@jbrowse/plugin-linear-genome-view 2.3.4 → 2.4.1

package/dist/LinearBareDisplay/index.d.ts

@@ -1,6 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-import { configSchemaFactory } from './configSchema';
-import { stateModelFactory } from './model';
 declare const _default: (pluginManager: PluginManager) => void;
 export default _default;
-export { configSchemaFactory, stateModelFactory };
+export { configSchemaFactory } from './configSchema';
+export { stateModelFactory } from './model';

package/dist/LinearBareDisplay/index.js

@@ -4,9 +4,7 @@ exports.stateModelFactory = exports.configSchemaFactory = void 0;
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 // locals
 const configSchema_1 = require("./configSchema");
-Object.defineProperty(exports, "configSchemaFactory", { enumerable: true, get: function () { return configSchema_1.configSchemaFactory; } });
 const model_1 = require("./model");
-Object.defineProperty(exports, "stateModelFactory", { enumerable: true, get: function () { return model_1.stateModelFactory; } });
 const BaseLinearDisplay_1 = require("../BaseLinearDisplay/");
 exports.default = (pluginManager) => {
     pluginManager.addDisplayType(() => {
@@ -21,4 +19,8 @@ exports.default = (pluginManager) => {
         });
     });
 };
+var configSchema_2 = require("./configSchema");
+Object.defineProperty(exports, "configSchemaFactory", { enumerable: true, get: function () { return configSchema_2.configSchemaFactory; } });
+var model_2 = require("./model");
+Object.defineProperty(exports, "stateModelFactory", { enumerable: true, get: function () { return model_2.stateModelFactory; } });
 //# sourceMappingURL=index.js.map

package/dist/LinearBareDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBareDisplay/index.ts"],"names":[],"mappings":";;;AACA,+EAAiE;AAEjE,SAAS;AACT,iDAAoD;AAkB3C,oGAlBA,kCAAmB,OAkBA;AAjB5B,mCAA2C;AAiBb,kGAjBrB,yBAAiB,OAiBqB;AAhB/C,6DAAkE;AAElE,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,kCAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,mCAAW,CAAC;YACrB,IAAI,EAAE,mBAAmB;YACzB,YAAY;YACZ,UAAU,EAAE,IAAA,yBAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,YAAY;YACvB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,8CAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBareDisplay/index.ts"],"names":[],"mappings":";;;AACA,+EAAiE;AAEjE,SAAS;AACT,iDAAoD;AACpD,mCAA2C;AAC3C,6DAAkE;AAElE,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,YAAY,GAAG,IAAA,kCAAmB,EAAC,aAAa,CAAC,CAAA;QACvD,OAAO,IAAI,mCAAW,CAAC;YACrB,IAAI,EAAE,mBAAmB;YACzB,YAAY;YACZ,UAAU,EAAE,IAAA,yBAAiB,EAAC,YAAY,CAAC;YAC3C,SAAS,EAAE,YAAY;YACvB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,8CAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,+CAAoD;AAA3C,mHAAA,mBAAmB,OAAA;AAC5B,iCAA2C;AAAlC,0GAAA,iBAAiB,OAAA"}

package/dist/LinearBareDisplay/model.d.ts

@@ -9,7 +9,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
-    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
@@ -128,6 +128,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -190,6 +191,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     renderSvg(opts: import("../LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
+        theme: import("@mui/material").ThemeOptions;
     }): Promise<JSX.Element>;
 } & {
     /**
@@ -200,11 +202,67 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
      * #getter
      */
     readonly rendererTypeName: any;
-}, import("mobx-state-tree")._NotCustomized, {
+}, {
+    type: string;
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+} & {
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: 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>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        renderInProgress: AbortController | undefined;
+        filled: boolean;
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
+            layout: any;
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;
-    height: number;
     id: string;
     rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;

package/dist/LinearBasicDisplay/index.d.ts

@@ -1,6 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-import configSchema from './configSchema';
-import modelFactory from './model';
 declare const _default: (pluginManager: PluginManager) => void;
 export default _default;
-export { modelFactory, configSchema };
+export { default as modelFactory } from './model';
+export { default as configSchema } from './configSchema';

package/dist/LinearBasicDisplay/index.js

@@ -8,9 +8,7 @@ const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const BaseLinearDisplay_1 = require("../BaseLinearDisplay");
 // locals
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.configSchema = configSchema_1.default;
 const model_1 = __importDefault(require("./model"));
-exports.modelFactory = model_1.default;
 exports.default = (pluginManager) => {
     pluginManager.addDisplayType(() => {
         const config = (0, configSchema_1.default)(pluginManager);
@@ -25,4 +23,8 @@ exports.default = (pluginManager) => {
         });
     });
 };
+var model_2 = require("./model");
+Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return __importDefault(model_2).default; } });
+var configSchema_2 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_2).default; } });
 //# sourceMappingURL=index.js.map

package/dist/LinearBasicDisplay/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBasicDisplay/index.ts"],"names":[],"mappings":";;;;;;AACA,+EAAiE;AACjE,4DAAiE;AAEjE,SAAS;AACT,kEAAyC;AAkBlB,uBAlBhB,sBAAY,CAkBgB;AAjBnC,oDAAkC;AAiBzB,uBAjBF,eAAY,CAiBE;AAfrB,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,MAAM,GAAG,IAAA,sBAAY,EAAC,aAAa,CAAC,CAAA;QAC1C,OAAO,IAAI,mCAAW,CAAC;YACrB,IAAI,EAAE,oBAAoB;YAC1B,WAAW,EAAE,uBAAuB;YACpC,YAAY,EAAE,MAAM;YACpB,UAAU,EAAE,IAAA,eAAY,EAAC,MAAM,CAAC;YAChC,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,8CAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearBasicDisplay/index.ts"],"names":[],"mappings":";;;;;;AACA,+EAAiE;AACjE,4DAAiE;AAEjE,SAAS;AACT,kEAAyC;AACzC,oDAAkC;AAElC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,MAAM,MAAM,GAAG,IAAA,sBAAY,EAAC,aAAa,CAAC,CAAA;QAC1C,OAAO,IAAI,mCAAW,CAAC;YACrB,IAAI,EAAE,oBAAoB;YAC1B,WAAW,EAAE,uBAAuB;YACpC,YAAY,EAAE,MAAM;YACpB,UAAU,EAAE,IAAA,eAAY,EAAC,MAAM,CAAC;YAChC,SAAS,EAAE,cAAc;YACzB,QAAQ,EAAE,kBAAkB;YAC5B,cAAc,EAAE,8CAA0B;SAC3C,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC,CAAA;AAED,iCAAiD;AAAxC,sHAAA,OAAO,OAAgB;AAChC,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}

package/dist/LinearBasicDisplay/model.d.ts

@@ -12,7 +12,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     type: import("mobx-state-tree").ISimpleType<string>;
     rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 } & {
-    height: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
     blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
         key: import("mobx-state-tree").ISimpleType<string>;
         region: import("mobx-state-tree").IModelType<{
@@ -32,34 +32,33 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
     }, {
         renderInProgress: AbortController | undefined;
-        filled: boolean;
+        filled: boolean; /**
+         * #property
+         */
         reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
         features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
         layout: any;
         status: string;
         error: unknown;
-        message: string | undefined; /**
-         * #getter
-         */
+        message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
             model: any;
         }) => any;
         renderProps: any;
     } & {
-        doReload(): void; /**
-         * #getter
-         */
+        doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
-        setLoading(abortController: AbortController): void; /**
-         * #action
-         */
+        setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
             features: Map<string, import("@jbrowse/core/util").Feature>;
             layout: any;
+            /**
+             * #method
+             */
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
@@ -68,7 +67,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>; /**
+     * #action
+     */
 } & {
     /**
      * #property
@@ -162,6 +163,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     estimatedRegionStatsP: Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats> | undefined;
     estimatedRegionStats: import("@jbrowse/core/data_adapters/BaseAdapter").Stats | undefined;
 } & {
+    readonly height: number;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
@@ -224,6 +226,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     renderSvg(opts: import("../LinearGenomeView").ExportSvgOptions & {
         overrideHeight: number;
+        theme: import("@mui/material").ThemeOptions;
     }): Promise<JSX.Element>;
 } & {
     /**
@@ -287,11 +290,76 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
      * #method
      */
     trackMenuItems(): MenuItem[];
-}, import("mobx-state-tree")._NotCustomized, {
+}, {
+    type: string;
+} & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<string>;
+    rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+} & {
+    heightPreConfig: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    blockState: import("mobx-state-tree").IMapType<import("mobx-state-tree").IModelType<{
+        key: import("mobx-state-tree").ISimpleType<string>;
+        region: import("mobx-state-tree").IModelType<{
+            refName: import("mobx-state-tree").ISimpleType<string>; /**
+             * #property
+             */
+            start: import("mobx-state-tree").ISimpleType<number>;
+            end: import("mobx-state-tree").ISimpleType<number>;
+            reversed: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
+        } & {
+            assemblyName: import("mobx-state-tree").ISimpleType<string>;
+        }, {
+            setRefName(newRefName: string): void;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+        reloadFlag: import("mobx-state-tree").IType<number | undefined, number, number>;
+        isLeftEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+        isRightEndOfDisplayedRegion: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    }, {
+        renderInProgress: AbortController | undefined;
+        filled: boolean; /**
+         * #property
+         */
+        reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+        features: Map<string, import("@jbrowse/core/util").Feature> | undefined;
+        layout: any;
+        status: string;
+        error: unknown;
+        message: string | undefined;
+        maxHeightReached: boolean;
+        ReactComponent: ({ model, }: {
+            model: any;
+        }) => any;
+        renderProps: any;
+    } & {
+        doReload(): void;
+        afterAttach(): void;
+        setStatus(message: string): void;
+        setLoading(abortController: AbortController): void;
+        setMessage(messageText: string): void;
+        setRendered(props: {
+            reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
+            features: Map<string, import("@jbrowse/core/util").Feature>;
+            layout: any;
+            /**
+             * #method
+             */
+            maxHeightReached: boolean;
+            renderProps: any;
+        } | undefined): void;
+        setError(error: unknown): void;
+        reload(): void;
+        beforeDestroy(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+    userBpPerPxLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    userByteSizeLimit: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>; /**
+     * #action
+     */
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: string;
-    height: number;
     id: string;
     rpcDriverName: string | undefined;
+    heightPreConfig: number | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;

package/dist/LinearGenomeView/components/CenterLine.js

@@ -26,13 +26,13 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
-const useStyles = (0, mui_1.makeStyles)()(() => ({
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
     centerLineContainer: {
         background: 'transparent',
         height: '100%',
         zIndex: 5,
         position: 'absolute',
-        border: '1px black dashed',
+        border: `1px ${theme.palette.action.active} dashed`,
         borderTop: 'none',
         borderBottom: 'none',
         pointerEvents: 'none',

package/dist/LinearGenomeView/components/CenterLine.js.map

@@ -1 +1 @@
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+{"version":3,"file":"CenterLine.js","sourceRoot":"","sources":["../../../src/LinearGenomeView/components/CenterLine.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAqC;AACrC,uCAA0C;AAC1C,2CAAqC;AAKrC,MAAM,SAAS,GAAG,IAAA,gBAAU,GAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;IACvC,mBAAmB,EAAE;QACnB,UAAU,EAAE,aAAa;QACzB,MAAM,EAAE,MAAM;QACd,MAAM,EAAE,CAAC;QACT,QAAQ,EAAE,UAAU;QACpB,MAAM,EAAE,OAAO,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,MAAM,SAAS;QACnD,SAAS,EAAE,MAAM;QACjB,YAAY,EAAE,MAAM;QACpB,aAAa,EAAE,MAAM;KACtB;IACD,cAAc,EAAE;QACd,QAAQ,EAAE,UAAU;QACpB,aAAa,EAAE,MAAM;QACrB,UAAU,EAAE,QAAQ;QACpB,UAAU,EAAE,MAAM;KACnB;CACF,CAAC,CAAC,CAAA;AAEH,SAAS,UAAU,CAAC,EAAE,KAAK,EAAkB;IAC3C,MAAM,EAAE,OAAO,EAAE,cAAc,EAAE,YAAY,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACtE,MAAM,GAAG,GAAG,IAAA,cAAM,EAAiB,IAAI,CAAC,CAAA;IACxC,MAAM,EAAE,OAAO,EAAE,GAAG,SAAS,EAAE,CAAA;IAC/B,MAAM,gBAAgB,GAAG,KAAK,GAAG,CAAC,CAAA;IAElC,OAAO,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,CACrB,sDACc,sBAAsB,EAClC,SAAS,EAAE,OAAO,CAAC,mBAAmB,EACtC,IAAI,EAAC,cAAc,EACnB,GAAG,EAAE,GAAG,EACR,KAAK,EAAE;YACL,IAAI,EAAE,GAAG,gBAAgB,IAAI;YAC7B,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,OAAO,EAAE,CAAC,CAAC;SAChC,IAEA,cAAc,IAAI,CACjB,sDAGc,iBAAiB,EAC7B,SAAS,EAAE,OAAO,CAAC,cAAc,EACjC,IAAI,EAAC,cAAc,EACnB,KAAK,EAAE;YACL,IAAI,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC;YAClC,GAAG,EAAE,YAAY;SAClB;QAGA,cAAc,CAAC,OAAO;;QAAG,GAAG;QAC5B,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAC/C,CACP,CACG,CACP,CAAC,CAAC,CAAC,IAAI,CAAA;AACV,CAAC;AAED,kBAAe,IAAA,qBAAQ,EAAC,UAAU,CAAC,CAAA"}

package/dist/LinearGenomeView/components/Cytobands.d.ts

@@ -0,0 +1,118 @@
+/// <reference types="react" />
+import { Base1DViewModel } from '@jbrowse/core/util/Base1DViewModel';
+import { ContentBlock } from '@jbrowse/core/util/blockTypes';
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+declare const _default: ({ overview, block, assembly, }: {
+    overview: Base1DViewModel;
+    assembly?: ({
+        configuration: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        error: unknown;
+        loaded: boolean;
+        loadingP: Promise<void> | undefined;
+        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: {
+            [x: string]: string;
+        } | undefined;
+        lowerCaseRefNameAliases: {
+            [x: string]: string;
+        } | undefined;
+        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+    } & {
+        readonly initialized: boolean;
+        readonly name: string;
+        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        readonly aliases: string[];
+        readonly displayName: string | undefined;
+        hasName(name: string): boolean;
+        readonly allAliases: string[];
+        readonly allRefNames: string[] | undefined;
+        readonly lowerCaseRefNames: string[] | undefined;
+        readonly allRefNamesWithLowerCase: string[] | undefined;
+        readonly rpcManager: any;
+        readonly refNameColors: string[];
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string;
+        getRefNameColor(refName: string): string | undefined;
+        isValidRefName(refName: string): boolean;
+    } & {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+        setError(e: unknown): void;
+        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+        setRefNameAliases(aliases: {
+            [x: string]: string;
+        }, lcAliases: {
+            [x: string]: string;
+        }): void;
+        setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+        setLoadingP(p?: Promise<void> | undefined): void;
+        load(): Promise<void>;
+        loadPre(): Promise<void>;
+    } & {
+        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
+            [x: string]: string;
+        }>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
+            [x: string]: string;
+        }>;
+    } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+        configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    }, {
+        error: unknown;
+        loaded: boolean;
+        loadingP: Promise<void> | undefined;
+        volatileRegions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        refNameAliases: {
+            [x: string]: string;
+        } | undefined;
+        lowerCaseRefNameAliases: {
+            [x: string]: string;
+        } | undefined;
+        cytobands: import("@jbrowse/core/util").Feature[] | undefined;
+    } & {
+        readonly initialized: boolean;
+        readonly name: string;
+        readonly regions: import("@jbrowse/core/assemblyManager/assembly").BasicRegion[] | undefined;
+        readonly aliases: string[];
+        readonly displayName: string | undefined;
+        hasName(name: string): boolean;
+        readonly allAliases: string[];
+        readonly allRefNames: string[] | undefined;
+        readonly lowerCaseRefNames: string[] | undefined;
+        readonly allRefNamesWithLowerCase: string[] | undefined;
+        readonly rpcManager: any;
+        readonly refNameColors: string[];
+    } & {
+        readonly refNames: string[] | undefined;
+    } & {
+        getCanonicalRefName(refName: string): string;
+        getRefNameColor(refName: string): string | undefined;
+        isValidRefName(refName: string): boolean;
+    } & {
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }: import("@jbrowse/core/assemblyManager/assembly").Loading): void;
+        setError(e: unknown): void;
+        setRegions(regions: import("@jbrowse/core/util").Region[]): void;
+        setRefNameAliases(aliases: {
+            [x: string]: string;
+        }, lcAliases: {
+            [x: string]: string;
+        }): void;
+        setCytobands(cytobands: import("@jbrowse/core/util").Feature[]): void;
+        setLoadingP(p?: Promise<void> | undefined): void;
+        load(): Promise<void>;
+        loadPre(): Promise<void>;
+    } & {
+        getAdapterMapEntry(adapterConf: unknown, options: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<import("@jbrowse/core/assemblyManager/assembly").RefNameMap>;
+        getRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
+            [x: string]: string;
+        }>;
+        getReverseRefNameMapForAdapter(adapterConf: unknown, opts: import("@jbrowse/core/assemblyManager/assembly").BaseOptions): Promise<{
+            [x: string]: string;
+        }>;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>) | undefined;
+    block: ContentBlock;
+}) => JSX.Element;
+export default _default;

package/dist/LinearGenomeView/components/Cytobands.js

@@ -0,0 +1,92 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mobx_react_1 = require("mobx-react");
+// locals
+const __1 = require("..");
+const util_1 = require("./util");
+// rounded rect from https://stackoverflow.com/a/45889603/2129219
+// prettier-ignore
+function rightRoundedRect(x, y, width, height, radius) {
+    return "M" + x + "," + y
+        + "h" + (width - radius)
+        + "a" + radius + "," + radius + " 0 0 1 " + radius + "," + radius
+        + "v" + (height - 2 * radius)
+        + "a" + radius + "," + radius + " 0 0 1 " + -radius + "," + radius
+        + "h" + (radius - width)
+        + "z";
+}
+// prettier-ignore
+function leftRoundedRect(x, y, width, height, radius) {
+    return "M" + (x + radius) + "," + y
+        + "h" + (width - radius)
+        + "v" + height
+        + "h" + (radius - width)
+        + "a" + radius + "," + radius + " 0 0 1 " + (-radius) + "," + (-radius)
+        + "v" + (2 * radius - height)
+        + "a" + radius + "," + radius + " 0 0 1 " + radius + "," + (-radius)
+        + "z";
+}
+const colorMap = {
+    gneg: 'rgb(227,227,227)',
+    gpos25: 'rgb(142,142,142)',
+    gpos50: 'rgb(85,85,85)',
+    gpos100: 'rgb(0,0,0)',
+    gpos75: 'rgb(57,57,57)',
+    gvar: 'rgb(0,0,0)',
+    stalk: 'rgb(127,127,127)',
+    acen: '#800',
+};
+exports.default = (0, mobx_react_1.observer)(function Cytobands({ overview, block, assembly, }) {
+    const { offsetPx, reversed } = block;
+    const cytobands = (0, util_1.getCytobands)(assembly, block.refName);
+    const coords = cytobands.map(f => {
+        const { refName, start, end, type } = f;
+        return [
+            overview.bpToPx({
+                refName,
+                coord: start,
+            }),
+            overview.bpToPx({
+                refName,
+                coord: end,
+            }),
+            type,
+        ];
+    });
+    const arr = cytobands || [];
+    const lcap = reversed ? arr.length - 1 : 0;
+    const rcap = reversed ? 0 : arr.length - 1;
+    let firstCent = true;
+    return (react_1.default.createElement("g", { transform: `translate(-${offsetPx})` }, coords.map(([start, end, type], index) => {
+        const key = `${start}-${end}-${type}`;
+        if (type === 'acen' && firstCent) {
+            firstCent = false;
+            return (react_1.default.createElement("polygon", { key: key, points: [
+                    [start, 0],
+                    [end, __1.HEADER_OVERVIEW_HEIGHT / 2],
+                    [start, __1.HEADER_OVERVIEW_HEIGHT],
+                ].toString(), fill: colorMap[type] }));
+        }
+        if (type === 'acen' && !firstCent) {
+            return (react_1.default.createElement("polygon", { key: key, points: [
+                    [start, __1.HEADER_OVERVIEW_HEIGHT / 2],
+                    [end, 0],
+                    [end, __1.HEADER_OVERVIEW_HEIGHT],
+                ].toString(), fill: colorMap[type] }));
+        }
+        if (lcap === index) {
+            return (react_1.default.createElement("path", { key: key, d: leftRoundedRect(Math.min(start, end), 0, Math.abs(end - start), __1.HEADER_OVERVIEW_HEIGHT, 8), fill: colorMap[type] }));
+        }
+        else if (rcap === index) {
+            return (react_1.default.createElement("path", { key: key, d: rightRoundedRect(Math.min(start, end), 0, Math.abs(end - start) - 2, __1.HEADER_OVERVIEW_HEIGHT, 8), fill: colorMap[type] }));
+        }
+        else {
+            return (react_1.default.createElement("rect", { key: key, x: Math.min(start, end), y: 0, width: Math.abs(end - start), height: __1.HEADER_OVERVIEW_HEIGHT, fill: colorMap[type] }));
+        }
+    })));
+});
+//# sourceMappingURL=Cytobands.js.map

package/dist/LinearGenomeView/components/Cytobands.js.map

@@ -0,0 +1 @@
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package/dist/LinearGenomeView/components/ExportSvgDialog.d.ts

@@ -2,7 +2,7 @@
 import { ExportSvgOptions } from '..';
 export default function ExportSvgDlg({ model, handleClose, }: {
     model: {
-        exportSvg(opts: ExportSvgOptions): void;
+        exportSvg(opts: ExportSvgOptions): Promise<void>;
     };
     handleClose: () => void;
 }): JSX.Element;

package/dist/LinearGenomeView/components/ExportSvgDialog.js

@@ -26,22 +26,38 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
 function LoadingMessage() {
     return (react_1.default.createElement("div", null,
         react_1.default.createElement(material_1.CircularProgress, { size: 20, style: { marginRight: 20 } }),
         react_1.default.createElement(material_1.Typography, { display: "inline" }, "Creating SVG")));
 }
+function useSvgLocal(key, val) {
+    return (0, util_1.useLocalStorage)('svg-' + key, val);
+}
 function ExportSvgDlg({ model, handleClose, }) {
-    // @ts-ignore
+    const session = (0, util_1.getSession)(model);
     const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
     const [rasterizeLayers, setRasterizeLayers] = (0, react_1.useState)(offscreenCanvas);
     const [loading, setLoading] = (0, react_1.useState)(false);
-    const [filename, setFilename] = (0, react_1.useState)('jbrowse.svg');
     const [error, setError] = (0, react_1.useState)();
+    const [filename, setFilename] = useSvgLocal('file', 'jbrowse.svg');
+    const [trackLabels, setTrackLabels] = useSvgLocal('tracklabels', 'offset');
+    const [themeName, setThemeName] = useSvgLocal('theme', session.themeName || 'default');
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
         react_1.default.createElement(material_1.DialogContent, null,
             error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : loading ? (react_1.default.createElement(LoadingMessage, null)) : null,
             react_1.default.createElement(material_1.TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
+            react_1.default.createElement("br", null),
+            react_1.default.createElement(material_1.TextField, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
+                react_1.default.createElement(material_1.MenuItem, { value: "offset" }, "Offset"),
+                react_1.default.createElement(material_1.MenuItem, { value: "overlay" }, "Overlay"),
+                react_1.default.createElement(material_1.MenuItem, { value: "left" }, "Left"),
+                react_1.default.createElement(material_1.MenuItem, { value: "none" }, "None")),
+            react_1.default.createElement("br", null),
+            session.allThemes ? (react_1.default.createElement(material_1.TextField, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (react_1.default.createElement(material_1.MenuItem, { key: key, value: key }, 
+            // @ts-expect-error
+            val.name || '(Unknown name)'))))) : null,
             offscreenCanvas ? (react_1.default.createElement(material_1.FormControlLabel, { control: react_1.default.createElement(material_1.Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (react_1.default.createElement(material_1.Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
@@ -49,7 +65,12 @@ function ExportSvgDlg({ model, handleClose, }) {
                     setLoading(true);
                     setError(undefined);
                     try {
-                        await model.exportSvg({ rasterizeLayers, filename });
+                        await model.exportSvg({
+                            rasterizeLayers,
+                            filename,
+                            trackLabels,
+                            themeName,
+                        });
                         handleClose();
                     }
                     catch (e) {