From 9bf0bab01ad7932c7471e664c8a857abe2f305d3 Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Thu, 26 Oct 2017 21:03:02 +0200
Subject: [PATCH] tweaks
---
src/mol-base/collections/ordered-set.ts | 5 +-
src/mol-base/collections/ordered-set/base.ts | 13 +-
.../ordered-set/segment-iterator.ts | 2 +-
src/mol-data/structure/model.ts | 348 +++++++++---------
4 files changed, 184 insertions(+), 184 deletions(-)
diff --git a/src/mol-base/collections/ordered-set.ts b/src/mol-base/collections/ordered-set.ts
index c11f95280..99325d25d 100644
--- a/src/mol-base/collections/ordered-set.ts
+++ b/src/mol-base/collections/ordered-set.ts
@@ -35,9 +35,8 @@ namespace OrderedSet {
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 getPredIndex1: (set: OrderedSet, x: number, start: number, end: number) => number = Base.getPredIndex1 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 getIntervalRange1: (set: OrderedSet, min: number, max: number, target: IndexRange) => IndexRange = Base.getIntervalRange 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 = Base.getIntervalRange as any;
export const segments = SegmentIterator
}
diff --git a/src/mol-base/collections/ordered-set/base.ts b/src/mol-base/collections/ordered-set/base.ts
index ebfb97fb1..654e816d2 100644
--- a/src/mol-base/collections/ordered-set/base.ts
+++ b/src/mol-base/collections/ordered-set/base.ts
@@ -70,15 +70,16 @@ export function getPredIndex(set: OrderedSetImpl, x: number) {
return typeof set === 'number' ? rangeSearchIndex(set, x) : binarySearchPredIndex(set as SortedArray, x);
}
-export function getPredIndex1(set: OrderedSetImpl, x: number, start: number, end: number) {
- return typeof set === 'number' ? rangeSearchIndex(set, x) : binarySearchPredIndexRange(set as SortedArray, x, start, end);
+export function getPredIndexInRange(set: OrderedSetImpl, x: number, { start, end }: { start: number, end: number }) {
+ 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);
- range.start = start;
- range.end = end;
- return range;
+ return { start, end };
}
export function union(a: OrderedSetImpl, b: OrderedSetImpl) {
diff --git a/src/mol-base/collections/ordered-set/segment-iterator.ts b/src/mol-base/collections/ordered-set/segment-iterator.ts
index e9063f0ea..078e4b697 100644
--- a/src/mol-base/collections/ordered-set/segment-iterator.ts
+++ b/src/mol-base/collections/ordered-set/segment-iterator.ts
@@ -41,7 +41,7 @@ class SegmentIterator implements Iterator<{ segmentIndex: number } & OrderedSet.
private updateValue() {
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.end = end;
this.setRange.start = end;
diff --git a/src/mol-data/structure/model.ts b/src/mol-data/structure/model.ts
index 5cbb92fe7..5ddeb9e03 100644
--- a/src/mol-data/structure/model.ts
+++ b/src/mol-data/structure/model.ts
@@ -1,174 +1,174 @@
-/**
- * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
- *
- * @author David Sehnal <david.sehnal@gmail.com>
- */
-
-import * as Data from './data'
-import { Selectors } from './selectors'
-import { Vec3, Mat4 } from '../../mol-base/math/linear-algebra'
-
-let _uid = 0;
-/** Model-related unique identifiers */
-export function getUid() { return _uid++; }
-
-/** Unit = essentially a list of residues (usually a chain) */
-export interface Unit extends Readonly<{
- operator: Unit.Operator,
- /** The static part (essentially residue annotations) */
- structure: Unit.Structure,
- /** 3D arrangement that often changes with time. */
- conformation: Unit.Conformation,
- /** 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,
- /** Property access */
- selectors: Selectors
-}> { }
-
-export namespace Unit {
- export interface Structure extends Readonly<{
- /** A globally unique identifier for this instance (to easily determine unique structures within a model) */
- id: number,
- /** Source data for this structure */
- data: Data.Structure,
- /** Reference to the data.entities table */
- entity: number,
- /** Reference to the data.chains table */
- chain: number,
- /** Indices into the data.residues table. */
- residues: ArrayLike<number>,
- /** Offsets of atoms in the residue layer. start = offsets[i], endExclusive = offsets[i + 1] */
- atomOffsets: ArrayLike<number>,
- /** Indices into data.atoms table */
- atoms: ArrayLike<number>
- /** Index of a residue in the corresponding residues array. */
- atomResidue: ArrayLike<number>
- }> { }
-
- export interface Conformation extends Readonly<{
- /** A globally unique identifier for this instance (to easily determine unique structures within a model) */
- id: number,
-
- positions: Data.Positions,
-
- /** Per residue secondary structure assignment. */
- secondaryStructure: Data.SecondaryStructures
- }> {
- '@spatialLookup': any, // TODO
- '@boundingSphere': Readonly<{ center: Vec3, radius: number }>,
- '@bonds': Data.Bonds
- }
-
- export namespace Conformation {
- export function spatialLookup(conformation: Conformation): any {
- throw 'not implemented'
- }
-
- export function boundingSphere(conformation: Conformation): any {
- throw 'not implemented'
- }
-
- export function bonds(conformation: Conformation): any {
- throw 'not implemented'
- }
- }
-
- export type OperatorKind =
- | { kind: 'identity' }
- | { kind: 'symmetry', id: string, hkl: Vec3 }
- | { kind: 'assembly', index: number }
- | { kind: 'custom' }
-
- export interface Operator extends Readonly<{
- kind: OperatorKind,
- transform: Mat4,
- inverse: Mat4
- }> { }
-
- export interface SpatialLookup {
- // TODO
- }
-}
-
-export interface Model extends Readonly<{
- units: Unit[],
-
- structure: { [id: number]: Unit.Structure },
- conformation: { [id: number]: Unit.Conformation }
-}> {
- '@unitLookup'?: Unit.SpatialLookup,
- /** bonds between units */
- '@unitBonds'?: Data.Bonds
-}
-
-export namespace Model {
- export function unitLookup(model: Model): Unit.SpatialLookup {
- throw 'not implemented';
- }
-
- export function unitBonds(model: Model): Data.Bonds {
- throw 'not implemented';
- }
-
- export function join(a: Model, b: Model): Model {
- return {
- units: [...a.units, ...b.units],
- structure: { ...a.structure, ...b.structure },
- conformation: { ...a.conformation, ...b.conformation }
- }
- }
-}
-
-export namespace Atom {
- /**
- * Represents a "packed reference" to an atom.
- * This is because selections can then be represented
- * a both number[] and Float64Array(), making it much
- * more efficient than storing an array of objects.
- */
- export type PackedReference = number
- export interface Reference { unit: number, atom: number }
- export type Selection = ArrayLike<PackedReference>
-
- const { _uint32, _float64 } = (function() {
- const data = new ArrayBuffer(8);
- return { _uint32: new Uint32Array(data), _float64: new Float64Array(data) };
- }());
-
- export function emptyRef(): Reference { return { unit: 0, atom: 0 }; }
-
- export function packRef(location: Reference) {
- _uint32[0] = location.unit;
- _uint32[1] = location.atom;
- return _float64[0];
- }
-
- export function unpackRef(ref: PackedReference) {
- return updateRef(ref, emptyRef());
- }
-
- export function updateRef(ref: PackedReference, location: Reference): Reference {
- _float64[0] = ref;
- location.unit = _uint32[0];
- location.atom = _uint32[1];
- return location;
- }
-}
-
-export interface Selector<T> {
- '@type': 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> {
- return { create } as Selector<T>;
-}
-
-export namespace Selector {
- export type Field<T> = (a: number, v?: T) => T;
-
- export type Category = { [s: string]: Selector<any> };
- 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]> }
-}
\ No newline at end of file
+// /**
+// * Copyright (c) 2017 molio contributors, licensed under MIT, See LICENSE file for more info.
+// *
+// * @author David Sehnal <david.sehnal@gmail.com>
+// */
+
+// import * as Data from './data'
+// import { Selectors } from './selectors'
+// import { Vec3, Mat4 } from '../../mol-base/math/linear-algebra'
+
+// let _uid = 0;
+// /** Model-related unique identifiers */
+// export function getUid() { return _uid++; }
+
+// /** Unit = essentially a list of residues (usually a chain) */
+// export interface Unit extends Readonly<{
+// operator: Unit.Operator,
+// /** The static part (essentially residue annotations) */
+// structure: Unit.Structure,
+// /** 3D arrangement that often changes with time. */
+// conformation: Unit.Conformation,
+// /** 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,
+// /** Property access */
+// selectors: Selectors
+// }> { }
+
+// export namespace Unit {
+// export interface Structure extends Readonly<{
+// /** A globally unique identifier for this instance (to easily determine unique structures within a model) */
+// id: number,
+// /** Source data for this structure */
+// data: Data.Structure,
+// /** Reference to the data.entities table */
+// entity: number,
+// /** Reference to the data.chains table */
+// chain: number,
+// /** Indices into the data.residues table. */
+// residues: ArrayLike<number>,
+// /** Offsets of atoms in the residue layer. start = offsets[i], endExclusive = offsets[i + 1] */
+// atomOffsets: ArrayLike<number>,
+// /** Indices into data.atoms table */
+// atoms: ArrayLike<number>
+// /** Index of a residue in the corresponding residues array. */
+// atomResidue: ArrayLike<number>
+// }> { }
+
+// export interface Conformation extends Readonly<{
+// /** A globally unique identifier for this instance (to easily determine unique structures within a model) */
+// id: number,
+
+// positions: Data.Positions,
+
+// /** Per residue secondary structure assignment. */
+// secondaryStructure: Data.SecondaryStructures
+// }> {
+// '@spatialLookup': any, // TODO
+// '@boundingSphere': Readonly<{ center: Vec3, radius: number }>,
+// '@bonds': Data.Bonds
+// }
+
+// export namespace Conformation {
+// export function spatialLookup(conformation: Conformation): any {
+// throw 'not implemented'
+// }
+
+// export function boundingSphere(conformation: Conformation): any {
+// throw 'not implemented'
+// }
+
+// export function bonds(conformation: Conformation): any {
+// throw 'not implemented'
+// }
+// }
+
+// export type OperatorKind =
+// | { kind: 'identity' }
+// | { kind: 'symmetry', id: string, hkl: Vec3 }
+// | { kind: 'assembly', index: number }
+// | { kind: 'custom' }
+
+// export interface Operator extends Readonly<{
+// kind: OperatorKind,
+// transform: Mat4,
+// inverse: Mat4
+// }> { }
+
+// export interface SpatialLookup {
+// // TODO
+// }
+// }
+
+// export interface Model extends Readonly<{
+// units: Unit[],
+
+// structure: { [id: number]: Unit.Structure },
+// conformation: { [id: number]: Unit.Conformation }
+// }> {
+// '@unitLookup'?: Unit.SpatialLookup,
+// /** bonds between units */
+// '@unitBonds'?: Data.Bonds
+// }
+
+// export namespace Model {
+// export function unitLookup(model: Model): Unit.SpatialLookup {
+// throw 'not implemented';
+// }
+
+// export function unitBonds(model: Model): Data.Bonds {
+// throw 'not implemented';
+// }
+
+// export function join(a: Model, b: Model): Model {
+// return {
+// units: [...a.units, ...b.units],
+// structure: { ...a.structure, ...b.structure },
+// conformation: { ...a.conformation, ...b.conformation }
+// }
+// }
+// }
+
+// export namespace Atom {
+// /**
+// * Represents a "packed reference" to an atom.
+// * This is because selections can then be represented
+// * a both number[] and Float64Array(), making it much
+// * more efficient than storing an array of objects.
+// */
+// export type PackedReference = number
+// export interface Reference { unit: number, atom: number }
+// export type Selection = ArrayLike<PackedReference>
+
+// const { _uint32, _float64 } = (function() {
+// const data = new ArrayBuffer(8);
+// return { _uint32: new Uint32Array(data), _float64: new Float64Array(data) };
+// }());
+
+// export function emptyRef(): Reference { return { unit: 0, atom: 0 }; }
+
+// export function packRef(location: Reference) {
+// _uint32[0] = location.unit;
+// _uint32[1] = location.atom;
+// return _float64[0];
+// }
+
+// export function unpackRef(ref: PackedReference) {
+// return updateRef(ref, emptyRef());
+// }
+
+// export function updateRef(ref: PackedReference, location: Reference): Reference {
+// _float64[0] = ref;
+// location.unit = _uint32[0];
+// location.atom = _uint32[1];
+// return location;
+// }
+// }
+
+// export interface Selector<T> {
+// '@type': 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> {
+// return { create } as Selector<T>;
+// }
+
+// export namespace Selector {
+// export type Field<T> = (a: number, v?: T) => T;
+
+// export type Category = { [s: string]: Selector<any> };
+// 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]> }
+// }
\ No newline at end of file
--
GitLab