@jbrowse/plugin-wiggle 3.6.5 → 4.0.0

package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/WiggleClusterDialogManual.js

@@ -1,145 +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 react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const material_1 = require("@mui/material");
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-const file_saver_1 = require("file-saver");
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mui_1 = require("tss-react/mui");
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    textAreaFont: {
-        fontFamily: 'Courier New',
-    },
-    mgap: {
-        display: 'flex',
-        flexDirection: 'column',
-        gap: theme.spacing(4),
-    },
-}));
-const WiggleClusterDialogManuals = (0, mobx_react_1.observer)(function ({ model, handleClose, children, }) {
-    const { classes } = useStyles();
-    const [paste, setPaste] = (0, react_1.useState)('');
-    const [ret, setRet] = (0, react_1.useState)();
-    const [error, setError] = (0, react_1.useState)();
-    const [loading, setLoading] = (0, react_1.useState)(false);
-    const [showAdvanced, setShowAdvanced] = (0, util_1.useLocalStorage)('cluster-showAdvanced', false);
-    const [clusterMethod, setClusterMethod] = (0, react_1.useState)('single');
-    const [samplesPerPixel, setSamplesPerPixel] = (0, react_1.useState)('1');
-    (0, react_1.useEffect)(() => {
-        ;
-        (async () => {
-            try {
-                setError(undefined);
-                setRet(undefined);
-                setLoading(true);
-                const view = (0, util_1.getContainingView)(model);
-                const { dynamicBlocks, bpPerPx } = view;
-                const { rpcManager } = (0, util_1.getSession)(model);
-                const { sourcesWithoutLayout, adapterConfig } = model;
-                const sessionId = (0, tracks_1.getRpcSessionId)(model);
-                const ret = (await rpcManager.call(sessionId, 'MultiWiggleGetScoreMatrix', {
-                    regions: dynamicBlocks.contentBlocks,
-                    sources: sourcesWithoutLayout,
-                    sessionId,
-                    adapterConfig,
-                    bpPerPx: bpPerPx / +samplesPerPixel,
-                }));
-                setRet(ret);
-            }
-            catch (e) {
-                if (!(0, util_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(model)) {
-                    console.error(e);
-                    setError(e);
-                }
-            }
-            finally {
-                setLoading(false);
-            }
-        })();
-    }, [model, samplesPerPixel]);
-    const results = ret
-        ? `inputMatrix<-matrix(c(${Object.values(ret)
-            .map(val => val.join(','))
-            .join(',\n')}
-),nrow=${Object.values(ret).length},byrow=TRUE)
-rownames(inputMatrix)<-c(${Object.keys(ret)
-            .map(key => `'${key}'`)
-            .join(',')})
-resultClusters<-hclust(dist(inputMatrix), method='${clusterMethod}')
-cat(resultClusters$order,sep='\\n')`
-        : undefined;
-    const resultsTsv = ret
-        ? Object.entries(ret)
-            .map(([key, val]) => [key, ...val].join('\t'))
-            .join('\n')
-        : undefined;
-    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [children, (0, jsx_runtime_1.jsxs)("div", { style: { marginTop: 50 }, children: [(0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsxs)("div", { style: {
-                                            display: 'flex',
-                                            gap: '8px',
-                                            flexWrap: 'wrap',
-                                            marginBottom: '16px',
-                                        }, children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                    (0, file_saver_1.saveAs)(new Blob([results || ''], {
-                                                        type: 'text/plain;charset=utf-8',
-                                                    }), 'cluster.R');
-                                                }, children: "Download Rscript" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                    (0, copy_to_clipboard_1.default)(results || '');
-                                                }, children: "Copy Rscript to clipboard" }), ' ', "or", ' ', (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                    (0, file_saver_1.saveAs)(new Blob([resultsTsv || ''], {
-                                                        type: 'text/plain;charset=utf-8',
-                                                    }), 'scores.tsv');
-                                                }, children: "Download TSV" })] }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                                                setShowAdvanced(!showAdvanced);
-                                            }, children: showAdvanced
-                                                ? 'Hide advanced options'
-                                                : 'Show advanced options' }) }), showAdvanced ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "h6", children: "Advanced options" }), (0, jsx_runtime_1.jsx)(material_1.RadioGroup, { children: Object.entries({
-                                                    single: 'Single',
-                                                    complete: 'Complete',
-                                                }).map(([key, val]) => ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { control: (0, jsx_runtime_1.jsx)(material_1.Radio, { checked: clusterMethod === key, onChange: () => {
-                                                            setClusterMethod(key);
-                                                        } }), label: val }, key))) }), (0, jsx_runtime_1.jsxs)("div", { style: { marginTop: 20 }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "This procedure samples the data at each 'pixel' across the visible by default" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Samples per pixel (>1 for denser sampling, between 0-1 for sparser sampling)", variant: "outlined", size: "small", value: samplesPerPixel, onChange: event => {
-                                                            setSamplesPerPixel(event.target.value);
-                                                        } })] })] })) : null, results ? ((0, jsx_runtime_1.jsx)("div", {})) : loading ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { variant: "h6", title: "Generating score matrix" })) : error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : null] }), (0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { variant: "subtitle2", gutterBottom: true, style: { marginTop: '16px' }, children: "Clustering Results:" }), (0, jsx_runtime_1.jsx)(material_1.TextField, { multiline: true, fullWidth: true, variant: "outlined", placeholder: "Paste results from Rscript here (sequence of numbers, one per line, specifying the new ordering)", rows: 10, value: paste, onChange: event => {
-                                            setPaste(event.target.value);
-                                        }, slotProps: {
-                                            input: {
-                                                classes: {
-                                                    input: classes.textAreaFont,
-                                                },
-                                            },
-                                        } })] })] })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
-                            const { sourcesWithoutLayout } = model;
-                            if (sourcesWithoutLayout) {
-                                try {
-                                    model.setLayout(paste
-                                        .split('\n')
-                                        .map(t => t.trim())
-                                        .filter(f => !!f)
-                                        .map(r => +r)
-                                        .map(idx => {
-                                        const ret = sourcesWithoutLayout[idx - 1];
-                                        if (!ret) {
-                                            throw new Error(`out of bounds at ${idx}`);
-                                        }
-                                        return ret;
-                                    }));
-                                }
-                                catch (e) {
-                                    console.error(e);
-                                    (0, util_1.getSession)(model).notifyError(`${e}`, e);
-                                }
-                            }
-                            handleClose();
-                        }, children: "Apply clustering" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                            handleClose();
-                        }, children: "Cancel" })] })] }));
-});
-exports.default = WiggleClusterDialogManuals;

package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/types.d.ts

@@ -1,7 +0,0 @@
-import type { Source } from '../../types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export interface ReducedModel {
-    sourcesWithoutLayout?: Source[];
-    adapterConfig: AnyConfigurationModel;
-    setLayout: (arg: Source[]) => void;
-}

package/dist/MultiLinearWiggleDisplay/components/WiggleClusterDialog/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.d.ts

@@ -1,5 +0,0 @@
-import type { WiggleDisplayModel } from '../model';
-declare const MultiLinearWiggleDisplayComponent: (props: {
-    model: WiggleDisplayModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default MultiLinearWiggleDisplayComponent;

package/dist/MultiLinearWiggleDisplay/components/WiggleDisplayComponent.js

@@ -1,14 +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_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-const mobx_react_1 = require("mobx-react");
-const YScaleBars_1 = __importDefault(require("./YScaleBars"));
-const MultiLinearWiggleDisplayComponent = (0, mobx_react_1.observer)(function (props) {
-    const { model } = props;
-    return ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)(plugin_linear_genome_view_1.BaseLinearDisplayComponent, { ...props }), (0, jsx_runtime_1.jsx)(YScaleBars_1.default, { model: model })] }));
-});
-exports.default = MultiLinearWiggleDisplayComponent;

package/dist/MultiLinearWiggleDisplay/components/YScaleBars.d.ts

@@ -1,7 +0,0 @@
-import type { WiggleDisplayModel } from '../model';
-export declare const YScaleBars: (props: {
-    model: WiggleDisplayModel;
-    orientation?: string;
-    exportSVG?: boolean;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default YScaleBars;

package/dist/MultiLinearWiggleDisplay/components/YScaleBars.js

@@ -1,28 +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.YScaleBars = void 0;
-const jsx_runtime_1 = require("react/jsx-runtime");
-const util_1 = require("@jbrowse/core/util");
-const mobx_react_1 = require("mobx-react");
-const FullHeightScaleBar_1 = __importDefault(require("./FullHeightScaleBar"));
-const IndividualScaleBars_1 = __importDefault(require("./IndividualScaleBars"));
-const Wrapper = (0, mobx_react_1.observer)(function ({ children, model, exportSVG, }) {
-    const { height } = model;
-    return exportSVG ? (children) : ((0, jsx_runtime_1.jsx)("svg", { style: {
-            position: 'absolute',
-            top: 0,
-            left: 0,
-            pointerEvents: 'none',
-            height,
-            width: (0, util_1.getContainingView)(model).width,
-        }, children: children }));
-});
-exports.YScaleBars = (0, mobx_react_1.observer)(function (props) {
-    const { model, orientation, exportSVG } = props;
-    const { showSidebar, stats, needsFullHeightScalebar, sources } = model;
-    return stats && sources ? ((0, jsx_runtime_1.jsx)(Wrapper, { ...props, children: showSidebar ? (needsFullHeightScalebar ? ((0, jsx_runtime_1.jsx)(FullHeightScaleBar_1.default, { model: model, orientation: orientation, exportSVG: exportSVG })) : ((0, jsx_runtime_1.jsx)(IndividualScaleBars_1.default, { model: model, orientation: orientation, exportSVG: exportSVG }))) : null })) : null;
-});
-exports.default = exports.YScaleBars;

package/dist/MultiLinearWiggleDisplay/components/util.d.ts

@@ -1,13 +0,0 @@
-import type { WiggleDisplayModel } from '../model';
-import type { GridRowId } from '@mui/x-data-grid';
-export declare function moveUp(arr: {
-    name: string;
-}[], sel: GridRowId[], by?: number): {
-    name: string;
-}[];
-export declare function moveDown(arr: {
-    name: string;
-}[], sel: GridRowId[], by?: number): {
-    name: string;
-}[];
-export declare function getOffset(model: WiggleDisplayModel): number;

package/dist/MultiLinearWiggleDisplay/components/util.js

@@ -1,45 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.moveUp = moveUp;
-exports.moveDown = moveDown;
-exports.getOffset = getOffset;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-function moveUp(arr, sel, by = 1) {
-    const idxs = sel
-        .map(l => arr.findIndex(v => v.name === l))
-        .sort((a, b) => a - b);
-    let lastIdx = 0;
-    for (const old of idxs) {
-        const idx = Math.max(lastIdx, old - by);
-        if (idx >= lastIdx) {
-            arr.splice(idx, 0, arr.splice(old, 1)[0]);
-        }
-        lastIdx = lastIdx + 1;
-    }
-    return arr;
-}
-function moveDown(arr, sel, by = 1) {
-    const idxs = sel
-        .map(l => arr.findIndex(v => v.name === l))
-        .sort((a, b) => b - a);
-    let lastIdx = arr.length - 1;
-    for (const old of idxs) {
-        const idx = Math.min(lastIdx, old + by);
-        if (idx <= lastIdx) {
-            arr.splice(idx, 0, arr.splice(old, 1)[0]);
-        }
-        lastIdx = lastIdx - 1;
-    }
-    return arr;
-}
-const trackLabelFontSize = 12.8;
-function getOffset(model) {
-    const { prefersOffset } = model;
-    const { trackLabels } = (0, util_1.getContainingView)(model);
-    const track = (0, util_1.getContainingTrack)(model);
-    const trackName = (0, configuration_1.getConf)(track, 'name');
-    return trackLabels === 'overlapping' && !prefersOffset
-        ? (0, util_1.measureText)(trackName, trackLabelFontSize) + 100
-        : 10;
-}

package/dist/MultiLinearWiggleDisplay/configSchema.d.ts

@@ -1,84 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function WiggleConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    defaultRendering: {
-        type: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        defaultValue: string;
-    };
-    renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        MultiXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        MultiDensityRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        MultiRowXYPlotRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        MultiLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-        MultiRowLineRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-    height: {
-        type: string;
-        defaultValue: number;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    autoscale: {
-        type: string;
-        defaultValue: string;
-        model: import("mobx-state-tree").ISimpleType<string>;
-        description: string;
-    };
-    minimalTicks: {
-        type: string;
-        defaultValue: boolean;
-        description: string;
-    };
-    minScore: {
-        type: string;
-        defaultValue: number;
-        description: string;
-    };
-    maxScore: {
-        type: string;
-        description: string;
-        defaultValue: number;
-    };
-    numStdDev: {
-        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;
-    };
-}, 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>>, undefined>>;

package/dist/MultiLinearWiggleDisplay/configSchema.js

@@ -1,44 +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 = WiggleConfigFactory;
-const configuration_1 = require("@jbrowse/core/configuration");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const SharedWiggleConfigSchema_1 = __importDefault(require("../shared/SharedWiggleConfigSchema"));
-function x() { }
-function WiggleConfigFactory(pluginManager) {
-    const MultiXYPlotRendererConfigSchema = pluginManager.getRendererType('MultiXYPlotRenderer').configSchema;
-    const MultiDensityRendererConfigSchema = pluginManager.getRendererType('MultiDensityRenderer').configSchema;
-    const MultiRowXYPlotRendererConfigSchema = pluginManager.getRendererType('MultiRowXYPlotRenderer').configSchema;
-    const MultiLineRendererConfigSchema = pluginManager.getRendererType('MultiLineRenderer').configSchema;
-    const MultiRowLineRendererConfigSchema = pluginManager.getRendererType('MultiRowLineRenderer').configSchema;
-    return (0, configuration_1.ConfigurationSchema)('MultiLinearWiggleDisplay', {
-        defaultRendering: {
-            type: 'stringEnum',
-            model: mobx_state_tree_1.types.enumeration('Rendering', [
-                'multirowxy',
-                'xyplot',
-                'multirowdensity',
-                'multiline',
-                'multirowline',
-            ]),
-            defaultValue: 'multirowxy',
-        },
-        renderers: (0, configuration_1.ConfigurationSchema)('RenderersConfiguration', {
-            MultiXYPlotRenderer: MultiXYPlotRendererConfigSchema,
-            MultiDensityRenderer: MultiDensityRendererConfigSchema,
-            MultiRowXYPlotRenderer: MultiRowXYPlotRendererConfigSchema,
-            MultiLineRenderer: MultiLineRendererConfigSchema,
-            MultiRowLineRenderer: MultiRowLineRendererConfigSchema,
-        }),
-        height: {
-            type: 'number',
-            defaultValue: 200,
-        },
-    }, {
-        baseConfiguration: (0, SharedWiggleConfigSchema_1.default)(),
-        explicitlyTyped: true,
-    });
-}

package/dist/MultiLinearWiggleDisplay/index.d.ts

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

package/dist/MultiLinearWiggleDisplay/index.js

@@ -1,57 +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;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = MultiLinearWiggleDisplayF;
-const react_1 = require("react");
-const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-const model_1 = __importDefault(require("./model"));
-function MultiLinearWiggleDisplayF(pluginManager) {
-    pluginManager.addDisplayType(() => {
-        const configSchema = (0, configSchema_1.default)(pluginManager);
-        return new DisplayType_1.default({
-            name: 'MultiLinearWiggleDisplay',
-            displayName: 'Multi-wiggle display',
-            configSchema,
-            stateModel: (0, model_1.default)(pluginManager, configSchema),
-            trackType: 'MultiQuantitativeTrack',
-            viewType: 'LinearGenomeView',
-            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/WiggleDisplayComponent')))),
-        });
-    });
-}