@jbrowse/plugin-alignments 2.14.0 → 2.15.1

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -1,9 +1,32 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
 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 react_1 = __importStar(require("react"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const clone_1 = __importDefault(require("clone"));
@@ -12,10 +35,12 @@ const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeature
 const util_1 = require("./util");
 const tagInfo_1 = require("./tagInfo");
 // local components
-const SuppAlignments_1 = __importDefault(require("./SuppAlignments"));
 const Flags_1 = __importDefault(require("./Flags"));
 const PairLink_1 = __importDefault(require("./PairLink"));
 const Formatter_1 = __importDefault(require("./Formatter"));
+// lazies
+const SupplementaryAlignments = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SupplementaryAlignments'))));
+const LinkedPairedAlignments = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LinkedPairedAlignments'))));
 const omit = ['clipPos', 'flags'];
 const AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
@@ -27,7 +52,8 @@ const AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
         react_1.default.createElement(BaseFeatureDetail_1.FeatureDetails, { ...props, omit: omit, 
             // @ts-expect-error
             descriptions: { ...tagInfo_1.tags, tags: tagInfo_1.tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (react_1.default.createElement(PairLink_1.default, { model: model, locString: value })) : (react_1.default.createElement(Formatter_1.default, { value: value })) }),
-        SA !== undefined ? (react_1.default.createElement(SuppAlignments_1.default, { model: model, tag: SA, feature: feat })) : null,
+        SA !== undefined ? (react_1.default.createElement(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null,
+        flags & 1 ? (react_1.default.createElement(LinkedPairedAlignments, { model: model, feature: feat })) : null,
         flags !== undefined ? react_1.default.createElement(Flags_1.default, { feature: feat, ...props }) : null));
 });
 exports.default = AlignmentsFeatureDetails;

package/dist/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.d.ts

@@ -0,0 +1 @@
+export { BreakendMultiLevelOptionDialog as default } from '@jbrowse/sv-core';

package/dist/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js

@@ -0,0 +1,6 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = void 0;
+// re-exported for react lazy
+var sv_core_1 = require("@jbrowse/sv-core");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendMultiLevelOptionDialog; } });

package/dist/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.d.ts

@@ -0,0 +1 @@
+export { BreakendSingleLevelOptionDialog as default } from '@jbrowse/sv-core';

package/dist/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js

@@ -0,0 +1,6 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = void 0;
+// re-exported for react lazy
+var sv_core_1 = require("@jbrowse/sv-core");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendSingleLevelOptionDialog; } });

package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { SimpleFeatureSerialized } from '@jbrowse/core/util';
+import { ViewType } from '@jbrowse/core/pluggableElementTypes';
+import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, }: {
+    model: AlignmentFeatureWidgetModel;
+    feature: SimpleFeatureSerialized;
+    viewType: ViewType;
+}): React.JSX.Element;

package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js

@@ -0,0 +1,92 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LaunchPairedEndBreakpointSplitViewPanel;
+const react_1 = __importStar(require("react"));
+const material_1 = require("@mui/material");
+const util_1 = require("@jbrowse/core/util");
+// lazies
+const BreakendMultiLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendMultiLevelOptionDialog'))));
+const BreakendSingleLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendSingleLevelOptionDialog'))));
+function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, }) {
+    const session = (0, util_1.getSession)(model);
+    const f1 = {
+        uniqueId: feature.uniqueId,
+        refName: feature.refName,
+        start: feature.start,
+        end: feature.end,
+        strand: feature.strand,
+    };
+    const f2 = {
+        uniqueId: `${feature.id}-mate`,
+        refName: feature.next_ref,
+        start: feature.next_pos,
+        end: feature.next_pos + 1,
+        strand: feature.strand,
+    };
+    return (react_1.default.createElement("div", null,
+        react_1.default.createElement(material_1.Typography, null, "Launch split view"),
+        react_1.default.createElement("ul", null,
+            react_1.default.createElement("li", null,
+                f1.refName,
+                ":",
+                (0, util_1.toLocale)(f1.start),
+                " -> ",
+                f2.refName,
+                ":",
+                (0, util_1.toLocale)(f2.start),
+                ' ',
+                react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+                        event.preventDefault();
+                        session.queueDialog(handleClose => [
+                            BreakendMultiLevelOptionDialog,
+                            {
+                                handleClose,
+                                model,
+                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
+                                // @ts-expect-error
+                                viewType,
+                                view: model.view,
+                                assemblyName: model.view.displayedRegions[0].assemblyName,
+                            },
+                        ]);
+                    } }, "(top/bottom)"),
+                ' ',
+                react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+                        event.preventDefault();
+                        session.queueDialog(handleClose => [
+                            BreakendSingleLevelOptionDialog,
+                            {
+                                handleClose,
+                                model,
+                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
+                                // @ts-expect-error
+                                viewType,
+                                view: model.view,
+                                assemblyName: model.view.displayedRegions[0].assemblyName,
+                            },
+                        ]);
+                    } }, "(single row)")))));
+}

package/dist/AlignmentsFeatureDetail/{LaunchBreakpointSplitViewPanel.js → LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js}

@@ -30,7 +30,8 @@ const util_1 = require("@jbrowse/core/util");
 const ui_1 = require("@jbrowse/core/ui");
 const getSAFeatures_1 = require("./getSAFeatures");
 // lazies
-const BreakendOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendOptionDialog'))));
+const BreakendMultiLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendMultiLevelOptionDialog'))));
+const BreakendSingleLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendSingleLevelOptionDialog'))));
 function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
     const session = (0, util_1.getSession)(model);
     const { view } = model;
@@ -60,26 +61,50 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
         }
     }
     return ret.length ? (react_1.default.createElement("div", null,
-        react_1.default.createElement(material_1.Typography, null, "Launch split views with breakend source and target"),
+        react_1.default.createElement(material_1.Typography, null, "Launch split view"),
         error ? react_1.default.createElement(ui_1.ErrorMessage, { error: error }) : null,
         react_1.default.createElement("ul", null, ret.map((arg, index) => {
             const [f1, f2] = arg;
             return (react_1.default.createElement("li", { key: `${JSON.stringify(arg)}-${index}` },
-                react_1.default.createElement(material_1.Tooltip, { title: "Top panel->Bottom panel" },
-                    react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
-                            event.preventDefault();
-                            session.queueDialog(handleClose => [
-                                BreakendOptionDialog,
-                                { handleClose, f1, f2, model, viewType },
-                            ]);
-                        } },
-                        f1.refName,
-                        ":",
-                        (0, util_1.toLocale)(f1.strand === 1 ? f1.end : f1.start),
-                        ' ',
-                        "-> ",
-                        f2.refName,
-                        ":",
-                        (0, util_1.toLocale)(f2.strand === 1 ? f2.start : f2.end)))));
+                f1.refName,
+                ":",
+                (0, util_1.toLocale)(f1.strand === 1 ? f1.end : f1.start),
+                " ->",
+                ' ',
+                f2.refName,
+                ":",
+                (0, util_1.toLocale)(f2.strand === 1 ? f2.start : f2.end),
+                ' ',
+                react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+                        event.preventDefault();
+                        session.queueDialog(handleClose => [
+                            BreakendMultiLevelOptionDialog,
+                            {
+                                handleClose,
+                                model,
+                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
+                                // @ts-expect-error
+                                viewType,
+                                view: model.view,
+                                assemblyName: model.view.displayedRegions[0].assemblyName,
+                            },
+                        ]);
+                    } }, "(top/bottom)"),
+                ' ',
+                react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+                        event.preventDefault();
+                        session.queueDialog(handleClose => [
+                            BreakendSingleLevelOptionDialog,
+                            {
+                                handleClose,
+                                model,
+                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
+                                // @ts-expect-error
+                                viewType,
+                                view: model.view,
+                                assemblyName: model.view.displayedRegions[0].assemblyName,
+                            },
+                        ]);
+                    } }, "(single row)")));
         })))) : null;
 }

package/dist/AlignmentsFeatureDetail/{SuppAlignments.d.ts → LinkedPairedAlignments.d.ts}

@@ -2,7 +2,6 @@ import React from 'react';
 import { SimpleFeatureSerialized } from '@jbrowse/core/util';
 import { AlignmentFeatureWidgetModel } from './stateModelFactory';
 export default function SuppAlignments(props: {
-    tag: string;
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
 }): React.JSX.Element;

package/dist/AlignmentsFeatureDetail/{SuppAlignments.js → LinkedPairedAlignments.js}

@@ -7,10 +7,9 @@ exports.default = SuppAlignments;
 const react_1 = __importDefault(require("react"));
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const util_1 = require("@jbrowse/core/util");
-const SuppAlignmentsLocStrings_1 = __importDefault(require("./SuppAlignmentsLocStrings"));
-const LaunchBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchBreakpointSplitViewPanel"));
+const LaunchPairedEndBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchPairedEndBreakpointSplitViewPanel"));
 function SuppAlignments(props) {
-    const { model, tag, feature } = props;
+    const { model, feature } = props;
     const session = (0, util_1.getSession)(model);
     const { pluginManager } = (0, util_1.getEnv)(session);
     let viewType;
@@ -20,7 +19,5 @@ function SuppAlignments(props) {
     catch (e) {
         // ignore
     }
-    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Supplementary alignments" },
-        react_1.default.createElement(SuppAlignmentsLocStrings_1.default, { model: model, tag: tag }),
-        viewType ? (react_1.default.createElement(LaunchBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
+    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Supplementary alignments" }, viewType ? (react_1.default.createElement(LaunchPairedEndBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
 }

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { SimpleFeatureSerialized } from '@jbrowse/core/util';
+import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+export default function SupplementaryAlignments(props: {
+    tag: string;
+    model: AlignmentFeatureWidgetModel;
+    feature: SimpleFeatureSerialized;
+}): React.JSX.Element;

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.js

@@ -0,0 +1,26 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = SupplementaryAlignments;
+const react_1 = __importDefault(require("react"));
+const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
+const util_1 = require("@jbrowse/core/util");
+const SupplementaryAlignmentsLocStrings_1 = __importDefault(require("./SupplementaryAlignmentsLocStrings"));
+const LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchSupplementaryAlignmentBreakpointSplitViewPanel"));
+function SupplementaryAlignments(props) {
+    const { model, tag, feature } = props;
+    const session = (0, util_1.getSession)(model);
+    const { pluginManager } = (0, util_1.getEnv)(session);
+    let viewType;
+    try {
+        viewType = pluginManager.getViewType('BreakpointSplitView');
+    }
+    catch (e) {
+        // ignore
+    }
+    return (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { ...props, title: "Supplementary alignments" },
+        react_1.default.createElement(SupplementaryAlignmentsLocStrings_1.default, { model: model, tag: tag }),
+        viewType ? (react_1.default.createElement(LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
+}

package/{esm/AlignmentsFeatureDetail/SuppAlignmentsLocStrings.d.ts → dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts}

@@ -1,6 +1,6 @@
 import React from 'react';
 import { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function SuppAlignmentsLocStrings({ tag, model, }: {
+export default function SupplementaryAlignmentsLocStrings({ tag, model, }: {
     tag: string;
     model: AlignmentFeatureWidgetModel;
 }): React.JSX.Element;

package/dist/AlignmentsFeatureDetail/{SuppAlignmentsLocStrings.js → SupplementaryAlignmentsLocStrings.js}

@@ -3,13 +3,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SuppAlignmentsLocStrings;
+exports.default = SupplementaryAlignmentsLocStrings;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
 // locals
 const MismatchParser_1 = require("../MismatchParser");
 const util_1 = require("./util");
-function SuppAlignmentsLocStrings({ tag, model, }) {
+function SupplementaryAlignmentsLocStrings({ tag, model, }) {
     return (react_1.default.createElement("div", null,
         react_1.default.createElement(material_1.Typography, null, "List of supplementary alignment locations"),
         react_1.default.createElement("ul", null, tag

package/dist/LinearAlignmentsDisplay/models/alignmentsModel.js

@@ -9,13 +9,12 @@ const util_1 = require("./util");
  * #stateModel LinearAlignmentsDisplayMixin
  */
 function LinearAlignmentsDisplayMixin(pluginManager, configSchema) {
-    const lowerPanelDisplays = (0, util_1.getLowerPanelDisplays)(pluginManager).map(f => f.stateModel);
     return mobx_state_tree_1.types.model({
         /**
          * #property
          * refers to LinearPileupDisplay sub-display model
          */
-        PileupDisplay: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.union(...lowerPanelDisplays)),
+        PileupDisplay: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.union(...(0, util_1.getLowerPanelDisplays)(pluginManager).map(f => f.stateModel))),
         /**
          * #property
          * refers to LinearSNPCoverageDisplay sub-display model

package/dist/LinearAlignmentsDisplay/models/util.js

@@ -2,10 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getLowerPanelDisplays = getLowerPanelDisplays;
 function getLowerPanelDisplays(pluginManager) {
-    return (pluginManager
+    return pluginManager
         .getDisplayElements()
-        // @ts-expect-error
         .filter(f => { var _a; return ((_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.type) === 'LinearAlignmentsDisplay'; })
-        // @ts-expect-error
-        .filter(f => { var _a; return (_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.lowerPanel; }));
+        .filter(f => { var _a; return (_a = f.subDisplay) === null || _a === void 0 ? void 0 : _a.lowerPanel; });
 }

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -37,7 +37,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement | undefined;
+        reactElement: React.ReactElement | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
@@ -48,10 +48,10 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             model: {
                 error?: unknown;
                 reload: () => void;
-                message: import("react").ReactNode;
+                message: React.ReactNode;
                 filled?: boolean;
                 status?: string;
-                reactElement?: import("react").ReactElement;
+                reactElement?: React.ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -62,7 +62,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement;
+            reactElement: React.ReactElement;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -150,7 +150,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     error: unknown;
     message: string | undefined;
 } & {
-    readonly RenderingComponent: import("react").FC<{
+    readonly RenderingComponent: React.FC<{
         model: {
             id: string;
             type: string;
@@ -171,7 +171,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         onHorizontalScroll?: () => void;
         blockState?: Record<string, any>;
     }>;
-    readonly DisplayBlurb: import("react").FC<{
+    readonly DisplayBlurb: React.FC<{
         model: {
             id: string;
             type: string;
@@ -181,9 +181,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree" /**
-             * #property
-             */).IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            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>>;
         }, {
@@ -196,7 +194,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly parentTrack: any;
     renderProps(): any;
     readonly rendererType: import("@jbrowse/core/pluggableElementTypes").RendererType;
-    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
     trackMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     readonly viewMenuActions: import("@jbrowse/core/ui").MenuItem[];
     regionCannotBeRendered(): null;
@@ -242,13 +240,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
+    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
     readonly blockType: "dynamicBlocks" | "staticBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
-    readonly TooltipComponent: import("react").FC<any>;
+    readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
-    readonly DisplayMessageComponent: undefined | import("react").FC<any>;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
@@ -345,7 +343,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
                 [x: string]: any;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>);
+        } & import("mobx-state-tree" /**
+         * #stateModel SharedLinearPileupDisplayMixin
+         * #category display
+         * extends `BaseLinearDisplay`
+         */).IStateTreeNode<AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<AnyConfigurationSchemaType>;
 } & {
     /**
@@ -419,7 +421,6 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
-        priority: number;
         onClick: () => void;
     })[];
 } & {
@@ -456,7 +457,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     }, {
         renderInProgress: AbortController | undefined;
         filled: boolean;
-        reactElement: import("react").ReactElement | undefined;
+        reactElement: React.ReactElement | undefined;
         features: Map<string, Feature> | undefined;
         layout: any;
         status: string;
@@ -467,10 +468,10 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
             model: {
                 error?: unknown;
                 reload: () => void;
-                message: import("react").ReactNode;
+                message: React.ReactNode;
                 filled?: boolean;
                 status?: string;
-                reactElement?: import("react").ReactElement;
+                reactElement?: React.ReactElement;
             };
         }) => import("react").JSX.Element | undefined;
         renderProps: any;
@@ -481,7 +482,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         setLoading(abortController: AbortController): void;
         setMessage(messageText: string): void;
         setRendered(props: {
-            reactElement: import("react").ReactElement;
+            reactElement: React.ReactElement;
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
@@ -523,8 +524,8 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     type: string;
     id: string;
     configuration: import("mobx-state-tree").ModelSnapshotType<Record<string, any>>;
-    rpcDriverName: string | undefined;
     heightPreConfig: number | undefined;
+    rpcDriverName: string | undefined;
     userBpPerPxLimit: number | undefined;
     userByteSizeLimit: number | undefined;
 } & import("mobx-state-tree")._NotCustomized>;

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -182,7 +182,11 @@ function SharedLinearPileupDisplayMixin(configSchema) {
         selectFeature(feature) {
             const session = (0, util_1.getSession)(self);
             if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                const featureWidget = session.addWidget('AlignmentsFeatureWidget', 'alignmentFeature', { featureData: feature.toJSON(), view: (0, util_1.getContainingView)(self) });
+                const featureWidget = session.addWidget('AlignmentsFeatureWidget', 'alignmentFeature', {
+                    featureData: feature.toJSON(),
+                    view: (0, util_1.getContainingView)(self),
+                    track: (0, util_1.getContainingTrack)(self),
+                });
                 session.showWidget(featureWidget);
             }
             session.setSelection(feature);
@@ -428,9 +432,12 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                     {
                         label: 'Color by tag...',
                         onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(doneCallback => [
+                            (0, util_1.getSession)(self).queueDialog(handleClose => [
                                 ColorByTagDialog,
-                                { model: self, handleClose: doneCallback },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },
@@ -442,20 +449,9 @@ function SharedLinearPileupDisplayMixin(configSchema) {
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
-                    {
-                        label: 'Filter by...',
-                        icon: ClearAll_1.default,
-                        priority: -1,
-                        onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(doneCallback => [
-                                FilterByTagDialog,
-                                { model: self, handleClose: doneCallback },
-                            ]);
-                        },
-                    },
                     {
                         label: 'Set feature height...',
-                        priority: -1,
+                        priority: 1,
                         subMenu: [
                             {
                                 label: 'Normal',
@@ -474,9 +470,12 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                             {
                                 label: 'Manually set height',
                                 onClick: () => {
-                                    (0, util_1.getSession)(self).queueDialog(doneCallback => [
+                                    (0, util_1.getSession)(self).queueDialog(handleClose => [
                                         SetFeatureHeightDialog,
-                                        { model: self, handleClose: doneCallback },
+                                        {
+                                            model: self,
+                                            handleClose,
+                                        },
                                     ]);
                                 },
                             },
@@ -484,10 +483,27 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                     },
                     {
                         label: 'Set max height...',
+                        priority: -1,
                         onClick: () => {
-                            (0, util_1.getSession)(self).queueDialog(doneCallback => [
+                            (0, util_1.getSession)(self).queueDialog(handleClose => [
                                 SetMaxHeightDialog,
-                                { model: self, handleClose: doneCallback },
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
+                            ]);
+                        },
+                    },
+                    {
+                        label: 'Filter by...',
+                        icon: ClearAll_1.default,
+                        onClick: () => {
+                            (0, util_1.getSession)(self).queueDialog(handleClose => [
+                                FilterByTagDialog,
+                                {
+                                    model: self,
+                                    handleClose,
+                                },
                             ]);
                         },
                     },

package/dist/LinearPileupDisplay/components/SetMaxHeightDialog.js

@@ -38,10 +38,10 @@ const SetMaxHeightDialog = (0, mobx_react_1.observer)(function (props) {
     const { classes } = useStyles();
     const { maxHeight = '' } = model;
     const [max, setMax] = (0, react_1.useState)(`${maxHeight}`);
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Filter options" },
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set max height" },
         react_1.default.createElement(material_1.DialogContent, { className: classes.root },
             react_1.default.createElement(material_1.Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
-            react_1.default.createElement(material_1.TextField, { value: max, onChange: event => {
+            react_1.default.createElement(material_1.TextField, { value: max, autoFocus: true, onChange: event => {
                     setMax(event.target.value);
                 }, placeholder: "Enter max height for layout" }),
             react_1.default.createElement(material_1.DialogActions, null,