@jbrowse/plugin-linear-comparative-view 2.11.1 → 2.12.0

package/esm/LinearSyntenyView/model.d.ts

@@ -32,7 +32,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     type: import("mobx-state-tree").ISimpleType<"LinearComparativeView">;
     trackSelectorType: import("mobx-state-tree").IType<string | undefined, string, string>;
     showIntraviewLinks: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    linkViews: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     interactToggled: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     middleComparativeHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
@@ -45,20 +44,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         type: import("mobx-state-tree").IType<string | undefined, string, string>;
         offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
         bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-        displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>; /**
-             * #property/
-             */
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
-             * #action
-             */
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
         tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
         hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -159,6 +145,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
             start: number;
             end: number;
+            type: string;
             regionNumber?: number | undefined;
             reversed?: boolean | undefined;
             refName: string;
@@ -215,14 +202,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 } | undefined;
                 lowerCaseRefNameAliases: {
                     [x: string]: string | undefined;
-                } | undefined;
+                } | undefined; /**
+                 * #property
+                 */
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean; /**
-                 * #property/
-                 */
+                readonly initialized: boolean;
                 readonly name: string;
                 readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
@@ -279,14 +266,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 } | undefined;
                 lowerCaseRefNameAliases: {
                     [x: string]: string | undefined;
-                } | undefined;
+                } | undefined; /**
+                 * #property
+                 */
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean; /**
-                 * #property/
-                 */
+                readonly initialized: boolean;
                 readonly name: string;
                 readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
@@ -356,7 +343,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             offset: number;
             start: number;
             end: number;
-            reversed: boolean;
+            reversed?: boolean | undefined;
         };
         readonly centerLineInfo: {
             coord: number;
@@ -367,7 +354,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             offset: number;
             start: number;
             end: number;
-            reversed: boolean;
+            reversed?: boolean | undefined;
         } | undefined;
     } & {
         afterCreate(): void;
@@ -380,20 +367,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         type: import("mobx-state-tree").IType<string | undefined, string, string>;
         offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
         bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-        displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>; /**
-             * #property/
-             */
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
-             * #action
-             */
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
         tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
         hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -427,7 +401,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     readonly refNames: string[][];
     readonly assemblyNames: string[];
 } & {
-    afterAttach(): void;
     beforeDestroy(): void;
     onSubviewAction(actionName: string, path: string, args?: unknown[] | undefined): void;
     setWidth(newWidth: number): void;
@@ -440,20 +413,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         type: import("mobx-state-tree").IType<string | undefined, string, string>;
         offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
         bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-        displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>; /**
-             * #property/
-             */
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
-             * #action
-             */
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
         tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
         hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -473,33 +433,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         type: string;
         offsetPx: number;
         bpPerPx: number;
-        displayedRegions: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>; /**
-             * #property/
-             */
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
-             * #action
-             */
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>; /**
-             * #property/
-             */
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
-             * #action
-             */
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>>;
+        displayedRegions: import("@jbrowse/core/util").Region[] & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>>;
         tracks: import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>>;
         hideHeader: boolean;
         hideHeaderOverview: boolean;
@@ -600,6 +534,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
             start: number;
             end: number;
+            type: string;
             regionNumber?: number | undefined;
             reversed?: boolean | undefined;
             refName: string;
@@ -656,14 +591,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 } | undefined;
                 lowerCaseRefNameAliases: {
                     [x: string]: string | undefined;
-                } | undefined;
+                } | undefined; /**
+                 * #property
+                 */
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean; /**
-                 * #property/
-                 */
+                readonly initialized: boolean;
                 readonly name: string;
                 readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
@@ -720,14 +655,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 } | undefined;
                 lowerCaseRefNameAliases: {
                     [x: string]: string | undefined;
-                } | undefined;
+                } | undefined; /**
+                 * #property
+                 */
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean; /**
-                 * #property/
-                 */
+                readonly initialized: boolean;
                 readonly name: string;
                 readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
@@ -797,7 +732,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             offset: number;
             start: number;
             end: number;
-            reversed: boolean;
+            reversed?: boolean | undefined;
         };
         readonly centerLineInfo: {
             coord: number;
@@ -808,7 +743,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             offset: number;
             start: number;
             end: number;
-            reversed: boolean;
+            reversed?: boolean | undefined;
         } | undefined;
     } & {
         afterCreate(): void;
@@ -821,20 +756,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         type: import("mobx-state-tree").IType<string | undefined, string, string>;
         offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
         bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-        displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>; /**
-             * #property/
-             */
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
-             * #action
-             */
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
         tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
         hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -935,6 +857,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         getSelectedRegions(leftOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined, rightOffset?: import("@jbrowse/plugin-linear-genome-view/src/LinearGenomeView").BpOffset | undefined): {
             start: number;
             end: number;
+            type: string;
             regionNumber?: number | undefined;
             reversed?: boolean | undefined;
             refName: string;
@@ -991,14 +914,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 } | undefined;
                 lowerCaseRefNameAliases: {
                     [x: string]: string | undefined;
-                } | undefined;
+                } | undefined; /**
+                 * #property
+                 */
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean; /**
-                 * #property/
-                 */
+                readonly initialized: boolean;
                 readonly name: string;
                 readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
@@ -1055,14 +978,14 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 } | undefined;
                 lowerCaseRefNameAliases: {
                     [x: string]: string | undefined;
-                } | undefined;
+                } | undefined; /**
+                 * #property
+                 */
                 cytobands: import("@jbrowse/core/util").Feature[] | undefined;
             } & {
                 getConf(arg: string): any;
             } & {
-                readonly initialized: boolean; /**
-                 * #property/
-                 */
+                readonly initialized: boolean;
                 readonly name: string;
                 readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
                 readonly aliases: string[];
@@ -1132,7 +1055,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             offset: number;
             start: number;
             end: number;
-            reversed: boolean;
+            reversed?: boolean | undefined;
         };
         readonly centerLineInfo: {
             coord: number;
@@ -1143,7 +1066,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
             offset: number;
             start: number;
             end: number;
-            reversed: boolean;
+            reversed?: boolean | undefined;
         } | undefined;
     } & {
         afterCreate(): void;
@@ -1156,20 +1079,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         type: import("mobx-state-tree").IType<string | undefined, string, string>;
         offsetPx: import("mobx-state-tree").IType<number | undefined, number, number>;
         bpPerPx: import("mobx-state-tree").IType<number | undefined, number, number>;
-        displayedRegions: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
-            refName: import("mobx-state-tree").ISimpleType<string>;
-            start: import("mobx-state-tree").ISimpleType<number>;
-            end: import("mobx-state-tree").ISimpleType<number>; /**
-             * #property/
-             */
-            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        } & {
-            assemblyName: import("mobx-state-tree").ISimpleType<string>; /**
-             * #action
-             */
-        }, {
-            setRefName(newRefName: string): void;
-        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        displayedRegions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[], import("@jbrowse/core/util").Region[]>, [undefined]>;
         tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
         hideHeader: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
         hideHeaderOverview: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
@@ -1184,7 +1094,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     }>>, import("mobx-state-tree")._NotCustomized>>): void;
     closeView(): void;
     setMiddleComparativeHeight(n: number): number;
-    toggleLinkViews(): void;
     activateTrackSelector(): import("@jbrowse/core/util").Widget | undefined;
     toggleTrack(trackId: string): boolean;
     showTrack(trackId: string, initialSnapshot?: {}): void;
@@ -1241,15 +1150,6 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
         type: string;
         description: string;
         icon?: undefined;
-    } | {
-        label: string;
-        type: string;
-        checked: boolean;
-        onClick: () => void;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        description?: undefined;
     } | {
         label: string;
         type: string;

package/esm/LinearSyntenyView/model.js

@@ -5,7 +5,6 @@ import { getSession } from '@jbrowse/core/util';
 import { saveAs } from 'file-saver';
 // icons
 import CropFreeIcon from '@mui/icons-material/CropFree';
-import LinkIcon from '@mui/icons-material/Link';
 import VisibilityIcon from '@mui/icons-material/Visibility';
 import PhotoCameraIcon from '@mui/icons-material/PhotoCamera';
 import { Curves } from './components/Icons';
@@ -98,13 +97,6 @@ export default function stateModelFactory(pluginManager) {
                         type: 'checkbox',
                         description: 'Draws per-base CIGAR level alignments',
                     },
-                    {
-                        label: 'Link views',
-                        type: 'checkbox',
-                        checked: self.linkViews,
-                        onClick: self.toggleLinkViews,
-                        icon: LinkIcon,
-                    },
                     {
                         label: 'Use curved lines',
                         type: 'checkbox',

package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.d.ts

@@ -1,5 +1,7 @@
 import React from 'react';
-declare const BreakpointAlignmentsFeatureDetail: ({ model }: {
-    model: any;
+declare const SyntenyFeatureDetail: ({ model, }: {
+    model: {
+        featureData: unknown;
+    };
 }) => React.JSX.Element;
-export default BreakpointAlignmentsFeatureDetail;
+export default SyntenyFeatureDetail;

package/esm/SyntenyFeatureDetail/SyntenyFeatureDetail.js

@@ -24,9 +24,7 @@ function Formatter({ value }) {
 function CustomFeatureDetails(props) {
     return (React.createElement(BaseAttributes, { ...props, formatter: (value) => React.createElement(Formatter, { value: value }) }));
 }
-const BreakpointAlignmentsFeatureDetail = observer(
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-({ model }) => {
+const SyntenyFeatureDetail = observer(function ({ model, }) {
     const { feature1, feature2 } = JSON.parse(JSON.stringify(model.featureData));
     return (React.createElement(Paper, { "data-testid": "alignment-side-drawer" },
         React.createElement(BaseCoreDetails, { title: "Feature 1", feature: feature1 }),
@@ -34,4 +32,4 @@ const BreakpointAlignmentsFeatureDetail = observer(
         React.createElement(CustomFeatureDetails, { feature: feature1 }),
         React.createElement(CustomFeatureDetails, { feature: feature2 })));
 });
-export default BreakpointAlignmentsFeatureDetail;
+export default SyntenyFeatureDetail;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "2.11.1",
+  "version": "2.12.0",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -61,5 +61,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
+  "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
 }