@jbrowse/plugin-alignments 2.10.1 → 2.10.3

package/dist/AlignmentsFeatureDetail/index.d.ts

@@ -1,51 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<any, any, any>;
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-} & {
-    type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
-}, {
-    error: unknown;
-} & {
-    setFeatureData(featureData: Record<string, unknown>): void;
-    clearFeatureData(): void;
-    setFormattedData(feat: Record<string, unknown>): void;
-    setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
-    setError(e: unknown): void;
-} & {
-    afterCreate(): void;
-}, {
-    type: "BaseFeatureWidget";
-} & 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<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<any, any, any>;
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
-}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    type: "BaseFeatureWidget";
-    id: string;
-    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    trackId: string | undefined;
-    trackType: string | undefined;
-    maxDepth: number | undefined;
-    formattedFields: any;
-    finalizedFeatureData: any;
-} & import("mobx-state-tree")._NotCustomized>;
-export default function register(pluginManager: PluginManager): void;
-export { configSchema };
+export default function AlignmentFeatureDetailsF(pluginManager: PluginManager): void;

package/dist/AlignmentsFeatureDetail/index.js

@@ -26,28 +26,17 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = exports.stateModelFactory = void 0;
 const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const WidgetType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/WidgetType"));
-const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
-const configSchema = (0, configuration_1.ConfigurationSchema)('AlignmentsFeatureWidget', {});
-exports.configSchema = configSchema;
-function stateModelFactory(pluginManager) {
-    const baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
-    return mobx_state_tree_1.types.compose(baseModel, mobx_state_tree_1.types.model('AlignmentsFeatureWidget', {
-        type: mobx_state_tree_1.types.literal('AlignmentsFeatureWidget'),
-    }));
-}
-exports.stateModelFactory = stateModelFactory;
-function register(pluginManager) {
+const configSchema_1 = require("./configSchema");
+const stateModelFactory_1 = require("./stateModelFactory");
+function AlignmentFeatureDetailsF(pluginManager) {
     pluginManager.addWidgetType(() => new WidgetType_1.default({
         name: 'AlignmentsFeatureWidget',
         heading: 'Feature details',
-        configSchema,
-        stateModel: stateModelFactory(pluginManager),
+        configSchema: configSchema_1.configSchema,
+        stateModel: (0, stateModelFactory_1.stateModelFactory)(pluginManager),
         ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AlignmentsFeatureDetail')))),
     }));
 }
-exports.default = register;
+exports.default = AlignmentFeatureDetailsF;

package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts

@@ -0,0 +1,22 @@
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import { ReducedFeature } from './getSAFeatures';
+export declare function getBreakpointSplitView({ f1, f2, view, }: {
+    f1: ReducedFeature;
+    f2: ReducedFeature;
+    view: LinearGenomeViewModel;
+}): {
+    type: string;
+    views: {
+        type: string;
+        displayedRegions: {
+            start: number;
+            end: number;
+            refName: string;
+            assemblyName: string;
+        }[];
+        hideHeader: boolean;
+        bpPerPx: number;
+        offsetPx: number;
+    }[];
+    displayName: string;
+};

package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.js

@@ -0,0 +1,50 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getBreakpointSplitView = void 0;
+const util_1 = require("@jbrowse/core/util");
+function getBreakpointSplitView({ f1, f2, view, }) {
+    const { assemblyName } = view.displayedRegions[0];
+    const { assemblyManager } = (0, util_1.getSession)(view);
+    const assembly = assemblyManager.get(assemblyName);
+    if (!assembly) {
+        throw new Error(`assembly ${assemblyName} not found`);
+    }
+    if (!assembly.regions) {
+        throw new Error(`assembly ${assemblyName} regions not loaded`);
+    }
+    const topRegion = assembly.regions.find(f => f.refName === f1.refName);
+    const bottomRegion = assembly.regions.find(f => f.refName === f2.refName);
+    if (!topRegion || !bottomRegion) {
+        throw new Error(`unable to find the refName for the top or bottom of the breakpoint view`);
+    }
+    const topMarkedRegion = [{ ...topRegion }, { ...topRegion }];
+    const bottomMarkedRegion = [{ ...bottomRegion }, { ...bottomRegion }];
+    const s = f1.strand === 1 ? f1.end : f1.start;
+    const e = f2.strand === 1 ? f2.start : f2.end;
+    topMarkedRegion[0].end = s;
+    topMarkedRegion[1].start = s + 1;
+    bottomMarkedRegion[0].end = e;
+    bottomMarkedRegion[1].start = e + 1;
+    const bpPerPx = 10;
+    return {
+        type: 'BreakpointSplitView',
+        views: [
+            {
+                type: 'LinearGenomeView',
+                displayedRegions: topMarkedRegion,
+                hideHeader: true,
+                bpPerPx,
+                offsetPx: (topRegion.start + s) / bpPerPx,
+            },
+            {
+                type: 'LinearGenomeView',
+                displayedRegions: bottomMarkedRegion,
+                hideHeader: true,
+                bpPerPx,
+                offsetPx: (bottomRegion.start + e) / bpPerPx,
+            },
+        ],
+        displayName: `breakend split detail`,
+    };
+}
+exports.getBreakpointSplitView = getBreakpointSplitView;

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -0,0 +1,51 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+import { Instance } from 'mobx-state-tree';
+export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+} & {
+    type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
+}, {
+    error: unknown;
+} & {
+    setFeatureData(featureData: Record<string, unknown>): void;
+    clearFeatureData(): void;
+    setFormattedData(feat: Record<string, unknown>): void;
+    setExtra(type?: string | undefined, trackId?: string | undefined, maxDepth?: number | undefined): void;
+    setError(e: unknown): void;
+} & {
+    afterCreate(): void;
+}, {
+    type: "BaseFeatureWidget";
+} & 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<"BaseFeatureWidget">;
+    featureData: import("mobx-state-tree").IType<any, any, any>;
+    formattedFields: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    maxDepth: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
+    id: string;
+    type: "BaseFeatureWidget";
+    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    trackId: string | undefined;
+    trackType: string | undefined;
+    maxDepth: number | undefined;
+    formattedFields: any;
+    finalizedFeatureData: any;
+} & import("mobx-state-tree")._NotCustomized>;
+export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;
+export type AlignmentFeatureWidgetModel = Instance<AlignmentFeatureWidgetStateModel>;

package/dist/AlignmentsFeatureDetail/stateModelFactory.js

@@ -0,0 +1,12 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.stateModelFactory = void 0;
+const mobx_state_tree_1 = require("mobx-state-tree");
+const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
+function stateModelFactory(pluginManager) {
+    const baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
+    return mobx_state_tree_1.types.compose(baseModel, mobx_state_tree_1.types.model('AlignmentsFeatureWidget', {
+        type: mobx_state_tree_1.types.literal('AlignmentsFeatureWidget'),
+    }));
+}
+exports.stateModelFactory = stateModelFactory;

package/dist/AlignmentsFeatureDetail/tagInfo.d.ts

@@ -0,0 +1,63 @@
+export declare const tags: {
+    AM: string;
+    AS: string;
+    BC: string;
+    BQ: string;
+    BZ: string;
+    CB: string;
+    CC: string;
+    CM: string;
+    CO: string;
+    CP: string;
+    CQ: string;
+    CR: string;
+    CS: string;
+    CT: string;
+    CY: string;
+    E2: string;
+    FI: string;
+    FS: string;
+    FZ: string;
+    GC: string;
+    GQ: string;
+    GS: string;
+    H0: string;
+    H1: string;
+    H2: string;
+    HI: string;
+    IH: string;
+    LB: string;
+    MC: string;
+    MD: string;
+    MF: string;
+    MI: string;
+    ML: string;
+    MM: string;
+    MQ: string;
+    NH: string;
+    NM: string;
+    OA: string;
+    OC: string;
+    OP: string;
+    OQ: string;
+    OX: string;
+    PG: string;
+    PQ: string;
+    PT: string;
+    PU: string;
+    Q2: string;
+    QT: string;
+    QX: string;
+    R2: string;
+    RG: string;
+    RT: string;
+    RX: string;
+    S2: string;
+    SA: string;
+    SM: string;
+    SQ: string;
+    TC: string;
+    TS: string;
+    U2: string;
+    UQ: string;
+};

package/dist/AlignmentsFeatureDetail/tagInfo.js

@@ -0,0 +1,66 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.tags = void 0;
+exports.tags = {
+    AM: 'The smallest template-independent mapping quality in the template',
+    AS: 'Alignment score generated by aligner',
+    BC: 'Barcode sequence identifying the sample',
+    BQ: 'Offset to base alignment quality (BAQ)',
+    BZ: 'Phred quality of the unique molecular barcode bases in the {OX} tag',
+    CB: 'Cell identifier',
+    CC: 'Reference name of the next hit',
+    CM: 'Edit distance between the color sequence and the color reference (see also {NM})',
+    CO: 'Free-text comments',
+    CP: 'Leftmost coordinate of the next hit',
+    CQ: 'Color read base qualities',
+    CR: 'Cellular barcode sequence bases (uncorrected)',
+    CS: 'Color read sequence',
+    CT: 'Complete read annotation tag, used for consensus annotation dummy features',
+    CY: 'Phred quality of the cellular barcode sequence in the {CR} tag',
+    E2: 'The 2nd most likely base calls',
+    FI: 'The index of segment in the template',
+    FS: 'Segment suffix',
+    FZ: 'Flow signal intensities',
+    GC: 'Reserved for backwards compatibility reasons',
+    GQ: 'Reserved for backwards compatibility reasons',
+    GS: 'Reserved for backwards compatibility reasons',
+    H0: 'Number of perfect hits',
+    H1: 'Number of 1-difference hits (see also {NM})',
+    H2: 'Number of 2-difference hits',
+    HI: 'Query hit index',
+    IH: 'Query hit total count',
+    LB: 'Library',
+    MC: 'CIGAR string for mate/next segment',
+    MD: 'String encoding mismatched and deleted reference bases',
+    MF: 'Reserved for backwards compatibility reasons',
+    MI: 'Molecular identifier; a string that uniquely identifies the molecule from which the record was derived',
+    ML: 'Base modification probabilities',
+    MM: 'Base modifications / methylation ',
+    MQ: 'Mapping quality of the mate/next segment',
+    NH: 'Number of reported alignments that contain the query in the current record',
+    NM: 'Edit distance to the reference',
+    OA: 'Original alignment',
+    OC: 'Original CIGAR (deprecated; use {OA} instead)',
+    OP: 'Original mapping position (deprecated; use {OA} instead)',
+    OQ: 'Original base quality',
+    OX: 'Original unique molecular barcode bases',
+    PG: 'Program',
+    PQ: 'Phred likelihood of the template',
+    PT: 'Read annotations for parts of the padded read sequence',
+    PU: 'Platform unit',
+    Q2: 'Phred quality of the mate/next segment sequence in the {R2} tag',
+    QT: 'Phred quality of the sample barcode sequence in the {BC} tag',
+    QX: 'Quality score of the unique molecular identifier in the {RX} tag',
+    R2: 'Sequence of the mate/next segment in the template',
+    RG: 'Read group',
+    RT: 'Reserved for backwards compatibility reasons',
+    RX: 'Sequence bases of the (possibly corrected) unique molecular identifier',
+    S2: 'Reserved for backwards compatibility reasons',
+    SA: 'Other canonical alignments in a chimeric alignment',
+    SM: 'Template-independent mapping quality',
+    SQ: 'Reserved for backwards compatibility reasons',
+    TC: 'The number of segments in the template',
+    TS: 'Transcript strand',
+    U2: 'Phred probability of the 2nd call being wrong conditional on the best being wrong',
+    UQ: 'Phred likelihood of the segment, conditional on the mapping being correct',
+};

package/dist/BamAdapter/BamAdapter.js

@@ -65,14 +65,13 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             const idToName = [];
             const nameToId = {};
             samHeader === null || samHeader === void 0 ? void 0 : samHeader.filter(l => l.tag === 'SQ').forEach((sqLine, refId) => {
-                sqLine.data.forEach(item => {
-                    if (item.tag === 'SN') {
-                        // this is the ref name
-                        const refName = item.value;
-                        nameToId[refName] = refId;
-                        idToName[refId] = refName;
-                    }
-                });
+                const SN = sqLine.data.find(item => item.tag === 'SN');
+                if (SN) {
+                    // this is the ref name
+                    const refName = SN.value;
+                    nameToId[refName] = refId;
+                    idToName[refId] = refName;
+                }
             });
             return { idToName, nameToId };
         });
@@ -144,7 +143,9 @@ class BamAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     }
                     if (tagFilter) {
                         const v = record.get(tagFilter.tag);
-                        if (!(v === '*' ? v !== undefined : `${v}` === tagFilter.value)) {
+                        if (!(tagFilter.value === '*'
+                            ? v !== undefined
+                            : `${v}` === tagFilter.value)) {
                             continue;
                         }
                     }

package/dist/CramAdapter/CramAdapter.js

@@ -22,12 +22,6 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     async configurePre() {
         const cramLocation = this.getConf('cramLocation');
         const craiLocation = this.getConf('craiLocation');
-        if (!cramLocation) {
-            throw new Error('missing cramLocation argument');
-        }
-        if (!craiLocation) {
-            throw new Error('missing craiLocation argument');
-        }
         const pm = this.pluginManager;
         const cram = new cram_1.IndexedCramFile({
             cramFilehandle: (0, io_1.openLocation)(cramLocation, pm),
@@ -40,6 +34,9 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             throw new Error('Error getting subadapter');
         }
         const seqConf = this.getConf('sequenceAdapter');
+        if (!seqConf) {
+            throw new Error('no sequenceAdapter supplied to CramAdapter config');
+        }
         const subadapter = await this.getSubAdapter(seqConf);
         return {
             cram,
@@ -86,8 +83,9 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             return chunkSeq.slice(trimStart, trimStart + trimLength);
         })
             .join('');
-        if (sequence.length !== end - start) {
-            throw new Error(`sequence fetch failed: fetching ${refName}:${(start - 1).toLocaleString()}-${end.toLocaleString()} returned ${sequence.length.toLocaleString()} bases, but should have returned ${(end - start).toLocaleString()}`);
+        const qlen = end - start;
+        if (sequence.length !== qlen) {
+            throw new Error(`fetching ${refName}:${(0, util_1.toLocale)(start - 1)}-${(0, util_1.toLocale)(end)} returned ${(0, util_1.toLocale)(sequence.length)} bases, should have returned ${(0, util_1.toLocale)(qlen)}`);
         }
         return sequence;
     }
@@ -104,14 +102,12 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             samHeader
                 .filter(l => l.tag === 'SQ')
                 .forEach((sqLine, refId) => {
-                sqLine.data.forEach(item => {
-                    if (item.tag === 'SN') {
-                        // this is the ref name
-                        const refName = item.value;
-                        nameToId[refName] = refId;
-                        idToName[refId] = refName;
-                    }
-                });
+                const SN = sqLine.data.find(item => item.tag === 'SN');
+                if (SN) {
+                    const refName = SN.value;
+                    nameToId[refName] = refId;
+                    idToName[refId] = refName;
+                }
             });
             const readGroups = samHeader
                 .filter(l => l.tag === 'RG')
@@ -161,7 +157,7 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const { signal, filterBy, statusCallback = () => { } } = opts || {};
         const { refName, start, end, originalRefName } = region;
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { cram } = await this.setup(opts);
+            const { cram, samHeader } = await this.setup(opts);
             const refId = this.refNameToId(refName);
             if (refId === undefined) {
                 console.warn('Unknown refName', refName);
@@ -183,9 +179,11 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                     }
                     if (tagFilter) {
                         const v = tagFilter.tag === 'RG'
-                            ? (_a = this.samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
+                            ? (_a = samHeader.readGroups) === null || _a === void 0 ? void 0 : _a[record.readGroupId]
                             : record.tags[tagFilter.tag];
-                        if (!(v === '*' ? v !== undefined : `${v}` === tagFilter.value)) {
+                        if (!(tagFilter.value === '*'
+                            ? v !== undefined
+                            : `${v}` === tagFilter.value)) {
                             continue;
                         }
                     }

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -46,28 +46,32 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
+        setMessage(messageText: string): void; /**
+         * #action
+         */
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
-            /**
-             * #action
-             */
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
-        setError(error: unknown): void; /**
-         * #action
-         */
+        setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
@@ -173,11 +177,11 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
             rendererTypeName: string;
             error: unknown;
-            message: string | undefined;
-        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>; /**
+            message: string | undefined; /**
              * #property
              */
+        } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
+            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>>;
         }, {
@@ -220,7 +224,9 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     afterAttach(): void;
 } & {
-    setCurrStatsBpPerPx(n: number): void;
+    setCurrStatsBpPerPx(n: number): void; /**
+     * #property
+     */
     setFeatureDensityStatsLimit(stats?: import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | undefined): void;
     getFeatureDensityStats(): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     setFeatureDensityStatsP(arg: any): void;
@@ -241,13 +247,17 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     readonly renderDelay: number;
     readonly TooltipComponent: import("react").FC<any>;
-    readonly selectedFeatureId: string | undefined;
+    readonly selectedFeatureId: string | undefined; /**
+     * #action
+     */
     readonly DisplayMessageComponent: import("react").FC<any> | undefined;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined; /**
+     * #action
+     */
     searchFeatureByID(id: string): [number, number, number, number] | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
@@ -450,28 +460,32 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         message: string | undefined;
         maxHeightReached: boolean;
         ReactComponent: ({ model, }: {
-            model: any;
-        }) => any;
+            model: {
+                error?: unknown;
+                reload: () => void;
+                message: import("react").ReactNode;
+                filled?: boolean | undefined;
+                status?: string | undefined;
+                reactElement?: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>> | undefined;
+            };
+        }) => import("react").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
         afterAttach(): void;
         setStatus(message: string): void;
         setLoading(abortController: AbortController): void;
-        setMessage(messageText: string): void;
+        setMessage(messageText: string): void; /**
+         * #action
+         */
         setRendered(props: {
             reactElement: import("react").ReactElement<any, string | import("react").JSXElementConstructor<any>>;
-            /**
-             * #action
-             */
             features: Map<string, Feature>;
             layout: any;
             maxHeightReached: boolean;
             renderProps: any;
         } | undefined): void;
-        setError(error: unknown): void; /**
-         * #action
-         */
+        setError(error: unknown): void;
         reload(): void;
         beforeDestroy(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -46,10 +46,10 @@ const shared_1 = require("../shared");
 const util_2 = require("../util");
 const color_1 = require("../shared/color");
 // async
-const FilterByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/FilterByTag'))));
-const ColorByTagDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ColorByTag'))));
-const SetFeatureHeightDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetFeatureHeight'))));
-const SetMaxHeightDlg = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetMaxHeight'))));
+const FilterByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/FilterByTag'))));
+const ColorByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/ColorByTag'))));
+const SetFeatureHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetFeatureHeight'))));
+const SetMaxHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetMaxHeight'))));
 // using a map because it preserves order
 const rendererTypes = new Map([
     ['pileup', 'PileupRenderer'],
@@ -421,7 +421,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                         label: 'Color by tag...',
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(doneCallback => [
-                                ColorByTagDlg,
+                                ColorByTagDialog,
                                 { model: self, handleClose: doneCallback },
                             ]);
                         },
@@ -439,7 +439,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                         icon: ClearAll_1.default,
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(doneCallback => [
-                                FilterByTagDlg,
+                                FilterByTagDialog,
                                 { model: self, handleClose: doneCallback },
                             ]);
                         },
@@ -465,7 +465,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                                 label: 'Manually set height',
                                 onClick: () => {
                                     (0, util_1.getSession)(self).queueDialog(doneCallback => [
-                                        SetFeatureHeightDlg,
+                                        SetFeatureHeightDialog,
                                         { model: self, handleClose: doneCallback },
                                     ]);
                                 },
@@ -476,7 +476,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                         label: 'Set max height...',
                         onClick: () => {
                             (0, util_1.getSession)(self).queueDialog(doneCallback => [
-                                SetMaxHeightDlg,
+                                SetMaxHeightDialog,
                                 { model: self, handleClose: doneCallback },
                             ]);
                         },