jbrowse-plugin-msaview 2.8.0 → 2.8.1

package/dist/MsaViewPanel/model.d.ts

@@ -53,7 +53,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     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]>;
     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("msa-parsers").MSAFormat>>;
+    msaFormat: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<import("react-msaview").MSAFormat>>;
 }, "height" | "id" | "type" | "allowedGappyness" | "colWidth" | "collapsed" | "currentAlignment" | "data" | "drawMsaLetters" | "featureFilters" | "gffFilehandle" | "hideGaps" | "highlightColumns" | "msaFilehandle" | "relativeTo" | "rowHeight" | "scrollX" | "scrollY" | "scrollZoom" | "showDomains" | "showOnly" | "subFeatureRows" | "treeFilehandle" | "treeMetadataFilehandle" | "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]>;
@@ -507,7 +507,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     setColorSchemeName(name: string): void;
     setBgColor(arg: boolean): void;
     setShowColumnStats(arg: boolean): void;
-    setMSAFormat(arg?: import("msa-parsers").MSAFormat): void;
+    setMSAFormat(arg?: import("react-msaview").MSAFormat): void;
 } & {
     headerHeight: number;
     status: {
@@ -594,7 +594,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     readonly noDomains: boolean;
     menuItems(): never[];
     readonly treeMetadata: Record<string, Record<string, string> | undefined>;
-    readonly MSA: import("msa-parsers").MSAParserType | null;
+    readonly MSA: import("react-msaview").MSAParserType | null;
     readonly numColumns: number;
     readonly tree: import("react-msaview").NodeWithIds;
     readonly rowNames: string[];
@@ -956,7 +956,7 @@ export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").
     bgColor: boolean;
     colorSchemeName: string;
     showColumnStats: boolean;
-    msaFormat: import("msa-parsers").MSAFormat | undefined;
+    msaFormat: import("react-msaview").MSAFormat | undefined;
     drawLabels: boolean;
     labelsAlignRight: boolean;
     treeAreaWidth: number;

package/dist/jbrowse-plugin-msaview.umd.production.min.js

@@ -46,7 +46,7 @@ In order to be iterable, non-array objects must have a [Symbol.iterator]() metho
 ${l[1]}`).join(`
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+`)}}),r()}}catch(R){l(R)}},onCancel:r}))}),tF=u$;var rF=p(Q());function Ga({children:e,value:t,index:r,...n}){return rF.default.createElement("div",{role:"tabpanel",hidden:t!==r,...n},t===r?e:null)}function yx({handleClose:e,feature:t,model:r}){let n=(0,oF.getSession)(r),i=!!UA(n.jbrowse)?.length,[s,a]=(0,wt.useState)("orthologs");return wt.default.createElement(nF.Dialog,{maxWidth:"xl",title:"Launch MSA view",open:!0,onClose:e},wt.default.createElement(qi.Tabs,{value:s,onChange:(c,l)=>{a(l)}},wt.default.createElement(qi.Tab,{label:"Orthologs (fast)",value:"orthologs"}),wt.default.createElement(qi.Tab,{label:"NCBI BLAST query",value:"ncbi_blast"}),i?wt.default.createElement(qi.Tab,{label:"Pre-loaded MSA datasets",value:"preloaded_msa"}):null,wt.default.createElement(qi.Tab,{label:"Manual upload",value:"manual_msa"})),wt.default.createElement(Ga,{value:s,index:"orthologs"},wt.default.createElement(VP,{handleClose:e,feature:t,model:r})),wt.default.createElement(Ga,{value:s,index:"ncbi_blast"},wt.default.createElement(px,{handleClose:e,feature:t,model:r})),i?wt.default.createElement(Ga,{value:s,index:"preloaded_msa"},wt.default.createElement(tF,{model:r,feature:t,handleClose:e})):null,wt.default.createElement(Ga,{value:s,index:"manual_msa"},wt.default.createElement(iP,{model:r,feature:t,handleClose:e})))}function f$(e){return e.name==="LinearBasicDisplay"}var d$=new Set(["gene","mRNA","transcript"]);function A$(e){return e.views(t=>{let r=t.contextMenuItems;return{contextMenuItems(){let n=(0,VA.getContainingTrack)(t),o=(0,VA.getSession)(n),i=u=>{o.queueDialog(d=>[yx,{model:n,handleClose:d,feature:u}])},s=t.contextMenuInfo,a=t.fetchFullFeature,c=t.contextMenuFeature,l=s&&a&&t.isGeneLike?()=>{a(s.item.featureId,s.displayedRegionIndex).then(u=>{u?i(u):o.notify("Could not load feature for MSA view","warning")}).catch(u=>{o.notifyError(`${u}`,u)})}:c&&d$.has(String(c.get("type")))?()=>{i(c)}:void 0;return[...r(),...l?[{label:"Launch MSA view",icon:yL,onClick:l}]:[]]}}})}function xx(e){e.addToExtensionPoint("Core-extendPluggableElement",t=>(f$(t)&&(t.stateModel=A$(t.stateModel)),t))}function Cx(e){e.addToExtensionPoint("LaunchView-MsaView",t=>{let{session:r,data:n,msaFileLocation:o,msaIndexedLocation:i,msaName:s,treeFileLocation:a,querySeqName:c,...l}=t;if(!n&&!o&&!i)throw new Error("No MSA data or file location provided when launching MSA view");return r.addView("MsaView",{type:"MsaView",...l,data:n,...a?{treeFilehandle:{...a,locationType:"UriLocation"}}:{},init:{msaUrl:o?.uri,msaIndexedLocation:i,msaName:s,querySeqName:c}}),t})}var bF=p(Q()),EF=p(sF());var b$=(0,bF.lazy)(()=>Promise.resolve().then(()=>(CF(),xF)));function Ix(e){e.addViewType(()=>new EF.default({name:"MsaView",stateModel:Ly(),ReactComponent:b$}))}var wF="2.8.1";var WA=class extends IF.default{constructor(){super(...arguments);this.name="MsaViewPlugin";this.version=wF;this.rootConfigurationSchema=r=>({msa:(0,Sx.ConfigurationSchema)("MSA",{datasets:vx.types.maybe(vx.types.array((0,Sx.ConfigurationSchema)("MSAEntry",{datasetId:{type:"string",defaultValue:""},description:{type:"string",defaultValue:""},name:{type:"string",defaultValue:""},adapter:r.pluggableConfigSchemaType("adapter")})))})})}install(r){Ix(r),xx(r),Cx(r),Gy(r),Hy(r)}configure(r){(0,SF.isAbstractMenuManager)(r.rootModel)&&r.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:Dw,onClick:n=>{n.addView("MsaView",{})}})}};return YF(E$);})();
 /*! Bundled license information:
 
 react-is/cjs/react-is.production.js: