@jbrowse/core 3.6.5 → 4.0.0

package/BaseFeatureWidget/SequenceFeatureDetails/model.js

@@ -1,81 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.SequenceFeatureDetailsF = SequenceFeatureDetailsF;
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("../../util");
-function localStorageSetNumber(key, value) {
-    (0, util_1.localStorageSetItem)(key, JSON.stringify(value));
-}
-function localStorageSetBoolean(key, value) {
-    (0, util_1.localStorageSetItem)(key, JSON.stringify(value));
-}
-const p = 'sequenceFeatureDetails';
-function SequenceFeatureDetailsF() {
-    return mobx_state_tree_1.types
-        .model('SequenceFeatureDetails')
-        .volatile(() => ({
-        showCoordinatesSetting: (0, util_1.localStorageGetItem)(`${p}-showCoordinatesSetting`) || 'none',
-        intronBp: (0, util_1.localStorageGetNumber)(`${p}-intronBp`, 10),
-        upDownBp: (0, util_1.localStorageGetNumber)(`${p}-upDownBp`, 100),
-        upperCaseCDS: (0, util_1.localStorageGetBoolean)(`${p}-upperCaseCDS`, true),
-        charactersPerRow: 100,
-        feature: undefined,
-        mode: '',
-    }))
-        .actions(self => ({
-        setFeature(f) {
-            self.feature = f;
-        },
-        setUpDownBp(f) {
-            self.upDownBp = f;
-        },
-        setIntronBp(f) {
-            self.intronBp = f;
-        },
-        setUpperCaseCDS(f) {
-            self.upperCaseCDS = f;
-        },
-        setShowCoordinates(f) {
-            self.showCoordinatesSetting = f;
-        },
-        setMode(mode) {
-            self.mode = mode;
-        },
-    }))
-        .views(self => ({
-        get showCoordinates() {
-            return self.showCoordinatesSetting !== 'none';
-        },
-        get showGenomicCoordsOption() {
-            return (self.mode === 'gene' ||
-                self.mode === 'gene_updownstream' ||
-                self.mode === 'genomic' ||
-                self.mode === 'genomic_sequence_updownstream');
-        },
-        get hasCDS() {
-            var _a, _b;
-            return (_b = (_a = self.feature) === null || _a === void 0 ? void 0 : _a.subfeatures) === null || _b === void 0 ? void 0 : _b.some(sub => sub.type === 'CDS');
-        },
-        get hasExon() {
-            var _a, _b;
-            return (_b = (_a = self.feature) === null || _a === void 0 ? void 0 : _a.subfeatures) === null || _b === void 0 ? void 0 : _b.some(sub => sub.type === 'exon');
-        },
-        get hasExonOrCDS() {
-            return this.hasExon || this.hasCDS;
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                localStorageSetNumber(`${p}-upDownBp`, self.upDownBp);
-                localStorageSetNumber(`${p}-intronBp`, self.intronBp);
-                localStorageSetBoolean(`${p}-upperCaseCDS`, self.upperCaseCDS);
-                (0, util_1.localStorageSetItem)(`${p}-showCoordinatesSetting`, self.showCoordinatesSetting);
-            }));
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                self.setMode(self.hasCDS ? 'cds' : self.hasExon ? 'cdna' : 'genomic');
-            }));
-        },
-    }));
-}

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.d.ts

@@ -1,16 +0,0 @@
-import type { SimpleFeatureSerialized } from '../../../util';
-import type { Feat } from '../../util';
-import type { SequenceFeatureDetailsModel } from '../model';
-declare const CDNASequence: ({ utr, cds, exons, sequence, upstream, downstream, feature, includeIntrons, collapseIntron, model, }: {
-    utr: Feat[];
-    cds: Feat[];
-    exons: Feat[];
-    sequence: string;
-    upstream?: string;
-    downstream?: string;
-    feature: SimpleFeatureSerialized;
-    includeIntrons?: boolean;
-    collapseIntron?: boolean;
-    model: SequenceFeatureDetailsModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default CDNASequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDNASequence.js

@@ -1,88 +0,0 @@
-"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 mobx_react_1 = require("mobx-react");
-const util_1 = require("../util");
-const SequenceDisplay_1 = __importDefault(require("./SequenceDisplay"));
-const CDNASequence = (0, mobx_react_1.observer)(function ({ utr, cds, exons, sequence, upstream, downstream, feature, includeIntrons, collapseIntron, model, }) {
-    var _a;
-    const { upperCaseCDS, intronBp, charactersPerRow, showCoordinates, showCoordinatesSetting, } = model;
-    const hasCds = cds.length > 0;
-    const chunks = (cds.length ? [...cds, ...utr].sort((a, b) => a.start - b.start) : exons).filter(f => f.start !== f.end);
-    const toLower = (s) => (upperCaseCDS ? s.toLowerCase() : s);
-    const toUpper = (s) => (upperCaseCDS ? s.toUpperCase() : s);
-    const strand = feature.strand === -1 ? -1 : 1;
-    const fullGenomicCoordinates = showCoordinatesSetting === 'genomic' && includeIntrons && !collapseIntron;
-    const mult = fullGenomicCoordinates ? strand : 1;
-    let coordStart = fullGenomicCoordinates
-        ? strand > 0
-            ? feature.start + 1 - ((upstream === null || upstream === void 0 ? void 0 : upstream.length) || 0)
-            : feature.end + ((upstream === null || upstream === void 0 ? void 0 : upstream.length) || 0)
-        : 0;
-    let currStart = 0;
-    let currRemainder = 0;
-    let upstreamChunk = null;
-    if (upstream) {
-        const { segments, remainder } = (0, util_1.splitString)({
-            str: toLower(upstream),
-            charactersPerRow,
-            showCoordinates,
-        });
-        upstreamChunk = ((0, jsx_runtime_1.jsx)(SequenceDisplay_1.default, { model: model, color: util_1.updownstreamColor, strand: mult, start: currStart, coordStart: coordStart, chunks: segments }));
-        currRemainder = remainder;
-        currStart = currStart + upstream.length * mult;
-        coordStart = coordStart + upstream.length * mult;
-    }
-    const middleChunks = [];
-    for (let idx = 0; idx < chunks.length; idx++) {
-        const chunk = chunks[idx];
-        const intron = sequence.slice(chunk.end, (_a = chunks[idx + 1]) === null || _a === void 0 ? void 0 : _a.start);
-        const s = sequence.slice(chunk.start, chunk.end);
-        const { segments, remainder } = (0, util_1.splitString)({
-            str: hasCds
-                ? chunk.type === 'CDS'
-                    ? toUpper(s)
-                    : toLower(s)
-                : toUpper(s),
-            charactersPerRow,
-            currRemainder,
-            showCoordinates,
-        });
-        middleChunks.push((0, jsx_runtime_1.jsx)(SequenceDisplay_1.default, { model: model, color: chunk.type === 'CDS' ? util_1.cdsColor : util_1.utrColor, strand: mult, start: currStart, coordStart: coordStart, chunks: segments }, `${JSON.stringify(chunk)}-mid`));
-        currRemainder = remainder;
-        currStart = currStart + s.length * mult;
-        coordStart = coordStart + s.length * mult;
-        if (intron && includeIntrons && idx < chunks.length - 1) {
-            const str = toLower(collapseIntron && intron.length > intronBp * 2
-                ? `${intron.slice(0, intronBp)}...${intron.slice(-intronBp)}`
-                : intron);
-            const { segments, remainder } = (0, util_1.splitString)({
-                str,
-                charactersPerRow,
-                currRemainder,
-                showCoordinates,
-            });
-            if (segments.length) {
-                middleChunks.push((0, jsx_runtime_1.jsx)(SequenceDisplay_1.default, { model: model, strand: mult, coordStart: coordStart, start: currStart, chunks: segments }, `${JSON.stringify(chunk)}-intron`));
-                currRemainder = remainder;
-                currStart = currStart + str.length * mult;
-                coordStart = coordStart + str.length * mult;
-            }
-        }
-    }
-    let downstreamChunk = null;
-    if (downstream) {
-        const { segments } = (0, util_1.splitString)({
-            str: toLower(downstream),
-            charactersPerRow,
-            currRemainder,
-            showCoordinates,
-        });
-        downstreamChunk = ((0, jsx_runtime_1.jsx)(SequenceDisplay_1.default, { start: currStart, model: model, strand: mult, chunks: segments, coordStart: coordStart, color: util_1.updownstreamColor }));
-    }
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [upstreamChunk, middleChunks, downstreamChunk] }));
-});
-exports.default = CDNASequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.d.ts

@@ -1,8 +0,0 @@
-import type { Feat } from '../../util';
-import type { SequenceFeatureDetailsModel } from '../model';
-declare const CDSSequence: ({ cds, sequence, model, }: {
-    cds: Feat[];
-    sequence: string;
-    model: SequenceFeatureDetailsModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default CDSSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/CDSSequence.js

@@ -1,20 +0,0 @@
-"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 mobx_react_1 = require("mobx-react");
-const util_1 = require("../../util");
-const util_2 = require("../util");
-const SequenceDisplay_1 = __importDefault(require("./SequenceDisplay"));
-const CDSSequence = (0, mobx_react_1.observer)(function ({ cds, sequence, model, }) {
-    const { charactersPerRow, showCoordinates } = model;
-    const { segments } = (0, util_2.splitString)({
-        str: (0, util_1.stitch)(cds, sequence),
-        charactersPerRow,
-        showCoordinates,
-    });
-    return ((0, jsx_runtime_1.jsx)(SequenceDisplay_1.default, { model: model, color: util_2.cdsColor, chunks: segments, start: 0 }));
-});
-exports.default = CDSSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.d.ts

@@ -1,10 +0,0 @@
-import type { SimpleFeatureSerialized } from '../../../util';
-import type { SequenceFeatureDetailsModel } from '../model';
-declare const GenomicSequence: ({ sequence, upstream, feature, downstream, model, }: {
-    sequence: string;
-    feature: SimpleFeatureSerialized;
-    upstream?: string;
-    downstream?: string;
-    model: SequenceFeatureDetailsModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default GenomicSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/GenomicSequence.js

@@ -1,56 +0,0 @@
-"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 mobx_react_1 = require("mobx-react");
-const util_1 = require("../util");
-const SequenceDisplay_1 = __importDefault(require("./SequenceDisplay"));
-const GenomicSequence = (0, mobx_react_1.observer)(function ({ sequence, upstream, feature, downstream, model, }) {
-    const { charactersPerRow, showCoordinatesSetting, showCoordinates } = model;
-    let currStart = 0;
-    let upstreamChunk = null;
-    let currRemainder = 0;
-    const strand = feature.strand === -1 ? -1 : 1;
-    const fullGenomicCoordinates = showCoordinatesSetting === 'genomic';
-    const mult = fullGenomicCoordinates ? strand : 1;
-    let coordStart = fullGenomicCoordinates
-        ? strand > 0
-            ? feature.start + 1 - ((upstream === null || upstream === void 0 ? void 0 : upstream.length) || 0)
-            : feature.end + ((upstream === null || upstream === void 0 ? void 0 : upstream.length) || 0)
-        : 0;
-    if (upstream) {
-        const { segments, remainder } = (0, util_1.splitString)({
-            str: upstream,
-            charactersPerRow,
-            showCoordinates,
-        });
-        upstreamChunk = ((0, jsx_runtime_1.jsx)(SequenceDisplay_1.default, { model: model, color: util_1.updownstreamColor, start: currStart, coordStart: coordStart, chunks: segments }));
-        currRemainder = remainder;
-        currStart = currStart + upstream.length * mult;
-        coordStart = coordStart + upstream.length * mult;
-    }
-    const { segments, remainder } = (0, util_1.splitString)({
-        str: sequence,
-        charactersPerRow,
-        showCoordinates,
-        currRemainder,
-    });
-    const middleChunk = ((0, jsx_runtime_1.jsx)(SequenceDisplay_1.default, { model: model, color: util_1.genomeColor, start: currStart, coordStart: coordStart, chunks: segments }));
-    currRemainder = remainder;
-    currStart += sequence.length * mult;
-    coordStart = coordStart + sequence.length * mult;
-    let downstreamChunk = null;
-    if (downstream) {
-        const { segments } = (0, util_1.splitString)({
-            str: downstream,
-            charactersPerRow,
-            currRemainder,
-            showCoordinates,
-        });
-        downstreamChunk = ((0, jsx_runtime_1.jsx)(SequenceDisplay_1.default, { start: currStart, model: model, chunks: segments, coordStart: coordStart, color: util_1.updownstreamColor }));
-    }
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [upstreamChunk, middleChunk, downstreamChunk] }));
-});
-exports.default = GenomicSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.d.ts

@@ -1,9 +0,0 @@
-import type { Feat } from '../../util';
-import type { SequenceFeatureDetailsModel } from '../model';
-declare const ProteinSequence: ({ cds, sequence, codonTable, model, }: {
-    cds: Feat[];
-    sequence: string;
-    codonTable: Record<string, string>;
-    model: SequenceFeatureDetailsModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default ProteinSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/ProteinSequence.js

@@ -1,25 +0,0 @@
-"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 mobx_react_1 = require("mobx-react");
-const util_1 = require("../../util");
-const util_2 = require("../util");
-const SequenceDisplay_1 = __importDefault(require("./SequenceDisplay"));
-const ProteinSequence = (0, mobx_react_1.observer)(function ({ cds, sequence, codonTable, model, }) {
-    const { charactersPerRow, showCoordinates } = model;
-    const str = (0, util_1.stitch)(cds, sequence);
-    let protein = '';
-    for (let i = 0; i < str.length; i += 3) {
-        protein += codonTable[str.slice(i, i + 3)] || '&';
-    }
-    const { segments } = (0, util_2.splitString)({
-        str: protein,
-        charactersPerRow,
-        showCoordinates,
-    });
-    return ((0, jsx_runtime_1.jsx)(SequenceDisplay_1.default, { model: model, color: util_2.proteinColor, chunks: segments, start: 0 }));
-});
-exports.default = ProteinSequence;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.d.ts

@@ -1,10 +0,0 @@
-import type { SequenceFeatureDetailsModel } from '../model';
-declare const SequenceDisplay: ({ chunks, start, color, strand, coordStart, model, }: {
-    chunks: string[];
-    start: number;
-    coordStart?: number;
-    strand?: number;
-    color?: string;
-    model: SequenceFeatureDetailsModel;
-}) => import("react/jsx-runtime").JSX.Element[];
-export default SequenceDisplay;

package/BaseFeatureWidget/SequenceFeatureDetails/seqtypes/SequenceDisplay.js

@@ -1,25 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const mobx_react_1 = require("mobx-react");
-const SequenceDisplay = (0, mobx_react_1.observer)(function ({ chunks, start, color, strand = 1, coordStart = start, model, }) {
-    const { charactersPerRow, showCoordinates } = model;
-    return chunks.map((chunk, idx) => {
-        var _a;
-        const f = coordStart - (start % charactersPerRow);
-        const prefix = (idx === 0 && start % charactersPerRow === 0) || idx > 0
-            ? `${`${f + idx * strand * charactersPerRow}`.padStart(4)}   `
-            : '';
-        const postfix = idx === chunks.length - 1 &&
-            (((_a = chunks.at(-1)) === null || _a === void 0 ? void 0 : _a.replaceAll(' ', '').length) || 0) +
-                (idx === 0 ? start % charactersPerRow : 0) !==
-                charactersPerRow
-            ? null
-            : showCoordinates
-                ? ' \n'
-                : '';
-        return ((0, jsx_runtime_1.jsxs)(react_1.Fragment, { children: [showCoordinates ? prefix : null, (0, jsx_runtime_1.jsx)("span", { style: { background: color }, children: chunk }), postfix] }, `${chunk}-${idx}`));
-    });
-});
-exports.default = SequenceDisplay;

package/BaseFeatureWidget/SequenceFeatureDetails/test_data/DLGAP3.d.ts

@@ -1,80 +0,0 @@
-declare namespace _default {
-    let source: string;
-    let type: string;
-    let start: number;
-    let end: number;
-    let strand: number;
-    let phase: number;
-    let refName: string;
-    let id: string;
-    let dbxref: string[];
-    let name: string;
-    let description: string;
-    let gbkey: string;
-    let gene: string;
-    let gene_biotype: string;
-    let gene_synonym: string[];
-    let 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;
-    }[];
-    let uniqueId: string;
-}
-export default _default;