@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,4 +1,4 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory.ts';
 declare const AlignmentsFeatureDetails: (props: {
     model: AlignmentFeatureWidgetModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -3,20 +3,20 @@ import { lazy } from 'react';
 import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
-import Flags from './Flags';
-import Formatter from './Formatter';
-import PairLink from './PairLink';
-import { tags } from './tagInfo';
-import { getTag } from './util';
-const SupplementaryAlignments = lazy(() => import('./SupplementaryAlignments'));
-const LinkedPairedAlignments = lazy(() => import('./LinkedPairedAlignments'));
-const FeatDefined = observer(function (props) {
+import Flags from "./Flags.js";
+import Formatter from "./Formatter.js";
+import PairLink from "./PairLink.js";
+import { tags } from "./tagInfo.js";
+import { getTag } from "./util.js";
+const SupplementaryAlignments = lazy(() => import("./SupplementaryAlignments.js"));
+const LinkedPairedAlignments = lazy(() => import("./LinkedPairedAlignments.js"));
+const FeatDefined = observer(function FeatDefined(props) {
     const { model, feat } = props;
     const flags = feat.flags;
     const SA = getTag('SA', feat);
     return (_jsxs(Paper, { "data-testid": "alignment-side-drawer", children: [_jsx(FeatureDetails, { ...props, descriptions: { tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (_jsx(PairLink, { model: model, locString: value })) : (_jsx(Formatter, { value: value })) }), SA !== undefined ? (_jsx(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null, flags != null ? (_jsxs(_Fragment, { children: [flags & 1 ? (_jsx(LinkedPairedAlignments, { model: model, feature: feat })) : null, _jsx(Flags, { flags: flags, ...props })] })) : null] }));
 });
-const AlignmentsFeatureDetails = observer(function (props) {
+const AlignmentsFeatureDetails = observer(function AlignmentsFeatureDetails(props) {
     const { model } = props;
     const { featureData } = model;
     const feat = structuredClone(featureData);

package/esm/AlignmentsFeatureDetail/BreakpointSplitViewChoiceDialog.d.ts

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

package/esm/AlignmentsFeatureDetail/BreakpointSplitViewChoiceDialog.js

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

package/esm/AlignmentsFeatureDetail/Flags.js

@@ -1,8 +1,8 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import SimpleField from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Checkbox, FormControlLabel, FormGroup } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     compact: {
         paddingRight: 0,

package/esm/AlignmentsFeatureDetail/Formatter.js

@@ -1,11 +1,11 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
-import copy from 'copy-to-clipboard';
 export default function Formatter({ value }) {
     const [show, setShow] = useState(false);
     const [copied, setCopied] = useState(false);
     const display = String(value);
-    return display.length > 100 ? (_jsxs(_Fragment, { children: [_jsx("button", { type: "button", onClick: () => {
+    return display.length > 100 ? (_jsxs(_Fragment, { children: [_jsx("button", { type: "button", onClick: async () => {
+                    const { default: copy } = await import('copy-to-clipboard');
                     copy(display);
                     setCopied(true);
                     setTimeout(() => {

package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts

@@ -1,6 +1,6 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory.ts';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-}): import("react/jsx-runtime").JSX.Element;
+}): import("react/jsx-runtime").JSX.Element | null;

package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js

@@ -1,9 +1,9 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { lazy } from 'react';
 import { SimpleFeature, getSession, toLocale } from '@jbrowse/core/util';
+import { getAssemblyName } from '@jbrowse/sv-core';
 import { Link, Typography } from '@mui/material';
-const BreakendMultiLevelOptionDialog = lazy(() => import('./BreakendMultiLevelOptionDialog'));
-const BreakendSingleLevelOptionDialog = lazy(() => import('./BreakendSingleLevelOptionDialog'));
+const BreakpointSplitViewChoiceDialog = lazy(() => import("./BreakpointSplitViewChoiceDialog.js"));
 export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }) {
     const session = getSession(model);
     const f1 = {
@@ -20,29 +20,18 @@ export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature
         end: feature.next_pos + 1,
         strand: feature.strand,
     };
-    return (_jsxs("div", { children: [_jsx(Typography, { children: "Launch split view" }), _jsx("ul", { children: _jsxs("li", { children: [f1.refName, ":", toLocale(f1.start), " -> ", f2.refName, ":", toLocale(f2.start), ' ', _jsx(Link, { href: "#", onClick: event => {
+    const assemblyName = getAssemblyName(model.view);
+    return assemblyName ? (_jsxs("div", { children: [_jsx(Typography, { children: "Launch split view" }), _jsx("ul", { children: _jsxs("li", { children: [f1.refName, ":", toLocale(f1.start), " -> ", f2.refName, ":", toLocale(f2.start), ' ', _jsx(Link, { href: "#", onClick: event => {
                                 event.preventDefault();
                                 session.queueDialog(handleClose => [
-                                    BreakendMultiLevelOptionDialog,
+                                    BreakpointSplitViewChoiceDialog,
                                     {
                                         handleClose,
                                         session,
                                         feature: new SimpleFeature({ ...f1, mate: f2 }),
                                         view: model.view,
-                                        assemblyName: model.view.displayedRegions[0].assemblyName,
+                                        assemblyName,
                                     },
                                 ]);
-                            }, children: "(top/bottom)" }), ' ', _jsx(Link, { href: "#", onClick: event => {
-                                event.preventDefault();
-                                session.queueDialog(handleClose => [
-                                    BreakendSingleLevelOptionDialog,
-                                    {
-                                        handleClose,
-                                        session,
-                                        feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                        view: model.view,
-                                        assemblyName: model.view.displayedRegions[0].assemblyName,
-                                    },
-                                ]);
-                            }, children: "(single row)" })] }) })] }));
+                            }, children: "(breakpoint split view)" })] }) })] })) : null;
 }

package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.d.ts

@@ -1,4 +1,4 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory.ts';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function LaunchBreakpointSplitViewPanel({ model, feature, }: {
     model: AlignmentFeatureWidgetModel;

package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js

@@ -2,10 +2,10 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { lazy, useEffect, useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { SimpleFeature, getSession, toLocale } from '@jbrowse/core/util';
+import { getAssemblyName } from '@jbrowse/sv-core';
 import { Link, Typography } from '@mui/material';
-import { getSAFeatures } from './getSAFeatures';
-const BreakendMultiLevelOptionDialog = lazy(() => import('./BreakendMultiLevelOptionDialog'));
-const BreakendSingleLevelOptionDialog = lazy(() => import('./BreakendSingleLevelOptionDialog'));
+import { getSAFeatures } from "./getSAFeatures.js";
+const BreakpointSplitViewChoiceDialog = lazy(() => import("./BreakpointSplitViewChoiceDialog.js"));
 export default function LaunchBreakpointSplitViewPanel({ model, feature, }) {
     const { view } = model;
     const [res, setRes] = useState();
@@ -32,40 +32,22 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, }) {
             ret.push([res[i], res[i + 1]]);
         }
     }
-    return ret.length ? (_jsxs("div", { children: [_jsx(Typography, { children: "Launch split view" }), error ? _jsx(ErrorMessage, { error: error }) : null, _jsx("ul", { children: ret.map((arg, index) => {
+    const session = getSession(model);
+    const assemblyName = getAssemblyName(model.view);
+    return ret.length && assemblyName ? (_jsxs("div", { children: [_jsx(Typography, { children: "Launch split view" }), error ? _jsx(ErrorMessage, { error: error }) : null, _jsx("ul", { children: ret.map((arg, index) => {
                     const [f1, f2] = arg;
-                    return (_jsxs("li", { children: [f1.refName, ":", toLocale(f1.strand === 1 ? f1.end : f1.start), " ->", ' ', f2.refName, ":", toLocale(f2.strand === 1 ? f2.start : f2.end), ' ', _jsx(TopBottomSplitViewLink, { model: model, f1: f1, f2: f2 }), ' ', _jsx(SideBySideViewLink, { model: model, f1: f1, f2: f2 })] }, `${JSON.stringify(arg)}-${index}`));
+                    return (_jsxs("li", { children: [f1.refName, ":", toLocale(f1.strand === 1 ? f1.end : f1.start), " ->", ' ', f2.refName, ":", toLocale(f2.strand === 1 ? f2.start : f2.end), ' ', _jsx(Link, { href: "#", onClick: event => {
+                                    event.preventDefault();
+                                    session.queueDialog(handleClose => [
+                                        BreakpointSplitViewChoiceDialog,
+                                        {
+                                            handleClose,
+                                            session,
+                                            feature: new SimpleFeature({ ...f1, mate: f2 }),
+                                            view: model.view,
+                                            assemblyName,
+                                        },
+                                    ]);
+                                }, children: "(breakpoint split view)" })] }, `${JSON.stringify(arg)}-${index}`));
                 }) })] })) : null;
 }
-function TopBottomSplitViewLink({ model, f1, f2, }) {
-    return (_jsx(Link, { href: "#", onClick: event => {
-            event.preventDefault();
-            const session = getSession(model);
-            session.queueDialog(handleClose => [
-                BreakendMultiLevelOptionDialog,
-                {
-                    handleClose,
-                    session,
-                    feature: new SimpleFeature({ ...f1, mate: f2 }),
-                    view: model.view,
-                    assemblyName: model.view.displayedRegions[0].assemblyName,
-                },
-            ]);
-        }, children: "(top/bottom)" }));
-}
-function SideBySideViewLink({ model, f1, f2, }) {
-    return (_jsx(Link, { href: "#", onClick: event => {
-            event.preventDefault();
-            const session = getSession(model);
-            session.queueDialog(handleClose => [
-                BreakendSingleLevelOptionDialog,
-                {
-                    handleClose,
-                    session,
-                    feature: new SimpleFeature({ ...f1, mate: f2 }),
-                    view: model.view,
-                    assemblyName: model.view.displayedRegions[0].assemblyName,
-                },
-            ]);
-        }, children: "(single row)" }));
-}

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts

@@ -1,4 +1,4 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory.ts';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function SuppAlignments(props: {
     model: AlignmentFeatureWidgetModel;

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -1,7 +1,7 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import { getEnv, getSession } from '@jbrowse/core/util';
-import LaunchPairedEndBreakpointSplitViewPanel from './LaunchPairedEndBreakpointSplitViewPanel';
+import LaunchPairedEndBreakpointSplitViewPanel from "./LaunchPairedEndBreakpointSplitViewPanel.js";
 export default function SuppAlignments(props) {
     const { model, feature } = props;
     const session = getSession(model);

package/esm/AlignmentsFeatureDetail/PairLink.d.ts

@@ -1,4 +1,4 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory.ts';
 export default function PairLink({ locString, model, }: {
     locString: string;
     model: AlignmentFeatureWidgetModel;

package/esm/AlignmentsFeatureDetail/PairLink.js

@@ -1,6 +1,6 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 import { Link } from '@mui/material';
-import { navToLoc } from './util';
+import { navToLoc } from "./util.js";
 export default function PairLink({ locString, model, }) {
     return (_jsx(Link, { onClick: event => {
             event.preventDefault();

package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts

@@ -1,4 +1,4 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory.ts';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function SupplementaryAlignments(props: {
     tag: string;

package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.js

@@ -1,8 +1,8 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import { getEnv, getSession } from '@jbrowse/core/util';
-import LaunchBreakpointSplitViewPanel from './LaunchSupplementaryAlignmentBreakpointSplitViewPanel';
-import SupplementaryAlignmentsLocStrings from './SupplementaryAlignmentsLocStrings';
+import LaunchBreakpointSplitViewPanel from "./LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js";
+import SupplementaryAlignmentsLocStrings from "./SupplementaryAlignmentsLocStrings.js";
 export default function SupplementaryAlignments(props) {
     const { model, tag, feature } = props;
     const session = getSession(model);

package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts

@@ -1,4 +1,4 @@
-import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory.ts';
 export default function SupplementaryAlignmentsLocStrings({ tag, model, }: {
     tag: string;
     model: AlignmentFeatureWidgetModel;

package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js

@@ -1,7 +1,8 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { toLocale } from '@jbrowse/core/util';
 import { Link, Typography } from '@mui/material';
-import { getLengthOnRef } from '../MismatchParser';
-import { navToLoc } from './util';
+import { navToLoc } from "./util.js";
+import { getLengthOnRef } from "../MismatchParser/index.js";
 export default function SupplementaryAlignmentsLocStrings({ tag, model, }) {
     return (_jsxs("div", { children: [_jsx(Typography, { children: "List of supplementary alignment locations" }), _jsx("ul", { children: tag
                     .split(';')
@@ -15,8 +16,8 @@ export default function SupplementaryAlignmentsLocStrings({ tag, model, }) {
                     const sp = start - extra;
                     const ep = end + extra;
                     const locString = `${saRef}:${Math.max(1, sp)}-${ep}`;
-                    const displayStart = start.toLocaleString('en-US');
-                    const displayEnd = end.toLocaleString('en-US');
+                    const displayStart = toLocale(start);
+                    const displayEnd = toLocale(end);
                     const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
                     return (_jsx("li", { children: _jsx(Link, { href: "#", onClick: async (event) => {
                                 event.preventDefault();

package/esm/AlignmentsFeatureDetail/configSchema.d.ts

@@ -1 +1 @@
-export declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export declare const configSchema: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;

package/esm/AlignmentsFeatureDetail/getSAFeatures.d.ts

@@ -3,7 +3,7 @@ import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export interface ReducedFeature {
     refName: string;
     start: number;
-    clipPos: number;
+    clipLengthAtStartOfRead: number;
     end: number;
     strand: number;
     seqLength: number;

package/esm/AlignmentsFeatureDetail/getSAFeatures.js

@@ -1,33 +1,34 @@
 import { getSession } from '@jbrowse/core/util';
-import { featurizeSA, getClip, getLengthSansClipping } from '../MismatchParser';
+import { featurizeSA, getClip, getLengthSansClipping, } from "../MismatchParser/index.js";
 export async function getSAFeatures({ view, feature, }) {
-    var _a;
     const { assemblyManager } = getSession(view);
     const cigar = feature.get('CIGAR');
     const origStrand = feature.get('strand');
-    const SA = ((_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a.SA) || '';
+    const SA = feature.get('tags')?.SA || '';
     const readName = feature.get('name');
-    const clipPos = getClip(cigar, 1);
+    const clipLengthAtStartOfRead = getClip(cigar, 1);
     const assembly = await assemblyManager.waitForAssembly(view.assemblyNames[0]);
     if (!assembly) {
         throw new Error('assembly not found');
     }
     const suppAlns = featurizeSA(SA, feature.id(), origStrand, readName, true);
-    const feat = feature.toJSON();
-    feat.clipPos = clipPos;
-    feat.strand = 1;
-    feat.mate = {
-        refName: readName,
-        start: clipPos,
-        end: clipPos + getLengthSansClipping(cigar),
+    const feat = {
+        ...feature.toJSON(),
+        clipLengthAtStartOfRead,
+        strand: 1,
+        mate: {
+            refName: readName,
+            start: clipLengthAtStartOfRead,
+            end: clipLengthAtStartOfRead + getLengthSansClipping(cigar),
+        },
     };
     const features = [feat, ...suppAlns];
-    for (const [idx, f] of features.entries()) {
-        f.refName = assembly.getCanonicalRefName(f.refName) || f.refName;
-        f.syntenyId = idx;
-        f.mate.syntenyId = idx;
+    for (const [i, feature_] of features.entries()) {
+        const f = feature_;
+        f.refName = assembly.getCanonicalRefName2(f.refName);
+        f.syntenyId = i;
+        f.mate.syntenyId = i;
         f.mate.uniqueId = `${f.uniqueId}_mate`;
     }
-    features.sort((a, b) => a.clipPos - b.clipPos);
-    return features;
+    return features.toSorted((a, b) => a.clipLengthAtStartOfRead - b.clipLengthAtStartOfRead);
 }

package/esm/AlignmentsFeatureDetail/index.js

@@ -1,13 +1,13 @@
 import { lazy } from 'react';
 import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType';
-import { configSchema } from './configSchema';
-import { stateModelFactory } from './stateModelFactory';
+import { configSchema } from "./configSchema.js";
+import { stateModelFactory } from "./stateModelFactory.js";
 export default function AlignmentFeatureDetailsF(pluginManager) {
     pluginManager.addWidgetType(() => new WidgetType({
         name: 'AlignmentsFeatureWidget',
         heading: 'Feature details',
         configSchema: configSchema,
         stateModel: stateModelFactory(pluginManager),
-        ReactComponent: lazy(() => import('./AlignmentsFeatureDetail')),
+        ReactComponent: lazy(() => import("./AlignmentsFeatureDetail.js")),
     }));
 }

package/esm/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts

@@ -1,4 +1,4 @@
-import type { ReducedFeature } from './getSAFeatures';
+import type { ReducedFeature } from './getSAFeatures.ts';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function getBreakpointSplitView({ f1, f2, view, }: {
     f1: ReducedFeature;
@@ -8,12 +8,11 @@ export declare function getBreakpointSplitView({ f1, f2, view, }: {
     type: string;
     views: {
         type: string;
-        displayedRegions: {
-            start: number;
-            end: number;
-            refName: string;
-            assemblyName: string;
-        }[];
+        displayedRegions: [import("@jbrowse/core/assemblyManager/assembly").BasicRegion & {
+            assemblyName?: string;
+        }, import("@jbrowse/core/assemblyManager/assembly").BasicRegion & {
+            assemblyName?: string;
+        }];
         hideHeader: boolean;
         bpPerPx: number;
         offsetPx: number;

package/esm/AlignmentsFeatureDetail/launchBreakpointSplitView.js

@@ -1,4 +1,5 @@
 import { getSession } from '@jbrowse/core/util';
+import { splitRegionAtPosition } from '@jbrowse/sv-core';
 export function getBreakpointSplitView({ f1, f2, view, }) {
     const { assemblyName } = view.displayedRegions[0];
     const { assemblyManager } = getSession(view);
@@ -14,14 +15,10 @@ export function getBreakpointSplitView({ f1, f2, view, }) {
     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 topMarkedRegion = splitRegionAtPosition(topRegion, s);
+    const bottomMarkedRegion = splitRegionAtPosition(bottomRegion, e);
     const bpPerPx = 10;
     return {
         type: 'BreakpointSplitView',

package/esm/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -1,17 +1,17 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
-import type { 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<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    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>>;
-    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+import type { Instance } from '@jbrowse/mobx-state-tree';
+export declare function stateModelFactory(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    featureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
+    formattedFields: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
+    view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    track: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    trackId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    trackType: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    maxDepth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{}, {
         showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
@@ -34,10 +34,10 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
+    descriptions: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 } & {
-    type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
     error: unknown;
 } & {
@@ -50,18 +50,18 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     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<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
-    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>>;
-    sequenceFeatureDetails: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{}, {
+} & Partial<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
+    featureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
+    formattedFields: import("@jbrowse/mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("@jbrowse/mobx-state-tree").IType<import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat, import("node_modules/@jbrowse/core/src/BaseFeatureWidget/types").MaybeSerializedFeat>;
+    view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    track: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
+    trackId: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    trackType: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    maxDepth: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<number>>;
+    sequenceFeatureDetails: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").IModelType<{}, {
         showCoordinatesSetting: string;
         intronBp: number;
         upDownBp: number;
@@ -84,20 +84,20 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         readonly hasExonOrCDS: boolean | undefined;
     } & {
         afterAttach(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
-}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
-    type: "BaseFeatureWidget";
+    }, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>, [undefined]>;
+    descriptions: import("@jbrowse/mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
+}>> & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & import("@jbrowse/mobx-state-tree")._NotCustomized, {
     id: string;
-    track: import("mobx-state-tree").ReferenceIdentifier | undefined;
-    view: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    type: "BaseFeatureWidget";
+    track: import("@jbrowse/mobx-state-tree").ReferenceIdentifier | undefined;
+    view: import("@jbrowse/mobx-state-tree").ReferenceIdentifier | undefined;
     trackId: string | undefined;
-    trackType: string | undefined;
     maxDepth: number | undefined;
-    sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
+    sequenceFeatureDetails: import("@jbrowse/mobx-state-tree").ModelSnapshotType<{}>;
     formattedFields: any;
+    trackType: string | undefined;
     descriptions: Record<string, unknown> | undefined;
     finalizedFeatureData: any;
-} & import("mobx-state-tree")._NotCustomized>;
+} & import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;
 export type AlignmentFeatureWidgetModel = Instance<AlignmentFeatureWidgetStateModel>;

package/esm/AlignmentsFeatureDetail/stateModelFactory.js

@@ -1,5 +1,5 @@
 import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
-import { types } from 'mobx-state-tree';
+import { types } from '@jbrowse/mobx-state-tree';
 export function stateModelFactory(pluginManager) {
     return types.compose(baseModelFactory(pluginManager), types.model('AlignmentsFeatureWidget', {
         type: types.literal('AlignmentsFeatureWidget'),

package/esm/AlignmentsFeatureDetail/util.d.ts

@@ -1,4 +1,4 @@
-import type { IAnyStateTreeNode } from 'mobx-state-tree';
+import type { IAnyStateTreeNode } from '@jbrowse/mobx-state-tree';
 export declare function getTag(tag: string, feat: {
     tags?: Record<string, unknown>;
     [key: string]: unknown;

package/esm/AlignmentsFeatureDetail/util.js

@@ -1,7 +1,6 @@
 import { getSession } from '@jbrowse/core/util';
 export function getTag(tag, feat) {
-    var _a;
-    return ((_a = feat.tags) === null || _a === void 0 ? void 0 : _a[tag]) || feat[tag];
+    return feat.tags?.[tag] || feat[tag];
 }
 export async function navToLoc(locString, model) {
     const session = getSession(model);