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Commit 9bf0bab0 authored by David Sehnal's avatar David Sehnal
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tweaks

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src/mol-base/collections/ordered-set.ts
+ 2
− 3
View file @ 9bf0bab0
...@@ -35,9 +35,8 @@ namespace OrderedSet { ...@@ -35,9 +35,8 @@ namespace OrderedSet {
export const subtract: (a: OrderedSet, b: OrderedSet) => OrderedSet = Base.subtract as any; export const subtract: (a: OrderedSet, b: OrderedSet) => OrderedSet = Base.subtract as any;
export const getPredIndex: (set: OrderedSet, x: number) => number = Base.getPredIndex as any; export const getPredIndex: (set: OrderedSet, x: number) => number = Base.getPredIndex as any;
export const getPredIndex1: (set: OrderedSet, x: number, start: number, end: number) => number = Base.getPredIndex1 as any; export const getPredIndexInRange: (set: OrderedSet, x: number, range: IndexRange) => number = Base.getPredIndexInRange as any;
export const getIntervalRange: (set: OrderedSet, min: number, max: number) => IndexRange = (set, min, max) => Base.getIntervalRange(set as any, min, max, IndexRange()); export const getIntervalRange: (set: OrderedSet, min: number, max: number) => IndexRange = Base.getIntervalRange as any;
export const getIntervalRange1: (set: OrderedSet, min: number, max: number, target: IndexRange) => IndexRange = Base.getIntervalRange as any;
export const segments = SegmentIterator export const segments = SegmentIterator
} }
......
src/mol-base/collections/ordered-set/base.ts
+ 7
− 6
View file @ 9bf0bab0
...@@ -70,15 +70,16 @@ export function getPredIndex(set: OrderedSetImpl, x: number) { ...@@ -70,15 +70,16 @@ export function getPredIndex(set: OrderedSetImpl, x: number) {
return typeof set === 'number' ? rangeSearchIndex(set, x) : binarySearchPredIndex(set as SortedArray, x); return typeof set === 'number' ? rangeSearchIndex(set, x) : binarySearchPredIndex(set as SortedArray, x);
} }
export function getPredIndex1(set: OrderedSetImpl, x: number, start: number, end: number) { export function getPredIndexInRange(set: OrderedSetImpl, x: number, { start, end }: { start: number, end: number }) {
return typeof set === 'number' ? rangeSearchIndex(set, x) : binarySearchPredIndexRange(set as SortedArray, x, start, end); if (typeof set === 'number') {
const ret = rangeSearchIndex(set, x);
return ret <= start ? start : ret >= end ? end : ret;
} else return binarySearchPredIndexRange(set as SortedArray, x, start, end);
} }
export function getIntervalRange(set: OrderedSetImpl, min: number, max: number, range: { start: number, end: number }) { export function getIntervalRange(set: OrderedSetImpl, min: number, max: number) {
const { start, end } = getStartEnd(set, min, max); const { start, end } = getStartEnd(set, min, max);
range.start = start; return { start, end };
range.end = end;
return range;
} }
export function union(a: OrderedSetImpl, b: OrderedSetImpl) { export function union(a: OrderedSetImpl, b: OrderedSetImpl) {
......
src/mol-base/collections/ordered-set/segment-iterator.ts
+ 1
− 1
View file @ 9bf0bab0
...@@ -41,7 +41,7 @@ class SegmentIterator implements Iterator<{ segmentIndex: number } & OrderedSet. ...@@ -41,7 +41,7 @@ class SegmentIterator implements Iterator<{ segmentIndex: number } & OrderedSet.
private updateValue() { private updateValue() {
const segmentEnd = OrderedSet.getAt(this.segments, this.segmentRange.start + 1); const segmentEnd = OrderedSet.getAt(this.segments, this.segmentRange.start + 1);
const end = OrderedSet.getPredIndex1(this.set, segmentEnd, this.setRange.start, this.setRange.end); const end = OrderedSet.getPredIndexInRange(this.set, segmentEnd, this.setRange);
this.value.start = this.setRange.start; this.value.start = this.setRange.start;
this.value.end = end; this.value.end = end;
this.setRange.start = end; this.setRange.start = end;
......
src/mol-data/structure/model.ts
+ 174
− 174
View file @ 9bf0bab0
/** // /**
* Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info. // * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
* // *
* @author David Sehnal <david.sehnal@gmail.com> // * @author David Sehnal <david.sehnal@gmail.com>
*/ // */
import * as Data from './data' // import * as Data from './data'
import { Selectors } from './selectors' // import { Selectors } from './selectors'
import { Vec3, Mat4 } from '../../mol-base/math/linear-algebra' // import { Vec3, Mat4 } from '../../mol-base/math/linear-algebra'
let _uid = 0; // let _uid = 0;
/** Model-related unique identifiers */ // /** Model-related unique identifiers */
export function getUid() { return _uid++; } // export function getUid() { return _uid++; }
/** Unit = essentially a list of residues (usually a chain) */ // /** Unit = essentially a list of residues (usually a chain) */
export interface Unit extends Readonly<{ // export interface Unit extends Readonly<{
operator: Unit.Operator, // operator: Unit.Operator,
/** The static part (essentially residue annotations) */ // /** The static part (essentially residue annotations) */
structure: Unit.Structure, // structure: Unit.Structure,
/** 3D arrangement that often changes with time. */ // /** 3D arrangement that often changes with time. */
conformation: Unit.Conformation, // conformation: Unit.Conformation,
/** Position of i-th atom. Special function for this because it's the only one that depends on "operator" */ // /** Position of i-th atom. Special function for this because it's the only one that depends on "operator" */
atomPosition(i: number, p: Vec3): Vec3, // atomPosition(i: number, p: Vec3): Vec3,
/** Property access */ // /** Property access */
selectors: Selectors // selectors: Selectors
}> { } // }> { }
export namespace Unit { // export namespace Unit {
export interface Structure extends Readonly<{ // export interface Structure extends Readonly<{
/** A globally unique identifier for this instance (to easily determine unique structures within a model) */ // /** A globally unique identifier for this instance (to easily determine unique structures within a model) */
id: number, // id: number,
/** Source data for this structure */ // /** Source data for this structure */
data: Data.Structure, // data: Data.Structure,
/** Reference to the data.entities table */ // /** Reference to the data.entities table */
entity: number, // entity: number,
/** Reference to the data.chains table */ // /** Reference to the data.chains table */
chain: number, // chain: number,
/** Indices into the data.residues table. */ // /** Indices into the data.residues table. */
residues: ArrayLike<number>, // residues: ArrayLike<number>,
/** Offsets of atoms in the residue layer. start = offsets[i], endExclusive = offsets[i + 1] */ // /** Offsets of atoms in the residue layer. start = offsets[i], endExclusive = offsets[i + 1] */
atomOffsets: ArrayLike<number>, // atomOffsets: ArrayLike<number>,
/** Indices into data.atoms table */ // /** Indices into data.atoms table */
atoms: ArrayLike<number> // atoms: ArrayLike<number>
/** Index of a residue in the corresponding residues array. */ // /** Index of a residue in the corresponding residues array. */
atomResidue: ArrayLike<number> // atomResidue: ArrayLike<number>
}> { } // }> { }
export interface Conformation extends Readonly<{ // export interface Conformation extends Readonly<{
/** A globally unique identifier for this instance (to easily determine unique structures within a model) */ // /** A globally unique identifier for this instance (to easily determine unique structures within a model) */
id: number, // id: number,
positions: Data.Positions, // positions: Data.Positions,
/** Per residue secondary structure assignment. */ // /** Per residue secondary structure assignment. */
secondaryStructure: Data.SecondaryStructures // secondaryStructure: Data.SecondaryStructures
}> { // }> {
'@spatialLookup': any, // TODO // '@spatialLookup': any, // TODO
'@boundingSphere': Readonly<{ center: Vec3, radius: number }>, // '@boundingSphere': Readonly<{ center: Vec3, radius: number }>,
'@bonds': Data.Bonds // '@bonds': Data.Bonds
} // }
export namespace Conformation { // export namespace Conformation {
export function spatialLookup(conformation: Conformation): any { // export function spatialLookup(conformation: Conformation): any {
throw 'not implemented' // throw 'not implemented'
} // }
export function boundingSphere(conformation: Conformation): any { // export function boundingSphere(conformation: Conformation): any {
throw 'not implemented' // throw 'not implemented'
} // }
export function bonds(conformation: Conformation): any { // export function bonds(conformation: Conformation): any {
throw 'not implemented' // throw 'not implemented'
} // }
} // }
export type OperatorKind = // export type OperatorKind =
| { kind: 'identity' } // | { kind: 'identity' }
| { kind: 'symmetry', id: string, hkl: Vec3 } // | { kind: 'symmetry', id: string, hkl: Vec3 }
| { kind: 'assembly', index: number } // | { kind: 'assembly', index: number }
| { kind: 'custom' } // | { kind: 'custom' }
export interface Operator extends Readonly<{ // export interface Operator extends Readonly<{
kind: OperatorKind, // kind: OperatorKind,
transform: Mat4, // transform: Mat4,
inverse: Mat4 // inverse: Mat4
}> { } // }> { }
export interface SpatialLookup { // export interface SpatialLookup {
// TODO // // TODO
} // }
} // }
export interface Model extends Readonly<{ // export interface Model extends Readonly<{
units: Unit[], // units: Unit[],
structure: { [id: number]: Unit.Structure }, // structure: { [id: number]: Unit.Structure },
conformation: { [id: number]: Unit.Conformation } // conformation: { [id: number]: Unit.Conformation }
}> { // }> {
'@unitLookup'?: Unit.SpatialLookup, // '@unitLookup'?: Unit.SpatialLookup,
/** bonds between units */ // /** bonds between units */
'@unitBonds'?: Data.Bonds // '@unitBonds'?: Data.Bonds
} // }
export namespace Model { // export namespace Model {
export function unitLookup(model: Model): Unit.SpatialLookup { // export function unitLookup(model: Model): Unit.SpatialLookup {
throw 'not implemented'; // throw 'not implemented';
} // }
export function unitBonds(model: Model): Data.Bonds { // export function unitBonds(model: Model): Data.Bonds {
throw 'not implemented'; // throw 'not implemented';
} // }
export function join(a: Model, b: Model): Model { // export function join(a: Model, b: Model): Model {
return { // return {
units: [...a.units, ...b.units], // units: [...a.units, ...b.units],
structure: { ...a.structure, ...b.structure }, // structure: { ...a.structure, ...b.structure },
conformation: { ...a.conformation, ...b.conformation } // conformation: { ...a.conformation, ...b.conformation }
} // }
} // }
} // }
export namespace Atom { // export namespace Atom {
/** // /**
* Represents a "packed reference" to an atom. // * Represents a "packed reference" to an atom.
* This is because selections can then be represented // * This is because selections can then be represented
* a both number[] and Float64Array(), making it much // * a both number[] and Float64Array(), making it much
* more efficient than storing an array of objects. // * more efficient than storing an array of objects.
*/ // */
export type PackedReference = number // export type PackedReference = number
export interface Reference { unit: number, atom: number } // export interface Reference { unit: number, atom: number }
export type Selection = ArrayLike<PackedReference> // export type Selection = ArrayLike<PackedReference>
const { _uint32, _float64 } = (function() { // const { _uint32, _float64 } = (function() {
const data = new ArrayBuffer(8); // const data = new ArrayBuffer(8);
return { _uint32: new Uint32Array(data), _float64: new Float64Array(data) }; // return { _uint32: new Uint32Array(data), _float64: new Float64Array(data) };
}()); // }());
export function emptyRef(): Reference { return { unit: 0, atom: 0 }; } // export function emptyRef(): Reference { return { unit: 0, atom: 0 }; }
export function packRef(location: Reference) { // export function packRef(location: Reference) {
_uint32[0] = location.unit; // _uint32[0] = location.unit;
_uint32[1] = location.atom; // _uint32[1] = location.atom;
return _float64[0]; // return _float64[0];
} // }
export function unpackRef(ref: PackedReference) { // export function unpackRef(ref: PackedReference) {
return updateRef(ref, emptyRef()); // return updateRef(ref, emptyRef());
} // }
export function updateRef(ref: PackedReference, location: Reference): Reference { // export function updateRef(ref: PackedReference, location: Reference): Reference {
_float64[0] = ref; // _float64[0] = ref;
location.unit = _uint32[0]; // location.unit = _uint32[0];
location.atom = _uint32[1]; // location.atom = _uint32[1];
return location; // return location;
} // }
} // }
export interface Selector<T> { // export interface Selector<T> {
'@type': T, // '@type': T,
create(m: Model, u: number): Selector.Field<T> // create(m: Model, u: number): Selector.Field<T>
} // }
export function Selector<T>(create: (m: Model, u: number) => (a: number, v?: T) => T): Selector<T> { // export function Selector<T>(create: (m: Model, u: number) => (a: number, v?: T) => T): Selector<T> {
return { create } as Selector<T>; // return { create } as Selector<T>;
} // }
export namespace Selector { // export namespace Selector {
export type Field<T> = (a: number, v?: T) => T; // export type Field<T> = (a: number, v?: T) => T;
export type Category = { [s: string]: Selector<any> }; // export type Category = { [s: string]: Selector<any> };
export type Unit<C extends Category> = { [F in keyof C]: Field<C[F]['@type']> } // export type Unit<C extends Category> = { [F in keyof C]: Field<C[F]['@type']> }
export type Set<S extends { [n: string]: Category }> = { [C in keyof S]: Unit<S[C]> } // export type Set<S extends { [n: string]: Category }> = { [C in keyof S]: Unit<S[C]> }
} // }
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