@jbrowse/plugin-linear-comparative-view 2.6.2 → 2.6.3

package/dist/LGVSyntenyDisplay/model.d.ts

@@ -86,21 +86,11 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
     configuration: AnyConfigurationSchemaType;
-    showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    mismatchAlpha: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    sortedBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        type: import("mobx-state-tree").ISimpleType<string>;
-        pos: import("mobx-state-tree").ISimpleType<number>;
-        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        refName: import("mobx-state-tree").ISimpleType<string>;
-        assemblyName: import("mobx-state-tree").ISimpleType<string>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
         type: import("mobx-state-tree").ISimpleType<string>;
         tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -250,45 +240,30 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    modificationTagMap: import("mobx").ObservableMap<string, string>; /**
-     * #property
-     */
     featureUnderMouseVolatile: Feature | undefined;
-    currSortBpPerPx: number;
-    modificationsReady: boolean;
-    sortReady: boolean;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
 } & {
-    setModificationsReady(flag: boolean): void;
     setTagsReady(flag: boolean): void;
-    setSortReady(flag: boolean): void;
-    setCurrSortBpPerPx(n: number): void;
     setMaxHeight(n: number): void;
     setFeatureHeight(n?: number | undefined): void;
     setNoSpacing(flag?: boolean | undefined): void;
     setColorScheme(colorScheme: {
         type: string;
         tag?: string | undefined;
+        extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy | undefined;
     }): void;
-    updateModificationColorMap(uniqueModifications: string[]): void;
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: Feature | undefined): void;
     selectFeature(feature: Feature): void;
-    clearSelected(): void;
     copyFeatureToClipboard(feature: Feature): void;
-    toggleSoftClipping(): void;
-    toggleMismatchAlpha(): void;
     setConfig(conf: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>): void;
-    setSortedBy(type: string, tag?: string | undefined): void;
-    setFilterBy(filter: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/model").Filter): void;
-} & {
-    reload(): void;
+    setFilterBy(filter: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin").Filter): void;
 } & {
     readonly rendererConfig: {
         [x: string]: any;
@@ -298,9 +273,8 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     readonly maxHeight: any;
     readonly featureHeightSetting: any;
-    readonly mismatchAlphaSetting: any;
     readonly featureUnderMouse: Feature | undefined;
-    readonly renderReady: boolean;
+    renderReady(): boolean;
 } & {
     readonly rendererTypeName: string;
     contextMenuItems(): ({
@@ -316,66 +290,31 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     })[];
     readonly DisplayBlurb: (props: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => import("react").JSX.Element | null;
     renderPropsPre(): any;
-    renderProps(): any;
-    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+    colorSchemeSubMenuItems(): {
         label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        type: string;
-        checked: boolean;
         onClick: () => void;
-        disabled?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        disabled: boolean;
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-        disabled?: undefined;
-    } | {
+    }[];
+    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
-        type?: undefined;
-        checked?: undefined;
-        disabled?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        type: string;
-        checked: any;
-        onClick: () => void;
-        icon?: undefined;
-        disabled?: undefined;
-        subMenu?: undefined;
     })[];
+} & {
+    renderProps(): any;
 } & {
     afterAttach(): void;
 } & {
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        label: string;
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+    })[];
 } & {
     afterCreate(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/LGVSyntenyDisplay/model.js

@@ -114,7 +114,7 @@ async function navToSynteny(feature, self) {
  */
 function stateModelFactory(schema) {
     return mobx_state_tree_1.types
-        .compose('LGVSyntenyDisplay', (0, plugin_alignments_1.linearPileupDisplayStateModelFactory)(schema), mobx_state_tree_1.types.model({
+        .compose('LGVSyntenyDisplay', (0, plugin_alignments_1.SharedLinearPileupDisplayMixin)(schema), mobx_state_tree_1.types.model({
         /**
          * #property
          */
@@ -142,11 +142,30 @@ function stateModelFactory(schema) {
                 ];
             },
         };
+    })
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems, colorSchemeSubMenuItems: superColorSchemeSubMenuItems, } = self;
+        return {
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Color scheme',
+                        subMenu: [...superColorSchemeSubMenuItems()],
+                    },
+                ];
+            },
+        };
     })
         .actions(self => ({
         afterCreate() {
-            // use color by strand to help indicate inversions better
-            self.setColorScheme({ type: 'strand' });
+            // use color by stand to help indicate inversions better on first load, otherwise use selected orientation
+            if (self.colorBy) {
+                self.setColorScheme({ ...self.colorBy });
+            }
+            else {
+                self.setColorScheme({ type: 'strand' });
+            }
         },
     }));
 }

package/dist/LinearSyntenyView/svgcomponents/SVGBackground.js

@@ -5,8 +5,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
+const color_1 = __importDefault(require("color"));
 function SVGBackground({ width, height, shift, }) {
     const theme = (0, material_1.useTheme)();
-    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+    return (react_1.default.createElement("rect", { width: width + shift * 2, height: height, fill: (0, color_1.default)(theme.palette.background.default).hex() }));
 }
 exports.default = SVGBackground;

package/esm/LGVSyntenyDisplay/model.d.ts

@@ -86,21 +86,11 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"LinearPileupDisplay">;
     configuration: AnyConfigurationSchemaType;
-    showSoftClipping: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     featureHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     noSpacing: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     fadeLikelihood: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     trackMaxHeight: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    mismatchAlpha: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    sortedBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
-        type: import("mobx-state-tree").ISimpleType<string>;
-        pos: import("mobx-state-tree").ISimpleType<number>;
-        tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-        refName: import("mobx-state-tree").ISimpleType<string>;
-        assemblyName: import("mobx-state-tree").ISimpleType<string>;
-    }, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     colorBy: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IModelType<{
         type: import("mobx-state-tree").ISimpleType<string>;
         tag: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -250,45 +240,30 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
-    modificationTagMap: import("mobx").ObservableMap<string, string>; /**
-     * #property
-     */
     featureUnderMouseVolatile: Feature | undefined;
-    currSortBpPerPx: number;
-    modificationsReady: boolean;
-    sortReady: boolean;
     tagsReady: boolean;
 } & {
     readonly autorunReady: boolean;
 } & {
-    setModificationsReady(flag: boolean): void;
     setTagsReady(flag: boolean): void;
-    setSortReady(flag: boolean): void;
-    setCurrSortBpPerPx(n: number): void;
     setMaxHeight(n: number): void;
     setFeatureHeight(n?: number | undefined): void;
     setNoSpacing(flag?: boolean | undefined): void;
     setColorScheme(colorScheme: {
         type: string;
         tag?: string | undefined;
+        extra?: import("@jbrowse/plugin-alignments/src/shared/color").ExtraColorBy | undefined;
     }): void;
-    updateModificationColorMap(uniqueModifications: string[]): void;
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: Feature | undefined): void;
     selectFeature(feature: Feature): void;
-    clearSelected(): void;
     copyFeatureToClipboard(feature: Feature): void;
-    toggleSoftClipping(): void;
-    toggleMismatchAlpha(): void;
     setConfig(conf: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>): void;
-    setSortedBy(type: string, tag?: string | undefined): void;
-    setFilterBy(filter: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/model").Filter): void;
-} & {
-    reload(): void;
+    setFilterBy(filter: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin").Filter): void;
 } & {
     readonly rendererConfig: {
         [x: string]: any;
@@ -298,9 +273,8 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
 } & {
     readonly maxHeight: any;
     readonly featureHeightSetting: any;
-    readonly mismatchAlphaSetting: any;
     readonly featureUnderMouse: Feature | undefined;
-    readonly renderReady: boolean;
+    renderReady(): boolean;
 } & {
     readonly rendererTypeName: string;
     contextMenuItems(): ({
@@ -316,66 +290,31 @@ declare function stateModelFactory(schema: AnyConfigurationSchemaType): import("
     })[];
     readonly DisplayBlurb: (props: import("@jbrowse/plugin-alignments/src/LinearPileupDisplay/components/LinearPileupDisplayBlurb").LinearPileupDisplayBlurbProps) => import("react").JSX.Element | null;
     renderPropsPre(): any;
-    renderProps(): any;
-    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+    colorSchemeSubMenuItems(): {
         label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        type: string;
-        checked: boolean;
         onClick: () => void;
-        disabled?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        disabled: boolean;
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-    } | {
-        label: string;
-        icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
-            muiName: string;
-        };
-        subMenu: {
-            label: string;
-            onClick: () => void;
-        }[];
-        type?: undefined;
-        checked?: undefined;
-        onClick?: undefined;
-        disabled?: undefined;
-    } | {
+    }[];
+    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
-        type?: undefined;
-        checked?: undefined;
-        disabled?: undefined;
-        subMenu?: undefined;
-    } | {
-        label: string;
-        type: string;
-        checked: any;
-        onClick: () => void;
-        icon?: undefined;
-        disabled?: undefined;
-        subMenu?: undefined;
     })[];
+} & {
+    renderProps(): any;
 } & {
     afterAttach(): void;
 } & {
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
+} & {
+    trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        label: string;
+        subMenu: {
+            label: string;
+            onClick: () => void;
+        }[];
+    })[];
 } & {
     afterCreate(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/LGVSyntenyDisplay/model.js

@@ -1,6 +1,6 @@
 import { ConfigurationReference, } from '@jbrowse/core/configuration';
 import { getSession, getContainingTrack, getContainingView, } from '@jbrowse/core/util';
-import { MismatchParser, linearPileupDisplayStateModelFactory, } from '@jbrowse/plugin-alignments';
+import { MismatchParser, SharedLinearPileupDisplayMixin, } from '@jbrowse/plugin-alignments';
 import { types } from 'mobx-state-tree';
 import { when } from 'mobx';
 const { parseCigar } = MismatchParser;
@@ -112,7 +112,7 @@ async function navToSynteny(feature, self) {
  */
 function stateModelFactory(schema) {
     return types
-        .compose('LGVSyntenyDisplay', linearPileupDisplayStateModelFactory(schema), types.model({
+        .compose('LGVSyntenyDisplay', SharedLinearPileupDisplayMixin(schema), types.model({
         /**
          * #property
          */
@@ -140,11 +140,30 @@ function stateModelFactory(schema) {
                 ];
             },
         };
+    })
+        .views(self => {
+        const { trackMenuItems: superTrackMenuItems, colorSchemeSubMenuItems: superColorSchemeSubMenuItems, } = self;
+        return {
+            trackMenuItems() {
+                return [
+                    ...superTrackMenuItems(),
+                    {
+                        label: 'Color scheme',
+                        subMenu: [...superColorSchemeSubMenuItems()],
+                    },
+                ];
+            },
+        };
     })
         .actions(self => ({
         afterCreate() {
-            // use color by strand to help indicate inversions better
-            self.setColorScheme({ type: 'strand' });
+            // use color by stand to help indicate inversions better on first load, otherwise use selected orientation
+            if (self.colorBy) {
+                self.setColorScheme({ ...self.colorBy });
+            }
+            else {
+                self.setColorScheme({ type: 'strand' });
+            }
         },
     }));
 }

package/esm/LinearSyntenyView/svgcomponents/SVGBackground.js

@@ -1,6 +1,7 @@
 import React from 'react';
 import { useTheme } from '@mui/material';
+import Color from 'color';
 export default function SVGBackground({ width, height, shift, }) {
     const theme = useTheme();
-    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: theme.palette.background.default }));
+    return (React.createElement("rect", { width: width + shift * 2, height: height, fill: Color(theme.palette.background.default).hex() }));
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-linear-comparative-view",
-  "version": "2.6.2",
+  "version": "2.6.3",
   "description": "JBrowse 2 linear comparative view",
   "keywords": [
     "jbrowse",
@@ -39,6 +39,7 @@
     "@mui/icons-material": "^5.0.1",
     "@popperjs/core": "^2.0.0",
     "clone": "^2.1.2",
+    "color": "^3.1.3",
     "copy-to-clipboard": "^3.3.1",
     "file-saver": "^2.0.0",
     "react-popper": "^2.0.0"
@@ -62,5 +63,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "bbea587a402d9974acdd804a33f4b77f31a2fd5f"
+  "gitHead": "ed402c87efb0904858d602c363bd1757d5742129"
 }