From 37a0b07d56be0a011f533078f77f77d9c588c563 Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Tue, 4 Jun 2019 17:52:02 -0700
Subject: [PATCH] stub for encoding config
---
package-lock.json | Bin 575779 -> 576329 bytes
src/mol-io/writer/cif.ts | 53 ++++++++++++++
src/mol-io/writer/cif/encoder/binary.ts | 7 +-
src/tests/browser/encoding-config.ts | 91 ++++++++++++++++++++++++
webpack.config.js | 1 +
5 files changed, 149 insertions(+), 3 deletions(-)
create mode 100644 src/tests/browser/encoding-config.ts
diff --git a/package-lock.json b/package-lock.json
index 6c89b0f359c83badbc08f0ea4223fd151c4475cc..e79e6e264ae78f3a1bc547133c07fb54afdc54c2 100644
GIT binary patch
delta 512
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delta 371
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diff --git a/src/mol-io/writer/cif.ts b/src/mol-io/writer/cif.ts
index c191d8a4b..762f1988f 100644
--- a/src/mol-io/writer/cif.ts
+++ b/src/mol-io/writer/cif.ts
@@ -53,5 +53,58 @@ export namespace CifWriter {
return ff && ff.binaryEncoding ? ArrayEncoder.fromEncoding(ff.binaryEncoding) : void 0;
}
}
+ };
+
+ export function createEncodingProviderFromJsonConfig(hints: EncodingStrategyHint[]): EncodingProvider {
+ return {
+ get(c, f) {
+ for (let i = 0; i < hints.length; i++) {
+ const hint = hints[i];
+ if (hint.categoryName === c && hint.columnName === f) {
+ return resolveEncoding(hint);
+ }
+ }
+ }
+ }
}
+
+ function resolveEncoding(hint: EncodingStrategyHint): ArrayEncoder | undefined {
+ const precision: number | undefined = hint.precision;
+ if (precision !== void 0) {
+ const multiplier = Math.pow(10, precision);
+ const fixedPoint = E.by(E.fixedPoint(multiplier));
+ switch (hint.encoding) {
+ case 'pack':
+ return fixedPoint.and(E.integerPacking);
+ case 'rle':
+ return fixedPoint.and(E.runLength).and(E.integerPacking);
+ case 'delta':
+ return fixedPoint.and(E.delta).and(E.integerPacking);
+ case 'delta-rle':
+ return fixedPoint.and(E.delta).and(E.runLength).and(E.integerPacking);
+ };
+ } else {
+ switch (hint.encoding) {
+ case 'pack':
+ return E.by(E.integerPacking);
+ case 'rle':
+ return E.by(E.runLength).and(E.integerPacking);
+ case 'delta':
+ return E.by(E.delta).and(E.integerPacking);
+ case 'delta-rle':
+ return E.by(E.delta).and(E.runLength).and(E.integerPacking);
+ }
+ }
+ }
+}
+
+// defines the information needed to encode certain fields: category and column name as well as encoding tag, precision is optional and identifies float columns
+// TODO would be nice to infer strategy and precision if needed
+export interface EncodingStrategyHint {
+ categoryName: string,
+ columnName: string,
+ // 'pack', 'rle', 'delta', or 'delta-rle'
+ encoding: string,
+ // number of decimal places to keep - must be specified to float columns
+ precision?: number
}
\ No newline at end of file
diff --git a/src/mol-io/writer/cif/encoder/binary.ts b/src/mol-io/writer/cif/encoder/binary.ts
index 9212bcea2..99ee50053 100644
--- a/src/mol-io/writer/cif/encoder/binary.ts
+++ b/src/mol-io/writer/cif/encoder/binary.ts
@@ -111,12 +111,13 @@ function getDefaultEncoder(type: Field.Type): ArrayEncoder {
}
function tryGetEncoder(categoryName: string, field: Field, format: Field.Format | undefined, provider: EncodingProvider | undefined) {
- if (format && format.encoder) {
+ // TODO made provider the first check - might break servers/model/query
+ if (provider && provider.get(categoryName, field.name)) {
+ return provider.get(categoryName, field.name);
+ } else if (format && format.encoder) {
return format.encoder;
} else if (field.defaultFormat && field.defaultFormat.encoder) {
return field.defaultFormat.encoder;
- } else if (provider) {
- return provider.get(categoryName, field.name);
} else {
return void 0;
}
diff --git a/src/tests/browser/encoding-config.ts b/src/tests/browser/encoding-config.ts
new file mode 100644
index 000000000..b02ed4ea8
--- /dev/null
+++ b/src/tests/browser/encoding-config.ts
@@ -0,0 +1,91 @@
+import './index.html'
+import { CIF, CifCategory, CifField, getCifFieldType } from '../../mol-io/reader/cif';
+import { CifWriter } from '../../mol-io/writer/cif';
+import { classifyFloatArray, classifyIntArray } from '../../mol-io/common/binary-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*',
+ binaryEncodingPovider: CifWriter.createEncodingProviderFromJsonConfig([
+ {
+ '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(classify(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
+ console.log(cif2.categories['atom_site'].getField('Cartn_x'));
+ // should have integer precision
+ console.log(cif2.categories['atom_site'].getField('Cartn_y'));
+ // should have 1 decimal place
+ console.log(cif2.categories['atom_site'].getField('Cartn_z'));
+ 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 classify(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') {
+ const encoder = classifyFloatArray(field.toFloatArray({ array: Float64Array }));
+ return CifWriter.Field.float(name, field.float, { valueKind: field.valueKind, encoder, typedArray: Float64Array });
+ } else {
+ const encoder = classifyIntArray(field.toIntArray({ array: Int32Array }));
+ return CifWriter.Field.int(name, field.int, { valueKind: field.valueKind, encoder, typedArray: Int32Array });
+ }
+}
\ No newline at end of file
diff --git a/webpack.config.js b/webpack.config.js
index 3de9e1565..c171386df 100644
--- a/webpack.config.js
+++ b/webpack.config.js
@@ -98,4 +98,5 @@ module.exports = [
createBrowserTest('render-spheres'),
createBrowserTest('render-structure'),
createBrowserTest('render-text'),
+ createBrowserTest('encoding-config')
]
\ No newline at end of file
--
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