@jbrowse/plugin-spreadsheet-view 2.6.1

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

@@ -0,0 +1,123 @@
+import React from 'react';
+import { types } from 'mobx-state-tree';
+import { observer } from 'mobx-react';
+import { MenuItem, Select, TextField } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType';
+const OPERATIONS = [
+    'equals',
+    'greater than',
+    'less than',
+    'between',
+    'not between',
+];
+// NOTE: assembly names, if present, are ignored in all of these predicates
+const OPERATION_PREDICATES = {
+    equals: (numberInCell, firstNumber) => {
+        return numberInCell === firstNumber;
+    },
+    'greater than': (numberInCell, firstNumber) => {
+        return numberInCell > firstNumber;
+    },
+    'less than': (numberInCell, firstNumber) => {
+        return numberInCell < firstNumber;
+    },
+    between: (numberInCell, firstNumber, secondNumber) => {
+        return (numberInCell > firstNumber &&
+            secondNumber !== undefined &&
+            numberInCell < secondNumber);
+    },
+};
+OPERATION_PREDICATES['not between'] = (numberInCell, firstNumber, secondNumber) => {
+    return !OPERATION_PREDICATES.between(numberInCell, firstNumber, secondNumber);
+};
+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(
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+({ filterModel }) => {
+    const { classes } = useStyles();
+    const operationChoices = OPERATIONS;
+    return (React.createElement(React.Fragment, null,
+        React.createElement(Select, { value: filterModel.operation, onChange: e => filterModel.setOperation(String(e.target.value)) }, operationChoices.map(name => (React.createElement(MenuItem, { key: name, value: name }, name)))),
+        ' ',
+        React.createElement(TextField, { label: "number", placeholder: "123", type: "number", error: filterModel.firstNumberIsInvalid, defaultValue: filterModel.firstNumber, onChange: evt => {
+                filterModel.setFirstNumber(parseFloat(evt.target.value));
+            }, className: classes.textFilterControl }),
+        filterModel.operation !== 'between' &&
+            filterModel.operation !== 'not between' ? null : (React.createElement(React.Fragment, null,
+            ' and ',
+            React.createElement(TextField, { label: "number", placeholder: "456", type: "number", error: filterModel.secondNumberIsInvalid, defaultValue: filterModel.secondNumber, onChange: evt => filterModel.setSecondNumber(parseFloat(evt.target.value)), className: classes.textFilterControl })))));
+});
+// MST model for the column filter control
+const FilterModelType = types
+    .model('ColumnNumberFilter', {
+    type: types.literal('Number'),
+    columnNumber: types.integer,
+    firstNumber: types.maybe(types.number),
+    secondNumber: types.maybe(types.number),
+    operation: types.optional(types.enumeration(OPERATIONS), OPERATIONS[0]),
+})
+    .views(self => ({
+    // returns a function that tests the given row
+    get predicate() {
+        if (typeof self.firstNumber !== 'number') {
+            return function alwaysTrue() {
+                return true;
+            };
+        }
+        const { firstNumber, secondNumber, operation, columnNumber } = self; // avoid closing over self
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        return function stringPredicate(_sheet, row) {
+            const { cellsWithDerived } = row;
+            const cell = cellsWithDerived[columnNumber];
+            if (!cell || !cell.text) {
+                return false;
+            }
+            const parsedCellText = parseFloat(cell.text);
+            if (typeof parsedCellText !== 'number') {
+                return false;
+            }
+            const predicate = OPERATION_PREDICATES[operation];
+            if (!predicate) {
+                throw new Error(`"${operation}" not implemented in location filter`);
+            }
+            return predicate(parsedCellText, firstNumber, secondNumber);
+        };
+    },
+}))
+    .actions(self => ({
+    setFirstNumber(n) {
+        self.firstNumber =
+            Number.isNaN(n) || typeof n !== 'number' ? undefined : n;
+    },
+    setSecondNumber(n) {
+        self.secondNumber =
+            Number.isNaN(n) || typeof n !== 'number' ? undefined : n;
+    },
+    setOperation(op) {
+        self.operation = op;
+    },
+}))
+    .volatile(() => ({ ReactComponent: FilterReactComponent }));
+const NumberColumn = MakeSpreadsheetColumnType('Number', {
+    compare(cellA, cellB) {
+        return parseFloat(cellA.text) - parseFloat(cellB.text);
+    },
+    FilterModelType,
+});
+export { NumberColumn, FilterModelType };
+//# sourceMappingURL=Number.js.map

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

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package/esm/SpreadsheetView/models/ColumnDataTypes/Text.d.ts

@@ -0,0 +1,28 @@
+import React from 'react';
+declare const ColumnTextFilter: import("mobx-state-tree").IModelType<{
+    type: import("mobx-state-tree").ISimpleType<"Text">;
+    columnNumber: import("mobx-state-tree").ISimpleType<number>;
+    stringToFind: import("mobx-state-tree").IType<string | undefined, string, string>;
+    operation: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+}, {
+    readonly predicate: (_sheet: any, row: any) => boolean;
+} & {
+    setString(s: string): void;
+    setOperation(op: string): void;
+} & {
+    ReactComponent: ({ filterModel }: {
+        filterModel: any;
+    }) => React.JSX.Element;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+declare const TextColumnType: 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 { TextColumnType as TextColumn, ColumnTextFilter as FilterModelType };

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

@@ -0,0 +1,124 @@
+import React from 'react';
+import { IconButton, TextField, MenuItem, InputAdornment, Select, } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType';
+import { types, getPropertyMembers } from 'mobx-state-tree';
+import { observer } from 'mobx-react';
+import { getPropertyType, getEnumerationValues, getSubType, } from '@jbrowse/core/util/mst-reflection';
+// icons
+import ClearIcon from '@mui/icons-material/Clear';
+const OPERATIONS = [
+    'equals',
+    'contains',
+    'does not contain',
+    'does not equal',
+    'starts with',
+    'ends with',
+];
+// NOTE: assembly names, if present, are ignored in all of these predicates
+const OPERATION_PREDICATES = {
+    contains: (textInCell, stringToFind) => {
+        return textInCell.toLowerCase().includes(stringToFind);
+    },
+    equals: (textInCell, stringToFind) => {
+        return textInCell.toLowerCase() === stringToFind;
+    },
+    'starts with': (textInCell, stringToFind) => {
+        return textInCell.toLowerCase().indexOf(stringToFind) === 0;
+    },
+    'ends with': (textInCell, stringToFind) => {
+        const index = textInCell.toLowerCase().indexOf(stringToFind);
+        if (index === -1) {
+            return false;
+        }
+        return index === textInCell.length - stringToFind.length;
+    },
+};
+OPERATION_PREDICATES['does not contain'] = (textInCell, stringToFind) => {
+    return !OPERATION_PREDICATES.contains(textInCell, stringToFind);
+};
+OPERATION_PREDICATES['does not equal'] = (textInCell, stringToFind) => {
+    return !OPERATION_PREDICATES.equals(textInCell, stringToFind);
+};
+const useStyles = makeStyles()({
+    textFilterControlAdornment: { marginRight: '-18px' },
+    textFilterControl: {
+        margin: 0,
+        '& .MuiInput-formControl': {
+            marginTop: 8,
+        },
+        '& .MuiInputLabel-formControl': {
+            top: '-7px',
+            '&.MuiInputLabel-shrink': {
+                top: '-3px',
+            },
+        },
+    },
+});
+// React component for the column filter control
+const FilterReactComponent = observer(
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+({ 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: "text", value: filterModel.stringToFind, onChange: evt => filterModel.setString(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.setString('') },
+                        React.createElement(ClearIcon, null)))),
+            } })));
+});
+// MST model for the column filter control
+const ColumnTextFilter = types
+    .model('ColumnTextFilter', {
+    type: types.literal('Text'),
+    columnNumber: types.integer,
+    stringToFind: '',
+    operation: types.optional(types.enumeration(OPERATIONS), OPERATIONS[0]),
+})
+    .views(self => ({
+    // returns a function that tests the given row
+    get predicate() {
+        const { stringToFind, columnNumber, operation } = self; // avoid closing over self
+        if (!stringToFind) {
+            return function alwaysTrue() {
+                return true;
+            };
+        }
+        const s = stringToFind.toLowerCase(); // case insensitive match
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        return function stringPredicate(_sheet, row) {
+            const { cellsWithDerived } = row;
+            const cell = cellsWithDerived[columnNumber];
+            if (!cell || !cell.text) {
+                return false;
+            }
+            const predicate = OPERATION_PREDICATES[operation];
+            if (!predicate) {
+                throw new Error(`"${operation}" not implemented in location filter`);
+            }
+            return predicate(cell.text, s);
+        };
+    },
+}))
+    .actions(self => ({
+    setString(s) {
+        self.stringToFind = s;
+    },
+    setOperation(op) {
+        self.operation = op;
+    },
+}))
+    .volatile(() => ({ ReactComponent: FilterReactComponent }));
+const TextColumnType = MakeSpreadsheetColumnType('Text', {
+    compare(cellA, cellB) {
+        return cellA.text.localeCompare(cellB.text);
+    },
+    FilterModelType: ColumnTextFilter,
+});
+export { TextColumnType as TextColumn, ColumnTextFilter as FilterModelType };
+//# sourceMappingURL=Text.js.map

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

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

@@ -0,0 +1,72 @@
+/// <reference types="react" />
+declare const ColumnTypes: {
+    Number: 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>;
+    Text: 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>;
+    LocString: 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>;
+    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>;
+    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>;
+    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>;
+};
+declare const AnyColumnType: import("mobx-state-tree").IAnyType;
+declare const AnyFilterModelType: import("mobx-state-tree").IAnyType;
+export { ColumnTypes, AnyColumnType, AnyFilterModelType };

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

@@ -0,0 +1,30 @@
+import LocString from './LocString';
+import LocRef from './LocRef';
+import LocStart from './LocStart';
+import LocEnd from './LocEnd';
+import { NumberColumn as Number } from './Number';
+import { TextColumn as Text } from './Text';
+import { types } from 'mobx-state-tree';
+const ColumnTypes = {
+    Number,
+    Text,
+    LocString,
+    LocRef,
+    LocStart,
+    LocEnd,
+};
+const allColumnTypes = Object.values(ColumnTypes);
+const AnyColumnType = types.union(...allColumnTypes);
+const AnyFilterModelType = types.union(...allColumnTypes
+    .map(columnType => {
+    // just instantiate the blank types to get their filter model types
+    const { FilterModelType } = columnType.create({
+        // @ts-expect-error
+        type: columnType.properties.type.value,
+    });
+    return FilterModelType;
+})
+    // some column types might not have filter machinery, filter those out
+    .filter(t => !!t));
+export { ColumnTypes, AnyColumnType, AnyFilterModelType };
+//# sourceMappingURL=index.js.map

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

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

@@ -0,0 +1,26 @@
+import { AnyFilterModelType as AnyColumnFilter } from './ColumnDataTypes';
+declare const model: import("mobx-state-tree").IModelType<{
+    rowFullText: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
+        type: import("mobx-state-tree").ISimpleType<"RowFullText">;
+        stringToFind: import("mobx-state-tree").IType<string | undefined, string, string>;
+    }, {
+        readonly predicate: (_sheet: unknown, row: {
+            cellsWithDerived: {
+                text: string;
+            }[];
+        }) => boolean;
+    } & {
+        setString(s: string): void;
+        clear(): void;
+    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    columnFilters: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyType>;
+}, {
+    readonly filters: any[];
+    setRowFullTextFilter(stringToFind: string): void;
+    rowPassesFilters(sheet: unknown, row: unknown): boolean;
+} & {
+    addBlankColumnFilter(columnNumber: number): void;
+    removeColumnFilter(filter: typeof AnyColumnFilter): boolean;
+    clearAllFilters(): void;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export default model;

package/esm/SpreadsheetView/models/FilterControls.js

@@ -0,0 +1,86 @@
+import { types, getParent } from 'mobx-state-tree';
+import { AnyFilterModelType as AnyColumnFilter } from './ColumnDataTypes';
+// filter that finds a simple string in any of the cells of a row
+const RowFullTextFilter = types
+    .model('RowFullTextFilter', {
+    type: types.literal('RowFullText'),
+    stringToFind: '',
+})
+    .views(self => ({
+    // returns a function that tests the given row
+    get predicate() {
+        let s = self.stringToFind; // avoid closing over self
+        if (!s) {
+            return function alwaysTrue() {
+                return true;
+            };
+        }
+        s = s.toLowerCase();
+        return function stringPredicate(_sheet, row) {
+            const { cellsWithDerived } = row;
+            for (const cell of cellsWithDerived) {
+                // note: case insensitive
+                if (cell.text && cell.text.toLowerCase().includes(s)) {
+                    return true;
+                }
+            }
+            return false;
+        };
+    },
+}))
+    .actions(self => ({
+    setString(s) {
+        self.stringToFind = s;
+    },
+    clear() {
+        self.stringToFind = '';
+    },
+}));
+const model = types
+    .model('SpreadsheetFilterControls', {
+    rowFullText: types.optional(RowFullTextFilter, () => ({
+        type: 'RowFullText',
+        stringToFind: '',
+    })),
+    columnFilters: types.array(AnyColumnFilter),
+})
+    .views(self => ({
+    get filters() {
+        return [self.rowFullText, ...self.columnFilters].filter(f => !!f);
+    },
+    setRowFullTextFilter(stringToFind) {
+        // @ts-expect-error
+        self.rowFullText = {
+            type: 'RowFullText',
+            stringToFind,
+        };
+    },
+    rowPassesFilters(sheet, row) {
+        for (let i = 0; i < this.filters.length; i += 1) {
+            if (!this.filters[i].predicate(sheet, row)) {
+                return false;
+            }
+        }
+        return true;
+    },
+}))
+    .actions(self => ({
+    addBlankColumnFilter(columnNumber) {
+        const { dataType } = 
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        getParent(self).spreadsheet.columns[columnNumber];
+        self.columnFilters.push({
+            type: dataType.type,
+            columnNumber,
+        });
+    },
+    removeColumnFilter(filter) {
+        return self.columnFilters.remove(filter);
+    },
+    clearAllFilters() {
+        self.columnFilters.clear();
+        self.rowFullText.clear();
+    },
+}));
+export default model;
+//# sourceMappingURL=FilterControls.js.map

package/esm/SpreadsheetView/models/FilterControls.js.map

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

@@ -0,0 +1,31 @@
+import { Instance } from 'mobx-state-tree';
+declare const ImportWizard: import("mobx-state-tree").IModelType<{
+    fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
+    selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
+}, {
+    fileTypes: string[];
+    fileSource: any;
+    error: unknown;
+    loading: boolean;
+} & {
+    readonly isReadyToOpen: any;
+    readonly canCancel: any;
+    readonly fileName: any;
+    readonly requiresUnzip: any;
+    isValidRefName(refName: string, assemblyName?: string): boolean;
+} & {
+    setSelectedAssemblyName(s: string): void;
+    setFileSource(newSource: unknown): void;
+    toggleHasColumnNameLine(): void;
+    setColumnNameLineNumber(newnumber: number): void;
+    setFileType(typeName: string): void;
+    setError(error: unknown): void;
+    setLoaded(): void;
+    cancelButton(): void;
+    import(assemblyName: string): Promise<void>;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+export type ImportWizardStateModel = typeof ImportWizard;
+export type ImportWizardModel = Instance<ImportWizardStateModel>;
+export default ImportWizard;