diff --git a/src/mol-io/writer/cif.ts b/src/mol-io/writer/cif.ts
index 3fd87a346b9ba50b9e0f1b768705ef490c07bff6..d80de4033505ff0e9165802f09e2ea0a75bb034e 100644
--- a/src/mol-io/writer/cif.ts
+++ b/src/mol-io/writer/cif.ts
@@ -68,7 +68,7 @@ export namespace CifWriter {
}
}
- function resolveEncoding(hint: EncodingStrategyHint): ArrayEncoder | undefined {
+ function resolveEncoding(hint: EncodingStrategyHint): ArrayEncoder {
const precision: number | undefined = hint.precision;
if (precision !== void 0) {
const multiplier = Math.pow(10, precision);
@@ -95,6 +95,7 @@ export namespace CifWriter {
return E.by(E.delta).and(E.runLength).and(E.integerPacking);
}
}
+ throw new Error('cannot be reached');
}
}
diff --git a/src/mol-io/writer/cif/encoder.ts b/src/mol-io/writer/cif/encoder.ts
index f0d95d18b7543d92f48c50d7f5f7897ed371befa..331e4184f71d39eaba5bc309bd16a2f3ef42c810 100644
--- a/src/mol-io/writer/cif/encoder.ts
+++ b/src/mol-io/writer/cif/encoder.ts
@@ -132,6 +132,36 @@ export namespace Category {
includeField(categoryName: string, fieldName: string): boolean,
}
+ export function whitelistBlacklistFilter(cat_whitelist: String[], cat_blacklist: String[], field_whitelist: String[], field_blacklist: String[]): Filter {
+ const wlcatcol = field_whitelist.map(it => it.split('.')[0]);
+ // blacklist has higher priority
+ return {
+ includeCategory(cat) {
+ // block if category in black
+ if (cat_blacklist.includes(cat)) {
+ return false;
+ } else {
+ // if there is a whitelist, the category has to be explicitly allowed
+ return cat_whitelist.length <= 0 ||
+ // otherwise include if whitelist contains category
+ cat_whitelist.indexOf(cat) !== -1;
+ }
+ },
+ includeField(cat, field) {
+ // column names are assumed to follow the pattern 'category_name.column_name'
+ const full = cat + '.' + field;
+ if (field_blacklist.includes(full)) {
+ return false;
+ } else {
+ // if for this category no whitelist entries exist
+ return !wlcatcol.includes(cat) ||
+ // otherwise must be specifically allowed
+ field_whitelist.includes(full);
+ }
+ }
+ }
+ }
+
export const DefaultFilter: Filter = {
includeCategory(cat) { return true; },
includeField(cat, field) { return true; }
diff --git a/src/tests/browser/encoding-config.ts b/src/tests/browser/encoding-config.ts
deleted file mode 100644
index a07e721160d50783b1a4b51f4c29b08e908112cb..0000000000000000000000000000000000000000
--- a/src/tests/browser/encoding-config.ts
+++ /dev/null
@@ -1,96 +0,0 @@
-import './index.html'
-import { CIF, CifCategory, CifField, getCifFieldType } from '../../mol-io/reader/cif';
-import { CifWriter } from '../../mol-io/writer/cif';
-
-async function parseCif(data: string|Uint8Array) {
- const comp = CIF.parse(data);
- const parsed = await comp.run();
- if (parsed.isError) throw parsed;
- return parsed.result;
-}
-
-async function downloadCif(url: string, isBinary: boolean) {
- const data = await fetch(url);
- return parseCif(isBinary ? new Uint8Array(await data.arrayBuffer()) : await data.text());
-}
-
-async function downloadFromPdb(pdb: string) {
- const parsed = await downloadCif(`https://webchem.ncbr.muni.cz/ModelServer/static/bcif/${pdb}`, true);
- return parsed.blocks[0];
-}
-
-async function init(props = {}) {
- const cif = await downloadFromPdb('1brr')
- const encoder = CifWriter.createEncoder({
- binary: true,
- encoderName: 'mol*',
- binaryAutoClassifyEncoding: true,
- binaryEncodingPovider: CifWriter.createEncodingProviderFromJsonConfig([
- // {
- // 'categoryName': 'atom_site',
- // 'columnName': 'Cartn_x',
- // 'encoding': 'delta',
- // 'precision': 3
- // },
- {
- 'categoryName': 'atom_site',
- 'columnName': 'Cartn_y',
- 'encoding': 'rle',
- 'precision': 0
- },
- {
- 'categoryName': 'atom_site',
- 'columnName': 'Cartn_z',
- 'encoding': 'delta',
- 'precision': 1
- },
- {
- 'categoryName': 'atom_site',
- 'columnName': 'label_seq_id',
- 'encoding': 'delta-rle'
- }
- ])
- });
-
- encoder.startDataBlock(cif.header);
- for (const c of cif.categoryNames) {
- const cat = cif.categories[c];
- const fields: CifWriter.Field[] = [];
- for (const f of cat.fieldNames) {
- fields.push(wrap(f, cat.getField(f)!))
- }
-
- encoder.writeCategory(getCategoryInstanceProvider(cif.categories[c], fields));
- }
- const ret = encoder.getData() as Uint8Array;
-
- const cif2 = (await parseCif(ret)).blocks[0];
- // should be untouched: delta encoding
- console.log(cif2.categories['atom_site'].getField('Cartn_x'));
- // should have rle encoding, 0 decimal places
- console.log(cif2.categories['atom_site'].getField('Cartn_y'));
- // should have delta encoding, 1 decimal place
- console.log(cif2.categories['atom_site'].getField('Cartn_z'));
- // should use delta-rle encoding
- console.log(cif2.categories['atom_site'].getField('label_seq_id'));
-}
-
-init()
-
-function getCategoryInstanceProvider(cat: CifCategory, fields: CifWriter.Field[]): CifWriter.Category {
- return {
- name: cat.name,
- instance: () => CifWriter.categoryInstance(fields, { data: cat, rowCount: cat.rowCount })
- };
-}
-
-function wrap(name: string, field: CifField): CifWriter.Field {
- const type = getCifFieldType(field);
- if (type['@type'] === 'str') {
- return { name, type: CifWriter.Field.Type.Str, value: field.str, valueKind: field.valueKind };
- } else if (type['@type'] === 'float') {
- return { name, type: CifWriter.Field.Type.Float, value: field.float, valueKind: field.valueKind };
- } else {
- return { name, type: CifWriter.Field.Type.Int, value: field.int, valueKind: field.valueKind };
- }
-}
\ No newline at end of file
diff --git a/webpack.config.js b/webpack.config.js
index c171386df79f848f39afbbc8d22abdbcc0666a77..3de9e1565111c706a5f326ff84f7f9f143cc4e28 100644
--- a/webpack.config.js
+++ b/webpack.config.js
@@ -98,5 +98,4 @@ module.exports = [
createBrowserTest('render-spheres'),
createBrowserTest('render-structure'),
createBrowserTest('render-text'),
- createBrowserTest('encoding-config')
]
\ No newline at end of file