From 01691f30502f74ded35535318fa0675d7926aa64 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Sun, 12 Sep 2021 23:20:59 -0700
Subject: [PATCH] lint: add keyword-spacing rule
---
.eslintrc.json | 6 +-
src/extensions/anvil/algorithm.ts | 6 +-
src/extensions/cellpack/model.ts | 2 +-
src/extensions/cellpack/state.ts | 4 +-
.../rcsb/assembly-symmetry/behavior.ts | 2 +-
src/extensions/rcsb/validation-report/prop.ts | 2 +-
src/mol-gl/shader-code.ts | 2 +-
src/mol-io/reader/psf/parser.ts | 2 +-
src/mol-math/linear-algebra/matrix/evd.ts | 6 +-
src/mol-model-formats/structure/cif-core.ts | 2 +-
.../shrake-rupley/radii.ts | 2 +-
src/mol-model/loci.ts | 4 +-
.../structure/structure/element/loci.ts | 2 +-
.../structure/representation-preset.ts | 4 +-
src/mol-plugin-state/manager/loci-label.ts | 2 +-
src/mol-plugin-ui/base.tsx | 2 +-
.../line-graph/line-graph-component.tsx | 44 ++++----
.../controls/line-graph/point-component.tsx | 2 +-
src/mol-plugin-ui/structure/focus.tsx | 2 +-
.../computed/accessible-surface-area.ts | 4 +-
.../sequence/best-database-mapping.ts | 2 +-
src/mol-plugin/util/toast.ts | 2 +-
src/mol-repr/shape/representation.ts | 2 +-
.../structure/visual/bond-inter-unit-line.ts | 2 +-
src/mol-repr/structure/visual/util/bond.ts | 2 +-
.../visual/util/polymer/trace-iterator.ts | 12 +-
src/mol-repr/volume/direct-volume.ts | 4 +-
src/mol-util/data-source.ts | 2 +-
src/mol-util/zip/bin.ts | 24 ++--
src/mol-util/zip/checksum.ts | 4 +-
src/mol-util/zip/deflate.ts | 104 +++++++++---------
src/mol-util/zip/huffman.ts | 34 +++---
src/mol-util/zip/inflate.ts | 58 +++++-----
src/mol-util/zip/util.ts | 18 +--
src/mol-util/zip/zip.ts | 32 +++---
src/servers/model/server/query.ts | 2 +-
36 files changed, 204 insertions(+), 202 deletions(-)
diff --git a/.eslintrc.json b/.eslintrc.json
index 75507b37c..3c1eb87b4 100644
--- a/.eslintrc.json
+++ b/.eslintrc.json
@@ -52,7 +52,8 @@
"space-before-function-paren": "off",
"func-call-spacing": "off",
"no-multi-spaces": "error",
- "block-spacing": "error"
+ "block-spacing": "error",
+ "keyword-spacing": "off"
},
"overrides": [
{
@@ -109,7 +110,8 @@
"named": "never",
"asyncArrow": "always"
}],
- "@typescript-eslint/func-call-spacing": ["error"]
+ "@typescript-eslint/func-call-spacing": ["error"],
+ "@typescript-eslint/keyword-spacing": ["error"]
}
}
]
diff --git a/src/extensions/anvil/algorithm.ts b/src/extensions/anvil/algorithm.ts
index 08bdcadd5..4427afb38 100644
--- a/src/extensions/anvil/algorithm.ts
+++ b/src/extensions/anvil/algorithm.ts
@@ -476,11 +476,11 @@ function adjustExtent(ctx: ANVILContext, membrane: MembraneCandidate, centroid:
}
function qValue(currentStats: HphobHphil, initialStats: HphobHphil): number {
- if(initialStats.hphob < 1) {
+ if (initialStats.hphob < 1) {
initialStats.hphob = 0.1;
}
- if(initialStats.hphil < 1) {
+ if (initialStats.hphil < 1) {
initialStats.hphil += 1;
}
@@ -505,7 +505,7 @@ function generateSpherePoints(ctx: ANVILContext, numberOfSpherePoints: number):
const { centroid, extent } = ctx;
const points = [];
let oldPhi = 0, h, theta, phi;
- for(let k = 1, kl = numberOfSpherePoints + 1; k < kl; k++) {
+ for (let k = 1, kl = numberOfSpherePoints + 1; k < kl; k++) {
h = -1 + 2 * (k - 1) / (2 * numberOfSpherePoints - 1);
theta = Math.acos(h);
phi = (k === 1 || k === numberOfSpherePoints) ? 0 : (oldPhi + 3.6 / Math.sqrt(2 * numberOfSpherePoints * (1 - h * h))) % (2 * Math.PI);
diff --git a/src/extensions/cellpack/model.ts b/src/extensions/cellpack/model.ts
index 8b060aafd..d57624cc3 100644
--- a/src/extensions/cellpack/model.ts
+++ b/src/extensions/cellpack/model.ts
@@ -415,7 +415,7 @@ export function createStructureFromCellPack(plugin: PluginContext, packing: Cell
if (ctx.shouldUpdate) await ctx.update(`${name} - structure`);
const structure = Structure.create(units);
- for(let i = 0, il = structure.models.length; i < il; ++i) {
+ for (let i = 0, il = structure.models.length; i < il; ++i) {
Model.TrajectoryInfo.set(structure.models[i], { size: il, index: i });
}
return { structure, assets, colors: skipColors ? undefined : colors };
diff --git a/src/extensions/cellpack/state.ts b/src/extensions/cellpack/state.ts
index bd5729272..e7bc842ab 100644
--- a/src/extensions/cellpack/state.ts
+++ b/src/extensions/cellpack/state.ts
@@ -84,7 +84,7 @@ const StructureFromCellpack = PluginStateTransform.BuiltIn({
},
dispose({ b, cache }) {
const assets = (cache as any).assets as Asset.Wrapper[];
- if(assets) {
+ if (assets) {
for (const a of assets) a.dispose();
}
@@ -137,7 +137,7 @@ const StructureFromAssemblies = PluginStateTransform.BuiltIn({
offsetInvariantId += maxInvariantId + 1;
}
structure = builder.getStructure();
- for(let i = 0, il = structure.models.length; i < il; ++i) {
+ for (let i = 0, il = structure.models.length; i < il; ++i) {
Model.TrajectoryInfo.set(structure.models[i], { size: il, index: i });
}
}
diff --git a/src/extensions/rcsb/assembly-symmetry/behavior.ts b/src/extensions/rcsb/assembly-symmetry/behavior.ts
index eed3800e6..9e032c809 100644
--- a/src/extensions/rcsb/assembly-symmetry/behavior.ts
+++ b/src/extensions/rcsb/assembly-symmetry/behavior.ts
@@ -85,7 +85,7 @@ export const InitAssemblySymmetry3D = StateAction.build({
const assemblySymmetryData = AssemblySymmetryDataProvider.get(a.data).value;
const symmetryIndex = assemblySymmetryData ? AssemblySymmetry.firstNonC1(assemblySymmetryData) : -1;
await AssemblySymmetryProvider.attach(propCtx, a.data, { symmetryIndex });
- } catch(e) {
+ } catch (e) {
plugin.log.error(`Assembly Symmetry: ${e}`);
return;
}
diff --git a/src/extensions/rcsb/validation-report/prop.ts b/src/extensions/rcsb/validation-report/prop.ts
index fa060c584..f1be4b10b 100644
--- a/src/extensions/rcsb/validation-report/prop.ts
+++ b/src/extensions/rcsb/validation-report/prop.ts
@@ -112,7 +112,7 @@ namespace ValidationReport {
}
export async function obtain(ctx: CustomProperty.Context, model: Model, props: ValidationReportProps): Promise<CustomProperty.Data<ValidationReport>> {
- switch(props.source.name) {
+ switch (props.source.name) {
case 'file': return open(ctx, model, props.source.params);
case 'server': return fetch(ctx, model, props.source.params);
}
diff --git a/src/mol-gl/shader-code.ts b/src/mol-gl/shader-code.ts
index 2e507084f..63836245a 100644
--- a/src/mol-gl/shader-code.ts
+++ b/src/mol-gl/shader-code.ts
@@ -137,7 +137,7 @@ import { cylinders_vert } from './shader/cylinders.vert';
import { cylinders_frag } from './shader/cylinders.frag';
export const CylindersShaderCode = ShaderCode('cylinders', cylinders_vert, cylinders_frag, { fragDepth: 'required', drawBuffers: 'optional' });
-import { text_vert }from './shader/text.vert';
+import { text_vert } from './shader/text.vert';
import { text_frag } from './shader/text.frag';
export const TextShaderCode = ShaderCode('text', text_vert, text_frag, { standardDerivatives: 'required', drawBuffers: 'optional' });
diff --git a/src/mol-io/reader/psf/parser.ts b/src/mol-io/reader/psf/parser.ts
index 7acca9aaf..7ef359df3 100644
--- a/src/mol-io/reader/psf/parser.ts
+++ b/src/mol-io/reader/psf/parser.ts
@@ -174,7 +174,7 @@ async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<
const id = readLine(state.tokenizer).trim();
- while(tokenizer.tokenEnd < tokenizer.length) {
+ while (tokenizer.tokenEnd < tokenizer.length) {
const line = readLine(state.tokenizer).trim();
if (line.includes('!NTITLE')) {
const numTitle = parseInt(line.split(reWhitespace)[0]);
diff --git a/src/mol-math/linear-algebra/matrix/evd.ts b/src/mol-math/linear-algebra/matrix/evd.ts
index 041048552..9feb5fcad 100644
--- a/src/mol-math/linear-algebra/matrix/evd.ts
+++ b/src/mol-math/linear-algebra/matrix/evd.ts
@@ -19,9 +19,9 @@ export namespace EVD {
return {
size,
matrix: Matrix.create(size, size),
- eigenValues: <any>new Float64Array(size),
- D: <any>new Float64Array(size),
- E: <any>new Float64Array(size)
+ eigenValues: <any> new Float64Array(size),
+ D: <any> new Float64Array(size),
+ E: <any> new Float64Array(size)
};
}
diff --git a/src/mol-model-formats/structure/cif-core.ts b/src/mol-model-formats/structure/cif-core.ts
index 55f869a79..091853b77 100644
--- a/src/mol-model-formats/structure/cif-core.ts
+++ b/src/mol-model-formats/structure/cif-core.ts
@@ -160,7 +160,7 @@ async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: Runti
ModelSymmetry.Provider.set(first, symmetry);
const bondCount = db.geom_bond._rowCount;
- if(bondCount > 0) {
+ if (bondCount > 0) {
const labelIndexMap: { [label: string]: number } = {};
const { label } = db.atom_site;
for (let i = 0, il = label.rowCount; i < il; ++i) {
diff --git a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts
index 80f24501e..ffb4a71ed 100644
--- a/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts
+++ b/src/mol-model-props/computed/accessible-surface-area/shrake-rupley/radii.ts
@@ -94,7 +94,7 @@ function determineRadiusAmino(atomId: string, element: ElementSymbol, compId: st
return atomId === 'NZ' ? 4 : 3;
case 'C':
switch (atomId) {
- case 'C': case 'CE1': case'CE2': case 'CE3': case 'CH2': case 'CZ': case 'CZ2': case 'CZ3':
+ case 'C': case 'CE1': case 'CE2': case 'CE3': case 'CH2': case 'CZ': case 'CZ2': case 'CZ3':
return 1;
case 'CA': case 'CB': case 'CE': case 'CG1': case 'CG2':
return 2;
diff --git a/src/mol-model/loci.ts b/src/mol-model/loci.ts
index 6b90c0221..64d264efd 100644
--- a/src/mol-model/loci.ts
+++ b/src/mol-model/loci.ts
@@ -262,9 +262,9 @@ namespace Loci {
export type Granularity = keyof typeof Granularity
export const GranularityOptions = ParamDefinition.objectToOptions(Granularity, k => {
switch (k) {
- case 'element': return'Atom/Coarse Element';
+ case 'element': return 'Atom/Coarse Element';
case 'elementInstances': return ['Atom/Coarse Element Instances', 'With Symmetry'];
- case 'structure': return'Structure/Shape';
+ case 'structure': return 'Structure/Shape';
default: return k.indexOf('Instances')
? [stringToWords(k), 'With Symmetry'] : stringToWords(k);
}
diff --git a/src/mol-model/structure/structure/element/loci.ts b/src/mol-model/structure/structure/element/loci.ts
index 083ea9baa..617f869a5 100644
--- a/src/mol-model/structure/structure/element/loci.ts
+++ b/src/mol-model/structure/structure/element/loci.ts
@@ -67,7 +67,7 @@ export namespace Loci {
export function isEmpty(loci: Loci) {
for (const u of loci.elements) {
- if(OrderedSet.size(u.indices) > 0) return false;
+ if (OrderedSet.size(u.indices) > 0) return false;
}
return true;
}
diff --git a/src/mol-plugin-state/builder/structure/representation-preset.ts b/src/mol-plugin-state/builder/structure/representation-preset.ts
index 119dd0f15..de9e8caf7 100644
--- a/src/mol-plugin-state/builder/structure/representation-preset.ts
+++ b/src/mol-plugin-state/builder/structure/representation-preset.ts
@@ -260,12 +260,12 @@ const coarseSurface = StructureRepresentationPresetProvider({
smoothness: 1,
visuals: ['structure-gaussian-surface-mesh']
});
- } else if(size === Structure.Size.Huge) {
+ } else if (size === Structure.Size.Huge) {
Object.assign(gaussianProps, {
radiusOffset: structure.isCoarseGrained ? 2 : 0,
smoothness: 1,
});
- } else if(structure.isCoarseGrained) {
+ } else if (structure.isCoarseGrained) {
Object.assign(gaussianProps, {
radiusOffset: 2,
smoothness: 1,
diff --git a/src/mol-plugin-state/manager/loci-label.ts b/src/mol-plugin-state/manager/loci-label.ts
index 1b7322cec..e36300411 100644
--- a/src/mol-plugin-state/manager/loci-label.ts
+++ b/src/mol-plugin-state/manager/loci-label.ts
@@ -48,7 +48,7 @@ export class LociLabelManager {
if (idx === -1 && action === MarkerAction.Highlight) {
this.locis.push(loci);
this.isDirty = true;
- } else if(idx !== -1 && action === MarkerAction.RemoveHighlight) {
+ } else if (idx !== -1 && action === MarkerAction.RemoveHighlight) {
arrayRemoveAtInPlace(this.locis, idx);
this.isDirty = true;
}
diff --git a/src/mol-plugin-ui/base.tsx b/src/mol-plugin-ui/base.tsx
index fef08ba42..20047db2e 100644
--- a/src/mol-plugin-ui/base.tsx
+++ b/src/mol-plugin-ui/base.tsx
@@ -85,7 +85,7 @@ export abstract class CollapsableControls<P = {}, S = {}, SS = {}> extends Plugi
}
componentDidUpdate(prevProps: P & CollapsableProps) {
- if(this.props.initiallyCollapsed !== undefined && prevProps.initiallyCollapsed !== this.props.initiallyCollapsed) {
+ if (this.props.initiallyCollapsed !== undefined && prevProps.initiallyCollapsed !== this.props.initiallyCollapsed) {
this.setState({ isCollapsed: this.props.initiallyCollapsed as any });
}
}
diff --git a/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx b/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx
index dd9e62b7a..b080af9cf 100644
--- a/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx
+++ b/src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx
@@ -49,11 +49,11 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
}
this.state.points.sort((a, b) => {
- if(a[0] === b[0]){
- if(a[0] === 0){
+ if (a[0] === b[0]){
+ if (a[0] === 0){
return a[1] - b[1];
}
- if(a[1] === 1){
+ if (a[1] === 1){
return b[1] - a[1];
}
return a[1] - b[1];
@@ -128,7 +128,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
}
private handleMouseDown = (id: number) => (event: any) => {
- if(id === 0 || id === this.state.points.length - 1){
+ if (id === 0 || id === this.state.points.length - 1){
return;
}
@@ -150,7 +150,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
}
private handleDrag(event: any) {
- if(this.selected === undefined){
+ if (this.selected === undefined){
return;
}
@@ -166,7 +166,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
updatedCopyPoint = Vec2.create(this.updatedX, this.updatedY);
} else if (svgP.x < padding) {
updatedCopyPoint = Vec2.create(padding, svgP.y);
- } else if(svgP.x > (this.width + (padding))) {
+ } else if (svgP.x > (this.width + (padding))) {
updatedCopyPoint = Vec2.create(this.width + padding, svgP.y);
} else if (svgP.y > (this.height + (padding))) {
updatedCopyPoint = Vec2.create(svgP.x, this.height + padding);
@@ -197,7 +197,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
return;
}
- if(selected === undefined || selected[0] === 0 || selected[0] === this.state.points.length - 1) {
+ if (selected === undefined || selected[0] === 0 || selected[0] === this.state.points.length - 1) {
this.setState({
copyPoint: undefined,
});
@@ -209,11 +209,11 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
const points = this.state.points.filter((_, i) => i !== selected[0]);
points.push(updatedPoint);;
points.sort((a, b) => {
- if(a[0] === b[0]){
- if(a[0] === 0){
+ if (a[0] === b[0]){
+ if (a[0] === 0){
return a[1] - b[1];
}
- if(a[1] === 1){
+ if (a[1] === 1){
return b[1] - a[1];
}
return a[1] - b[1];
@@ -238,7 +238,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
const points = this.state.points;
const padding = this.padding / 2;
- if(svgP.x < (padding) ||
+ if (svgP.x < (padding) ||
svgP.x > (this.width + (padding)) ||
svgP.y > (this.height + (padding)) ||
svgP.y < (this.padding / 2)) {
@@ -247,11 +247,11 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
const newPoint = this.unNormalizePoint(Vec2.create(svgP.x, svgP.y));
points.push(newPoint);
points.sort((a, b) => {
- if(a[0] === b[0]){
- if(a[0] === 0){
+ if (a[0] === b[0]){
+ if (a[0] === 0){
return a[1] - b[1];
}
- if(a[1] === 1){
+ if (a[1] === 1){
return b[1] - a[1];
}
return a[1] - b[1];
@@ -263,14 +263,14 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
}
private deletePoint = (i: number) => (event: any) => {
- if(i === 0 || i === this.state.points.length - 1){ return; }
+ if (i === 0 || i === this.state.points.length - 1){ return; }
const points = this.state.points.filter((_, j) => j !== i);
points.sort((a, b) => {
- if(a[0] === b[0]){
- if(a[0] === 0){
+ if (a[0] === b[0]){
+ if (a[0] === 0){
return a[1] - b[1];
}
- if(a[1] === 1){
+ if (a[1] === 1){
return b[1] - a[1];
}
return a[1] - b[1];
@@ -283,7 +283,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
}
private handleLeave() {
- if(this.selected === undefined) {
+ if (this.selected === undefined) {
return;
}
@@ -320,7 +320,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
}
private refCallBack(element: any) {
- if(element){
+ if (element){
this.myRef = element;
}
}
@@ -329,7 +329,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
const points: any[] = [];
let point: Vec2;
for (let i = 0; i < this.state.points.length; i++){
- if(i !== 0 && i !== this.state.points.length - 1){
+ if (i !== 0 && i !== this.state.points.length - 1){
point = this.normalizePoint(this.state.points[i]);
points.push(<PointComponent
key={i}
@@ -359,7 +359,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
let normalizedY: number;
let reverseY: number;
- for(const point of this.state.points){
+ for (const point of this.state.points){
min = this.padding / 2;
maxX = this.width + min;
maxY = this.height + min;
diff --git a/src/mol-plugin-ui/controls/line-graph/point-component.tsx b/src/mol-plugin-ui/controls/line-graph/point-component.tsx
index d3c752eea..94c2a1e79 100644
--- a/src/mol-plugin-ui/controls/line-graph/point-component.tsx
+++ b/src/mol-plugin-ui/controls/line-graph/point-component.tsx
@@ -29,7 +29,7 @@ export class PointComponent extends React.Component<any, {show: boolean}> {
}
public render() {
- return([
+ return ([
<circle
r="10"
key={`${this.props.id}circle`}
diff --git a/src/mol-plugin-ui/structure/focus.tsx b/src/mol-plugin-ui/structure/focus.tsx
index a5ab8d5f2..1aa66ec00 100644
--- a/src/mol-plugin-ui/structure/focus.tsx
+++ b/src/mol-plugin-ui/structure/focus.tsx
@@ -77,7 +77,7 @@ function getFocusEntries(structure: Structure) {
for (let i = 0, il = u.elements.length; i < il; ++i) {
const eI = u.elements[i];
const rI = residueIndex[eI];
- if(rI !== prev) {
+ if (rI !== prev) {
l.element = eI;
addSymmetryGroupEntries(entityEntries, l, ug, 'residue');
prev = rI;
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.ts b/src/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.ts
index 44cd1568f..10a12d4c8 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/computed/accessible-surface-area.ts
@@ -69,7 +69,7 @@ export const AccessibleSurfaceArea = PluginBehavior.create<{ autoAttach: boolean
//
function accessibleSurfaceAreaLabel(loci: Loci): string | undefined {
- if(loci.kind === 'element-loci') {
+ if (loci.kind === 'element-loci') {
if (loci.elements.length === 0) return;
const accessibleSurfaceArea = AccessibleSurfaceAreaProvider.get(loci.structure).value;
@@ -96,7 +96,7 @@ function accessibleSurfaceAreaLabel(loci: Loci): string | undefined {
return `Accessible Surface Area ${residueCount}: ${cummulativeArea.toFixed(2)} \u212B<sup>2</sup>`;
- } else if(loci.kind === 'structure-loci') {
+ } else if (loci.kind === 'structure-loci') {
const accessibleSurfaceArea = AccessibleSurfaceAreaProvider.get(loci.structure).value;
if (!accessibleSurfaceArea || loci.structure.customPropertyDescriptors.hasReference(AccessibleSurfaceAreaProvider.descriptor)) return;
diff --git a/src/mol-plugin/behavior/dynamic/custom-props/sequence/best-database-mapping.ts b/src/mol-plugin/behavior/dynamic/custom-props/sequence/best-database-mapping.ts
index 186ba57f0..9336cf6ac 100644
--- a/src/mol-plugin/behavior/dynamic/custom-props/sequence/best-database-mapping.ts
+++ b/src/mol-plugin/behavior/dynamic/custom-props/sequence/best-database-mapping.ts
@@ -58,7 +58,7 @@ export const BestDatabaseSequenceMapping = PluginBehavior.create<{ autoAttach: b
//
function bestDatabaseSequenceMappingLabel(loci: Loci): string | undefined {
- if(loci.kind === 'element-loci') {
+ if (loci.kind === 'element-loci') {
if (loci.elements.length === 0) return;
const e = loci.elements[0];
diff --git a/src/mol-plugin/util/toast.ts b/src/mol-plugin/util/toast.ts
index 7aa3d02cb..977b1155a 100644
--- a/src/mol-plugin/util/toast.ts
+++ b/src/mol-plugin/util/toast.ts
@@ -85,7 +85,7 @@ export class PluginToastManager extends StatefulPluginComponent<{
private hide(e: PluginToastManager.Entry | undefined) {
if (!e) return;
if (e.timeout !== void 0) clearTimeout(e.timeout);
- e.hide = <any>void 0;
+ e.hide = <any> void 0;
if (this.updateState({ entries: this.state.entries.delete(e.id) })) this.events.changed.next(void 0);
}
diff --git a/src/mol-repr/shape/representation.ts b/src/mol-repr/shape/representation.ts
index af0b769ee..2ad1cf89d 100644
--- a/src/mol-repr/shape/representation.ts
+++ b/src/mol-repr/shape/representation.ts
@@ -217,7 +217,7 @@ export function ShapeRepresentation<D, G extends Geometry, P extends Geometry.Pa
Representation.updateState(_state, state);
},
setTheme(theme: Theme) {
- if(isDebugMode) {
+ if (isDebugMode) {
console.warn('The `ShapeRepresentation` theme is fixed to `ShapeGroupColorTheme` and `ShapeGroupSizeTheme`. Colors are taken from `Shape.getColor` and sizes from `Shape.getSize`');
}
},
diff --git a/src/mol-repr/structure/visual/bond-inter-unit-line.ts b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
index f31a76652..5578b8011 100644
--- a/src/mol-repr/structure/visual/bond-inter-unit-line.ts
+++ b/src/mol-repr/structure/visual/bond-inter-unit-line.ts
@@ -75,7 +75,7 @@ function createInterUnitBondLines(ctx: VisualContext, structure: Structure, them
return LinkStyle.Dashed;
} else if (o === 3) {
return LinkStyle.Triple;
- }else if (aromaticBonds && BondType.is(f, BondType.Flag.Aromatic)) {
+ } else if (aromaticBonds && BondType.is(f, BondType.Flag.Aromatic)) {
return LinkStyle.Aromatic;
} else if (o === 2) {
return LinkStyle.Double;
diff --git a/src/mol-repr/structure/visual/util/bond.ts b/src/mol-repr/structure/visual/util/bond.ts
index 983a7612a..5e2ddafd6 100644
--- a/src/mol-repr/structure/visual/util/bond.ts
+++ b/src/mol-repr/structure/visual/util/bond.ts
@@ -100,7 +100,7 @@ export function makeInterBondIgnoreTest(structure: Structure, props: BondProps):
const b = edges[edgeIndex];
const uA = structure.unitMap.get(b.unitA);
const uB = structure.unitMap.get(b.unitB);
- if(isHydrogen(uA, uA.elements[b.indexA]) || isHydrogen(uB, uB.elements[b.indexB])) return true;
+ if (isHydrogen(uA, uA.elements[b.indexA]) || isHydrogen(uB, uB.elements[b.indexB])) return true;
}
if (!allBondTypes) {
diff --git a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
index d8561b58f..e191b3c01 100644
--- a/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
+++ b/src/mol-repr/structure/visual/util/polymer/trace-iterator.ts
@@ -289,7 +289,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
Vec3.copy(this.p0, this.p3);
Vec3.copy(this.p1, this.p3);
Vec3.copy(this.p2, this.p3);
- } else if(isHelixPrev1) {
+ } else if (isHelixPrev1) {
Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p2, this.p3), 2);
Vec3.add(this.p2, this.p3, tmpDir);
Vec3.add(this.p1, this.p2, tmpDir);
@@ -299,7 +299,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
if (isHelix) {
Vec3.copy(this.p0, this.p2);
Vec3.copy(this.p1, this.p2);
- } else if(isHelixPrev2) {
+ } else if (isHelixPrev2) {
Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p1, this.p2), 2);
Vec3.add(this.p1, this.p2, tmpDir);
Vec3.add(this.p0, this.p1, tmpDir);
@@ -307,7 +307,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
} else if (isHelix !== isHelixPrev3) {
if (isHelix) {
Vec3.copy(this.p0, this.p1);
- } else if(isHelixPrev3) {
+ } else if (isHelixPrev3) {
Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p0, this.p1), 2);
Vec3.add(this.p0, this.p1, tmpDir);
}
@@ -318,7 +318,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
Vec3.copy(this.p4, this.p3);
Vec3.copy(this.p5, this.p3);
Vec3.copy(this.p6, this.p3);
- } else if(isHelixNext1) {
+ } else if (isHelixNext1) {
Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p4, this.p3), 2);
Vec3.add(this.p4, this.p3, tmpDir);
Vec3.add(this.p5, this.p4, tmpDir);
@@ -328,7 +328,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
if (isHelix) {
Vec3.copy(this.p5, this.p4);
Vec3.copy(this.p6, this.p4);
- } else if(isHelixNext2) {
+ } else if (isHelixNext2) {
Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p5, this.p4), 2);
Vec3.add(this.p5, this.p4, tmpDir);
Vec3.add(this.p6, this.p5, tmpDir);
@@ -336,7 +336,7 @@ export class AtomicPolymerTraceIterator implements Iterator<PolymerTraceElement>
} else if (isHelix !== isHelixNext3) {
if (isHelix) {
Vec3.copy(this.p6, this.p5);
- } else if(isHelixNext3) {
+ } else if (isHelixNext3) {
Vec3.scale(tmpDir, Vec3.sub(tmpDir, this.p6, this.p5), 2);
Vec3.add(this.p6, this.p5, tmpDir);
}
diff --git a/src/mol-repr/volume/direct-volume.ts b/src/mol-repr/volume/direct-volume.ts
index d4a7bfcec..042219514 100644
--- a/src/mol-repr/volume/direct-volume.ts
+++ b/src/mol-repr/volume/direct-volume.ts
@@ -35,7 +35,7 @@ function getBoundingBox(gridDimension: Vec3, transform: Mat4) {
export function createDirectVolume2d(ctx: RuntimeContext, webgl: WebGLContext, volume: Volume, directVolume?: DirectVolume) {
const gridDimension = volume.grid.cells.space.dimensions as Vec3;
const { width, height } = getVolumeTexture2dLayout(gridDimension);
- if(Math.max(width, height) > webgl.maxTextureSize / 2) {
+ if (Math.max(width, height) > webgl.maxTextureSize / 2) {
throw new Error('volume too large for direct-volume rendering');
}
@@ -77,7 +77,7 @@ function getUnitToCartn(grid: Grid) {
export function createDirectVolume3d(ctx: RuntimeContext, webgl: WebGLContext, volume: Volume, directVolume?: DirectVolume) {
const gridDimension = volume.grid.cells.space.dimensions as Vec3;
- if(Math.max(...gridDimension) > webgl.max3dTextureSize / 2) {
+ if (Math.max(...gridDimension) > webgl.max3dTextureSize / 2) {
throw new Error('volume too large for direct-volume rendering');
}
diff --git a/src/mol-util/data-source.ts b/src/mol-util/data-source.ts
index 609d1a9d5..794c2e4d4 100644
--- a/src/mol-util/data-source.ts
+++ b/src/mol-util/data-source.ts
@@ -247,7 +247,7 @@ function processAjax<T extends DataType>(req: XMLHttpRequest, type: T): DataResp
}
function getRequestResponseType(type: DataType): XMLHttpRequestResponseType {
- switch(type) {
+ switch (type) {
case 'json': return 'json';
case 'xml': return 'document';
case 'string': return 'text';
diff --git a/src/mol-util/zip/bin.ts b/src/mol-util/zip/bin.ts
index a1a175389..38111eff9 100644
--- a/src/mol-util/zip/bin.ts
+++ b/src/mol-util/zip/bin.ts
@@ -35,7 +35,7 @@ export function writeUint(buff: Uint8Array, p: number, n: number) {
function readASCII(buff: Uint8Array, p: number, l: number){
let s = '';
- for(let i = 0; i < l; i++) s += String.fromCharCode(buff[p + i]);
+ for (let i = 0; i < l; i++) s += String.fromCharCode(buff[p + i]);
return s;
}
@@ -49,10 +49,10 @@ function pad(n: string) {
export function readUTF8(buff: Uint8Array, p: number, l: number) {
let s = '', ns;
- for(let i = 0; i < l; i++) s += '%' + pad(buff[p + i].toString(16));
+ for (let i = 0; i < l; i++) s += '%' + pad(buff[p + i].toString(16));
try {
ns = decodeURIComponent(s);
- } catch(e) {
+ } catch (e) {
return readASCII(buff, p, l);
}
return ns;
@@ -61,21 +61,21 @@ export function readUTF8(buff: Uint8Array, p: number, l: number) {
export function writeUTF8(buff: Uint8Array, p: number, str: string) {
const strl = str.length;
let i = 0;
- for(let ci = 0; ci < strl; ci++) {
+ for (let ci = 0; ci < strl; ci++) {
const code = str.charCodeAt(ci);
- if((code & (0xffffffff - (1 << 7) + 1)) === 0) {
+ if ((code & (0xffffffff - (1 << 7) + 1)) === 0) {
buff[p + i] = (code);
i++;
- } else if((code & (0xffffffff - (1 << 11) + 1)) === 0) {
+ } else if ((code & (0xffffffff - (1 << 11) + 1)) === 0) {
buff[p + i] = (192 | (code >> 6));
buff[p + i + 1] = (128 | ((code >> 0) & 63));
i += 2;
- } else if((code & (0xffffffff - (1 << 16) + 1)) === 0) {
+ } else if ((code & (0xffffffff - (1 << 16) + 1)) === 0) {
buff[p + i] = (224 | (code >> 12));
buff[p + i + 1] = (128 | ((code >> 6) & 63));
buff[p + i + 2] = (128 | ((code >> 0) & 63));
i += 3;
- } else if((code & (0xffffffff - (1 << 21) + 1)) === 0) {
+ } else if ((code & (0xffffffff - (1 << 21) + 1)) === 0) {
buff[p + i] = (240 | (code >> 18));
buff[p + i + 1] = (128 | ((code >> 12) & 63));
buff[p + i + 2] = (128 | ((code >> 6) & 63));
@@ -89,15 +89,15 @@ export function writeUTF8(buff: Uint8Array, p: number, str: string) {
export function sizeUTF8(str: string) {
const strl = str.length;
let i = 0;
- for(let ci = 0; ci < strl; ci++) {
+ for (let ci = 0; ci < strl; ci++) {
const code = str.charCodeAt(ci);
if ((code & (0xffffffff - (1 << 7) + 1)) === 0) {
i++ ;
- } else if((code & (0xffffffff - (1 << 11) + 1)) === 0) {
+ } else if ((code & (0xffffffff - (1 << 11) + 1)) === 0) {
i += 2;
- } else if((code & (0xffffffff - (1 << 16) + 1)) === 0) {
+ } else if ((code & (0xffffffff - (1 << 16) + 1)) === 0) {
i += 3;
- } else if((code & (0xffffffff - (1 << 21) + 1)) === 0) {
+ } else if ((code & (0xffffffff - (1 << 21) + 1)) === 0) {
i += 4;
} else {
throw new Error('e');
diff --git a/src/mol-util/zip/checksum.ts b/src/mol-util/zip/checksum.ts
index 2ea3851a4..5bfaa03f3 100644
--- a/src/mol-util/zip/checksum.ts
+++ b/src/mol-util/zip/checksum.ts
@@ -35,9 +35,9 @@ export function adler(data: Uint8Array, o: number, len: number) {
let a = 1, b = 0;
let off = o;
const end = o + len;
- while(off < end) {
+ while (off < end) {
const eend = Math.min(off + 5552, end);
- while(off < eend) {
+ while (off < eend) {
a += data[off++];
b += a;
}
diff --git a/src/mol-util/zip/deflate.ts b/src/mol-util/zip/deflate.ts
index 498f6e463..217f92993 100644
--- a/src/mol-util/zip/deflate.ts
+++ b/src/mol-util/zip/deflate.ts
@@ -45,19 +45,19 @@ function deflateChunk(ctx: DeflateContext, count: number) {
const end = Math.min(i + count, dlen);
- for(; i < end; i++) {
+ for (; i < end; i++) {
c = nc;
- if(i + 1 < dlen - 2) {
+ if (i + 1 < dlen - 2) {
nc = _hash(data, i + 1);
const ii = ((i + 1) & 0x7fff);
prev[ii] = strt[nc];
strt[nc] = ii;
}
- if(cvrd <= i) {
- if((li > 14000 || lc > 26697) && (dlen - i) > 100) {
- if(cvrd < i) {
+ if (cvrd <= i) {
+ if ((li > 14000 || lc > 26697) && (dlen - i) > 100) {
+ if (cvrd < i) {
lits[li] = i - cvrd;
li += 2;
cvrd = i;
@@ -68,11 +68,11 @@ function deflateChunk(ctx: DeflateContext, count: number) {
}
let mch = 0;
- if(i < dlen - 2) {
+ if (i < dlen - 2) {
mch = _bestMatch(data, i, prev, c, Math.min(opt[2], dlen - i), opt[3]);
}
- if(mch !== 0) {
+ if (mch !== 0) {
const len = mch >>> 16, dst = mch & 0xffff;
const lgi = _goodIndex(len, U.of0); U.lhst[257 + lgi]++;
const dgi = _goodIndex(dst, U.df0); U.dhst[dgi]++; ebits += U.exb[lgi] + U.dxb[dgi];
@@ -120,10 +120,10 @@ export async function _deflateRaw(runtime: RuntimeContext, data: Uint8Array, out
const ctx = DeflateContext(data, out, opos, lvl);
const { dlen } = ctx;
- if(lvl === 0) {
+ if (lvl === 0) {
let { i, pos } = ctx;
- while(i < dlen) {
+ while (i < dlen) {
const len = Math.min(0xffff, dlen - i);
_putsE(out, pos, (i + len === dlen ? 1 : 0));
pos = _copyExact(data, i, len, out, pos + 8);
@@ -132,7 +132,7 @@ export async function _deflateRaw(runtime: RuntimeContext, data: Uint8Array, out
return pos >>> 3;
}
- if(dlen > 2) {
+ if (dlen > 2) {
ctx.nc = _hash(data, 0);
ctx.strt[ctx.nc] = 0;
}
@@ -147,15 +147,15 @@ export async function _deflateRaw(runtime: RuntimeContext, data: Uint8Array, out
let { li, cvrd, pos } = ctx;
const { i, lits, bs, ebits } = ctx;
- if(bs !== i || data.length === 0) {
- if(cvrd < i) {
+ if (bs !== i || data.length === 0) {
+ if (cvrd < i) {
lits[li] = i - cvrd;
li += 2;
cvrd = i;
}
pos = _writeBlock(1, lits, li, ebits, data, bs, i - bs, out, pos);
}
- while((pos & 7) !== 0) pos++;
+ while ((pos & 7) !== 0) pos++;
return pos >>> 3;
}
@@ -163,21 +163,21 @@ function _bestMatch(data: Uint8Array, i: number, prev: Uint16Array, c: number, n
let ci = (i & 0x7fff), pi = prev[ci];
// console.log("----", i);
let dif = ((ci - pi + (1 << 15)) & 0x7fff);
- if(pi === ci || c !== _hash(data, i - dif)) return 0;
+ if (pi === ci || c !== _hash(data, i - dif)) return 0;
let tl = 0, td = 0; // top length, top distance
const dlim = Math.min(0x7fff, i);
- while(dif <= dlim && --chain !== 0 && pi !== ci /* && c==UZIP.F._hash(data,i-dif)*/) {
- if(tl === 0 || (data[i + tl] === data[i + tl - dif])) {
+ while (dif <= dlim && --chain !== 0 && pi !== ci /* && c==UZIP.F._hash(data,i-dif)*/) {
+ if (tl === 0 || (data[i + tl] === data[i + tl - dif])) {
let cl = _howLong(data, i, dif);
- if(cl > tl) {
- tl = cl; td = dif; if(tl >= nice) break; //*
- if(dif + 2 < cl) cl = dif + 2;
+ if (cl > tl) {
+ tl = cl; td = dif; if (tl >= nice) break; //*
+ if (dif + 2 < cl) cl = dif + 2;
let maxd = 0; // pi does not point to the start of the word
- for(let j = 0; j < cl - 2; j++) {
+ for (let j = 0; j < cl - 2; j++) {
const ei = (i - dif + j + (1 << 15)) & 0x7fff;
const li = prev[ei];
const curd = (ei - li + (1 << 15)) & 0x7fff;
- if(curd > maxd) { maxd = curd; pi = ei; }
+ if (curd > maxd) { maxd = curd; pi = ei; }
}
}
}
@@ -189,11 +189,11 @@ function _bestMatch(data: Uint8Array, i: number, prev: Uint16Array, c: number, n
}
function _howLong(data: Uint8Array, i: number, dif: number) {
- if(data[i] !== data[i - dif] || data[i + 1] !== data[i + 1 - dif] || data[i + 2] !== data[i + 2 - dif]) return 0;
+ if (data[i] !== data[i - dif] || data[i + 1] !== data[i + 1 - dif] || data[i + 2] !== data[i + 2 - dif]) return 0;
const oi = i, l = Math.min(data.length, i + 258);
i += 3;
// while(i+4<l && data[i]==data[i-dif] && data[i+1]==data[i+1-dif] && data[i+2]==data[i+2-dif] && data[i+3]==data[i+3-dif]) i+=4;
- while(i < l && data[i] === data[i - dif]) i++;
+ while (i < l && data[i] === data[i - dif]) i++;
return i - oi;
}
@@ -217,9 +217,9 @@ function _writeBlock(BFINAL: number, lits: Uint32Array, li: number, ebits: numbe
let dynSize = ebits + contSize(U.ltree, U.lhst) + contSize(U.dtree, U.dhst);
dynSize += 14 + 3 * numh + contSize(U.itree, U.ihst) + (U.ihst[16] * 2 + U.ihst[17] * 3 + U.ihst[18] * 7);
- for(let j = 0; j < 286; j++) U.lhst[j] = 0;
- for(let j = 0; j < 30; j++) U.dhst[j] = 0;
- for(let j = 0; j < 19; j++) U.ihst[j] = 0;
+ for (let j = 0; j < 286; j++) U.lhst[j] = 0;
+ for (let j = 0; j < 30; j++) U.dhst[j] = 0;
+ for (let j = 0; j < 19; j++) U.ihst[j] = 0;
const BTYPE = (cstSize < fxdSize && cstSize < dynSize) ? 0 : (fxdSize < dynSize ? 1 : 2);
_putsF(out, pos, BFINAL);
@@ -227,14 +227,14 @@ function _writeBlock(BFINAL: number, lits: Uint32Array, li: number, ebits: numbe
pos += 3;
// let opos = pos;
- if(BTYPE === 0) {
- while((pos & 7) !== 0) pos++;
+ if (BTYPE === 0) {
+ while ((pos & 7) !== 0) pos++;
pos = _copyExact(data, o0, l0, out, pos);
} else {
let ltree: number[], dtree: number[];
- if(BTYPE === 1) {
+ if (BTYPE === 1) {
ltree = U.fltree; dtree = U.fdtree;
- } else if(BTYPE === 2) {
+ } else if (BTYPE === 2) {
makeCodes(U.ltree, ML); revCodes(U.ltree, ML);
makeCodes(U.dtree, MD); revCodes(U.dtree, MD);
makeCodes(U.itree, MH); revCodes(U.itree, MH);
@@ -245,7 +245,7 @@ function _writeBlock(BFINAL: number, lits: Uint32Array, li: number, ebits: numbe
_putsE(out, pos, numd - 1); pos += 5; // 30
_putsE(out, pos, numh - 4); pos += 4; // 19
- for(let i = 0; i < numh; i++) _putsE(out, pos + i * 3, U.itree[(U.ordr[i] << 1) + 1]);
+ for (let i = 0; i < numh; i++) _putsE(out, pos + i * 3, U.itree[(U.ordr[i] << 1) + 1]);
pos += 3 * numh;
pos = _codeTiny(lset, U.itree, out, pos);
pos = _codeTiny(dset, U.itree, out, pos);
@@ -254,11 +254,11 @@ function _writeBlock(BFINAL: number, lits: Uint32Array, li: number, ebits: numbe
}
let off = o0;
- for(let si = 0; si < li; si += 2) {
+ for (let si = 0; si < li; si += 2) {
const qb = lits[si], len = (qb >>> 23), end = off + (qb & ((1 << 23) - 1));
- while(off < end) pos = _writeLit(data[off++], ltree, out, pos);
+ while (off < end) pos = _writeLit(data[off++], ltree, out, pos);
- if(len !== 0) {
+ if (len !== 0) {
const qc = lits[si + 1], dst = (qc >> 16), lgi = (qc >> 8) & 255, dgi = (qc & 255);
pos = _writeLit(257 + lgi, ltree, out, pos);
_putsE(out, pos, len - U.of0[lgi]); pos += U.exb[lgi];
@@ -298,26 +298,26 @@ function getTrees() {
const numl = _lenCodes(U.ltree, lset);
const dset: number[] = [];
const numd = _lenCodes(U.dtree, dset);
- for(let i = 0; i < lset.length; i += 2) U.ihst[lset[i]]++;
- for(let i = 0; i < dset.length; i += 2) U.ihst[dset[i]]++;
+ for (let i = 0; i < lset.length; i += 2) U.ihst[lset[i]]++;
+ for (let i = 0; i < dset.length; i += 2) U.ihst[dset[i]]++;
const MH = _hufTree(U.ihst, U.itree, 7);
let numh = 19;
- while(numh > 4 && U.itree[(U.ordr[numh - 1] << 1) + 1] === 0) numh--;
+ while (numh > 4 && U.itree[(U.ordr[numh - 1] << 1) + 1] === 0) numh--;
return [ML, MD, MH, numl, numd, numh, lset, dset] as const;
}
function contSize(tree: number[], hst: NumberArray) {
let s = 0;
- for(let i = 0; i < hst.length; i++) s += hst[i] * tree[(i << 1) + 1];
+ for (let i = 0; i < hst.length; i++) s += hst[i] * tree[(i << 1) + 1];
return s;
}
function _codeTiny(set: number[], tree: number[], out: Uint8Array, pos: number) {
- for(let i = 0; i < set.length; i += 2) {
+ for (let i = 0; i < set.length; i += 2) {
const l = set[i], rst = set[i + 1]; // console.log(l, pos, tree[(l<<1)+1]);
pos = _writeLit(l, tree, out, pos);
const rsl = l === 16 ? 2 : (l === 17 ? 3 : 7);
- if(l > 15) {
+ if (l > 15) {
_putsE(out, pos, rst);
pos += rsl;
}
@@ -328,19 +328,19 @@ function _codeTiny(set: number[], tree: number[], out: Uint8Array, pos: number)
function _lenCodes(tree: number[], set: number[]) {
let len = tree.length;
- while(len !== 2 && tree[len - 1] === 0) len -= 2; // when no distances, keep one code with length 0
- for(let i = 0; i < len; i += 2) {
+ while (len !== 2 && tree[len - 1] === 0) len -= 2; // when no distances, keep one code with length 0
+ for (let i = 0; i < len; i += 2) {
const l = tree[i + 1], nxt = (i + 3 < len ? tree[i + 3] : -1), nnxt = (i + 5 < len ? tree[i + 5] : -1), prv = (i === 0 ? -1 : tree[i - 1]);
- if(l === 0 && nxt === l && nnxt === l) {
+ if (l === 0 && nxt === l && nnxt === l) {
let lz = i + 5;
- while(lz + 2 < len && tree[lz + 2] === l) lz += 2;
+ while (lz + 2 < len && tree[lz + 2] === l) lz += 2;
const zc = Math.min((lz + 1 - i) >>> 1, 138);
- if(zc < 11) set.push(17, zc - 3);
+ if (zc < 11) set.push(17, zc - 3);
else set.push(18, zc - 11);
i += zc * 2 - 2;
- } else if(l === prv && nxt === l && nnxt === l) {
+ } else if (l === prv && nxt === l && nnxt === l) {
let lz = i + 5;
- while(lz + 2 < len && tree[lz + 2] === l) lz += 2;
+ while (lz + 2 < len && tree[lz + 2] === l) lz += 2;
const zc = Math.min((lz + 1 - i) >>> 1, 6);
set.push(16, zc - 3);
i += zc * 2 - 2;
@@ -353,11 +353,11 @@ function _lenCodes(tree: number[], set: number[]) {
function _goodIndex(v: number, arr: number[]) {
let i = 0;
- if(arr[i | 16] <= v) i |= 16;
- if(arr[i | 8] <= v) i |= 8;
- if(arr[i | 4] <= v) i |= 4;
- if(arr[i | 2] <= v) i |= 2;
- if(arr[i | 1] <= v) i |= 1;
+ if (arr[i | 16] <= v) i |= 16;
+ if (arr[i | 8] <= v) i |= 8;
+ if (arr[i | 4] <= v) i |= 4;
+ if (arr[i | 2] <= v) i |= 2;
+ if (arr[i | 1] <= v) i |= 1;
return i;
}
diff --git a/src/mol-util/zip/huffman.ts b/src/mol-util/zip/huffman.ts
index 16d5263b4..6caf1f974 100644
--- a/src/mol-util/zip/huffman.ts
+++ b/src/mol-util/zip/huffman.ts
@@ -19,14 +19,14 @@ export type HufTree = {
export function _hufTree(hst: NumberArray, tree: number[], MAXL: number) {
const list: HufTree[] = [];
const hl = hst.length, tl = tree.length;
- for(let i = 0; i < tl; i += 2) {
+ for (let i = 0; i < tl; i += 2) {
tree[i] = 0;
tree[i + 1] = 0;
}
- for(let i = 0; i < hl; i++) if(hst[i] !== 0) list.push({ lit: i, f: hst[i], d: undefined as any });
+ for (let i = 0; i < hl; i++) if (hst[i] !== 0) list.push({ lit: i, f: hst[i], d: undefined as any });
const end = list.length, l2 = list.slice(0);
- if(end === 0) return 0; // empty histogram (usually for dist)
- if(end === 1) {
+ if (end === 0) return 0; // empty histogram (usually for dist)
+ if (end === 1) {
const lit = list[0].lit, l2 = lit === 0 ? 1 : 0;
tree[(lit << 1) + 1] = 1;
tree[(l2 << 1) + 1] = 1;
@@ -41,13 +41,13 @@ export function _hufTree(hst: NumberArray, tree: number[], MAXL: number) {
r: b,
d: 0
};
- while(i1 !== end - 1) {
- if(i0 !== i1 && (i2 === end || list[i0].f < list[i2].f)) {
+ while (i1 !== end - 1) {
+ if (i0 !== i1 && (i2 === end || list[i0].f < list[i2].f)) {
a = list[i0++];
} else {
a = list[i2++];
}
- if(i0 !== i1 && (i2 === end || list[i0].f < list[i2].f)) {
+ if (i0 !== i1 && (i2 === end || list[i0].f < list[i2].f)) {
b = list[i0++];
} else {
b = list[i2++];
@@ -61,16 +61,16 @@ export function _hufTree(hst: NumberArray, tree: number[], MAXL: number) {
};
}
let maxl = setDepth(list[i1 - 1], 0);
- if(maxl > MAXL) {
+ if (maxl > MAXL) {
restrictDepth(l2, MAXL, maxl);
maxl = MAXL;
}
- for(let i = 0; i < end; i++) tree[(l2[i].lit << 1) + 1] = l2[i].d;
+ for (let i = 0; i < end; i++) tree[(l2[i].lit << 1) + 1] = l2[i].d;
return maxl;
}
function setDepth(t: HufTree, d: number): number {
- if(t.lit !== -1) {
+ if (t.lit !== -1) {
t.d = d;
return d;
}
@@ -82,8 +82,8 @@ function restrictDepth(dps: HufTree[], MD: number, maxl: number) {
const bCost = 1 << (maxl - MD);
dps.sort(function (a: HufTree, b: HufTree){ return b.d === a.d ? a.f - b.f : b.d - a.d; });
- for(i = 0; i < dps.length; i++) {
- if(dps[i].d > MD) {
+ for (i = 0; i < dps.length; i++) {
+ if (dps[i].d > MD) {
const od = dps[i].d;
dps[i].d = MD;
dbt += bCost - (1 << (maxl - od));
@@ -92,20 +92,20 @@ function restrictDepth(dps: HufTree[], MD: number, maxl: number) {
}
}
dbt = dbt >>> (maxl - MD);
- while(dbt > 0) {
+ while (dbt > 0) {
const od = dps[i].d;
- if(od < MD) {
+ if (od < MD) {
dps[i].d++;
dbt -= (1 << (MD - od - 1));
} else {
i++;
}
}
- for(; i >= 0; i--) {
- if(dps[i].d === MD && dbt < 0) {
+ for (; i >= 0; i--) {
+ if (dps[i].d === MD && dbt < 0) {
dps[i].d--;
dbt++;
}
}
- if(dbt !== 0) console.log('debt left');
+ if (dbt !== 0) console.log('debt left');
}
\ No newline at end of file
diff --git a/src/mol-util/zip/inflate.ts b/src/mol-util/zip/inflate.ts
index 0428a24f6..145a01c6e 100644
--- a/src/mol-util/zip/inflate.ts
+++ b/src/mol-util/zip/inflate.ts
@@ -13,7 +13,7 @@ import { RuntimeContext } from '../../mol-task';
function InflateContext(data: Uint8Array, buf?: Uint8Array) {
const noBuf = buf === undefined;
- if(buf === undefined) buf = new Uint8Array((data.length >>> 2) << 3);
+ if (buf === undefined) buf = new Uint8Array((data.length >>> 2) << 3);
return {
data,
buf,
@@ -31,7 +31,7 @@ function inflateBlocks(ctx: InflateContext, count: number) {
let iBlock = 0;
- while(BFINAL === 0 && iBlock < count) {
+ while (BFINAL === 0 && iBlock < count) {
let lmap, dmap;
let ML = 0, MD = 0;
@@ -40,12 +40,12 @@ function inflateBlocks(ctx: InflateContext, count: number) {
const BTYPE = _bitsF(data, pos + 1, 2);
pos += 3;
- if(BTYPE === 0) {
+ if (BTYPE === 0) {
// uncompressed block
- if((pos & 7) !== 0) pos += 8 - (pos & 7);
+ if ((pos & 7) !== 0) pos += 8 - (pos & 7);
const p8 = (pos >>> 3) + 4;
const len = data[p8 - 4] | (data[p8 - 3] << 8);
- if(noBuf) buf = _check(buf, off + len);
+ if (noBuf) buf = _check(buf, off + len);
buf.set(new Uint8Array(data.buffer, data.byteOffset + p8, len), off);
pos = ((p8 + len) << 3);
off += len;
@@ -53,30 +53,30 @@ function inflateBlocks(ctx: InflateContext, count: number) {
}
// grow output buffer if not provided
- if(noBuf) buf = _check(buf, off + (1 << 17));
+ if (noBuf) buf = _check(buf, off + (1 << 17));
- if(BTYPE === 1) {
+ if (BTYPE === 1) {
// block compressed with fixed Huffman codes
lmap = U.flmap;
dmap = U.fdmap;
ML = (1 << 9) - 1;
MD = (1 << 5) - 1;
- } else if(BTYPE === 2) {
+ } else if (BTYPE === 2) {
// block compressed with dynamic Huffman codes
const HLIT = _bitsE(data, pos, 5) + 257;
const HDIST = _bitsE(data, pos + 5, 5) + 1;
const HCLEN = _bitsE(data, pos + 10, 4) + 4;
pos += 14;
- for(let i = 0; i < 38; i += 2) {
+ for (let i = 0; i < 38; i += 2) {
U.itree[i] = 0;
U.itree[i + 1] = 0;
}
let tl = 1;
- for(let i = 0; i < HCLEN; i++) {
+ for (let i = 0; i < HCLEN; i++) {
const l = _bitsE(data, pos + i * 3, 3);
U.itree[(U.ordr[i] << 1) + 1] = l;
- if(l > tl) tl = l;
+ if (l > tl) tl = l;
}
pos += 3 * HCLEN;
makeCodes(U.itree, tl);
@@ -99,17 +99,17 @@ function inflateBlocks(ctx: InflateContext, count: number) {
throw new Error(`unknown BTYPE ${BTYPE}`);
}
- while(true) {
+ while (true) {
const code = lmap[_get17(data, pos) & ML];
pos += code & 15;
const lit = code >>> 4;
- if((lit >>> 8) === 0) {
+ if ((lit >>> 8) === 0) {
buf[off++] = lit;
- } else if(lit === 256) {
+ } else if (lit === 256) {
break;
} else {
let end = off + lit - 254;
- if(lit > 264) {
+ if (lit > 264) {
const ebs = U.ldef[lit - 257];
end = off + (ebs >>> 3) + _bitsE(data, pos, ebs & 7);
pos += ebs & 7;
@@ -122,8 +122,8 @@ function inflateBlocks(ctx: InflateContext, count: number) {
const dst = (dbs >>> 4) + _bitsF(data, pos, dbs & 15);
pos += dbs & 15;
- if(noBuf) buf = _check(buf, off + (1 << 17));
- while(off < end) {
+ if (noBuf) buf = _check(buf, off + (1 << 17));
+ while (off < end) {
buf[off] = buf[off++ - dst];
buf[off] = buf[off++ - dst];
buf[off] = buf[off++ - dst];
@@ -142,10 +142,10 @@ function inflateBlocks(ctx: InflateContext, count: number) {
// https://tools.ietf.org/html/rfc1951
export async function _inflate(runtime: RuntimeContext, data: Uint8Array, buf?: Uint8Array) {
- if(data[0] === 3 && data[1] === 0) return (buf ? buf : new Uint8Array(0));
+ if (data[0] === 3 && data[1] === 0) return (buf ? buf : new Uint8Array(0));
const ctx = InflateContext(data, buf);
- while(ctx.BFINAL === 0) {
+ while (ctx.BFINAL === 0) {
if (runtime.shouldUpdate) {
await runtime.update({ message: 'Inflating blocks...', current: ctx.pos, max: data.length });
}
@@ -156,7 +156,7 @@ export async function _inflate(runtime: RuntimeContext, data: Uint8Array, buf?:
function _check(buf: Uint8Array, len: number) {
const bl = buf.length;
- if(len <= bl) return buf;
+ if (len <= bl) return buf;
const nbuf = new Uint8Array(Math.max(bl << 1, len));
nbuf.set(buf, 0);
return nbuf;
@@ -164,28 +164,28 @@ function _check(buf: Uint8Array, len: number) {
function _decodeTiny(lmap: NumberArray, LL: number, len: number, data: Uint8Array, pos: number, tree: number[]) {
let i = 0;
- while(i < len) {
+ while (i < len) {
const code = lmap[_get17(data, pos) & LL];
pos += code & 15;
const lit = code >>> 4;
- if(lit <= 15) {
+ if (lit <= 15) {
tree[i] = lit;
i++;
} else {
let ll = 0, n = 0;
- if(lit === 16) {
+ if (lit === 16) {
n = (3 + _bitsE(data, pos, 2));
pos += 2;
ll = tree[i - 1];
- } else if(lit === 17) {
+ } else if (lit === 17) {
n = (3 + _bitsE(data, pos, 3));
pos += 3;
- } else if(lit === 18) {
+ } else if (lit === 18) {
n = (11 + _bitsE(data, pos, 7));
pos += 7;
}
const ni = i + n;
- while(i < ni) {
+ while (i < ni) {
tree[i] = ll;
i++;
}
@@ -197,14 +197,14 @@ function _decodeTiny(lmap: NumberArray, LL: number, len: number, data: Uint8Arra
function _copyOut(src: number[], off: number, len: number, tree: number[]) {
let mx = 0, i = 0;
const tl = tree.length >>> 1;
- while(i < len) {
+ while (i < len) {
const v = src[i + off];
tree[(i << 1)] = 0;
tree[(i << 1) + 1] = v;
- if(v > mx)mx = v;
+ if (v > mx)mx = v;
i++;
}
- while(i < tl) {
+ while (i < tl) {
tree[(i << 1)] = 0;
tree[(i << 1) + 1] = 0;
i++;
diff --git a/src/mol-util/zip/util.ts b/src/mol-util/zip/util.ts
index f9b4eb732..f5eec31fd 100644
--- a/src/mol-util/zip/util.ts
+++ b/src/mol-util/zip/util.ts
@@ -35,7 +35,7 @@ export const U = (function (){
(function (){
const len = 1 << 15;
- for(let i = 0; i < len; i++) {
+ for (let i = 0; i < len; i++) {
let x = i;
x = (((x & 0xaaaaaaaa) >>> 1) | ((x & 0x55555555) << 1));
x = (((x & 0xcccccccc) >>> 2) | ((x & 0x33333333) << 2));
@@ -45,10 +45,10 @@ export const U = (function (){
}
function pushV(tgt: number[], n: number, sv: number) {
- while(n-- !== 0) tgt.push(0, sv);
+ while (n-- !== 0) tgt.push(0, sv);
}
- for(let i = 0; i < 32; i++) {
+ for (let i = 0; i < 32; i++) {
U.ldef[i] = (U.of0[i] << 3) | U.exb[i];
U.ddef[i] = (U.df0[i] << 4) | U.dxb[i];
}
@@ -86,15 +86,15 @@ export const U = (function (){
export function codes2map(tree: number[], MAX_BITS: number, map: Uint16Array) {
const max_code = tree.length;
const r15 = U.rev15;
- for(let i = 0; i < max_code; i += 2) {
- if(tree[i + 1] !== 0) {
+ for (let i = 0; i < max_code; i += 2) {
+ if (tree[i + 1] !== 0) {
const lit = i >> 1;
const cl = tree[i + 1], val = (lit << 4) | cl; // : (0x8000 | (U.of0[lit-257]<<7) | (U.exb[lit-257]<<4) | cl);
const rest = (MAX_BITS - cl);
let i0 = tree[i] << rest;
const i1 = i0 + (1 << rest);
// tree[i]=r15[i0]>>>(15-MAX_BITS);
- while(i0 !== i1) {
+ while (i0 !== i1) {
const p0 = r15[i0] >>> (15 - MAX_BITS);
map[p0] = val; i0++;
}
@@ -106,8 +106,8 @@ export function makeCodes(tree: number[], MAX_BITS: number) { // code, length
const max_code = tree.length;
const bl_count = U.bl_count;
- for(let i = 0; i <= MAX_BITS; i++) bl_count[i] = 0;
- for(let i = 1; i < max_code; i += 2) bl_count[tree[i]]++;
+ for (let i = 0; i <= MAX_BITS; i++) bl_count[i] = 0;
+ for (let i = 1; i < max_code; i += 2) bl_count[tree[i]]++;
const next_code = U.next_code; // smallest code for each length
@@ -129,7 +129,7 @@ export function makeCodes(tree: number[], MAX_BITS: number) { // code, length
export function revCodes(tree: number[], MAX_BITS: number) {
const r15 = U.rev15, imb = 15 - MAX_BITS;
- for(let i = 0; i < tree.length; i += 2) {
+ for (let i = 0; i < tree.length; i += 2) {
const i0 = (tree[i] << (MAX_BITS - tree[i + 1]));
tree[i] = r15[i0] >>> imb;
}
diff --git a/src/mol-util/zip/zip.ts b/src/mol-util/zip/zip.ts
index 173cd9f90..b81bccf49 100644
--- a/src/mol-util/zip/zip.ts
+++ b/src/mol-util/zip/zip.ts
@@ -20,7 +20,7 @@ export async function unzip(runtime: RuntimeContext, buf: ArrayBuffer, onlyNames
const data = new Uint8Array(buf);
let eocd = data.length - 4;
- while(readUint(data, eocd) !== 0x06054b50) eocd--;
+ while (readUint(data, eocd) !== 0x06054b50) eocd--;
let o = eocd;
o += 4; // sign = 0x06054b50
@@ -35,7 +35,7 @@ export async function unzip(runtime: RuntimeContext, buf: ArrayBuffer, onlyNames
const coffs = readUint(data, o); o += 4;
o = coffs;
- for(let i = 0; i < cnu; i++) {
+ for (let i = 0; i < cnu; i++) {
// const sign = readUint(data, o);
o += 4;
o += 4; // versions;
@@ -93,15 +93,15 @@ async function _readLocal(runtime: RuntimeContext, data: Uint8Array, o: number,
o += nlen; // console.log(name);
o += elen;
- if(onlyNames) {
+ if (onlyNames) {
out[name] = { size: usize, csize };
return;
}
const file = new Uint8Array(data.buffer, o);
- if(cmpr === 0) {
+ if (cmpr === 0) {
out[name] = new Uint8Array(file.buffer.slice(o, o + csize));
- } else if(cmpr === 8) {
+ } else if (cmpr === 8) {
const buf = new Uint8Array(usize);
await inflateRaw(runtime, file, buf);
out[name] = buf;
@@ -141,14 +141,14 @@ export async function ungzip(runtime: RuntimeContext, file: Uint8Array, buf?: Ui
}
if (flg & 8) { // FNAME
let zero = o;
- while(file[zero] !== 0) ++zero;
+ while (file[zero] !== 0) ++zero;
// const name = readUTF8(file, o, zero - o)
// console.log('FNAME', name, zero - o)
o = zero + 1;
}
if (flg & 16) { // FCOMMENT
let zero = o;
- while(file[zero] !== 0) ++zero;
+ while (file[zero] !== 0) ++zero;
// const comment = readUTF8(file, o, zero - o)
// console.log('FCOMMENT', comment)
o = zero + 1;
@@ -175,7 +175,7 @@ export async function ungzip(runtime: RuntimeContext, file: Uint8Array, buf?: Ui
}
export async function deflate(runtime: RuntimeContext, data: Uint8Array, opts?: { level: number }/* , buf, off*/) {
- if(opts === undefined) opts = { level: 6 };
+ if (opts === undefined) opts = { level: 6 };
let off = 0;
const buf = new Uint8Array(50 + Math.floor(data.length * 1.1));
buf[off] = 120; buf[off + 1] = 156; off += 2;
@@ -189,7 +189,7 @@ export async function deflate(runtime: RuntimeContext, data: Uint8Array, opts?:
}
async function deflateRaw(runtime: RuntimeContext, data: Uint8Array, opts?: { level: number }) {
- if(opts === undefined) opts = { level: 6 };
+ if (opts === undefined) opts = { level: 6 };
const buf = new Uint8Array(50 + Math.floor(data.length * 1.1));
const off = await _deflateRaw(runtime, data, buf, 0, opts.level);
return new Uint8Array(buf.buffer, 0, off);
@@ -202,7 +202,7 @@ export function Zip(obj: { [k: string]: Uint8Array }, noCmpr = false) {
export async function zip(runtime: RuntimeContext, obj: { [k: string]: Uint8Array }, noCmpr = false) {
let tot = 0;
const zpd: { [k: string]: { cpr: boolean, usize: number, crc: number, file: Uint8Array } } = {};
- for(const p in obj) {
+ for (const p in obj) {
const cpr = !_noNeed(p) && !noCmpr, buf = obj[p];
const crcValue = crc(buf, 0, buf.length);
zpd[p] = {
@@ -213,20 +213,20 @@ export async function zip(runtime: RuntimeContext, obj: { [k: string]: Uint8Arra
};
}
- for(const p in zpd) tot += zpd[p].file.length + 30 + 46 + 2 * sizeUTF8(p);
+ for (const p in zpd) tot += zpd[p].file.length + 30 + 46 + 2 * sizeUTF8(p);
tot += 22;
const data = new Uint8Array(tot);
let o = 0;
const fof = [];
- for(const p in zpd) {
+ for (const p in zpd) {
const file = zpd[p]; fof.push(o);
o = _writeHeader(data, o, p, file, 0);
}
let i = 0;
const ioff = o;
- for(const p in zpd) {
+ for (const p in zpd) {
const file = zpd[p];
fof.push(o);
o = _writeHeader(data, o, p, file, 1, fof[i++]);
@@ -253,7 +253,7 @@ function _writeHeader(data: Uint8Array, o: number, p: string, obj: { cpr: boolea
const file = obj.file;
writeUint(data, o, t === 0 ? 0x04034b50 : 0x02014b50); o += 4; // sign
- if(t === 1) o += 2; // ver made by
+ if (t === 1) o += 2; // ver made by
writeUshort(data, o, 20); o += 2; // ver
writeUshort(data, o, 0); o += 2; // gflip
writeUshort(data, o, obj.cpr ? 8 : 0); o += 2; // cmpr
@@ -266,14 +266,14 @@ function _writeHeader(data: Uint8Array, o: number, p: string, obj: { cpr: boolea
writeUshort(data, o, sizeUTF8(p)); o += 2; // nlen
writeUshort(data, o, 0); o += 2; // elen
- if(t === 1) {
+ if (t === 1) {
o += 2; // comment length
o += 2; // disk number
o += 6; // attributes
writeUint(data, o, roff); o += 4; // usize
}
const nlen = writeUTF8(data, o, p); o += nlen;
- if(t === 0) {
+ if (t === 0) {
data.set(file, o);
o += file.length;
}
diff --git a/src/servers/model/server/query.ts b/src/servers/model/server/query.ts
index 1fe8899a9..fc502db27 100644
--- a/src/servers/model/server/query.ts
+++ b/src/servers/model/server/query.ts
@@ -166,7 +166,7 @@ async function resolveMultiFile(job: Job) {
encoder.startDataBlock(structure.cifFrame.header);
hasDataBlock = true;
await resolveJobEntry(entry, structure, encoder);
- } catch(e) {
+ } catch (e) {
if (!hasDataBlock) {
header = createErrorDataBlock(entry, encoder);
}
--
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