@jbrowse/plugin-alignments 3.7.0 → 4.0.0

package/dist/LinearReadCloudDisplay/model.js

@@ -1,213 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-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;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const util_1 = require("@jbrowse/core/util");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const LinearReadDisplayBaseMixin_1 = require("../shared/LinearReadDisplayBaseMixin");
-const LinearReadDisplayWithLayoutMixin_1 = require("../shared/LinearReadDisplayWithLayoutMixin");
-const LinearReadDisplayWithPairFiltersMixin_1 = require("../shared/LinearReadDisplayWithPairFiltersMixin");
-const chainToSimpleFeature_1 = require("../shared/chainToSimpleFeature");
-const menuItems_1 = require("../shared/menuItems");
-const SetFeatureHeightDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetFeatureHeightDialog'))));
-function stateModelFactory(configSchema) {
-    return mobx_state_tree_1.types
-        .compose('LinearReadCloudDisplay', pluggableElementTypes_1.BaseDisplay, (0, plugin_linear_genome_view_1.TrackHeightMixin)(), (0, plugin_linear_genome_view_1.FeatureDensityMixin)(), (0, LinearReadDisplayBaseMixin_1.LinearReadDisplayBaseMixin)(), (0, LinearReadDisplayWithLayoutMixin_1.LinearReadDisplayWithLayoutMixin)(), (0, LinearReadDisplayWithPairFiltersMixin_1.LinearReadDisplayWithPairFiltersMixin)(), mobx_state_tree_1.types.model({
-        type: mobx_state_tree_1.types.literal('LinearReadCloudDisplay'),
-        configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        drawCloud: false,
-        noSpacing: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        trackMaxHeight: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
-    }))
-        .volatile(() => ({
-        layoutHeight: 0,
-    }))
-        .views(self => ({
-        get colorBy() {
-            var _a;
-            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
-        },
-        get filterBy() {
-            var _a;
-            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
-        },
-        get featureHeightSetting() {
-            var _a;
-            return (_a = self.featureHeight) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'featureHeight');
-        },
-    }))
-        .actions(self => ({
-        reload() {
-            self.error = undefined;
-        },
-        setNoSpacing(flag) {
-            self.noSpacing = flag;
-        },
-        setMaxHeight(n) {
-            self.trackMaxHeight = n;
-        },
-        setLayoutHeight(n) {
-            self.layoutHeight = n;
-        },
-        selectFeature(chain) {
-            const session = (0, util_1.getSession)(self);
-            const syntheticFeature = (0, chainToSimpleFeature_1.chainToSimpleFeature)(chain);
-            if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                const featureWidget = session.addWidget('AlignmentsFeatureWidget', 'alignmentFeature', {
-                    featureData: syntheticFeature.toJSON(),
-                    view: (0, util_1.getContainingView)(self),
-                    track: (0, util_1.getContainingTrack)(self),
-                });
-                session.showWidget(featureWidget);
-            }
-            session.setSelection(syntheticFeature);
-        },
-        setDrawCloud(b) {
-            self.drawCloud = b;
-        },
-    }))
-        .views(self => {
-        const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
-        return {
-            renderProps() {
-                return {
-                    ...superRenderProps(),
-                    notReady: !self.chainData,
-                };
-            },
-            trackMenuItems() {
-                return [
-                    ...superTrackMenuItems(),
-                    {
-                        label: 'Set feature height...',
-                        subMenu: [
-                            {
-                                label: 'Normal',
-                                onClick: () => {
-                                    self.setFeatureHeight(7);
-                                    self.setNoSpacing(false);
-                                },
-                            },
-                            {
-                                label: 'Compact',
-                                onClick: () => {
-                                    self.setFeatureHeight(3);
-                                    self.setNoSpacing(true);
-                                },
-                            },
-                            {
-                                label: 'Manually set height...',
-                                onClick: () => {
-                                    (0, util_1.getSession)(self).queueDialog(handleClose => [
-                                        SetFeatureHeightDialog,
-                                        {
-                                            model: self,
-                                            handleClose,
-                                        },
-                                    ]);
-                                },
-                            },
-                        ],
-                    },
-                    {
-                        label: 'Toggle read cloud (y-coordinate proportional to TLEN)',
-                        type: 'checkbox',
-                        checked: self.drawCloud,
-                        onClick: () => {
-                            self.setDrawCloud(!self.drawCloud);
-                        },
-                    },
-                    {
-                        label: 'Draw singletons',
-                        type: 'checkbox',
-                        checked: self.drawSingletons,
-                        onClick: () => {
-                            self.setDrawSingletons(!self.drawSingletons);
-                        },
-                    },
-                    {
-                        label: 'Draw proper pairs',
-                        type: 'checkbox',
-                        checked: self.drawProperPairs,
-                        onClick: () => {
-                            self.setDrawProperPairs(!self.drawProperPairs);
-                        },
-                    },
-                    {
-                        label: 'Flip strand relative to primary alignment for long read chains',
-                        type: 'checkbox',
-                        checked: self.flipStrandLongReadChains,
-                        onClick: () => {
-                            self.setFlipStrandLongReadChains(!self.flipStrandLongReadChains);
-                        },
-                    },
-                    (0, menuItems_1.getFilterByMenuItem)(self),
-                    (0, menuItems_1.getColorSchemeMenuItem)(self),
-                ];
-            },
-            async renderSvg(opts) {
-                const { renderSvg } = await Promise.resolve().then(() => __importStar(require('../shared/renderSvgUtil')));
-                if (self.drawCloud) {
-                    const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeatsCloud')));
-                    return renderSvg(self, opts, drawFeats);
-                }
-                else {
-                    const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeatsStack')));
-                    return renderSvg(self, opts, drawFeats);
-                }
-            },
-        };
-    })
-        .actions(self => ({
-        afterAttach() {
-            ;
-            (async () => {
-                try {
-                    const { doAfterAttach } = await Promise.resolve().then(() => __importStar(require('../shared/afterAttach')));
-                    const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeatsAbstract')));
-                    doAfterAttach(self, drawFeats);
-                }
-                catch (e) {
-                    console.error(e);
-                    self.setError(e);
-                }
-            })();
-        },
-    }));
-}
-exports.default = stateModelFactory;

package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -1,12 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-type Coord = [number, number];
-declare const SNPCoverageTooltip: (props: {
-    model: {
-        featureUnderMouse?: Feature;
-    };
-    height: number;
-    offsetMouseCoord: Coord;
-    clientMouseCoord: Coord;
-    clientRect?: DOMRect;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default SNPCoverageTooltip;

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -1,15 +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 plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const mobx_react_1 = require("mobx-react");
-const TooltipContents_1 = __importDefault(require("./TooltipContents"));
-const SNPCoverageTooltip = (0, mobx_react_1.observer)(function (props) {
-    const { model } = props;
-    const { featureUnderMouse: feat } = model;
-    return feat && feat.get('type') === 'skip' ? null : ((0, jsx_runtime_1.jsx)(plugin_wiggle_1.Tooltip, { TooltipContents: TooltipContents_1.default, ...props }));
-});
-exports.default = SNPCoverageTooltip;

package/dist/LinearSNPCoverageDisplay/components/TooltipContents.d.ts

@@ -1,14 +0,0 @@
-import type { Feature } from '@jbrowse/core/util';
-interface Props {
-    feature: Feature;
-    model: {
-        visibleModifications: Map<string, {
-            color: string;
-            base: string;
-            strand: string;
-        }>;
-        simplexModifications?: Set<string>;
-    };
-}
-declare const TooltipContents: import("react").ForwardRefExoticComponent<Props & import("react").RefAttributes<HTMLDivElement>>;
-export default TooltipContents;

package/dist/LinearSNPCoverageDisplay/components/TooltipContents.js

@@ -1,177 +0,0 @@
-"use strict";
-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 mui_1 = require("tss-react/mui");
-const modificationData_1 = require("../../shared/modificationData");
-const useStyles = (0, mui_1.makeStyles)()(() => ({
-    td: {
-        whiteSpace: 'nowrap',
-    },
-    table: {
-        width: '100%',
-        tableLayout: 'auto',
-    },
-}));
-const toP = (s = 0) => +s.toFixed(1);
-const pct = (n, total = 1) => `${toP((n / (total || 1)) * 100)}%`;
-function getModificationColor(base, model) {
-    var _a;
-    if (!base.startsWith('mod_') && !base.startsWith('nonmod_')) {
-        return undefined;
-    }
-    if (base.startsWith('nonmod_')) {
-        return 'blue';
-    }
-    return (_a = model.visibleModifications.get(base.replace(/^mod_/, ''))) === null || _a === void 0 ? void 0 : _a.color;
-}
-function isModification(base) {
-    return base.startsWith('mod_') || base.startsWith('nonmod_');
-}
-function getModificationType(base) {
-    return base.replace(/^(mod_|nonmod_)/, '');
-}
-function formatStrandCounts(score) {
-    const neg = score['-1'] ? `${score['-1']}(-)` : '';
-    const pos = score['1'] ? `${score['1']}(+)` : '';
-    return neg + pos;
-}
-function shouldShowPercentage(base) {
-    return base !== 'depth' && base !== 'skip';
-}
-function getModificationLabel(base, model) {
-    const isNonmod = base.startsWith('nonmod_');
-    if (isNonmod) {
-        const genomicBase = base.replace('nonmod_', '');
-        return `Unmodified ${genomicBase}`;
-    }
-    const modType = getModificationType(base);
-    const mod = model.visibleModifications.get(modType);
-    if (mod) {
-        const modName = (0, modificationData_1.getModificationName)(modType);
-        return modName;
-    }
-    return base.toUpperCase();
-}
-function getDuplexModificationLabel(base, model) {
-    const isNonmod = base.startsWith('nonmod_');
-    if (isNonmod) {
-        const genomicBase = base.replace('nonmod_', '');
-        return `Unmodified ${genomicBase}`;
-    }
-    const modType = getModificationType(base);
-    const mod = model.visibleModifications.get(modType);
-    if (!mod) {
-        return base.toUpperCase();
-    }
-    const modName = (0, modificationData_1.getModificationName)(modType);
-    return modName;
-}
-function ColorSquare({ base, model }) {
-    const color = getModificationColor(base, model);
-    if (!color) {
-        return null;
-    }
-    return (0, jsx_runtime_1.jsx)("div", { style: { width: 10, height: 10, background: color } });
-}
-function TableHeader() {
-    return ((0, jsx_runtime_1.jsx)("thead", { children: (0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("th", {}), (0, jsx_runtime_1.jsx)("th", { children: "Base" }), (0, jsx_runtime_1.jsx)("th", { children: "Count" }), (0, jsx_runtime_1.jsx)("th", { children: "% of Reads" }), (0, jsx_runtime_1.jsx)("th", { children: "Strands" }), (0, jsx_runtime_1.jsx)("th", { children: "Avg Prob" })] }) }));
-}
-function TotalRow({ readsCounted }) {
-    return ((0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", {}), (0, jsx_runtime_1.jsx)("td", { children: "Total" }), (0, jsx_runtime_1.jsx)("td", { children: readsCounted }), (0, jsx_runtime_1.jsx)("td", { children: " " }), (0, jsx_runtime_1.jsx)("td", { children: " " }), (0, jsx_runtime_1.jsx)("td", { children: " " })] }));
-}
-function RefRow({ referenceBase, reference, readsCounted, }) {
-    return ((0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", {}), (0, jsx_runtime_1.jsxs)("td", { children: ["REF ", referenceBase ? `(${referenceBase.toUpperCase()})` : ''] }), (0, jsx_runtime_1.jsx)("td", { children: reference.entryDepth }), (0, jsx_runtime_1.jsx)("td", { children: pct(reference.entryDepth, readsCounted) }), (0, jsx_runtime_1.jsx)("td", { children: formatStrandCounts(reference) }), (0, jsx_runtime_1.jsx)("td", { children: " " })] }));
-}
-function DuplexModificationRow({ base, score, readsCounted, model, tdClass, rowKey, }) {
-    return ((0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", { children: (0, jsx_runtime_1.jsx)(ColorSquare, { model: model, base: base }) }), (0, jsx_runtime_1.jsx)("td", { children: getDuplexModificationLabel(base, model) }), (0, jsx_runtime_1.jsx)("td", { className: tdClass, children: score.entryDepth }), (0, jsx_runtime_1.jsx)("td", { children: shouldShowPercentage(base)
-                    ? pct(score.entryDepth, readsCounted)
-                    : '---' }), (0, jsx_runtime_1.jsx)("td", { children: formatStrandCounts(score) }), (0, jsx_runtime_1.jsx)("td", { children: score.avgProbability !== undefined ? pct(score.avgProbability) : '' })] }, rowKey));
-}
-function SimplexOrRegularRow({ base, score, isMod, readsCounted, model, tdClass, rowKey, }) {
-    return ((0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", { children: (0, jsx_runtime_1.jsx)(ColorSquare, { model: model, base: base }) }), (0, jsx_runtime_1.jsx)("td", { children: isMod ? getModificationLabel(base, model) : base.toUpperCase() }), (0, jsx_runtime_1.jsx)("td", { className: tdClass, children: score.entryDepth }), (0, jsx_runtime_1.jsx)("td", { children: shouldShowPercentage(base)
-                    ? pct(score.entryDepth, readsCounted)
-                    : '---' }), (0, jsx_runtime_1.jsx)("td", { children: formatStrandCounts(score) }), (0, jsx_runtime_1.jsx)("td", { children: score.avgProbability !== undefined ? pct(score.avgProbability) : '' })] }, rowKey));
-}
-function ModificationRows({ info, readsCounted, model, tdClass, }) {
-    const consolidatedEntries = {};
-    for (const [key, entry] of Object.entries(info)) {
-        for (const [base, score] of Object.entries(entry)) {
-            const isNonmod = base.startsWith('nonmod_');
-            if (isNonmod) {
-                const modType = getModificationType(base);
-                const mod = model.visibleModifications.get(modType);
-                const genomicBase = (mod === null || mod === void 0 ? void 0 : mod.base) || 'X';
-                const consolidatedKey = `${key}_nonmod_${genomicBase}`;
-                if (!consolidatedEntries[consolidatedKey]) {
-                    consolidatedEntries[consolidatedKey] = {
-                        base: `nonmod_${genomicBase}`,
-                        score: {
-                            entryDepth: 0,
-                            '1': 0,
-                            '-1': 0,
-                            avgProbability: 0,
-                        },
-                        isNonmod: true,
-                    };
-                }
-                const consolidated = consolidatedEntries[consolidatedKey];
-                consolidated.score.entryDepth += score.entryDepth;
-                consolidated.score['1'] += score['1'];
-                consolidated.score['-1'] += score['-1'];
-                if (score.avgProbability !== undefined) {
-                    const prevAvg = consolidated.score.avgProbability || 0;
-                    const prevCount = consolidated.score.entryDepth - score.entryDepth;
-                    consolidated.score.avgProbability =
-                        prevCount > 0
-                            ? (prevAvg * prevCount +
-                                score.avgProbability * score.entryDepth) /
-                                consolidated.score.entryDepth
-                            : score.avgProbability;
-                }
-            }
-            else {
-                consolidatedEntries[`${key}_${base}`] = {
-                    base,
-                    score: { ...score },
-                    isNonmod: false,
-                };
-            }
-        }
-    }
-    return ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: Object.entries(consolidatedEntries).map(([rowKey, { base, score, isNonmod }]) => {
-            var _a;
-            const modType = getModificationType(base);
-            const isMod = isModification(base) || isNonmod;
-            const isSimplex = !isNonmod && isMod && ((_a = model.simplexModifications) === null || _a === void 0 ? void 0 : _a.has(modType));
-            const posStrandCount = score['1'] || 0;
-            const negStrandCount = score['-1'] || 0;
-            if (isNonmod) {
-                return ((0, jsx_runtime_1.jsx)(SimplexOrRegularRow, { base: base, score: score, isMod: true, isSimplex: false, readsCounted: readsCounted, model: model, tdClass: tdClass, rowKey: rowKey }, rowKey));
-            }
-            if (isMod &&
-                !isSimplex &&
-                (posStrandCount > 0 || negStrandCount > 0)) {
-                return ((0, jsx_runtime_1.jsx)(DuplexModificationRow, { base: base, score: score, posStrandCount: posStrandCount, negStrandCount: negStrandCount, readsCounted: readsCounted, model: model, tdClass: tdClass, rowKey: rowKey }, rowKey));
-            }
-            return ((0, jsx_runtime_1.jsx)(SimplexOrRegularRow, { base: base, score: score, isMod: isMod, isSimplex: isSimplex, readsCounted: readsCounted, model: model, tdClass: tdClass, rowKey: rowKey }, rowKey));
-        }) }));
-}
-const TooltipContents = (0, react_1.forwardRef)(function TooltipContents2(props, reactRef) {
-    const { feature, model } = props;
-    const { classes } = useStyles();
-    const start = feature.get('start') + 1;
-    const end = feature.get('end');
-    const name = feature.get('refName');
-    const { refbase: referenceBase, readsCounted, depth, ref: reference, ...info } = feature.get('snpinfo');
-    return ((0, jsx_runtime_1.jsx)("div", { ref: reactRef, children: (0, jsx_runtime_1.jsxs)("table", { children: [(0, jsx_runtime_1.jsx)("caption", { children: [
-                        name,
-                        start === end
-                            ? (0, util_1.toLocale)(start)
-                            : `${(0, util_1.toLocale)(start)}..${(0, util_1.toLocale)(end)}`,
-                    ]
-                        .filter(f => !!f)
-                        .join(':') }), (0, jsx_runtime_1.jsx)(TableHeader, {}), (0, jsx_runtime_1.jsxs)("tbody", { children: [(0, jsx_runtime_1.jsx)(TotalRow, { readsCounted: readsCounted }), (0, jsx_runtime_1.jsx)(RefRow, { referenceBase: referenceBase, reference: reference, readsCounted: readsCounted }), (0, jsx_runtime_1.jsx)(ModificationRows, { info: info, readsCounted: readsCounted, model: model, tdClass: classes.td })] })] }) }));
-});
-exports.default = TooltipContents;

package/dist/LinearSNPCoverageDisplay/configSchema.d.ts

@@ -1,80 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    autoscale: {
-        type: string;
-        defaultValue: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-    };
-    minScore: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    maxScore: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    scaleType: {
-        type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-        defaultValue: string;
-    };
-    inverted: {
-        type: string;
-        description: string;
-        defaultValue: boolean;
-    };
-    multiTicks: {
-        type: string;
-        description: string;
-        defaultValue: boolean;
-    };
-    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        SNPCoverageRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    colorBy: {
-        type: string;
-        description: string;
-        defaultValue: {
-            type: string;
-        };
-    };
-    filterBy: {
-        type: string;
-        description: string;
-        defaultValue: {
-            flagInclude: number;
-            flagExclude: number;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    maxFeatureScreenDensity: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    fetchSizeLimit: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    height: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    mouseover: {
-        type: string;
-        description: string;
-        defaultValue: string;
-        contextVariable: string[];
-    };
-    jexlFilters: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;

package/dist/LinearSNPCoverageDisplay/configSchema.js

@@ -1,62 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = SNPCoverageConfigFactory;
-const configuration_1 = require("@jbrowse/core/configuration");
-const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("../shared/util");
-function x() { }
-function SNPCoverageConfigFactory(pluginManager) {
-    return (0, configuration_1.ConfigurationSchema)('LinearSNPCoverageDisplay', {
-        autoscale: {
-            type: 'stringEnum',
-            defaultValue: 'local',
-            model: mobx_state_tree_1.types.enumeration('Autoscale type', ['local']),
-            description: 'performs local autoscaling (no other options for SNP Coverage available)',
-        },
-        minScore: {
-            type: 'number',
-            defaultValue: Number.MIN_VALUE,
-            description: 'minimum value for the y-scale',
-        },
-        maxScore: {
-            type: 'number',
-            description: 'maximum value for the y-scale',
-            defaultValue: Number.MAX_VALUE,
-        },
-        scaleType: {
-            type: 'stringEnum',
-            model: mobx_state_tree_1.types.enumeration('Scale type', ['linear', 'log']),
-            description: 'The type of scale to use',
-            defaultValue: 'linear',
-        },
-        inverted: {
-            type: 'boolean',
-            description: 'draw upside down',
-            defaultValue: false,
-        },
-        multiTicks: {
-            type: 'boolean',
-            description: 'Display multiple values for the ticks',
-            defaultValue: false,
-        },
-        renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
-            SNPCoverageRenderer: pluginManager.getRendererType('SNPCoverageRenderer').configSchema,
-        }),
-        colorBy: {
-            type: 'frozen',
-            description: 'color scheme to use',
-            defaultValue: {
-                type: 'normal',
-            },
-        },
-        filterBy: {
-            type: 'frozen',
-            description: 'default filters to use',
-            defaultValue: util_1.defaultFilterFlags,
-        },
-    }, {
-        baseConfiguration: plugin_linear_genome_view_1.baseLinearDisplayConfigSchema,
-        explicitlyTyped: true,
-    });
-}

package/dist/LinearSNPCoverageDisplay/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function register(pluginManager: PluginManager): void;

package/dist/LinearSNPCoverageDisplay/index.js

@@ -1,24 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = register;
-const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
-const configSchema_1 = __importDefault(require("./configSchema"));
-const model_1 = __importDefault(require("./model"));
-function register(pluginManager) {
-    pluginManager.addDisplayType(() => {
-        const configSchema = (0, configSchema_1.default)(pluginManager);
-        return new DisplayType_1.default({
-            name: 'LinearSNPCoverageDisplay',
-            displayName: 'SNPCoverage display',
-            configSchema,
-            stateModel: (0, model_1.default)(pluginManager, configSchema),
-            trackType: 'AlignmentsTrack',
-            viewType: 'LinearGenomeView',
-            ReactComponent: plugin_wiggle_1.LinearWiggleDisplayReactComponent,
-        });
-    });
-}