@jbrowse/plugin-spreadsheet-view 2.6.1

package/esm/SpreadsheetView/importAdapters/VcfImport.d.ts

@@ -0,0 +1,13 @@
+/// <reference types="node" />
+import { RowSet, Column, ParseOptions } from './ImportUtils';
+export declare function parseVcfBuffer(buffer: Buffer, options?: ParseOptions): {
+    rowSet: RowSet;
+    columnDisplayOrder: number[];
+    hasColumnNames: boolean;
+    columns: Column[];
+    assemblyName: string | undefined;
+};
+export declare function splitVcfFileHeaderAndBody(wholeFile: string): {
+    header: string;
+    body: string;
+};

package/esm/SpreadsheetView/importAdapters/VcfImport.js

@@ -0,0 +1,103 @@
+import VCF from '@gmod/vcf';
+import { VcfFeature } from '@jbrowse/plugin-variants';
+import { bufferToString, } from './ImportUtils';
+const vcfCoreColumns = [
+    { name: 'CHROM', type: 'Text' },
+    { name: 'POS', type: 'Number' },
+    { name: 'ID', type: 'Text' },
+    { name: 'REF', type: 'Text' },
+    { name: 'ALT', type: 'Text' },
+    { name: 'QUAL', type: 'Number' },
+    { name: 'FILTER', type: 'Text' },
+    { name: 'INFO', type: 'Text' },
+    { name: 'FORMAT', type: 'Text' }, // 8
+];
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+function vcfRecordToRow(vcfParser, line, lineNumber) {
+    const vcfVariant = vcfParser.parseLine(line);
+    const vcfFeature = new VcfFeature({
+        variant: vcfVariant,
+        parser: vcfParser,
+        id: `vcf-${lineNumber}`,
+    });
+    const data = line.split('\t').map(d => (d === '.' ? '' : d));
+    // no format column, add blank
+    if (data.length === 8) {
+        data.push('');
+    }
+    const row = {
+        id: String(lineNumber + 1),
+        extendedData: { vcfFeature: vcfFeature.toJSON() },
+        cells: data.map((text, columnNumber) => {
+            return {
+                columnNumber,
+                text,
+            };
+        }),
+    };
+    return row;
+}
+export function parseVcfBuffer(buffer, options = {}) {
+    const { selectedAssemblyName } = options;
+    let { header, body } = splitVcfFileHeaderAndBody(bufferToString(buffer));
+    const rows = [];
+    const vcfParser = new VCF({ header });
+    header = ''; // garbage collect
+    body.split(/\n|\r\n|\r/).forEach((line, lineNumber) => {
+        if (/\S/.test(line)) {
+            rows.push(vcfRecordToRow(vcfParser, line, lineNumber));
+        }
+    });
+    body = ''; // garbage collect
+    const rowSet = {
+        isLoaded: true,
+        rows,
+    };
+    const columnDisplayOrder = [];
+    const columns = [];
+    for (let i = 0; i < vcfCoreColumns.length; i += 1) {
+        columnDisplayOrder.push(i);
+        columns[i] = {
+            name: vcfCoreColumns[i].name,
+            dataType: { type: vcfCoreColumns[i].type },
+        };
+    }
+    for (let i = 0; i < vcfParser.samples.length; i += 1) {
+        const oi = vcfCoreColumns.length + i;
+        columnDisplayOrder.push(oi);
+        columns[oi] = { name: vcfParser.samples[i], dataType: { type: 'Text' } };
+    }
+    columnDisplayOrder.push(columnDisplayOrder.length);
+    columns.unshift({
+        name: 'Location',
+        dataType: { type: 'LocString' },
+        isDerived: true,
+        derivationFunctionText: `jexl:{text:row.extendedData.vcfFeature.refName+':'\n
+    +row.extendedData.vcfFeature.start+'..'+row.extendedData.vcfFeature.end, extendedData:\n
+    {refName:row.extendedData.vcfFeature.refName,start:row.extendedData.vcfFeature.start,end:row.extendedData.vcfFeature.end}}`,
+    });
+    return {
+        rowSet,
+        columnDisplayOrder,
+        hasColumnNames: true,
+        columns,
+        assemblyName: selectedAssemblyName,
+    };
+}
+export function splitVcfFileHeaderAndBody(wholeFile) {
+    // split into header and the rest of the file
+    let headerEndIndex = 0;
+    let prevChar;
+    for (; headerEndIndex < wholeFile.length; headerEndIndex += 1) {
+        const c = wholeFile[headerEndIndex];
+        if (prevChar === '\n' && c !== '#') {
+            break;
+        }
+        prevChar = c;
+    }
+    return {
+        header: wholeFile.slice(0, Math.max(0, headerEndIndex)),
+        body: wholeFile.slice(headerEndIndex),
+    };
+}
+//# sourceMappingURL=VcfImport.js.map

package/esm/SpreadsheetView/importAdapters/VcfImport.js.map

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package/esm/SpreadsheetView/index.d.ts

@@ -0,0 +1,4 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;
+export { type SpreadsheetViewModel, type SpreadsheetViewStateModel, } from './models/SpreadsheetView';

package/esm/SpreadsheetView/index.js

@@ -0,0 +1,14 @@
+import { lazy } from 'react';
+import { ViewType } from '@jbrowse/core/pluggableElementTypes';
+import stateModel from './models/SpreadsheetView';
+export default (pluginManager) => {
+    pluginManager.addViewType(() => {
+        return new ViewType({
+            name: 'SpreadsheetView',
+            displayName: 'Spreadsheet view',
+            stateModel,
+            ReactComponent: lazy(() => import('./components/SpreadsheetView')),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/SpreadsheetView/index.js.map

@@ -0,0 +1 @@
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package/esm/SpreadsheetView/models/ColumnDataTypes/LocEnd.d.ts

@@ -0,0 +1,13 @@
+/// <reference types="react" />
+declare const LocEnd: import("mobx-state-tree").IModelType<{
+    type: import("mobx-state-tree").ISimpleType<string>;
+}, {
+    DataCellReactComponent: import("react").FC<any> | null;
+    FilterModelType: any;
+    displayName: string;
+    categoryName: string | undefined;
+} & {
+    compare: any;
+    readonly hasFilter: boolean;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default LocEnd;

package/esm/SpreadsheetView/models/ColumnDataTypes/LocEnd.js

@@ -0,0 +1,16 @@
+import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType';
+import { FilterModelType as NumberFilterModel } from './Number';
+import { types } from 'mobx-state-tree';
+const FilterModelType = types.compose(NumberFilterModel, types.model({
+    type: types.literal('LocEnd'),
+}));
+const LocEnd = MakeSpreadsheetColumnType('LocEnd', {
+    categoryName: 'Location',
+    displayName: 'End',
+    compare(cellA, cellB) {
+        return parseFloat(cellA.text) - parseFloat(cellB.text);
+    },
+    FilterModelType,
+});
+export default LocEnd;
+//# sourceMappingURL=LocEnd.js.map

package/esm/SpreadsheetView/models/ColumnDataTypes/LocEnd.js.map

@@ -0,0 +1 @@
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package/esm/SpreadsheetView/models/ColumnDataTypes/LocRef.d.ts

@@ -0,0 +1,13 @@
+/// <reference types="react" />
+declare const LocRef: import("mobx-state-tree").IModelType<{
+    type: import("mobx-state-tree").ISimpleType<string>;
+}, {
+    DataCellReactComponent: import("react").FC<any> | null;
+    FilterModelType: any;
+    displayName: string;
+    categoryName: string | undefined;
+} & {
+    compare: any;
+    readonly hasFilter: boolean;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default LocRef;

package/esm/SpreadsheetView/models/ColumnDataTypes/LocRef.js

@@ -0,0 +1,16 @@
+import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType';
+import { FilterModelType as NumberFilterModel } from './Text';
+import { types } from 'mobx-state-tree';
+const FilterModelType = types.compose(NumberFilterModel, types.model({
+    type: types.literal('LocRef'),
+}));
+const LocRef = MakeSpreadsheetColumnType('LocRef', {
+    categoryName: 'Location',
+    displayName: 'Reference seq',
+    compare(cellA, cellB) {
+        return cellA.text.localeCompare(cellB.text);
+    },
+    FilterModelType,
+});
+export default LocRef;
+//# sourceMappingURL=LocRef.js.map

package/esm/SpreadsheetView/models/ColumnDataTypes/LocRef.js.map

@@ -0,0 +1 @@
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package/esm/SpreadsheetView/models/ColumnDataTypes/LocStart.d.ts

@@ -0,0 +1,13 @@
+/// <reference types="react" />
+declare const LocStart: import("mobx-state-tree").IModelType<{
+    type: import("mobx-state-tree").ISimpleType<string>;
+}, {
+    DataCellReactComponent: import("react").FC<any> | null;
+    FilterModelType: any;
+    displayName: string;
+    categoryName: string | undefined;
+} & {
+    compare: any;
+    readonly hasFilter: boolean;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default LocStart;

package/esm/SpreadsheetView/models/ColumnDataTypes/LocStart.js

@@ -0,0 +1,16 @@
+import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType';
+import { types } from 'mobx-state-tree';
+import { FilterModelType as NumberFilterModel } from './Number';
+const FilterModelType = types.compose(NumberFilterModel, types.model({
+    type: types.literal('LocStart'),
+}));
+const LocStart = MakeSpreadsheetColumnType('LocStart', {
+    categoryName: 'Location',
+    displayName: 'Start',
+    compare(cellA, cellB) {
+        return parseFloat(cellA.text) - parseFloat(cellB.text);
+    },
+    FilterModelType,
+});
+export default LocStart;
+//# sourceMappingURL=LocStart.js.map

package/esm/SpreadsheetView/models/ColumnDataTypes/LocStart.js.map

@@ -0,0 +1 @@
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package/esm/SpreadsheetView/models/ColumnDataTypes/LocString.d.ts

@@ -0,0 +1,13 @@
+import React from 'react';
+declare const LocStringColumnType: import("mobx-state-tree").IModelType<{
+    type: import("mobx-state-tree").ISimpleType<string>;
+}, {
+    DataCellReactComponent: React.FC<any> | null;
+    FilterModelType: any;
+    displayName: string;
+    categoryName: string | undefined;
+} & {
+    compare: any;
+    readonly hasFilter: boolean;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default LocStringColumnType;

package/esm/SpreadsheetView/models/ColumnDataTypes/LocString.js

@@ -0,0 +1,185 @@
+import React from 'react';
+import { IconButton, TextField, MenuItem, InputAdornment, Select, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import { observer } from 'mobx-react';
+import { types, getParent, getPropertyMembers } from 'mobx-state-tree';
+// jbrowse imports
+import { getPropertyType, getEnumerationValues, getSubType, } from '@jbrowse/core/util/mst-reflection';
+import { doesIntersect2, isContainedWithin, compareLocs, getSession, parseLocString, } from '@jbrowse/core/util';
+// icons
+import ClearIcon from '@mui/icons-material/Clear';
+// locals
+import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType';
+const useStyles = makeStyles()({
+    textFilterControlAdornment: { marginRight: '-18px' },
+    textFilterControl: {
+        '& .MuiInput-formControl': {
+            marginTop: 8,
+        },
+        '& .MuiInputLabel-formControl': {
+            top: '-7px',
+            '&.MuiInputLabel-shrink': {
+                top: '-3px',
+            },
+        },
+    },
+});
+// React component for the column filter control
+const FilterReactComponent = observer(function ({ filterModel, }) {
+    const { classes } = useStyles();
+    const operationChoices = getEnumerationValues(getSubType(getPropertyType(getPropertyMembers(filterModel), 'operation')));
+    return (React.createElement(React.Fragment, null,
+        React.createElement(Select, { value: filterModel.operation, onChange: event => filterModel.setOperation(String(event.target.value)) }, operationChoices.map(name => (React.createElement(MenuItem, { key: name, value: name }, name)))),
+        ' ',
+        React.createElement(TextField, { label: "range", placeholder: "chr1:100-200", error: filterModel.locStringIsInvalid, value: filterModel.locString, onChange: evt => filterModel.setLocString(evt.target.value), className: classes.textFilterControl, InputProps: {
+                endAdornment: (React.createElement(InputAdornment, { className: classes.textFilterControlAdornment, position: "end" },
+                    React.createElement(IconButton, { "aria-label": "clear filter", onClick: () => filterModel.setLocString('') },
+                        React.createElement(ClearIcon, null)))),
+            } })));
+});
+const OPERATIONS = [
+    'overlaps with',
+    'contained within',
+    'fully contains',
+    'does not overlap',
+    'not contained within',
+    'does not contain',
+];
+// NOTE: assembly names, if present, are ignored in all of these predicates
+const OPERATION_PREDICATES = {
+    'overlaps with': (cellLocation, specifiedLocation) => {
+        return (cellLocation.refName === specifiedLocation.refName &&
+            doesIntersect2(cellLocation.start, cellLocation.end, specifiedLocation.start, specifiedLocation.end));
+    },
+    'contained within': (cellLocation, specifiedLocation) => {
+        return (cellLocation.refName === specifiedLocation.refName &&
+            isContainedWithin(cellLocation.start, cellLocation.end, specifiedLocation.start, specifiedLocation.end));
+    },
+    'fully contains': (cellLocation, specifiedLocation) => {
+        return (cellLocation.refName === specifiedLocation.refName &&
+            isContainedWithin(specifiedLocation.start, specifiedLocation.end, cellLocation.start, cellLocation.end));
+    },
+};
+OPERATION_PREDICATES['does not overlap'] = (cellLocation, specifiedLocation) => {
+    return !OPERATION_PREDICATES['overlaps with'](cellLocation, specifiedLocation);
+};
+OPERATION_PREDICATES['not contained within'] = (cellLocation, specifiedLocation) => {
+    return !OPERATION_PREDICATES['contained within'](cellLocation, specifiedLocation);
+};
+OPERATION_PREDICATES['does not contain'] = (cellLocation, specifiedLocation) => {
+    return !OPERATION_PREDICATES['fully contains'](cellLocation, specifiedLocation);
+};
+// MST model for the column filter control
+const FilterModelType = types
+    .model('ColumnLocStringFilter', {
+    type: types.literal('LocString'),
+    columnNumber: types.integer,
+    locString: '',
+    operation: types.optional(types.enumeration(OPERATIONS), OPERATIONS[0]),
+})
+    .views(self => ({
+    get locStringIsInvalid() {
+        if (self.locString) {
+            const parsed = this.parsedLocString;
+            return (!parsed ||
+                parsed.refName === '' ||
+                typeof parsed.start !== 'number' ||
+                typeof parsed.end !== 'number' ||
+                parsed.start > parsed.end);
+        }
+        return false;
+    },
+    get parsedLocString() {
+        const session = getSession(self);
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        const model = getParent(self, 3).spreadsheet;
+        const { assemblyName } = model;
+        try {
+            return parseLocString(self.locString, refName => session.assemblyManager.isValidRefName(refName, assemblyName));
+        }
+        catch (e) {
+            return undefined;
+        }
+    },
+}))
+    .views(self => ({
+    // returns a function that tests the given row
+    get predicate() {
+        const { locString, locStringIsInvalid, parsedLocString, operation, columnNumber, } = self; // avoid closing over self
+        if (!locString || locStringIsInvalid || !parsedLocString) {
+            return function alwaysTrue() {
+                return true;
+            };
+        }
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        return function stringPredicate(_sheet, row) {
+            const { cellsWithDerived: cells } = row;
+            const cell = cells[columnNumber];
+            if (!cell || !cell.text || !cell.extendedData) {
+                return false;
+            }
+            const parsedCellText = cell.extendedData;
+            if (!parsedCellText.refName) {
+                return false;
+            }
+            const predicate = OPERATION_PREDICATES[operation];
+            if (!predicate) {
+                throw new Error(`"${operation}" not implemented in location filter`);
+            }
+            return predicate(parsedCellText, parsedLocString);
+        };
+    },
+}))
+    .actions(self => ({
+    setLocString(s) {
+        self.locString = s;
+    },
+    setOperation(op) {
+        self.operation = op;
+    },
+}))
+    .volatile(() => ({ ReactComponent: FilterReactComponent }));
+// opens a new LGV at the location described in the locString in the cell text
+async function locationLinkClick(
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+spreadsheet, _columnNumber, 
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+cell) {
+    const session = getSession(spreadsheet);
+    const { assemblyName } = spreadsheet;
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    const { id } = getParent(spreadsheet);
+    const newViewId = `${id}_${assemblyName}`;
+    let view = session.views.find(v => v.id === newViewId);
+    if (!view) {
+        view = session.addView('LinearGenomeView', {
+            id: newViewId,
+        });
+    }
+    await view.navToLocString(cell.text, assemblyName);
+}
+const DataCellReactComponent = observer(function ({ cell, columnNumber, spreadsheet, }) {
+    return (React.createElement("a", { onClick: async (evt) => {
+            evt.preventDefault();
+            const session = getSession(spreadsheet);
+            try {
+                await locationLinkClick(spreadsheet, columnNumber, cell);
+            }
+            catch (e) {
+                console.error(e);
+                session.notify(`${e}`, 'error');
+            }
+        }, title: "open a new linear genome view here", href: "#link" }, cell.text));
+});
+const LocStringColumnType = MakeSpreadsheetColumnType('LocString', {
+    categoryName: 'Location',
+    displayName: 'Full location',
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    compare(cellA, cellB) {
+        return compareLocs(cellA.extendedData, cellB.extendedData);
+    },
+    FilterModelType,
+    DataCellReactComponent,
+});
+export default LocStringColumnType;
+//# sourceMappingURL=LocString.js.map

package/esm/SpreadsheetView/models/ColumnDataTypes/LocString.js.map

@@ -0,0 +1 @@
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package/esm/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.d.ts

@@ -0,0 +1,19 @@
+import React from 'react';
+/** utility function for assembling the MST model of a column data type */
+export default function MakeSpreadsheetColumnType(name: string, { DataCellReactComponent, FilterModelType, compare, displayName, categoryName, }: {
+    compare?: any;
+    DataCellReactComponent?: React.FC<any> | null;
+    FilterModelType?: any;
+    displayName?: string;
+    categoryName?: string;
+}): import("mobx-state-tree").IModelType<{
+    type: import("mobx-state-tree").ISimpleType<string>;
+}, {
+    DataCellReactComponent: React.FC<any> | null;
+    FilterModelType: any;
+    displayName: string;
+    categoryName: string | undefined;
+} & {
+    compare: any;
+    readonly hasFilter: boolean;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.js

@@ -0,0 +1,21 @@
+import { types } from 'mobx-state-tree';
+/** utility function for assembling the MST model of a column data type */
+export default function MakeSpreadsheetColumnType(name, { DataCellReactComponent = null, FilterModelType = null, compare, displayName = undefined, categoryName = undefined, }) {
+    return types
+        .model(`ColumnDataType${name}`, {
+        type: types.literal(name),
+    })
+        .volatile(() => ({
+        DataCellReactComponent,
+        FilterModelType: FilterModelType,
+        displayName: displayName || name,
+        categoryName,
+    }))
+        .views(() => ({
+        compare,
+        get hasFilter() {
+            return !!FilterModelType;
+        },
+    }));
+}
+//# sourceMappingURL=MakeSpreadsheetColumnType.js.map

package/esm/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.js.map

@@ -0,0 +1 @@
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package/esm/SpreadsheetView/models/ColumnDataTypes/Number.d.ts

@@ -0,0 +1,30 @@
+import React from 'react';
+declare const FilterModelType: import("mobx-state-tree").IModelType<{
+    type: import("mobx-state-tree").ISimpleType<"Number">;
+    columnNumber: import("mobx-state-tree").ISimpleType<number>;
+    firstNumber: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    secondNumber: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<number>>;
+    operation: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+}, {
+    readonly predicate: (_sheet: any, row: any) => boolean;
+} & {
+    setFirstNumber(n: number): void;
+    setSecondNumber(n: number): void;
+    setOperation(op: string): void;
+} & {
+    ReactComponent: ({ filterModel }: {
+        filterModel: any;
+    }) => React.JSX.Element;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+declare const NumberColumn: import("mobx-state-tree").IModelType<{
+    type: import("mobx-state-tree").ISimpleType<string>;
+}, {
+    DataCellReactComponent: React.FC<any> | null;
+    FilterModelType: any;
+    displayName: string;
+    categoryName: string | undefined;
+} & {
+    compare: any;
+    readonly hasFilter: boolean;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export { NumberColumn, FilterModelType };