@jbrowse/plugin-variants 2.17.0 → 3.0.0

package/dist/VcfTabixAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/extensionPoints.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function ExtensionPointsF(pluginManager: PluginManager): void;

package/dist/extensionPoints.js

@@ -1,51 +1,39 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = ExtensionPointsF;
+const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 function ExtensionPointsF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
-            const regexGuess = /\.vcf\.b?gz$/i;
-            const adapterName = 'VcfTabixAdapter';
             const fileName = (0, tracks_1.getFileName)(file);
             const indexName = index && (0, tracks_1.getFileName)(index);
-            const obj = {
-                type: adapterName,
-                vcfGzLocation: file,
-                index: {
-                    location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
-                    indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
-                },
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
+            if ((0, util_1.testAdapter)(fileName, /\.vcf\.b?gz$/i, adapterHint, 'VcfTabixAdapter')) {
+                return {
+                    type: 'VcfTabixAdapter',
+                    vcfGzLocation: file,
+                    index: {
+                        location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
+                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
+                    },
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.vcf(\.gz)?$/i, adapterHint, 'VcfAdapter')) {
+                return {
+                    type: 'VcfAdapter',
+                    vcfLocation: file,
+                };
             }
-            if (adapterHint === adapterName) {
-                return obj;
+            else {
+                return adapterGuesser(file, index, adapterHint);
             }
-            return adapterGuesser(file, index, adapterHint);
         };
     });
     pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {
         return (adapterName) => {
-            if (adapterName === 'VcfTabixAdapter' || adapterName === 'VcfAdapter') {
-                return 'VariantTrack';
-            }
-            return trackTypeGuesser(adapterName);
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const regexGuess = /\.vcf$/i;
-            const adapterName = 'VcfAdapter';
-            const fileName = (0, tracks_1.getFileName)(file);
-            if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                return {
-                    type: adapterName,
-                    vcfLocation: file,
-                };
-            }
-            return adapterGuesser(file, index, adapterHint);
+            return ['VcfTabixAdapter', 'VcfAdapter'].includes(adapterName)
+                ? 'VariantTrack'
+                : trackTypeGuesser(adapterName);
         };
     });
 }

package/dist/getMultiVariantFeaturesAutorun.d.ts

@@ -0,0 +1,16 @@
+import type { SampleInfo, Source } from './types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
+export declare function getMultiVariantFeaturesAutorun(self: {
+    configuration: AnyConfigurationModel;
+    adapterConfig: AnyConfigurationModel;
+    sources?: Source[];
+    minorAlleleFrequencyFilter: number;
+    statsReadyAndRegionNotTooLarge: boolean;
+    adapterProps: () => Record<string, unknown>;
+    setError: (error: unknown) => void;
+    setFeatures: (f: Feature[]) => void;
+    setMessage: (str: string) => void;
+    setHasPhased: (arg: boolean) => void;
+    setSampleInfo: (arg: Record<string, SampleInfo>) => void;
+}): void;

package/dist/getMultiVariantFeaturesAutorun.js

@@ -0,0 +1,41 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getMultiVariantFeaturesAutorun = getMultiVariantFeaturesAutorun;
+const util_1 = require("@jbrowse/core/util");
+const aborting_1 = require("@jbrowse/core/util/aborting");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
+function getMultiVariantFeaturesAutorun(self) {
+    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
+        try {
+            const view = (0, util_1.getContainingView)(self);
+            if (!view.initialized || !self.statsReadyAndRegionNotTooLarge) {
+                return;
+            }
+            const { rpcManager } = (0, util_1.getSession)(self);
+            const { sources, minorAlleleFrequencyFilter, adapterConfig } = self;
+            if (sources) {
+                const sessionId = (0, tracks_1.getRpcSessionId)(self);
+                const { sampleInfo, hasPhased, features } = (await rpcManager.call(sessionId, 'MultiVariantGetSimplifiedFeatures', {
+                    regions: view.dynamicBlocks.contentBlocks,
+                    sources,
+                    minorAlleleFrequencyFilter,
+                    sessionId,
+                    adapterConfig,
+                }));
+                if ((0, mobx_state_tree_1.isAlive)(self)) {
+                    self.setHasPhased(hasPhased);
+                    self.setSampleInfo(sampleInfo);
+                    self.setFeatures(features.map(f => new util_1.SimpleFeature(f)));
+                }
+            }
+        }
+        catch (e) {
+            console.error(e);
+            if (!(0, aborting_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(self)) {
+                (0, util_1.getSession)(self).notifyError(`${e}`, e);
+            }
+        }
+    }, { delay: 1000 }));
+}

package/dist/getMultiVariantSourcesAutorun.d.ts

@@ -0,0 +1,11 @@
+import type { Source } from './types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function getMultiVariantSourcesAutorun(self: {
+    configuration: AnyConfigurationModel;
+    adapterConfig: AnyConfigurationModel;
+    adapterProps: () => Record<string, unknown>;
+    setSourcesLoading: (aborter: string) => void;
+    setError: (error: unknown) => void;
+    setMessage: (str: string) => void;
+    setSources: (sources: Source[]) => void;
+}): void;

package/dist/getMultiVariantSourcesAutorun.js

@@ -0,0 +1,37 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getMultiVariantSourcesAutorun = getMultiVariantSourcesAutorun;
+const util_1 = require("@jbrowse/core/util");
+const aborting_1 = require("@jbrowse/core/util/aborting");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
+function getMultiVariantSourcesAutorun(self) {
+    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
+        try {
+            const view = (0, util_1.getContainingView)(self);
+            if (!view.initialized) {
+                return;
+            }
+            const { rpcManager } = (0, util_1.getSession)(self);
+            const { adapterConfig } = self;
+            const token = (0, stopToken_1.createStopToken)();
+            self.setSourcesLoading(token);
+            const sessionId = (0, tracks_1.getRpcSessionId)(self);
+            const sources = (await rpcManager.call(sessionId, 'MultiVariantGetSources', {
+                sessionId,
+                adapterConfig,
+            }));
+            if ((0, mobx_state_tree_1.isAlive)(self)) {
+                self.setSources(sources);
+            }
+        }
+        catch (e) {
+            if (!(0, aborting_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(self)) {
+                console.error(e);
+                (0, util_1.getSession)(self).notifyError(`${e}`, e);
+            }
+        }
+    }, { delay: 1000 }));
+}

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class VariantsPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -4,15 +4,22 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.VcfFeature = void 0;
-const VcfAdapter_1 = __importDefault(require("./VcfAdapter"));
-const VcfTabixAdapter_1 = __importDefault(require("./VcfTabixAdapter"));
-const extensionPoints_1 = __importDefault(require("./extensionPoints"));
-const VariantTrack_1 = __importDefault(require("./VariantTrack"));
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
 const ChordVariantDisplay_1 = __importDefault(require("./ChordVariantDisplay"));
 const LinearVariantDisplay_1 = __importDefault(require("./LinearVariantDisplay"));
+const MultiLinearVariantDisplay_1 = __importDefault(require("./MultiLinearVariantDisplay"));
+const MultiLinearVariantMatrixDisplay_1 = __importDefault(require("./MultiLinearVariantMatrixDisplay"));
+const MultiLinearVariantMatrixRenderer_1 = __importDefault(require("./MultiLinearVariantMatrixRenderer"));
+const MultiLinearVariantRenderer_1 = __importDefault(require("./MultiLinearVariantRenderer"));
 const StructuralVariantChordRenderer_1 = __importDefault(require("./StructuralVariantChordRenderer"));
 const VariantFeatureWidget_1 = __importDefault(require("./VariantFeatureWidget"));
+const MultiVariantGetGenotypeMatrix_1 = require("./VariantRPC/MultiVariantGetGenotypeMatrix");
+const MultiVariantGetSimplifiedFeatures_1 = require("./VariantRPC/MultiVariantGetSimplifiedFeatures");
+const MultiVariantGetSources_1 = require("./VariantRPC/MultiVariantGetSources");
+const VariantTrack_1 = __importDefault(require("./VariantTrack"));
+const VcfAdapter_1 = __importDefault(require("./VcfAdapter"));
+const VcfTabixAdapter_1 = __importDefault(require("./VcfTabixAdapter"));
+const extensionPoints_1 = __importDefault(require("./extensionPoints"));
 class VariantsPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
@@ -25,8 +32,15 @@ class VariantsPlugin extends Plugin_1.default {
         (0, VariantTrack_1.default)(pluginManager);
         (0, extensionPoints_1.default)(pluginManager);
         (0, LinearVariantDisplay_1.default)(pluginManager);
+        (0, MultiLinearVariantMatrixDisplay_1.default)(pluginManager);
+        (0, MultiLinearVariantDisplay_1.default)(pluginManager);
+        (0, MultiLinearVariantRenderer_1.default)(pluginManager);
+        (0, MultiLinearVariantMatrixRenderer_1.default)(pluginManager);
         (0, StructuralVariantChordRenderer_1.default)(pluginManager);
         (0, ChordVariantDisplay_1.default)(pluginManager);
+        pluginManager.addRpcMethod(() => new MultiVariantGetSources_1.MultiVariantGetSources(pluginManager));
+        pluginManager.addRpcMethod(() => new MultiVariantGetGenotypeMatrix_1.MultiVariantGetGenotypeMatrix(pluginManager));
+        pluginManager.addRpcMethod(() => new MultiVariantGetSimplifiedFeatures_1.MultiVariantGetSimplifiedFeatures(pluginManager));
     }
 }
 exports.default = VariantsPlugin;

package/dist/shared/BulkEditPanel.d.ts

@@ -0,0 +1,5 @@
+import type { Source } from '../types';
+export default function BulkEditPanel({ onClose, currLayout, }: {
+    currLayout: Source[];
+    onClose: (arg?: Source[]) => void;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/BulkEditPanel.js

@@ -0,0 +1,84 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = BulkEditPanel;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()({
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+});
+function BulkEditPanel({ onClose, currLayout, }) {
+    const { classes } = useStyles();
+    const [val, setVal] = (0, react_1.useState)('');
+    const [error, setError] = (0, react_1.useState)();
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Paste CSV or TSV. If a header column is present. First line is a header. If a column called \"name\" is present, it uses that to connect to IDs in the table, otherwise it uses the first column no." }), error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null, (0, jsx_runtime_1.jsx)(material_1.TextField, { variant: "outlined", multiline: true, minRows: 5, placeholder: 'name,population\nHG00098,GBR\nHG00101,GBR\nHG00459,CHS\n...', maxRows: 10, fullWidth: true, value: val, onChange: event => {
+                            setVal(event.target.value);
+                        }, slotProps: {
+                            input: {
+                                classes: {
+                                    input: classes.textAreaFont,
+                                },
+                            },
+                        } })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                            const lines = val
+                                .split('\n')
+                                .map(f => f.trim())
+                                .filter(f => !!f);
+                            const fields = lines[0].split(/[,\t]/gm);
+                            if (fields.includes('name')) {
+                                setError('');
+                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
+                                const newData = Object.fromEntries(lines.slice(1).map(line => {
+                                    const cols = line.split(/[,\t]/gm);
+                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
+                                    return [
+                                        newRecord.name,
+                                        {
+                                            ...newRecord,
+                                            ...oldLayout[newRecord.name],
+                                        },
+                                    ];
+                                }));
+                                onClose(currLayout.map(record => ({
+                                    ...record,
+                                    ...newData[record.name],
+                                })));
+                            }
+                            else {
+                                setError(new Error('No "name" column found on line 1'));
+                            }
+                        }, children: "Update rows" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
+                            const lines = val
+                                .split('\n')
+                                .map(f => f.trim())
+                                .filter(f => !!f);
+                            const fields = lines[0].split(/[,\t]/gm);
+                            if (fields.includes('name')) {
+                                setError('');
+                                const oldLayout = Object.fromEntries(currLayout.map(record => [record.name, record]));
+                                const newData = Object.fromEntries(lines.slice(1).map(line => {
+                                    const cols = line.split(/[,\t]/gm);
+                                    const newRecord = Object.fromEntries(cols.map((col, idx) => [fields[idx], col]));
+                                    return [
+                                        newRecord.name,
+                                        {
+                                            ...newRecord,
+                                            ...oldLayout[newRecord.name],
+                                        },
+                                    ];
+                                }));
+                                onClose(currLayout.map(record => ({
+                                    ...newData[record.name],
+                                })));
+                            }
+                            else {
+                                setError(new Error('No "name" column found on line 1'));
+                            }
+                        }, children: "Replace rows" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "inherit", onClick: () => {
+                            onClose();
+                        }, children: "Cancel" })] })] }));
+}

package/dist/shared/ClusterDialog.d.ts

@@ -0,0 +1,11 @@
+import type { Source } from '../types';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export default function ClusterDialog({ model, handleClose, }: {
+    model: {
+        sources?: Source[];
+        minorAlleleFrequencyFilter?: number;
+        adapterConfig: AnyConfigurationModel;
+        setLayout: (arg: Source[]) => void;
+    };
+    handleClose: () => void;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/shared/ClusterDialog.js

@@ -0,0 +1,109 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = ClusterDialog;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const material_1 = require("@mui/material");
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+const file_saver_1 = require("file-saver");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    textAreaFont: {
+        fontFamily: 'Courier New',
+    },
+    mgap: {
+        display: 'flex',
+        flexDirection: 'column',
+        gap: theme.spacing(4),
+    },
+}));
+function ClusterDialog({ model, handleClose, }) {
+    const { classes } = useStyles();
+    const [results, setResults] = (0, react_1.useState)();
+    const [error, setError] = (0, react_1.useState)();
+    const [paste, setPaste] = (0, react_1.useState)('');
+    (0, react_1.useEffect)(() => {
+        ;
+        (async () => {
+            try {
+                setError(undefined);
+                const view = (0, util_1.getContainingView)(model);
+                if (!view.initialized) {
+                    return;
+                }
+                const { rpcManager } = (0, util_1.getSession)(model);
+                const { sources, minorAlleleFrequencyFilter, adapterConfig } = model;
+                const sessionId = (0, tracks_1.getRpcSessionId)(model);
+                const ret = (await rpcManager.call(sessionId, 'MultiVariantGetGenotypeMatrix', {
+                    regions: view.dynamicBlocks.contentBlocks,
+                    sources,
+                    minorAlleleFrequencyFilter,
+                    sessionId,
+                    adapterConfig,
+                }));
+                const entries = Object.values(ret);
+                const keys = Object.keys(ret);
+                const text = `try(library(fastcluster), silent=TRUE)
+inputMatrix<-matrix(c(${entries.map(val => val.genotypes.join(',')).join(',\n')}
+),nrow=${entries.length},byrow=TRUE)
+rownames(inputMatrix)<-c(${keys.map(key => `'${key}'`).join(',')})
+resultClusters<-hclust(dist(inputMatrix), method='single')
+cat(resultClusters$order,sep='\\n')`;
+                setResults(text);
+            }
+            catch (e) {
+                if (!(0, util_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(model)) {
+                    console.error(e);
+                    setError(e);
+                }
+            }
+        })();
+    }, [model]);
+    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, title: "Cluster by genotype", onClose: handleClose, children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: (0, jsx_runtime_1.jsxs)("div", { className: classes.mgap, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "This page will produce an R script that will perform hierarchical clustering on the visible genotype data using `hclust`." }), (0, jsx_runtime_1.jsx)(material_1.Typography, { children: "You can then paste the results in this form to specify the row ordering." }), results ? ((0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsxs)("div", { children: ["Step 1:", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                                            (0, file_saver_1.saveAs)(new Blob([results || ''], {
+                                                type: 'text/plain;charset=utf-8',
+                                            }), 'cluster.R');
+                                        }, children: "Download Rscript" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                                            (0, copy_to_clipboard_1.default)(results || '');
+                                        }, children: "Copy Rscript to clipboard" }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Step 2. Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
+                                                setPaste(event.target.value);
+                                            }, slotProps: {
+                                                input: {
+                                                    classes: {
+                                                        input: classes.textAreaFont,
+                                                    },
+                                                },
+                                            } }) })] }) })) : ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { variant: "h6", title: "Generating genotype matrix" })), error ? (0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error }) : null] }) }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { disabled: !results, variant: "contained", onClick: () => {
+                            const { sources } = model;
+                            if (sources) {
+                                try {
+                                    model.setLayout(paste
+                                        .split('\n')
+                                        .map(t => t.trim())
+                                        .filter(f => !!f)
+                                        .map(r => +r)
+                                        .map(idx => {
+                                        const ret = sources[idx - 1];
+                                        if (!ret) {
+                                            throw new Error(`out of bounds at ${idx}`);
+                                        }
+                                        return ret;
+                                    }));
+                                }
+                                catch (e) {
+                                    console.error(e);
+                                    setError(e);
+                                }
+                            }
+                            handleClose();
+                        }, children: "Apply clustering" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" })] })] }));
+}

package/dist/shared/ColorLegend.d.ts

@@ -0,0 +1,10 @@
+import type { Source } from '../types';
+declare const ColorLegend: ({ model, labelWidth, }: {
+    model: {
+        canDisplayLabels: boolean;
+        rowHeight: number;
+        sources?: Source[];
+    };
+    labelWidth: number;
+}) => import("react/jsx-runtime").JSX.Element | null;
+export default ColorLegend;

package/dist/shared/ColorLegend.js

@@ -0,0 +1,22 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
+const RectBg_1 = __importDefault(require("./RectBg"));
+const ColorLegend = (0, mobx_react_1.observer)(function ({ model, labelWidth, }) {
+    const { canDisplayLabels, rowHeight, sources } = model;
+    const svgFontSize = (0, util_1.clamp)(rowHeight, 8, 12);
+    const colorBoxWidth = 15;
+    const hasColors = sources === null || sources === void 0 ? void 0 : sources.some(s => s.color);
+    const legendWidth = labelWidth + (hasColors ? colorBoxWidth + 5 : 0);
+    return sources ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [canDisplayLabels ? ((0, jsx_runtime_1.jsx)(RectBg_1.default, { y: 0, x: 0, width: legendWidth, height: (sources.length + 0.25) * rowHeight })) : null, sources.map((source, idx) => {
+                const { color, name, label } = source;
+                return ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [color ? ((0, jsx_runtime_1.jsx)(RectBg_1.default, { y: idx * rowHeight, x: 0, width: colorBoxWidth + 0.5, height: rowHeight + 0.5, color: color })) : null, canDisplayLabels ? ((0, jsx_runtime_1.jsx)("text", { y: idx * rowHeight + svgFontSize, x: color ? colorBoxWidth + 2 : 0, fontSize: svgFontSize, children: label || name })) : null] }, `${label}-${idx}`));
+            })] })) : null;
+});
+exports.default = ColorLegend;

package/dist/shared/HelpfulTips.d.ts

@@ -0,0 +1 @@
+export default function HelpfulTips(): import("react/jsx-runtime").JSX.Element;

package/dist/shared/HelpfulTips.js

@@ -0,0 +1,7 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = HelpfulTips;
+const jsx_runtime_1 = require("react/jsx-runtime");
+function HelpfulTips() {
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: ["Helpful tips", (0, jsx_runtime_1.jsxs)("ul", { children: [(0, jsx_runtime_1.jsx)("li", { children: "You can select rows in the table with the checkboxes" }), (0, jsx_runtime_1.jsx)("li", { children: "Multi-select is enabled with shift-click and control-click" }), (0, jsx_runtime_1.jsx)("li", { children: "The \"Move selected items up/down\" can re-arrange subtracks" }), (0, jsx_runtime_1.jsx)("li", { children: "Sorting the data grid itself can also re-arrange subtracks" }), (0, jsx_runtime_1.jsx)("li", { children: "Changes are applied when you hit Submit" }), (0, jsx_runtime_1.jsx)("li", { children: "You can click and drag the dialog box to move it on the screen" }), (0, jsx_runtime_1.jsx)("li", { children: "Columns in the table can be hidden using a vertical '...' menu on the right side of each column" })] })] }));
+}

package/dist/shared/LegendBar.d.ts

@@ -0,0 +1,18 @@
+import type { Source } from '../types';
+interface ReducedModel {
+    scrollTop: number;
+    totalHeight: number;
+    rowHeight: number;
+    lineZoneHeight?: number;
+    sources?: Source[];
+    canDisplayLabels: boolean;
+    height: number;
+    samplePloidy?: Record<string, number>;
+    id: string;
+}
+export declare const LegendBar: (props: {
+    model: ReducedModel;
+    orientation?: string;
+    exportSVG?: boolean;
+}) => import("react/jsx-runtime").JSX.Element | null;
+export default LegendBar;

package/dist/shared/LegendBar.js

@@ -0,0 +1,32 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.LegendBar = void 0;
+const jsx_runtime_1 = require("react/jsx-runtime");
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
+const ColorLegend_1 = __importDefault(require("./ColorLegend"));
+const Wrapper = (0, mobx_react_1.observer)(function ({ children, model, exportSVG, }) {
+    const { id, scrollTop, height } = model;
+    const clipid = `legend-${id}`;
+    return exportSVG ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: clipid, children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: 1000, height: height }) }) }), (0, jsx_runtime_1.jsx)("g", { clipPath: `url(#${clipid})`, children: (0, jsx_runtime_1.jsx)("g", { transform: `translate(0,${-scrollTop})`, children: children }) })] })) : ((0, jsx_runtime_1.jsx)("svg", { style: {
+            position: 'absolute',
+            top: 0,
+            left: 0,
+            zIndex: 100,
+            pointerEvents: 'none',
+            height: model.totalHeight,
+            width: (0, util_1.getContainingView)(model).width,
+        }, children: children }));
+});
+exports.LegendBar = (0, mobx_react_1.observer)(function (props) {
+    const { model } = props;
+    const { canDisplayLabels, rowHeight, sources } = model;
+    const svgFontSize = (0, util_1.clamp)(rowHeight, 8, 12);
+    return sources ? ((0, jsx_runtime_1.jsx)(Wrapper, { ...props, children: (0, jsx_runtime_1.jsx)(ColorLegend_1.default, { model: model, labelWidth: (0, util_1.max)(sources
+                .map(s => (0, util_1.measureText)(s.label, svgFontSize) + 10)
+                .map(width => (canDisplayLabels ? width : 20)), 0) }) })) : null;
+});
+exports.default = exports.LegendBar;

package/dist/shared/MAFFilterDialog.d.ts

@@ -0,0 +1,8 @@
+declare const MAFFilterDialog: ({ model, handleClose, }: {
+    model: {
+        minorAlleleFrequencyFilter?: number;
+        setMafFilter: (arg: number) => void;
+    };
+    handleClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element;
+export default MAFFilterDialog;

package/dist/shared/MAFFilterDialog.js

@@ -0,0 +1,28 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()({
+    root: {
+        width: 500,
+    },
+});
+const MAFFilterDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
+    const { minorAlleleFrequencyFilter = '' } = model;
+    const { classes } = useStyles();
+    const [maf, setMaf] = (0, react_1.useState)(`${minorAlleleFrequencyFilter}`);
+    return ((0, jsx_runtime_1.jsx)(material_1.Dialog, { open: true, onClose: handleClose, title: "Set minor allele frequency (MAF)", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { className: classes.root, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Set minor allele frequency cutoff track. This will filter out rare variants that might not contribute to meaningful large scale patterns" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: maf, autoFocus: true, placeholder: "Enter MAF", onChange: event => {
+                        setMaf(event.target.value);
+                    } }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
+                                if (!Number.isNaN(+maf)) {
+                                    model.setMafFilter(+maf);
+                                }
+                                handleClose();
+                            }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                                handleClose();
+                            }, children: "Cancel" })] })] }) }));
+});
+exports.default = MAFFilterDialog;