@jbrowse/plugin-variants 2.10.2 → 2.11.0

package/dist/LinearVariantDisplay/model.d.ts

@@ -45,8 +45,15 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/dist/VariantFeatureWidget/stateModelFactory.d.ts

@@ -38,8 +38,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    type: "BaseFeatureWidget";
     id: string;
+    type: "BaseFeatureWidget";
     track: import("mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;

package/dist/VcfFeature/util.d.ts

@@ -3,5 +3,5 @@ import VCF from '@gmod/vcf';
  * Get a sequence ontology (SO) term that describes the variant type
  */
 export declare function getSOTermAndDescription(ref: string, alt: string[], parser: VCF): string[];
-export declare function getSOAndDescFromAltDefs(ref: string, alt: string, parser: VCF): string[];
+export declare function getSOAndDescFromAltDefs(alt: string, parser: VCF): string[];
 export declare function getSOAndDescByExamination(ref: string, alt: string): string[];

package/dist/VcfFeature/util.js

@@ -25,7 +25,7 @@ function getSOTermAndDescription(ref, alt, parser) {
     const soTerms = new Set();
     let descriptions = new Set();
     alt.forEach(a => {
-        let [soTerm, description] = getSOAndDescFromAltDefs(ref, a, parser);
+        let [soTerm, description] = getSOAndDescFromAltDefs(a, parser);
         if (!soTerm) {
             ;
             [soTerm, description] = getSOAndDescByExamination(ref, a);
@@ -58,7 +58,7 @@ function getSOTermAndDescription(ref, alt, parser) {
     return [];
 }
 exports.getSOTermAndDescription = getSOTermAndDescription;
-function getSOAndDescFromAltDefs(ref, alt, parser) {
+function getSOAndDescFromAltDefs(alt, parser) {
     if (typeof alt === 'string' && !alt.startsWith('<')) {
         return [];
     }
@@ -74,7 +74,7 @@ function getSOAndDescFromAltDefs(ref, alt, parser) {
     // try to look for a definition for a parent term if we can
     const modAlt = alt.split(':');
     if (modAlt.length > 1) {
-        return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, -1).join(':')}>`, parser);
+        return getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser);
     }
     // no parent
     return [];

package/esm/LinearVariantDisplay/model.d.ts

@@ -45,8 +45,15 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;

package/esm/VariantFeatureWidget/stateModelFactory.d.ts

@@ -38,8 +38,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
     maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    type: "BaseFeatureWidget";
     id: string;
+    type: "BaseFeatureWidget";
     track: import("mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;

package/esm/VcfFeature/util.d.ts

@@ -3,5 +3,5 @@ import VCF from '@gmod/vcf';
  * Get a sequence ontology (SO) term that describes the variant type
  */
 export declare function getSOTermAndDescription(ref: string, alt: string[], parser: VCF): string[];
-export declare function getSOAndDescFromAltDefs(ref: string, alt: string, parser: VCF): string[];
+export declare function getSOAndDescFromAltDefs(alt: string, parser: VCF): string[];
 export declare function getSOAndDescByExamination(ref: string, alt: string): string[];

package/esm/VcfFeature/util.js

@@ -22,7 +22,7 @@ export function getSOTermAndDescription(ref, alt, parser) {
     const soTerms = new Set();
     let descriptions = new Set();
     alt.forEach(a => {
-        let [soTerm, description] = getSOAndDescFromAltDefs(ref, a, parser);
+        let [soTerm, description] = getSOAndDescFromAltDefs(a, parser);
         if (!soTerm) {
             ;
             [soTerm, description] = getSOAndDescByExamination(ref, a);
@@ -54,7 +54,7 @@ export function getSOTermAndDescription(ref, alt, parser) {
     }
     return [];
 }
-export function getSOAndDescFromAltDefs(ref, alt, parser) {
+export function getSOAndDescFromAltDefs(alt, parser) {
     if (typeof alt === 'string' && !alt.startsWith('<')) {
         return [];
     }
@@ -70,7 +70,7 @@ export function getSOAndDescFromAltDefs(ref, alt, parser) {
     // try to look for a definition for a parent term if we can
     const modAlt = alt.split(':');
     if (modAlt.length > 1) {
-        return getSOAndDescFromAltDefs(ref, `<${modAlt.slice(0, -1).join(':')}>`, parser);
+        return getSOAndDescFromAltDefs(`<${modAlt.slice(0, -1).join(':')}>`, parser);
     }
     // no parent
     return [];

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "2.10.2",
+  "version": "2.11.0",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -41,7 +41,7 @@
     "@gmod/tabix": "^1.5.6",
     "@gmod/vcf": "^5.0.9",
     "@mui/icons-material": "^5.0.2",
-    "@mui/x-data-grid": "^6.0.1",
+    "@mui/x-data-grid": "^7.0.0",
     "generic-filehandle": "^3.0.0"
   },
   "peerDependencies": {
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "7ca3b7db337ebd88853e2d96cdab940ed550c4fb"
+  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
 }