTreeOrder(order: import("react-msaview").TreeOrder): void;
     setDrawNodeBubbles(arg: boolean): void;
@@ -671,6 +669,17 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly rowNamesSet: Map<string, number>;
     readonly resolvedClades: import("react-msaview").ResolvedClade[];
     readonly cladeGutterWidth: number;
+    readonly treeDrawn: boolean;
+    readonly treeTips: {
+        names: string[];
+        depth: number;
+    };
+    readonly maxTipLabelWidth: number;
+    readonly labelColumnWidth: number;
+    readonly fittedTreeAreaWidth: number;
+    readonly effectiveTreeAreaWidth: number;
+    readonly effectiveTreeWidth: number;
+    readonly showTreeText: boolean;
     readonly mouseOverRowName: string | undefined;
     readonly hoveredInsertion: {
         rowName: string;
@@ -736,7 +745,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly totalWidth: number;
 } & {
     readonly showMsaLetters: boolean;
-    readonly showTreeText: boolean;
 } & {
     readonly columnTrackContent: Map<string, {
         values?: number[];
@@ -747,9 +755,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     columnTrackModel(track: import("react-msaview").ColumnTrackSpec): import("react-msaview").BasicTrack;
     readonly columnTrackModels: import("react-msaview").BasicTrack[];
 } & {
-    readonly labelWidthMap: Map<string, number>;
-    readonly labelWidthScale: number;
-    readonly labelsWidth: number;
     readonly secondaryStructureConsensus: string | undefined;
     readonly secondaryStructureArcs: import("react-msaview").Arc[] | undefined;
     readonly adapterTrackModels: import("react-msaview").BasicTrack[];
@@ -1122,11 +1127,11 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
     displayName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
     minimized: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-}, "id" | "type" | "autoTreeAreaWidth" | "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"> & Omit<Omit<Omit<{}, "autoTreeAreaWidth" | "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
+}, "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"> & Omit<Omit<Omit<{}, "drawLabels" | "drawNodeBubbles" | "drawNodeLabels" | "drawTree" | "labelsAlignRight" | "overviewHeight" | "showBranchLen" | "showTreeOverview" | "treeAreaWidth" | "treeOrder" | "treeWidth"> & {
     drawLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     labelsAlignRight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-    treeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    treeWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
+    treeAreaWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    treeWidth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
     showBranchLen: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     treeOrder: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").TreeOrder>, [undefined]>;
     drawTree: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -1134,7 +1139,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawNodeLabels: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     showTreeOverview: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     overviewHeight: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<number>, [undefined]>;
-    autoTreeAreaWidth: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
 }, "bgColor" | "colorSchemeName" | "customColorScheme" | "msaFormat" | "showColumnStats"> & {
     bgColor: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<boolean>, [undefined]>;
     colorSchemeName: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
@@ -1523,7 +1527,7 @@ 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>;
-}>, "id" | "type" | "autoTreeAreaWidth" | "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"> & ({
+}>, "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;
@@ -1531,8 +1535,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
-    treeAreaWidth: number;
-    treeWidth: number;
+    treeAreaWidth: number | undefined;
+    treeWidth: number | undefined;
     showBranchLen: boolean;
     treeOrder: import("react-msaview").TreeOrder;
     drawTree: boolean;
@@ -1540,7 +1544,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
     overviewHeight: number;
-    autoTreeAreaWidth: boolean;
     columnTracks: import("react-msaview").ColumnTrackSpec[];
     id: string;
     showDomains: boolean;
@@ -1669,8 +1672,8 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     msaFormat: import("msa-parsers").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
-    treeAreaWidth: number;
-    treeWidth: number;
+    treeAreaWidth: number | undefined;
+    treeWidth: number | undefined;
     showBranchLen: boolean;
     treeOrder: import("react-msaview").TreeOrder;
     drawTree: boolean;
@@ -1678,7 +1681,6 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     drawNodeLabels: boolean;
     showTreeOverview: boolean;
     overviewHeight: number;
-    autoTreeAreaWidth: boolean;
     columnTracks?: undefined;
     id: string;
     showDomains: boolean;

package/dist/chunks/{AboutDialog-YNPKL64P.js → AboutDialog-IRBPUPJK.js}

@@ -1,2 +1,2 @@
-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);var l="8.4.1";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-YNPKL64P.js.map
+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);var l="9.0.0";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-IRBPUPJK.js.map

package/dist/chunks/{AboutDialog-YNPKL64P.js.map → AboutDialog-IRBPUPJK.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx", "../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/version.ts"],
-  "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", "export const version = '8.4.1'\n"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/AboutDialog.tsx", "../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/version.ts"],
+  "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", "export const version = '9.0.0'\n"],
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package/dist/chunks/{AnnotationFileDialog-NJGKHAVR.js → AnnotationFileDialog-FCYYZ4JN.js}

@@ -1,2 +1,2 @@
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+//# sourceMappingURL=AnnotationFileDialog-FCYYZ4JN.js.map

package/dist/chunks/{AnnotationFileDialog-NJGKHAVR.js.map → AnnotationFileDialog-FCYYZ4JN.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/AnnotationFileDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/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 {\n  annotationsToGFF,\n  interProScanResponseToAnnotations,\n} from 'msa-parsers'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { InterProScanResponse } from 'msa-parsers'\n\n// GFF3 as the CLI writes it, or the JSON an InterProScan run returns. Both\n// arrive as text and the model keeps GFF, so the JSON is converted on the way\n// in rather than given a second path through the model\nfunction toGFF(text: string) {\n  const trimmed = text.trimStart()\n  if (!trimmed.startsWith('{')) {\n    return text\n  }\n  const response: InterProScanResponse = JSON.parse(trimmed)\n  return annotationsToGFF(interProScanResponseToAnnotations(response))\n}\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' ? 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package/dist/chunks/ExportSVGDialog-TYYPI6VB.js

@@ -0,0 +1,2 @@
+import{a as p}from"./chunk-YOTSFJMU.js";import{a as P}from"./chunk-CVLB4VFP.js";import{a as R}from"./chunk-DNFD5II2.js";import{a as q}from"./chunk-BX4Z274Q.js";import{a as W}from"./chunk-J6KYLXRD.js";import{b as a}from"./chunk-FY3BTKY4.js";var t=a(W(),1),i=a(R(),1),e=a(q(),1),v=a(P(),1);function z(r){requestAnimationFrame(()=>{requestAnimationFrame(r)})}var O=(0,v.observer)(function({model:r,onClose:c}){let[s,f]=(0,t.useState)(!0),[n,x]=(0,t.useState)(!0),[o,k]=(0,t.useState)("viewport"),[h,y]=(0,t.useState)(),[m,d]=(0,t.useState)(!1),T=(0,e.useTheme)(),{totalWidth:C,totalHeight:b,effectiveTreeAreaWidth:w,rowPanelsWidth:M,turnedOnTracks:A,totalTrackAreaHeight:S,numColumns:F,leaves:G,showMsaLetters:I,treeOverviewHeight:D}=r,E=A.length>0,H=C+w+M,L=b+(n?S:0)+D,g=I&&o==="entire"?F*G.length:0,V=g>1e5;return t.default.createElement(i.Dialog,{onClose:()=>{c()},open:!0,title:"Export SVG"},t.default.createElement(e.DialogContent,null,h?t.default.createElement(i.ErrorMessage,{error:h}):null,t.default.createElement(e.Typography,null,"Settings:"),t.default.createElement(p,{label:"Include minimap?",disabled:o==="entire",checked:s,onChange:()=>{f(!s)}}),E?t.default.createElement(p,{label:"Include tracks?",checked:n,onChange:()=>{x(!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:l=>{let{value:u}=l.target;(u==="entire"||u==="viewport")&&k(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"})))),V?t.default.createElement(e.Alert,{severity:"warning",style:{marginTop:8}},"The entire MSA is ",Math.round(H),"x",Math.round(L)," pixels and draws"," ",Math.round(g/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:()=>{d(!0),z(()=>{r.exportSVG({theme:T,includeMinimap:s,includeTracks:E&&n,exportType:o}).then(()=>{c()}).catch(l=>{console.error(l),y(l)}).finally(()=>{d(!1)})})}},m?"Exporting\u2026":"Export"),t.default.createElement(e.Button,{variant:"contained",color:"secondary",onClick:()=>{c()}},"Cancel")))}),_=O;export{_ as default};
+//# sourceMappingURL=ExportSVGDialog-TYYPI6VB.js.map

package/dist/chunks/ExportSVGDialog-TYYPI6VB.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/ExportSVGDialog.tsx"],
+  "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog, ErrorMessage } from '@jbrowse/core/ui'\nimport {\n  Alert,\n  Button,\n  CircularProgress,\n  DialogActions,\n  DialogContent,\n  FormControl,\n  FormControlLabel,\n  FormLabel,\n  Radio,\n  RadioGroup,\n  Typography,\n  useTheme,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport Checkbox2 from '../Checkbox2.tsx'\n\nimport type { MsaViewModel } from '../../model.ts'\n\n// Run after the browser has painted. A requestAnimationFrame callback still\n// runs *before* the frame it was queued for, so one alone hands the main thread\n// to the render with the spinner not yet on screen; the second fires once that\n// frame is out.\nfunction afterPaint(fn: () => void) {\n  requestAnimationFrame(() => {\n    requestAnimationFrame(fn)\n  })\n}\n\nconst ExportSVGDialog = observer(function ({\n  model,\n  onClose,\n}: {\n  model: MsaViewModel\n  onClose: () => void\n}) {\n  const [includeMinimap, setIncludeMinimap] = useState(true)\n  const [includeTracks, setIncludeTracks] = useState(true)\n  const [exportType, setExportType] = useState<'entire' | 'viewport'>(\n    'viewport',\n  )\n  const [error, setError] = useState<unknown>()\n  const [exporting, setExporting] = useState(false)\n  const theme = useTheme()\n  const {\n    totalWidth,\n    totalHeight,\n    effectiveTreeAreaWidth,\n    rowPanelsWidth,\n    turnedOnTracks,\n    totalTrackAreaHeight,\n    numColumns,\n    leaves,\n    showMsaLetters,\n    treeOverviewHeight,\n  } = model\n  const hasTracks = turnedOnTracks.length > 0\n  const entireWidth = totalWidth + effectiveTreeAreaWidth + rowPanelsWidth\n  const entireHeight =\n    totalHeight +\n    (includeTracks ? totalTrackAreaHeight : 0) +\n    treeOverviewHeight\n  // the background is one raster image whatever its size, so what the figure\n  // actually costs is its residue letters: each is an svg element of its own.\n  // Past roughly this many the export runs to tens of seconds and can exhaust\n  // the tab's memory outright\n  const glyphs =\n    showMsaLetters && exportType === 'entire' ? numColumns * leaves.length : 0\n  const isLargeExport = glyphs > 100_000\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Export SVG\"\n    >\n      <DialogContent>\n        {error ? <ErrorMessage error={error} /> : null}\n        <Typography>Settings:</Typography>\n        <Checkbox2\n          label=\"Include minimap?\"\n          disabled={exportType === 'entire'}\n          checked={includeMinimap}\n          onChange={() => {\n            setIncludeMinimap(!includeMinimap)\n          }}\n        />\n        {hasTracks ? (\n          <Checkbox2\n            label=\"Include tracks?\"\n            checked={includeTracks}\n            onChange={() => {\n              setIncludeTracks(!includeTracks)\n            }}\n          />\n        ) : null}\n        <div>\n          <FormControl>\n            <FormLabel>Export type</FormLabel>\n            <RadioGroup\n              value={exportType}\n              onChange={event => {\n                const { value } = event.target\n                if (value === 'entire' || value === 'viewport') {\n                  setExportType(value)\n                }\n              }}\n            >\n              <FormControlLabel\n                value=\"entire\"\n                control={<Radio />}\n                label=\"Entire MSA\"\n              />\n              <FormControlLabel\n                value=\"viewport\"\n                control={<Radio />}\n                label=\"Current viewport only\"\n              />\n            </RadioGroup>\n          </FormControl>\n        </div>\n        {isLargeExport ? (\n          <Alert severity=\"warning\" style={{ marginTop: 8 }}>\n            The entire MSA is {Math.round(entireWidth)}x\n            {Math.round(entireHeight)} pixels and draws{' '}\n            {Math.round(glyphs / 1000)}k residue letters, each its own SVG\n            element. Export may be slow or fail \u2014 zooming out far enough to hide\n            the letters exports the same alignment as an image instead.\n          </Alert>\n        ) : null}\n      </DialogContent>\n      <DialogActions>\n        <Button\n          variant=\"contained\"\n          color=\"primary\"\n          // rendering runs on the main thread and a large figure holds it for\n          // seconds; without this the button stays live through the freeze and\n          // a second click starts a second export\n          disabled={exporting}\n          startIcon={\n            exporting ? <CircularProgress size={16} color=\"inherit\" /> : null\n          }\n          onClick={() => {\n            setExporting(true)\n            afterPaint(() => {\n              void model\n                .exportSVG({\n                  theme,\n                  includeMinimap,\n                  includeTracks: hasTracks && includeTracks,\n                  exportType,\n                })\n                .then(() => {\n                  onClose()\n                })\n                .catch((e: unknown) => {\n                  console.error(e)\n                  setError(e)\n                })\n                .finally(() => {\n                  setExporting(false)\n                })\n            })\n          }}\n        >\n          {exporting ? 'Exporting\u2026' : 'Export'}\n        </Button>\n        <Button\n          variant=\"contained\"\n          color=\"secondary\"\n          onClick={() => {\n            onClose()\n          }}\n        >\n          Cancel\n        </Button>\n      </DialogActions>\n    </Dialog>\n  )\n})\n\nexport default ExportSVGDialog\n"],
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+  "names": ["import_react", "import_ui", "import_material", "import_mobx_react", "afterPaint", "fn", "ExportSVGDialog", "model", "onClose", "includeMinimap", "setIncludeMinimap", "includeTracks", "setIncludeTracks", "exportType", "setExportType", "error", "setError", "exporting", "setExporting", "theme", "totalWidth", "totalHeight", "effectiveTreeAreaWidth", "rowPanelsWidth", "turnedOnTracks", "totalTrackAreaHeight", "numColumns", "leaves", "showMsaLetters", "treeOverviewHeight", "hasTracks", "entireWidth", "entireHeight", "glyphs", "isLargeExport", "React", "Checkbox2", "event", "value", "e", "ExportSVGDialog_default"]
+}

package/dist/chunks/{FeatureDialog-7XXL6XUK.js → FeatureDialog-ZBX3XQZ5.js}

@@ -1,2 +1,2 @@
 import{a as C}from"./chunk-CVLB4VFP.js";import{a as F}from"./chunk-DNFD5II2.js";import{a as k}from"./chunk-BX4Z274Q.js";import{a as T}from"./chunk-J6KYLXRD.js";import{b as c}from"./chunk-FY3BTKY4.js";var e=c(T(),1),p=c(F(),1),t=c(k(),1),s=c(C(),1);function w(n,a){return[n.accession,n.name,n.description].some(o=>o?.toLowerCase().includes(a))}var x=(0,s.observer)(function({model:n,accessions:a}){let o=u=>{for(let m of a)n.setFilter(m,u)};return e.default.createElement("div",null,e.default.createElement(t.Button,{onClick:()=>{o(!0)}},"Toggle all on"),e.default.createElement(t.Button,{onClick:()=>{o(!1)}},"Toggle all off"))}),v=(0,s.observer)(function({model:n}){let{annotationTypes:a,annotations:o,featureColors:u,fillPalette:m}=n,[f,h]=(0,e.useState)(""),g=f.trim().toLowerCase(),d=[...a.values()].filter(l=>!g||w(l,g)),i=new Map,E=new Map;for(let l of o){let{accession:r}=l;i.set(r,(i.get(r)??0)+1),E.has(r)||E.set(r,u.get(l)?.fill??m[r])}return e.default.createElement(e.default.Fragment,null,e.default.createElement(t.TextField,{label:"Filter",size:"small",value:f,onChange:l=>{h(l.target.value)}}),e.default.createElement(x,{model:n,accessions:d.map(l=>l.accession)}),e.default.createElement(t.Table,{size:"small"},e.default.createElement(t.TableHead,null,e.default.createElement(t.TableRow,null,e.default.createElement(t.TableCell,{padding:"checkbox"}),e.default.createElement(t.TableCell,null,"color"),e.default.createElement(t.TableCell,null,"accession"),e.default.createElement(t.TableCell,null,"name"),e.default.createElement(t.TableCell,null,"count"),e.default.createElement(t.TableCell,null,"description"))),e.default.createElement(t.TableBody,null,d.map(({accession:l,name:r,description:b})=>e.default.createElement(t.TableRow,{key:l},e.default.createElement(t.TableCell,{padding:"checkbox"},e.default.createElement(t.Checkbox,{checked:!n.turnedOffFeatures.get(l),onChange:()=>{n.setFilter(l,!!n.turnedOffFeatures.get(l))}})),e.default.createElement(t.TableCell,null,e.default.createElement("div",{style:{width:20,height:20,background:E.get(l)}})),e.default.createElement(t.TableCell,null,l),e.default.createElement(t.TableCell,null,r),e.default.createElement(t.TableCell,null,i.get(l)),e.default.createElement(t.TableCell,null,b))))))}),y=(0,s.observer)(function({onClose:n,model:a}){return e.default.createElement(p.Dialog,{onClose:()=>{n()},open:!0,title:"Feature filters",maxWidth:"xl"},e.default.createElement(t.DialogContent,null,e.default.createElement(v,{model:a})))}),D=y;export{D as default};
-//# sourceMappingURL=FeatureDialog-7XXL6XUK.js.map
+//# sourceMappingURL=FeatureDialog-ZBX3XQZ5.js.map

package/dist/chunks/{FeatureDialog-7XXL6XUK.js.map → FeatureDialog-ZBX3XQZ5.js.map}

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/react-msaview@8.4.1_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/FeatureDialog.tsx"],
+  "sources": ["../../node_modules/.pnpm/react-msaview@9.0.0_3e54acfe76b6ad0d26e91cd532b7f775/node_modules/react-msaview/src/components/dialogs/FeatureDialog.tsx"],
   "sourcesContent": ["import React, { useState } from 'react'\n\nimport { Dialog } from '@jbrowse/core/ui'\nimport {\n  Button,\n  Checkbox,\n  DialogContent,\n  Table,\n  TableBody,\n  TableCell,\n  TableHead,\n  TableRow,\n  TextField,\n} from '@mui/material'\nimport { observer } from 'mobx-react'\n\nimport type { MsaViewModel } from '../../model.ts'\nimport type { Annotation } from '../../types.ts'\n\nfunction matches(type: Annotation, query: string) {\n  return [type.accession, type.name, type.description].some(field =>\n    field?.toLowerCase().includes(query),\n  )\n}\n\nconst Toggles = observer(function ({\n  model,\n  accessions,\n}: {\n  model: MsaViewModel\n  accessions: string[]\n}) {\n  const setAll = (shown: boolean) => {\n    for (const accession of accessions) {\n      model.setFilter(accession, shown)\n    }\n  }\n  return (\n    <div>\n      <Button\n        onClick={() => {\n          setAll(true)\n        }}\n      >\n        Toggle all on\n      </Button>\n\n      <Button\n        onClick={() => {\n          setAll(false)\n        }}\n      >\n        Toggle all off\n      </Button>\n    </div>\n  )\n})\n\nconst FeatureTable = observer(function ({ model }: { model: MsaViewModel }) {\n  const { annotationTypes, annotations, featureColors, fillPalette } = model\n  const [query, setQuery] = useState('')\n  const needle = query.trim().toLowerCase()\n  const types = [...annotationTypes.values()].filter(\n    type => !needle || matches(type, needle),\n  )\n  const counts = new Map<string, number>()\n  const swatches = new Map<string, string>()\n  for (const annot of annotations) {\n    const { accession } = annot\n    counts.set(accession, (counts.get(accession) ?? 0) + 1)\n    if (!swatches.has(accession)) {\n      swatches.set(\n        accession,\n        featureColors.get(annot)?.fill ?? fillPalette[accession]!,\n      )\n    }\n  }\n  return (\n    <>\n      <TextField\n        label=\"Filter\"\n        size=\"small\"\n        value={query}\n        onChange={event => {\n          setQuery(event.target.value)\n        }}\n      />\n      <Toggles model={model} accessions={types.map(t => t.accession)} />\n      <Table size=\"small\">\n        <TableHead>\n          <TableRow>\n            <TableCell padding=\"checkbox\" />\n            <TableCell>color</TableCell>\n            <TableCell>accession</TableCell>\n            <TableCell>name</TableCell>\n            <TableCell>count</TableCell>\n            <TableCell>description</TableCell>\n          </TableRow>\n        </TableHead>\n        <TableBody>\n          {types.map(({ accession, name, description }) => (\n            <TableRow key={accession}>\n              <TableCell padding=\"checkbox\">\n                <Checkbox\n                  checked={!model.turnedOffFeatures.get(accession)}\n                  onChange={() => {\n                    model.setFilter(\n                      accession,\n                      !!model.turnedOffFeatures.get(accession),\n                    )\n                  }}\n                />\n              </TableCell>\n              <TableCell>\n                <div\n                  style={{\n                    width: 20,\n                    height: 20,\n                    background: swatches.get(accession),\n                  }}\n                />\n              </TableCell>\n              <TableCell>{accession}</TableCell>\n              <TableCell>{name}</TableCell>\n              <TableCell>{counts.get(accession)}</TableCell>\n              <TableCell>{description}</TableCell>\n            </TableRow>\n          ))}\n        </TableBody>\n      </Table>\n    </>\n  )\n})\n\nconst FeatureTypeDialog = observer(function ({\n  onClose,\n  model,\n}: {\n  onClose: () => void\n  model: MsaViewModel\n}) {\n  return (\n    <Dialog\n      onClose={() => {\n        onClose()\n      }}\n      open\n      title=\"Feature filters\"\n      maxWidth=\"xl\"\n    >\n      <DialogContent>\n        <FeatureTable model={model} />\n      </DialogContent>\n    </Dialog>\n  )\n})\n\nexport default FeatureTypeDialog\n"],
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package/dist/chunks/{LaunchMsaViewDialog-C53VHT52.js → LaunchMsaViewDialog-GJAUPGFC.js}

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