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+import * as Data from '../../reader/cif/data-model'
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+import { CifWriter } from '../cif';
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+import decodeMsgPack from '../../common/msgpack/decode'
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+import { EncodedFile, EncodedCategory } from '../../common/binary-cif';
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+import Field from '../../reader/cif/binary/field';
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+import * as C from '../cif/encoder';
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+
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+const cartn_x = Data.CifField.ofNumbers([1.001, 1.002, 1.003, 1.004, 1.005, 1.006, 1.007, 1.008, 1.009]);
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+const cartn_y = Data.CifField.ofNumbers([-3.0, -2.666, -2.3333, -2.0, -1.666, -1.333, -1.0, -0.666, -0.333]);
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+const cartn_z = Data.CifField.ofNumbers([1, 2, 3, 4, 5, 6, 7, 8, 9].map(i => Math.sqrt(i)));
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+const label_seq_id = Data.CifField.ofNumbers([1, 2, 3, 6, 11, 23, 47, 106, 235]);
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+const atom_site = Data.CifCategory.ofFields('atom_site', { 'Cartn_x': cartn_x, 'Cartn_y': cartn_y, 'Cartn_z': cartn_z, 'label_seq_id': label_seq_id });
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+const field1 = Data.CifField.ofNumbers([1, 2, 3, 6, 11, 23, 47, 106, 235]);
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+const field2 = Data.CifField.ofNumbers([-1, -2, -3, -6, -11, -23, -47, -106, -235]);
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+const other_fields = Data.CifCategory.ofFields('other_fields', { 'field1': field1, 'field2': field2 });
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+
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+const encoding_aware_encoder = CifWriter.createEncoder({
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+ binary: true,
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+ binaryAutoClassifyEncoding: true,
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+ binaryEncodingPovider: CifWriter.createEncodingProviderFromJsonConfig([
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+ {
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+ 'categoryName': 'atom_site',
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+ 'columnName': 'Cartn_y',
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+ 'encoding': 'rle',
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+ 'precision': 0
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+ },
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+ {
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+ 'categoryName': 'atom_site',
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+ 'columnName': 'Cartn_z',
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+ 'encoding': 'delta',
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+ 'precision': 1
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+ },
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+ {
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+ 'categoryName': 'atom_site',
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+ 'columnName': 'label_seq_id',
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+ 'encoding': 'delta-rle'
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+ }
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+ ])
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+});
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+
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+describe('encoding-config', () => {
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+ const decoded = process(encoding_aware_encoder);
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+
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+ const decoded_atom_site = decoded.blocks[0].categories['atom_site'];
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+ const decoded_cartn_x = decoded_atom_site.getField('Cartn_x')!;
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+ const decoded_cartn_y = decoded_atom_site.getField('Cartn_y')!;
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+ const decoded_cartn_z = decoded_atom_site.getField('Cartn_z')!;
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+ const decoded_label_seq_id = decoded_atom_site.getField('label_seq_id')!;
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+
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+ const delta = 0.001;
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+ function assert(e: ArrayLike<number>, a: ArrayLike<number>) {
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+ expect(e.length).toBe(a.length);
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+ for (let i = 0; i < e.length; i++) {
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+ expect(Math.abs(e[i] - a[i])).toBeLessThan(delta);
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+ }
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+ }
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+
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+ function join(field: Data.CifField) {
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+ return field.binaryEncoding!.map(e => e.kind).join();
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+ }
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+
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+ it('strategy', () => {
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+ expect(join(decoded_cartn_x)).toBe('FixedPoint,Delta,IntegerPacking,ByteArray');
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+ expect(join(decoded_cartn_y)).toBe('FixedPoint,RunLength,IntegerPacking,ByteArray');
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+ expect(join(decoded_cartn_z)).toBe('FixedPoint,Delta,IntegerPacking,ByteArray');
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+ expect(join(decoded_label_seq_id)).toBe('Delta,RunLength,IntegerPacking,ByteArray');
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+ });
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+
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+ it('precision', () => {
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+ assert(decoded_cartn_x.toFloatArray(), cartn_x.toFloatArray());
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+ assert(decoded_cartn_y.toFloatArray(), cartn_y.toFloatArray().map(d => Math.round(d)));
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+ assert(decoded_cartn_z.toFloatArray(), cartn_z.toFloatArray().map(d => Math.round(d * 10) / 10));
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+ assert(decoded_label_seq_id.toIntArray(), label_seq_id.toIntArray());
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+ });
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+});
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+
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+const filter_aware_encoder1 = CifWriter.createEncoder({
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+ binary: true,
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+ binaryAutoClassifyEncoding: true
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+});
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+filter_aware_encoder1.setFilter(C.Category.filterOf('atom_site\n' +
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+'\n' +
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+'atom_site.Cartn_x\n' +
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+'atom_site.Cartn_y\n'));
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+
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+const filter_aware_encoder2 = CifWriter.createEncoder({
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+ binary: true
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+});
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+filter_aware_encoder2.setFilter(C.Category.filterOf('!atom_site\n' +
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+'\n' +
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+'!other_fields.field2\n'));
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+
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+describe('filtering-config', () => {
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+ const decoded1 = process(filter_aware_encoder1);
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+
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+ const atom_site1 = decoded1.blocks[0].categories['atom_site'];
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+ const cartn_x1 = atom_site1.getField('Cartn_x');
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+ const cartn_y1 = atom_site1.getField('Cartn_y');
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+ const cartn_z1 = atom_site1.getField('Cartn_z');
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+ const label_seq_id1 = atom_site1.getField('label_seq_id');
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+ const fields1 = decoded1.blocks[0].categories['other_fields'];
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+
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+ it('whitelist-filtering', () => {
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+ expect(atom_site1).toBeDefined();
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+ expect(cartn_x1).toBeDefined();
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+ expect(cartn_y1).toBeDefined();
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+ expect(cartn_z1).toBeUndefined();
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+ expect(label_seq_id1).toBeUndefined();
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+ expect(fields1).toBeUndefined();
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+ });
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+
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+ const decoded2 = process(filter_aware_encoder2);
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+
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+ const atom_site2 = decoded2.blocks[0].categories['atom_site'];
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+ const fields2 = decoded2.blocks[0].categories['other_fields'];
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+ const field12 = fields2.getField('field1');
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+ const field22 = fields2.getField('field2');
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+
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+ it('blacklist-filtering', () => {
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+ expect(atom_site2).toBeUndefined();
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+ expect(fields2).toBeDefined();
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+ expect(field12).toBeDefined();
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+ expect(field22).toBeUndefined();
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+ });
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+});
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+
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+function process(encoder: C.Encoder) {
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+ encoder.startDataBlock('test');
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+
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+ for (const cat of [atom_site, other_fields]) {
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+ const fields: CifWriter.Field[] = [];
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+ for (const f of cat.fieldNames) {
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+ fields.push(wrap(f, cat.getField(f)!))
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+ }
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+ encoder.writeCategory(getCategoryInstanceProvider(cat, fields));
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+ }
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+
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+ const encoded = encoder.getData() as Uint8Array;
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+
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+ const unpacked = decodeMsgPack(encoded) as EncodedFile;
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+ return Data.CifFile(unpacked.dataBlocks.map(block => {
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+ const cats = Object.create(null);
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+ for (const cat of block.categories) cats[cat.name.substr(1)] = Category(cat);
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+ return Data.CifBlock(block.categories.map(c => c.name.substr(1)), cats, block.header);
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+ }));
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+}
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+
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+
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+function getCategoryInstanceProvider(cat: Data.CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
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+ return {
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+ name: cat.name,
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+ instance: () => CifWriter.categoryInstance(fields, { data: cat, rowCount: cat.rowCount })
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+ };
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+}
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+
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+function wrap(name: string, field: Data.CifField): CifWriter.Field {
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+ const type = Data.getCifFieldType(field);
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+ if (type['@type'] === 'str') {
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+ return { name, type: CifWriter.Field.Type.Str, value: field.str, valueKind: field.valueKind };
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+ } else if (type['@type'] === 'float') {
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+ return { name, type: CifWriter.Field.Type.Float, value: field.float, valueKind: field.valueKind };
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+ } else {
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+ return { name, type: CifWriter.Field.Type.Int, value: field.int, valueKind: field.valueKind };
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+ }
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+}
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+
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+function Category(data: EncodedCategory): Data.CifCategory {
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+ const map = Object.create(null);
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+ const cache = Object.create(null);
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+ for (const col of data.columns) map[col.name] = col;
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+ return {
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+ rowCount: data.rowCount,
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+ name: data.name.substr(1),
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+ fieldNames: data.columns.map(c => c.name),
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+ getField(name) {
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+ const col = map[name];
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+ if (!col) return void 0;
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+ if (!!cache[name]) return cache[name];
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+ cache[name] = Field(col);
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+ return cache[name];
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+ }
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+ }
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+}
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Alexander Rose