jbrowse-plugin-mafviewer 1.0.8 → 1.1.1

package/dist/LinearMafDisplay/stateModel.js

@@ -1,10 +1,13 @@
-import { types } from 'mobx-state-tree';
 import { ConfigurationReference, getConf, } from '@jbrowse/core/configuration';
 import { getEnv, getSession } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
+import { ascending } from 'd3-array';
+import { cluster, hierarchy } from 'd3-hierarchy';
+import { autorun } from 'mobx';
+import { addDisposer, isAlive, types } from 'mobx-state-tree';
 import SetRowHeightDialog from './components/SetRowHeight';
-function isStrs(array) {
-    return typeof array[0] === 'string';
-}
+import { maxLength, setBrLength, } from './types';
+import { normalize } from '../util';
 /**
  * #stateModel LinearMafDisplay
  * extends LinearBasicDisplay
@@ -38,12 +41,28 @@ export default function stateModelFactory(configSchema, pluginManager) {
          * #property
          */
         mismatchRendering: true,
+        /**
+         * #property
+         */
+        showBranchLen: false,
+        /**
+         * #property
+         */
+        treeAreaWidth: 80,
     }))
         .volatile(() => ({
         /**
          * #volatile
          */
         prefersOffset: true,
+        /**
+         * #volatile
+         */
+        volatileSamples: [],
+        /**
+         * #volatile
+         */
+        tree: undefined,
     }))
         .actions(self => ({
         /**
@@ -70,17 +89,15 @@ export default function stateModelFactory(configSchema, pluginManager) {
         setMismatchRendering(f) {
             self.mismatchRendering = f;
         },
-    }))
-        .views(self => ({
         /**
-         * #getter
+         * #action
          */
-        get samples() {
-            const r = self.adapterConfig.samples;
-            return isStrs(r)
-                ? r.map(elt => ({ id: elt, label: elt, color: undefined }))
-                : r;
+        setSamples({ samples, tree }) {
+            self.volatileSamples = samples;
+            self.tree = tree;
         },
+    }))
+        .views(self => ({
         /**
          * #getter
          */
@@ -98,14 +115,74 @@ export default function stateModelFactory(configSchema, pluginManager) {
                 type: 'LinearMafRenderer',
             }, getEnv(self));
         },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         */
+        get root() {
+            return self.tree
+                ? hierarchy(self.tree, d => d.children)
+                    // todo: investigate whether needed, typescript says children always true
+                    .sum(d => (d.children ? 0 : 1))
+                    .sort((a, b) => ascending(a.data.length || 1, b.data.length || 1))
+                : undefined;
+        },
+    }))
+        .views(self => ({
+        /**
+         * #getter
+         * generates a new tree that is clustered with x,y positions
+         */
+        get hierarchy() {
+            const r = self.root;
+            if (r) {
+                const width = self.treeAreaWidth;
+                const clust = cluster()
+                    .size([this.totalHeight, width])
+                    .separation(() => 1);
+                clust(r);
+                setBrLength(r, (r.data.length = 0), width / maxLength(r));
+                return r;
+            }
+            else {
+                return undefined;
+            }
+        },
+        /**
+         * #getter
+         */
+        get samples() {
+            return this.rowNames ? normalize(this.rowNames) : self.volatileSamples;
+        },
+        /**
+         * #getter
+         */
+        get totalHeight() {
+            return this.samples.length * self.rowHeight;
+        },
+        /**
+         * #getter
+         */
+        get leaves() {
+            return self.root?.leaves();
+        },
+        /**
+         * #getter
+         */
+        get rowNames() {
+            return this.leaves?.map(n => n.data.name);
+        },
     }))
         .views(self => {
-        const { 
-        // eslint-disable-next-line @typescript-eslint/unbound-method
-        trackMenuItems: superTrackMenuItems, 
-        // eslint-disable-next-line @typescript-eslint/unbound-method
-        renderProps: superRenderProps, } = self;
+        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
         return {
+            /**
+             * #getter
+             */
+            get treeWidth() {
+                return self.hierarchy ? self.treeAreaWidth : 0;
+            },
             /**
              * #method
              */
@@ -159,8 +236,31 @@ export default function stateModelFactory(configSchema, pluginManager) {
             },
         };
     })
+        .actions(self => ({
+        afterCreate() {
+            addDisposer(self, autorun(async () => {
+                try {
+                    const { rpcManager } = getSession(self);
+                    const sessionId = getRpcSessionId(self);
+                    const results = (await rpcManager.call(sessionId, 'MafGetSamples', {
+                        sessionId,
+                        adapterConfig: self.adapterConfig,
+                        statusCallback: (message) => {
+                            if (isAlive(self)) {
+                                self.setMessage(message);
+                            }
+                        },
+                    }));
+                    self.setSamples(results);
+                }
+                catch (e) {
+                    console.error(e);
+                    getSession(self).notifyError(`${e}`, e);
+                }
+            }));
+        },
+    }))
         .actions(self => {
-        // eslint-disable-next-line @typescript-eslint/unbound-method
         const { renderSvg: superRenderSvg } = self;
         return {
             /**

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package/dist/LinearMafDisplay/types.d.ts

@@ -0,0 +1,17 @@
+import type { HierarchyNode } from 'd3-hierarchy';
+export interface NodeWithIds {
+    id: string;
+    name: string;
+    children: NodeWithIds[];
+    length?: number;
+    noTree?: boolean;
+}
+export interface NodeWithIdsAndLength {
+    id: string;
+    name: string;
+    children: NodeWithIdsAndLength[];
+    noTree?: boolean;
+    length: number;
+}
+export declare function maxLength(d: HierarchyNode<NodeWithIds>): number;
+export declare function setBrLength(d: HierarchyNode<NodeWithIds>, y0: number, k: number): void;

package/dist/LinearMafDisplay/types.js

@@ -0,0 +1,16 @@
+import { max } from 'd3-array';
+// basically same as maxLength from https://observablehq.com/@d3/tree-of-life
+export function maxLength(d) {
+    return ((d.data.length || 0) + (d.children ? max(d.children, maxLength) || 0 : 0));
+}
+// basically same as setRadius from https://observablehq.com/@d3/tree-of-life
+export function setBrLength(d, y0, k) {
+    // @ts-expect-error
+    d.len = (y0 += Math.max(d.data.length || 0, 0)) * k;
+    if (d.children) {
+        d.children.forEach(d => {
+            setBrLength(d, y0, k);
+        });
+    }
+}
+//# sourceMappingURL=types.js.map

package/dist/LinearMafDisplay/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/LinearMafDisplay/types.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAoB9B,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,CAA6B;IACrD,OAAO,CACL,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAC1E,CAAA;AACH,CAAC;AACD,6EAA6E;AAC7E,MAAM,UAAU,WAAW,CACzB,CAA6B,EAC7B,EAAU,EACV,CAAS;IAET,mBAAmB;IACnB,CAAC,CAAC,GAAG,GAAG,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;IAEnD,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;QACf,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACrB,WAAW,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,CAAA;QACvB,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC"}

package/dist/LinearMafRenderer/LinearMafRenderer.d.ts

@@ -25,12 +25,12 @@ export default class LinearMafRenderer extends FeatureRendererType {
         height: number;
         canvasRecordedData: any;
         features: Map<string, Feature>;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         width: number;
         height: number;
-        reactElement: React.JSX.Element;
+        reactElement: import("react/jsx-runtime").JSX.Element;
         features: Map<string, Feature>;
         html?: string;
     } | {
@@ -38,7 +38,7 @@ export default class LinearMafRenderer extends FeatureRendererType {
         height: number;
         imageData: any;
         features: Map<string, Feature>;
-        reactElement?: import("react").ReactElement;
+        reactElement?: React.ReactElement;
         html?: string;
     }>;
 }

package/dist/LinearMafRenderer/LinearMafRenderer.js

@@ -4,7 +4,7 @@ import { featureSpanPx, renderToAbstractCanvas, } from '@jbrowse/core/util';
 import { getColorBaseMap, getContrastBaseMap } from './util';
 function makeImageData({ ctx, renderArgs, }) {
     const { regions, bpPerPx, rowHeight, showAllLetters, theme: configTheme, mismatchRendering, samples, rowProportion, features, } = renderArgs;
-    const [region] = regions;
+    const region = regions[0];
     const h = rowHeight * rowProportion;
     const theme = createJBrowseTheme(configTheme);
     const colorForBase = getColorBaseMap(theme);
@@ -26,7 +26,7 @@ function makeImageData({ ctx, renderArgs, }) {
             const alignment = origAlignment.toLowerCase();
             const row = sampleToRowMap.get(sample);
             if (row === undefined) {
-                throw new Error(`unknown sample encountered: ${sample}`);
+                continue;
             }
             const t = rowHeight * row;
             // gaps
@@ -65,7 +65,7 @@ function makeImageData({ ctx, renderArgs, }) {
                 if (seq[i] !== '-') {
                     if (c !== '-') {
                         const l = leftPx + scale * o;
-                        if (seq[i] !== c) {
+                        if (seq[i] !== c && c !== ' ') {
                             ctx.fillStyle = mismatchRendering
                                 ? // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                                     (colorForBase[c] ?? 'black')
@@ -92,8 +92,10 @@ function makeImageData({ ctx, renderArgs, }) {
                         const offset = (scale - charSizeW) / 2 + 1;
                         const c = alignment[i];
                         if ((showAllLetters || seq[i] !== c) && c !== '-') {
-                            ctx.fillStyle = contrastForBase[c] ?? 'white';
-                            ctx.fillText(origAlignment[i], l + offset, hp2 + t + 3);
+                            ctx.fillStyle = mismatchRendering
+                                ? (contrastForBase[c] ?? 'white')
+                                : 'black';
+                            ctx.fillText(origAlignment[i] || '', l + offset, hp2 + t + 3);
                         }
                         o++;
                     }
@@ -112,7 +114,7 @@ function makeImageData({ ctx, renderArgs, }) {
             const alignment = origAlignment.toLowerCase();
             const row = sampleToRowMap.get(sample);
             if (row === undefined) {
-                throw new Error(`unknown sample encountered: ${sample}`);
+                continue;
             }
             const t = rowHeight * row;
             ctx.beginPath();
@@ -120,7 +122,7 @@ function makeImageData({ ctx, renderArgs, }) {
             for (let i = 0, o = 0; i < alignment.length; i++) {
                 let ins = '';
                 while (seq[i] === '-') {
-                    if (alignment[i] !== '-') {
+                    if (alignment[i] !== '-' && alignment[i] !== ' ') {
                         ins += alignment[i];
                     }
                     i++;
@@ -150,8 +152,8 @@ export default class LinearMafRenderer extends FeatureRendererType {
     }
     async render(renderProps) {
         const { regions, bpPerPx, samples, rowHeight } = renderProps;
-        const [region] = regions;
-        const height = samples.length * rowHeight + 100;
+        const region = regions[0];
+        const height = samples.length * (rowHeight + 1) + 100;
         const width = (region.end - region.start) / bpPerPx;
         const features = await this.getFeatures(renderProps);
         const res = await renderToAbstractCanvas(width, height, renderProps, ctx => {

package/dist/LinearMafRenderer/LinearMafRenderer.js.map

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package/dist/LinearMafRenderer/components/ReactComponent.js

@@ -1,6 +1,6 @@
+import React from 'react';
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
-import React from 'react';
 const LinearMafRendering = observer(function (props) {
     return React.createElement(PrerenderedCanvas, { ...props });
 });

package/dist/LinearMafRenderer/components/ReactComponent.js.map

@@ -1 +1 @@
-{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/components/ReactComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAA;AACpD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AACrC,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,KAG7C;IACC,OAAO,oBAAC,iBAAiB,OAAK,KAAK,GAAI,CAAA;AACzC,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}
+{"version":3,"file":"ReactComponent.js","sourceRoot":"","sources":["../../../src/LinearMafRenderer/components/ReactComponent.tsx"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAA;AACpD,OAAO,EAAE,QAAQ,EAAE,MAAM,YAAY,CAAA;AAErC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,UAAU,KAG7C;IACC,OAAO,oBAAC,iBAAiB,OAAK,KAAK,GAAI,CAAA;AACzC,CAAC,CAAC,CAAA;AAEF,eAAe,kBAAkB,CAAA"}

package/dist/LinearMafRenderer/index.js

@@ -1,6 +1,6 @@
-import configSchema from './configSchema';
 import LinearMafRenderer from './LinearMafRenderer';
 import ReactComponent from './components/ReactComponent';
+import configSchema from './configSchema';
 export default function LinearMafRendererF(pluginManager) {
     pluginManager.addRendererType(() => new LinearMafRenderer({
         name: 'LinearMafRenderer',

package/dist/LinearMafRenderer/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/index.ts"],"names":[],"mappings":"AACA,OAAO,YAAY,MAAM,gBAAgB,CAAA;AACzC,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,cAAc,MAAM,6BAA6B,CAAA;AAExD,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,iBAAiB,CAAC;QACpB,IAAI,EAAE,mBAAmB;QACzB,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/LinearMafRenderer/index.ts"],"names":[],"mappings":"AAEA,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,cAAc,MAAM,6BAA6B,CAAA;AACxD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,aAAa,CAAC,eAAe,CAC3B,GAAG,EAAE,CACH,IAAI,iBAAiB,CAAC;QACpB,IAAI,EAAE,mBAAmB;QACzB,cAAc;QACd,YAAY;QACZ,aAAa;KACd,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js

@@ -1,9 +1,9 @@
 import React, { useState } from 'react';
-import { Button, FormControl, FormControlLabel, FormLabel, Paper, Radio, RadioGroup, TextField, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-import { getSession, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
 import { ErrorMessage, FileSelector } from '@jbrowse/core/ui';
+import { getSession, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
+import { Button, FormControl, FormControlLabel, FormLabel, Paper, Radio, RadioGroup, TextField, } from '@mui/material';
 import { getRoot } from 'mobx-state-tree';
+import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     textbox: {
         width: '100%',
@@ -23,6 +23,7 @@ export default function MultiMAFWidget({ model }) {
     const [samples, setSamples] = useState('');
     const [loc, setLoc] = useState();
     const [indexLoc, setIndexLoc] = useState();
+    const [nhLoc, setNhLoc] = useState();
     const [error, setError] = useState();
     const [trackName, setTrackName] = useState('MAF track');
     const [fileTypeChoice, setFileTypeChoice] = useState('BigMafAdapter');
@@ -35,28 +36,34 @@ export default function MultiMAFWidget({ model }) {
                 React.createElement(FormLabel, null, "File type"),
                 React.createElement(RadioGroup, { value: fileTypeChoice, onChange: event => {
                         setFileTypeChoice(event.target.value);
-                    } },
-                    React.createElement(FormControlLabel, { value: "BigMafAdapter", control: React.createElement(Radio, null), checked: fileTypeChoice === 'BigMafAdapter', label: "bigMaf" }),
-                    React.createElement(FormControlLabel, { value: "MafTabixAdapter", control: React.createElement(Radio, null), checked: fileTypeChoice === 'MafTabixAdapter', label: "mafTabix" }))),
+                    } }, ['BigMafAdapter', 'MafTabixAdapter', 'BgzipTaffyAdapter'].map(r => (React.createElement(FormControlLabel, { value: r, control: React.createElement(Radio, null), checked: fileTypeChoice === r, label: r }))))),
             fileTypeChoice === 'BigMafAdapter' ? (React.createElement(FileSelector, { location: loc, name: "Path to bigMaf", rootModel: rootModel, setLocation: arg => {
                     setLoc(arg);
-                } })) : (React.createElement(React.Fragment, null,
+                } })) : fileTypeChoice === 'MafTabixAdapter' ? (React.createElement(React.Fragment, null,
                 React.createElement(FormControl, null,
                     React.createElement(FormLabel, null, "Index type"),
                     React.createElement(RadioGroup, { value: fileTypeChoice, onChange: event => {
                             setIndexTypeChoice(event.target.value);
-                        } },
-                        React.createElement(FormControlLabel, { value: "TBI", control: React.createElement(Radio, null), checked: indexTypeChoice === 'TBI', label: "TBI" }),
-                        React.createElement(FormControlLabel, { value: "CSI", control: React.createElement(Radio, null), checked: indexTypeChoice === 'CSI', label: "CSI" }))),
-                React.createElement(FileSelector, { location: loc, name: "Path to MAF tabix", setLocation: arg => {
+                        } }, ['TBI', 'CSI'].map(r => (React.createElement(FormControlLabel, { value: r, control: React.createElement(Radio, null), checked: fileTypeChoice === r, label: r }))))),
+                React.createElement(FileSelector, { location: loc, name: "Path to MAF tabix", rootModel: rootModel, setLocation: arg => {
+                        setLoc(arg);
+                    } }),
+                React.createElement(FileSelector, { location: indexLoc, name: "Path to MAF tabix index", rootModel: rootModel, setLocation: arg => {
+                        setIndexLoc(arg);
+                    } }))) : (React.createElement(React.Fragment, null,
+                React.createElement(FileSelector, { location: loc, name: "Path to TAF.gz (Bgzipped TAF)", rootModel: rootModel, setLocation: arg => {
                         setLoc(arg);
-                    }, rootModel: rootModel }),
-                React.createElement(FileSelector, { location: indexLoc, name: "Path to MAF tabix index", setLocation: arg => {
+                    } }),
+                React.createElement(FileSelector, { location: indexLoc, name: "Path to TAF.gz.tai (TAF index)", rootModel: rootModel, setLocation: arg => {
                         setIndexLoc(arg);
-                    }, rootModel: rootModel })))),
-        React.createElement(TextField, { multiline: true, rows: 10, value: samples, onChange: event => {
-                setSamples(event.target.value);
-            }, placeholder: 'Enter sample names from the MAF file, one per line, or JSON formatted array of samples', variant: "outlined", fullWidth: true }),
+                    } })))),
+        React.createElement("div", null,
+            React.createElement(FileSelector, { location: nhLoc, name: "Path to newick tree (.nh)", rootModel: rootModel, setLocation: arg => {
+                    setNhLoc(arg);
+                } }),
+            React.createElement(TextField, { multiline: true, rows: 10, value: samples, onChange: event => {
+                    setSamples(event.target.value);
+                }, helperText: "Sample names (optional if .nh supplied, required if not)", placeholder: 'Enter sample names from the MAF file, one per line, or JSON formatted array of samples', variant: "outlined", fullWidth: true })),
         React.createElement(TextField, { value: trackName, helperText: "Track name", onChange: event => {
                 setTrackName(event.target.value);
             } }),
@@ -85,16 +92,26 @@ export default function MultiMAFWidget({ model }) {
                                     type: fileTypeChoice,
                                     bigBedLocation: loc,
                                     samples: sampleNames,
+                                    nhLocation: nhLoc,
                                 }
-                                : {
-                                    type: fileTypeChoice,
-                                    bedGzLocation: loc,
-                                    index: {
-                                        indexType: indexTypeChoice,
-                                        location: indexLoc,
+                                : fileTypeChoice === 'MafTabixAdapter'
+                                    ? {
+                                        type: fileTypeChoice,
+                                        bedGzLocation: loc,
+                                        nhLocation: nhLoc,
+                                        index: {
+                                            indexType: indexTypeChoice,
+                                            location: indexLoc,
+                                        },
+                                        samples: sampleNames,
+                                    }
+                                    : {
+                                        type: fileTypeChoice,
+                                        tafGzLocation: loc,
+                                        taiLocation: indexLoc,
+                                        nhLocation: nhLoc,
+                                        samples: sampleNames,
                                     },
-                                    samples: sampleNames,
-                                },
                         });
                         model.view?.showTrack(trackId);
                     }

package/dist/MafAddTrackWorkflow/AddTrackWorkflow.js.map

@@ -1 +1 @@
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package/dist/MafRPC/index.d.ts

@@ -0,0 +1,16 @@
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Region } from '@jbrowse/core/util';
+export declare class MafGetSamples extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name: string;
+    execute(args: {
+        adapterConfig: AnyConfigurationModel;
+        stopToken?: string;
+        sessionId: string;
+        headers?: Record<string, string>;
+        regions: Region[];
+        bpPerPx: number;
+    }, rpcDriverClassName: string): Promise<any>;
+}
+export default function MafRPCF(pluginManager: PluginManager): void;

package/dist/MafRPC/index.js

@@ -0,0 +1,19 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
+import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions';
+export class MafGetSamples extends RpcMethodTypeWithFiltersAndRenameRegions {
+    name = 'MafGetSamples';
+    async execute(args, rpcDriverClassName) {
+        const pm = this.pluginManager;
+        const deserializedArgs = await this.deserializeArguments(args, rpcDriverClassName);
+        const { regions, adapterConfig, sessionId } = deserializedArgs;
+        const { dataAdapter } = await getAdapter(pm, sessionId, adapterConfig);
+        // @ts-expect-error
+        return dataAdapter.getSamples(regions, deserializedArgs);
+    }
+}
+export default function MafRPCF(pluginManager) {
+    pluginManager.addRpcMethod(() => {
+        return new MafGetSamples(pluginManager);
+    });
+}
+//# sourceMappingURL=index.js.map

package/dist/MafRPC/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/MafRPC/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AACzE,OAAO,wCAAwC,MAAM,8EAA8E,CAAA;AAMnI,MAAM,OAAO,aAAc,SAAQ,wCAAwC;IACzE,IAAI,GAAG,eAAe,CAAA;IAEtB,KAAK,CAAC,OAAO,CACX,IAOC,EACD,kBAA0B;QAE1B,MAAM,EAAE,GAAG,IAAI,CAAC,aAAa,CAAA;QAC7B,MAAM,gBAAgB,GAAG,MAAM,IAAI,CAAC,oBAAoB,CACtD,IAAI,EACJ,kBAAkB,CACnB,CAAA;QACD,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,GAAG,gBAAgB,CAAA;QAC9D,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,UAAU,CAAC,EAAE,EAAE,SAAS,EAAE,aAAa,CAAC,CAAA;QAEtE,mBAAmB;QACnB,OAAO,WAAW,CAAC,UAAU,CAAC,OAAO,EAAE,gBAAgB,CAAC,CAAA;IAC1D,CAAC;CACF;AAED,MAAM,CAAC,OAAO,UAAU,OAAO,CAAC,aAA4B;IAC1D,aAAa,CAAC,YAAY,CAAC,GAAG,EAAE;QAC9B,OAAO,IAAI,aAAa,CAAC,aAAa,CAAC,CAAA;IACzC,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/dist/MafTabixAdapter/MafTabixAdapter.d.ts

@@ -13,5 +13,13 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
     getRefNames(): Promise<string[]>;
     getHeader(): Promise<unknown>;
     getFeatures(query: Region): import("rxjs").Observable<Feature>;
+    getSamples(_query: Region): Promise<{
+        samples: {
+            id: string;
+            label: string;
+            color?: string;
+        }[];
+        tree: Record<string, any> | undefined;
+    }>;
     freeResources(): void;
 }