@jbrowse/core 2.1.4 → 2.1.6

package/BaseFeatureWidget/SequenceHelpDialog.js

@@ -0,0 +1,51 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
+// icons
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const Settings_1 = __importDefault(require("@mui/icons-material/Settings"));
+const useStyles = (0, mui_1.makeStyles)()(theme => ({
+    closeButton: {
+        position: 'absolute',
+        right: theme.spacing(1),
+        top: theme.spacing(1),
+        color: theme.palette.grey[500],
+    },
+    dialogContent: {},
+}));
+function HelpDialog({ handleClose, }) {
+    const { classes } = useStyles();
+    return (react_1.default.createElement(material_1.Dialog, { maxWidth: "xl", open: true, onClose: () => handleClose() },
+        react_1.default.createElement(material_1.DialogTitle, null,
+            "Feature sequence panel",
+            handleClose ? (react_1.default.createElement(material_1.IconButton, { className: classes.closeButton, onClick: () => handleClose() },
+                react_1.default.createElement(Close_1.default, null))) : null),
+        react_1.default.createElement(material_1.Divider, null),
+        react_1.default.createElement(material_1.DialogContent, { className: classes.dialogContent },
+            react_1.default.createElement(material_1.Typography, { paragraph: true }, "The \"Feature sequence\" panel shows the underlying genomic sequence for a given feature, fetched from the reference genome."),
+            react_1.default.createElement(material_1.Typography, null, "For gene features, this panel does special calculations to e.g. stitch together the coding sequence, the options are:"),
+            react_1.default.createElement("ul", null,
+                react_1.default.createElement("li", null, "CDS - shows the stitched together CDS sequences"),
+                react_1.default.createElement("li", null, "Protein - the translated coding sequence, with the \"standard\" genetic code"),
+                react_1.default.createElement("li", null, "cDNA - shows the UTRs and stitched together CDS sequences"),
+                react_1.default.createElement("li", null, "Gene w/ introns - the sequence underlying the entire gene including including introns, with UTR and CDS highlighted"),
+                react_1.default.createElement("li", null, "Gene w/ Nbp introns - same \"Gene w/ introns\", but limiting to a subset of the intron sequence displayed"),
+                react_1.default.createElement("li", null, "Gene +/- Nbp up+down stream - same as \"Gene w/ introns\" but with up and downstream sequence displayed"),
+                react_1.default.createElement("li", null, "Gene +/- Nbp up+down stream, Nbp introns - same as \"Gene w/ introns\", but with limited intron sequence displayed and up and downstream sequence")),
+            react_1.default.createElement(material_1.Typography, { paragraph: true }, "For other feature types, the options are:"),
+            react_1.default.createElement("ul", null,
+                react_1.default.createElement("li", null, "Feature sequence - the reference genome sequence underlying the feature"),
+                react_1.default.createElement("li", null, "Feature sequence +/- Nbp up+down stream - the reference genome sequence underlying the feature, with the up and downstream sequence")),
+            react_1.default.createElement(material_1.Typography, null,
+                "Note: you can use the \"gear icon\" ",
+                react_1.default.createElement(Settings_1.default, null),
+                " to edit the number of bp displayed up/downstream and in the intron region")),
+        react_1.default.createElement(material_1.DialogActions, null,
+            react_1.default.createElement(material_1.Button, { onClick: () => handleClose(), autoFocus: true, variant: "contained" }, "Close"))));
+}
+exports.default = HelpDialog;

package/BaseFeatureWidget/SequencePanel.d.ts

@@ -0,0 +1,10 @@
+import React from 'react';
+import { ParentFeat, SeqState } from './util';
+interface SequencePanelProps {
+    sequence: SeqState;
+    feature: ParentFeat;
+    mode: string;
+    intronBp?: number;
+}
+declare const SequencePanel: React.ForwardRefExoticComponent<SequencePanelProps & React.RefAttributes<HTMLDivElement>>;
+export default SequencePanel;

package/BaseFeatureWidget/SequencePanel.js

@@ -0,0 +1,72 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const util_1 = require("../util");
+const util_2 = require("./util");
+const SequenceBox_1 = require("./SequenceBox");
+const SequencePanel = react_1.default.forwardRef((props, ref) => {
+    const { feature, mode, intronBp = 10 } = props;
+    let { sequence: { seq, upstream = '', downstream = '' }, } = props;
+    const { subfeatures = [] } = feature;
+    const children = subfeatures
+        .sort((a, b) => a.start - b.start)
+        .map(sub => ({
+        ...sub,
+        start: sub.start - feature.start,
+        end: sub.end - feature.start,
+    }));
+    // we filter duplicate entries in cds and exon lists duplicate entries may be
+    // rare but was seen in Gencode v36 track NCList, likely a bug on GFF3 or
+    // probably worth ignoring here (produces broken protein translations if
+    // included)
+    //
+    // position 1:224,800,006..225,203,064 gene ENSG00000185842.15 first
+    // transcript ENST00000445597.6
+    //
+    // http://localhost:3000/?config=test_data%2Fconfig.json&session=share-FUl7G1isvF&password=HXh5Y
+    let cds = (0, util_2.dedupe)(children.filter(sub => sub.type === 'CDS'));
+    let utr = (0, util_2.dedupe)(children.filter(sub => sub.type.match(/utr/i)));
+    let exons = (0, util_2.dedupe)(children.filter(sub => sub.type === 'exon'));
+    if (!utr.length && cds.length && exons.length) {
+        utr = (0, util_2.calculateUTRs)(cds, exons);
+    }
+    if (!utr.length && cds.length && !exons.length) {
+        utr = (0, util_2.calculateUTRs2)(cds, {
+            start: 0,
+            end: feature.end - feature.start,
+            type: 'gene',
+        });
+    }
+    if (feature.strand === -1) {
+        // doing this in a single assignment is needed because downstream and
+        // upstream are swapped so this avoids a temp variable
+        ;
+        [seq, upstream, downstream] = [
+            (0, util_1.revcom)(seq),
+            (0, util_1.revcom)(downstream),
+            (0, util_1.revcom)(upstream),
+        ];
+        cds = (0, util_2.revlist)(cds, seq.length);
+        exons = (0, util_2.revlist)(exons, seq.length);
+        utr = (0, util_2.revlist)(utr, seq.length);
+    }
+    const codonTable = (0, util_1.generateCodonTable)(util_1.defaultCodonTable);
+    return (react_1.default.createElement("div", { ref: ref, "data-testid": "sequence_panel" },
+        react_1.default.createElement("div", { style: {
+                fontFamily: 'monospace',
+                wordWrap: 'break-word',
+                overflow: 'auto',
+                fontSize: 12,
+                maxWidth: 600,
+                maxHeight: 500,
+            } },
+            `>${feature.name ||
+                feature.id ||
+                feature.refName + ':' + (feature.start + 1) + '-' + feature.end}-${mode}\n`,
+            react_1.default.createElement("br", null),
+            mode === 'genomic' ? (react_1.default.createElement(SequenceBox_1.Genomic, { sequence: seq })) : mode === 'genomic_sequence_updown' ? (react_1.default.createElement(SequenceBox_1.Genomic, { sequence: seq, upstream: upstream, downstream: downstream })) : mode === 'cds' ? (react_1.default.createElement(SequenceBox_1.GeneCDS, { cds: cds, sequence: seq })) : mode === 'cdna' ? (react_1.default.createElement(SequenceBox_1.GenecDNA, { exons: exons, cds: cds, utr: utr, sequence: seq, intronBp: intronBp })) : mode === 'protein' ? (react_1.default.createElement(SequenceBox_1.GeneProtein, { cds: cds, codonTable: codonTable, sequence: seq })) : mode === 'gene' ? (react_1.default.createElement(SequenceBox_1.GenecDNA, { exons: exons, cds: cds, utr: utr, sequence: seq, includeIntrons: true, intronBp: intronBp })) : mode === 'gene_collapsed_intron' ? (react_1.default.createElement(SequenceBox_1.GenecDNA, { exons: exons, cds: cds, sequence: seq, utr: utr, includeIntrons: true, collapseIntron: true, intronBp: intronBp })) : mode === 'gene_updownstream' ? (react_1.default.createElement(SequenceBox_1.GenecDNA, { exons: exons, cds: cds, sequence: seq, utr: utr, upstream: upstream, downstream: downstream, includeIntrons: true, intronBp: intronBp })) : mode === 'gene_updownstream_collapsed_intron' ? (react_1.default.createElement(SequenceBox_1.GenecDNA, { exons: exons, cds: cds, sequence: seq, utr: utr, upstream: upstream, downstream: downstream, includeIntrons: true, collapseIntron: true, intronBp: intronBp })) : (react_1.default.createElement("div", null, "Unknown type")))));
+});
+exports.default = SequencePanel;

package/BaseFeatureWidget/index.d.ts

@@ -8,10 +8,13 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 }, {
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
+    setExtra(type?: string, trackId?: string): void;
 } & {
     afterCreate(): void;
 }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
@@ -22,11 +25,15 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+    trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+    trackType: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
 }>>, {
     id: string;
     type: "BaseFeatureWidget";
     track: import("mobx-state-tree").ReferenceIdentifier | undefined;
     view: import("mobx-state-tree").ReferenceIdentifier | undefined;
+    trackId: string | undefined;
+    trackType: string | undefined;
     formattedFields: any;
     finalizedFeatureData: any;
 }>;

package/BaseFeatureWidget/index.js

@@ -6,8 +6,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = exports.configSchema = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const mobx_1 = require("mobx");
-const configuration_1 = require("../configuration");
 const clone_1 = __importDefault(require("clone"));
+const configuration_1 = require("../configuration");
+const util_1 = require("../util");
 const mst_1 = require("../util/types/mst");
 const configSchema = (0, configuration_1.ConfigurationSchema)('BaseFeatureWidget', {});
 exports.configSchema = configSchema;
@@ -32,8 +33,9 @@ function stateModelFactory(pluginManager) {
         unformattedFeatureData: mobx_state_tree_1.types.frozen(),
         view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
         track: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('track', 'stateModel')),
+        trackId: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
+        trackType: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
     })
-        .volatile(() => ({}))
         .actions(self => ({
         setFeatureData(featureData) {
             self.unformattedFeatureData = featureData;
@@ -44,20 +46,34 @@ function stateModelFactory(pluginManager) {
         setFormattedData(feat) {
             self.featureData = feat;
         },
+        setExtra(type, trackId) {
+            self.trackId = trackId;
+            self.trackType = type;
+        },
     }))
         .actions(self => ({
         afterCreate() {
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
+                var _a, _b;
+                self.setExtra((_a = self.track) === null || _a === void 0 ? void 0 : _a.type, (_b = self.track) === null || _b === void 0 ? void 0 : _b.configuration.trackId);
                 const { unformattedFeatureData, track } = self;
+                const session = (0, util_1.getSession)(self);
                 if (unformattedFeatureData) {
                     const feature = (0, clone_1.default)(unformattedFeatureData);
+                    const f = (obj, arg2) => (0, configuration_1.getConf)(obj, ['formatDetails', arg2], { feature });
                     if (track) {
                         // eslint-disable-next-line no-underscore-dangle
-                        feature.__jbrowsefmt = (0, configuration_1.getConf)(track, ['formatDetails', 'feature'], { feature });
+                        feature.__jbrowsefmt = {
+                            ...f(session, 'feature'),
+                            ...f(track, 'feature'),
+                        };
                         const depth = (0, configuration_1.getConf)(track, ['formatDetails', 'depth']);
-                        formatSubfeatures(feature, depth, subfeature => {
+                        formatSubfeatures(feature, depth, sub => {
                             // eslint-disable-next-line no-underscore-dangle
-                            subfeature.__jbrowsefmt = (0, configuration_1.getConf)(track, ['formatDetails', 'subfeatures'], { feature: subfeature });
+                            sub.__jbrowsefmt = {
+                                ...f(session, 'subfeature'),
+                                ...f(track, 'subfeature'),
+                            };
                         });
                     }
                     self.setFormattedData(feature);

package/BaseFeatureWidget/test_data/DLGAP3.d.ts

@@ -0,0 +1,80 @@
+declare namespace _default {
+    const source: string;
+    const type: string;
+    const start: number;
+    const end: number;
+    const strand: number;
+    const phase: number;
+    const refName: string;
+    const id: string;
+    const dbxref: string[];
+    const name: string;
+    const description: string;
+    const gbkey: string;
+    const gene: string;
+    const gene_biotype: string;
+    const gene_synonym: string[];
+    const subfeatures: {
+        source: string;
+        type: string;
+        start: number;
+        end: number;
+        strand: number;
+        phase: number;
+        refName: string;
+        id: string;
+        parent: string;
+        dbxref: string[];
+        name: string;
+        gbkey: string;
+        gene: string;
+        product: string;
+        tag: string;
+        transcript_id: string;
+        subfeatures: ({
+            source: string;
+            type: string;
+            start: number;
+            end: number;
+            strand: number;
+            phase: number;
+            refName: string;
+            parent: string;
+            dbxref: string[];
+            gbkey: string;
+            gene: string;
+            product: string;
+            tag: string;
+            transcript_id: string;
+            uniqueId: string;
+            parentId: string;
+            id?: undefined;
+            name?: undefined;
+            protein_id?: undefined;
+        } | {
+            source: string;
+            type: string;
+            start: number;
+            end: number;
+            strand: number;
+            phase: number;
+            refName: string;
+            id: string;
+            parent: string;
+            dbxref: string[];
+            name: string;
+            gbkey: string;
+            gene: string;
+            product: string;
+            protein_id: string;
+            tag: string;
+            uniqueId: string;
+            parentId: string;
+            transcript_id?: undefined;
+        })[];
+        uniqueId: string;
+        parentId: string;
+    }[];
+    const uniqueId: string;
+}
+export default _default;