diff --git a/src/mol-base/collections/_spec/table.spec.ts b/src/mol-base/collections/_spec/table.spec.ts
index 537579793d9bcc799abc9443d854ed28f3f7e3aa..aa7662ab48736aad7e2be9c8c6c815c66dc4b6af 100644
--- a/src/mol-base/collections/_spec/table.spec.ts
+++ b/src/mol-base/collections/_spec/table.spec.ts
@@ -40,8 +40,9 @@ describe('column', () => {
expect(numStr.toArray()).toEqual(['1', '2']);
});
- it('permutation', () => {
- expect(Column.permutation(arr, [1, 0, 3, 2]).toArray()).toEqual([2, 1, 4, 3]);
+ it('view', () => {
+ expect(Column.view(arr, [1, 0, 3, 2]).toArray()).toEqual([2, 1, 4, 3]);
+ expect(Column.view(arr, [1, 3]).toArray()).toEqual([2, 4]);
});
it('map to array', () => {
diff --git a/src/mol-base/collections/column.ts b/src/mol-base/collections/column.ts
index 941e25afcc9a390b861d31bdc5744b45817d58c5..e510026600e82f5e08c7b7e739b159f492da262f 100644
--- a/src/mol-base/collections/column.ts
+++ b/src/mol-base/collections/column.ts
@@ -12,12 +12,13 @@ interface Column<T> {
readonly rowCount: number,
value(row: number): T,
valueKind(row: number): Column.ValueKind,
- toArray(params?: Column.ToArrayParams): ReadonlyArray<T>,
+ toArray(params?: Column.ToArrayParams<T>): ReadonlyArray<T>,
areValuesEqual(rowA: number, rowB: number): boolean
}
namespace Column {
export type Type<T = any> = Type.Str | Type.Int | Type.Float | Type.Vector | Type.Matrix | Type.Aliased<T>
+ export type ArrayCtor<T> = { new(size: number): ArrayLike<T> }
export namespace Type {
export type Str = { T: string, kind: 'str' }
@@ -37,8 +38,8 @@ namespace Column {
export function aliased<T>(t: Type): Aliased<T> { return t as any as Aliased<T>; }
}
- export interface ToArrayParams {
- array?: { new(size: number): ArrayLike<number> },
+ export interface ToArrayParams<T> {
+ array?: ArrayCtor<T>,
start?: number,
/** Last row (exclusive) */
end?: number
@@ -85,7 +86,7 @@ namespace Column {
return windowColumn(column, start, end);
}
- export function permutation<T>(column: Column<T>, indices: ArrayLike<number>, checkIndentity = true) {
+ export function view<T>(column: Column<T>, indices: ArrayLike<number>, checkIndentity = true) {
return columnPermutation(column, indices, checkIndentity);
}
@@ -94,12 +95,12 @@ namespace Column {
return createFirstIndexMapOfColumn(column);
}
- export function mapToArray<T, S>(column: Column<T>, f: (v: T) => S, ctor?: { new(size: number): ArrayLike<number> }): ArrayLike<S> {
+ export function mapToArray<T, S>(column: Column<T>, f: (v: T) => S, ctor?: ArrayCtor<S>): ArrayLike<S> {
return mapToArrayImpl(column, f, ctor || Array);
}
/** Makes the column backned by an array. Useful for columns that accessed often. */
- export function asArrayColumn<T>(c: Column<T>, array?: ToArrayParams['array']): Column<T> {
+ export function asArrayColumn<T>(c: Column<T>, array?: ArrayCtor<T>): Column<T> {
if (c['@array']) return c;
if (!c.isDefined) return Undefined(c.rowCount, c['@type']) as any as Column<T>;
return arrayColumn({ array: c.toArray({ array }), type: c['@type'] as any, valueKind: c.valueKind });
@@ -220,7 +221,8 @@ function windowFull<T>(c: Column<T>, start: number, end: number): Column<T> {
};
}
-function isIdentity(map: ArrayLike<number>) {
+function isIdentity(map: ArrayLike<number>, rowCount: number) {
+ if (map.length !== rowCount) return false;
for (let i = 0, _i = map.length; i < _i; i++) {
if (map[i] !== i) return false;
}
@@ -229,22 +231,22 @@ function isIdentity(map: ArrayLike<number>) {
function columnPermutation<T>(c: Column<T>, map: ArrayLike<number>, checkIdentity: boolean): Column<T> {
if (!c.isDefined) return c;
- if (checkIdentity && isIdentity(map)) return c;
- if (!c['@array']) return permutationArray(c, map);
- return permutationFull(c, map);
+ if (checkIdentity && isIdentity(map, c.rowCount)) return c;
+ if (!c['@array']) return arrayView(c, map);
+ return viewFull(c, map);
}
-function permutationArray<T>(c: Column<T>, map: ArrayLike<number>): Column<T> {
+function arrayView<T>(c: Column<T>, map: ArrayLike<number>): Column<T> {
const array = c['@array']!;
- const ret = new (array as any).constructor(c.rowCount);
- for (let i = 0, _i = c.rowCount; i < _i; i++) ret[i] = array[map[i]];
+ const ret = new (array as any).constructor(map.length);
+ for (let i = 0, _i = map.length; i < _i; i++) ret[i] = array[map[i]];
return arrayColumn({ array: ret, type: c['@type'], valueKind: c.valueKind });
}
-function permutationFull<T>(c: Column<T>, map: ArrayLike<number>): Column<T> {
+function viewFull<T>(c: Column<T>, map: ArrayLike<number>): Column<T> {
const v = c.value, vk = c.valueKind, ave = c.areValuesEqual;
const value: Column<T>['value'] = row => v(map[row]);
- const rowCount = c.rowCount;
+ const rowCount = map.length;
return {
'@type': c['@type'],
'@array': void 0,
@@ -261,20 +263,20 @@ function permutationFull<T>(c: Column<T>, map: ArrayLike<number>): Column<T> {
};
}
-function mapToArrayImpl<T, S>(c: Column<T>, f: (v: T) => S, ctor: { new(size: number): ArrayLike<number> }): ArrayLike<S> {
+function mapToArrayImpl<T, S>(c: Column<T>, f: (v: T) => S, ctor: Column.ArrayCtor<S>): ArrayLike<S> {
const ret = new ctor(c.rowCount) as any;
for (let i = 0, _i = c.rowCount; i < _i; i++) ret[i] = f(c.value(i));
return ret;
}
export namespace ColumnHelpers {
- export function getArrayBounds(rowCount: number, params?: Column.ToArrayParams) {
+ export function getArrayBounds(rowCount: number, params?: Column.ToArrayParams<any>) {
const start = params && typeof params.start !== 'undefined' ? Math.max(Math.min(params.start, rowCount - 1), 0) : 0;
const end = params && typeof params.end !== 'undefined' ? Math.min(params.end, rowCount) : rowCount;
return { start, end };
}
- export function createArray(rowCount: number, params?: Column.ToArrayParams) {
+ export function createArray(rowCount: number, params?: Column.ToArrayParams<any>) {
const c = params && typeof params.array !== 'undefined' ? params.array : Array;
const { start, end } = getArrayBounds(rowCount, params);
return { array: new c(end - start) as any[], start, end };
@@ -285,7 +287,7 @@ export namespace ColumnHelpers {
return target;
}
- export function createAndFillArray(rowCount: number, value: (row: number) => any, params?: Column.ToArrayParams) {
+ export function createAndFillArray(rowCount: number, value: (row: number) => any, params?: Column.ToArrayParams<any>) {
const { array, start } = createArray(rowCount, params);
return fillArrayValues(value, array, start);
}
@@ -294,7 +296,7 @@ export namespace ColumnHelpers {
return !!data.buffer && typeof data.byteLength === 'number' && typeof data.BYTES_PER_ELEMENT === 'number';
}
- export function typedArrayWindow(data: any, params?: Column.ToArrayParams): ReadonlyArray<number> {
+ export function typedArrayWindow(data: any, params?: Column.ToArrayParams<any>): ReadonlyArray<number> {
const { constructor, buffer, length, byteOffset, BYTES_PER_ELEMENT } = data;
const { start, end } = getArrayBounds(length, params);
if (start === 0 && end === length) return data;
diff --git a/src/mol-base/collections/integer/_spec/segmentation.spec.ts b/src/mol-base/collections/integer/_spec/segmentation.spec.ts
index c77fbb86ff81b0e8d7fbfacd27b64d2bcb9b8144..2c08ce9293b77d5c793f567ff457472d4a260530 100644
--- a/src/mol-base/collections/integer/_spec/segmentation.spec.ts
+++ b/src/mol-base/collections/integer/_spec/segmentation.spec.ts
@@ -19,12 +19,17 @@ describe('segments', () => {
expect(p).toBe(Interval.ofBounds(0, 2))
});
+ it('ofOffsetts', () => {
+ const p = Segmentation.ofOffsets([10, 12], Interval.ofBounds(10, 14));
+ expect(p.segments).toEqual(new Int32Array([0, 2, 4]))
+ });
+
it('map', () => {
const segs = Segmentation.create([0, 1, 2]);
expect(segs.segmentMap).toEqual(new Int32Array([0, 1]));
expect(Segmentation.getSegment(segs, 0)).toBe(0);
expect(Segmentation.getSegment(segs, 1)).toBe(1);
- })
+ });
it('iteration', () => {
const it = Segmentation.transientSegments(segs, data);
diff --git a/src/mol-base/collections/integer/impl/segmentation.ts b/src/mol-base/collections/integer/impl/segmentation.ts
index a821db8ae880befef3c9f668722ef22b3ec08a0f..254191098fcaaf6932cb653565b3ea4f08e20e81 100644
--- a/src/mol-base/collections/integer/impl/segmentation.ts
+++ b/src/mol-base/collections/integer/impl/segmentation.ts
@@ -10,7 +10,7 @@ import Interval from '../interval'
import SortedArray from '../sorted-array'
import Segs from '../segmentation'
-type Segmentation = { segments: SortedArray, segmentMap: ArrayLike<number>, count: number }
+type Segmentation = { segments: SortedArray, segmentMap: Int32Array, count: number }
export function create(values: ArrayLike<number>): Segmentation {
const segments = SortedArray.ofSortedArray(values);
@@ -24,6 +24,16 @@ export function create(values: ArrayLike<number>): Segmentation {
return { segments, segmentMap, count: values.length - 1 };
}
+export function ofOffsets(offsets: ArrayLike<number>, bounds: Interval): Segmentation {
+ const s = Interval.start(bounds);
+ const segments = new Int32Array(offsets.length + 1);
+ for (let i = 0, _i = offsets.length; i < _i; i++) {
+ segments[i] = offsets[i] - s;
+ }
+ segments[offsets.length] = Interval.end(bounds) - s;
+ return create(segments);
+}
+
export function count({ count }: Segmentation) { return count; }
export function getSegment({ segmentMap }: Segmentation, value: number) { return segmentMap[value]; }
diff --git a/src/mol-base/collections/integer/segmentation.ts b/src/mol-base/collections/integer/segmentation.ts
index 3be8cc7c345bc8be093020576abdbc21f55877f0..275b44f6dacc6e97de063b157692ef1241d6dd6b 100644
--- a/src/mol-base/collections/integer/segmentation.ts
+++ b/src/mol-base/collections/integer/segmentation.ts
@@ -13,6 +13,7 @@ namespace Segmentation {
export interface Segment { index: number, start: number, end: number }
export const create: (segs: ArrayLike<number>) => Segmentation = Impl.create as any;
+ export const ofOffsets: (offsets: ArrayLike<number>, bounds: Interval) => Segmentation = Impl.ofOffsets as any;
export const count: (segs: Segmentation) => number = Impl.count as any;
export const getSegment: (segs: Segmentation, value: number) => number = Impl.getSegment as any;
diff --git a/src/mol-base/collections/table.ts b/src/mol-base/collections/table.ts
index 087edc66b7f8f054432c0f24d7bc510fac41d6d0..fad8188538d32cdfdfa7faa03d4e76a55b23ca17 100644
--- a/src/mol-base/collections/table.ts
+++ b/src/mol-base/collections/table.ts
@@ -83,7 +83,7 @@ namespace Table {
ret._rowCount = table._rowCount;
ret._columns = table._columns;
for (const c of table._columns) {
- ret[c] = Column.permutation((table as any)[c], indices, false);
+ ret[c] = Column.view((table as any)[c], indices, false);
}
return ret;
}
diff --git a/src/mol-data/model.ts b/src/mol-data/model.ts
index a9e450a0affa6b279eaccead06ddcc39de8eddb2..db02acf8aa71c13249c452eb500693b51834e39b 100644
--- a/src/mol-data/model.ts
+++ b/src/mol-data/model.ts
@@ -5,9 +5,8 @@
*/
import * as Formats from './model/formats'
-//import CommonProperties from './model/properties/common'
-import MacromoleculeTree from './model/properties/macromolecule-tree'
-import Conformation from './model/properties/conformation'
+import MacromoleculeData from './model/data/macromolecule'
+import ConformationData from './model/data/conformation'
import Segmentation from '../mol-base/collections/integer/segmentation'
/**
@@ -22,9 +21,8 @@ interface Model extends Readonly<{
sourceData: Formats.RawData,
- //common: CommonProperties,
- macromolecule: MacromoleculeTree,
- conformation: Conformation,
+ macromolecule: MacromoleculeData,
+ conformation: ConformationData,
// used for diffing.
version: {
@@ -35,8 +33,7 @@ interface Model extends Readonly<{
atomCount: number,
segments: Readonly<{
chains: Segmentation,
- residues: Segmentation,
- entities: Segmentation
+ residues: Segmentation
}>
}> { }
diff --git a/src/mol-data/model/builders/mmcif.ts b/src/mol-data/model/builders/mmcif.ts
index e9a26ff171bf7d642e9467c727124489d7a362e1..24ad91e491a3827f9c358bbfe431c9a73263029a 100644
--- a/src/mol-data/model/builders/mmcif.ts
+++ b/src/mol-data/model/builders/mmcif.ts
@@ -7,6 +7,7 @@
import { RawData } from '../formats'
import { Frame as mmCIF } from '../../../mol-io/reader/cif/schema/mmcif'
import Model from '../../model'
+//import Column from '../../../mol-base/collections/column'
import Interval from '../../../mol-base/collections/integer/interval'
import Segmentation from '../../../mol-base/collections/integer/segmentation'
import uuId from '../../../mol-base/utils/uuid'
@@ -20,40 +21,28 @@ function findModelBounds(data: mmCIF, startIndex: number) {
return Interval.ofBounds(startIndex, endIndex);
}
-function segment(data: mmCIF, bounds: Interval) {
+function segmentOffsets(data: mmCIF, bounds: Interval) {
const start = Interval.start(bounds), end = Interval.end(bounds);
- const residues = [0], chains = [0], entities = [0];
+ const residues = [start], chains = [start];
const { label_entity_id, auth_asym_id, auth_seq_id, pdbx_PDB_ins_code, label_comp_id } = data.atom_site;
- let offset = 1;
for (let i = start + 1; i < end; i++) {
- const newEntity = !label_entity_id.areValuesEqual(i - 1, i);
- const newChain = newEntity || !auth_asym_id.areValuesEqual(i - 1, i);
+ const newChain = !label_entity_id.areValuesEqual(i - 1, i) || !auth_asym_id.areValuesEqual(i - 1, i);
const newResidue = newChain
|| !auth_seq_id.areValuesEqual(i - 1, i)
|| !pdbx_PDB_ins_code.areValuesEqual(i - 1, i)
|| !label_comp_id.areValuesEqual(i - 1, i);
- if (newEntity) entities[entities.length] = offset;
- if (newResidue) residues[residues.length] = offset;
- if (newChain) chains[chains.length] = offset;
- offset++;
+ if (newResidue) residues[residues.length] = i;
+ if (newChain) chains[chains.length] = i;
}
- residues[residues.length] = offset;
- chains[chains.length] = offset;
- entities[entities.length] = offset;
-
- return {
- residues: Segmentation.create(residues),
- chains: Segmentation.create(chains),
- entities: Segmentation.create(entities)
- };
+ return { residues, chains };
}
function createModel(raw: RawData, data: mmCIF, bounds: Interval): Model {
- const segments = segment(data, bounds);
+ const segments = segmentOffsets(data, bounds);
return {
id: uuId(),
sourceData: raw,
@@ -63,7 +52,10 @@ function createModel(raw: RawData, data: mmCIF, bounds: Interval): Model {
conformation: 0 as any,
version: { data: 0, conformation: 0 },
atomCount: Interval.size(bounds),
- segments
+ segments: {
+ residues: Segmentation.ofOffsets(segments.residues, bounds),
+ chains: Segmentation.ofOffsets(segments.chains, bounds),
+ }
};
}
diff --git a/src/mol-data/model/properties/conformation.ts b/src/mol-data/model/data/conformation.ts
similarity index 100%
rename from src/mol-data/model/properties/conformation.ts
rename to src/mol-data/model/data/conformation.ts
diff --git a/src/mol-data/model/properties/macromolecule-tree.ts b/src/mol-data/model/data/macromolecule.ts
similarity index 100%
rename from src/mol-data/model/properties/macromolecule-tree.ts
rename to src/mol-data/model/data/macromolecule.ts
diff --git a/src/mol-data/model/properties/secondary-structure.ts b/src/mol-data/model/data/secondary-structure.ts
similarity index 100%
rename from src/mol-data/model/properties/secondary-structure.ts
rename to src/mol-data/model/data/secondary-structure.ts
diff --git a/src/mol-data/model/properties/transforms.ts b/src/mol-data/model/data/transforms.ts
similarity index 100%
rename from src/mol-data/model/properties/transforms.ts
rename to src/mol-data/model/data/transforms.ts
diff --git a/src/mol-io/reader/cif/data-model.ts b/src/mol-io/reader/cif/data-model.ts
index d353c534a9b4e573282cc8bf0dcf6b71bf7718a5..3d8c6edf42b20ebef5f940c392c81bab6792f92d 100644
--- a/src/mol-io/reader/cif/data-model.ts
+++ b/src/mol-io/reader/cif/data-model.ts
@@ -69,9 +69,9 @@ export interface Field {
areValuesEqual(rowA: number, rowB: number): boolean,
- toStringArray(params?: Column.ToArrayParams): ReadonlyArray<string>,
- toIntArray(params?: Column.ToArrayParams): ReadonlyArray<number>,
- toFloatArray(params?: Column.ToArrayParams): ReadonlyArray<number>
+ toStringArray(params?: Column.ToArrayParams<string>): ReadonlyArray<string>,
+ toIntArray(params?: Column.ToArrayParams<number>): ReadonlyArray<number>,
+ toFloatArray(params?: Column.ToArrayParams<number>): ReadonlyArray<number>
}
export function getMatrix(category: Category, field: string, rows: number, cols: number, row: number) {