white-/blacklist filtering

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');
     }
 }
 

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; }

src/tests/browser/encoding-config.ts

@@ -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 };
-    }
-}

webpack.config.js

@@ -98,5 +98,4 @@ module.exports = [
     createBrowserTest('render-spheres'),
     createBrowserTest('render-structure'),
     createBrowserTest('render-text'),
-    createBrowserTest('encoding-config')
 ]