From 1cee84d9afe87a58503ce0e2d63fa16093655305 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alexander.rose@weirdbyte.de>
Date: Thu, 23 Jan 2020 10:14:03 -0800
Subject: [PATCH] fix formating
---
src/apps/basic-wrapper/superposition.ts | 20 ++--
src/apps/chem-comp-bond/create-table.ts | 4 +-
src/apps/structure-info/volume.ts | 4 +-
src/examples/proteopedia-wrapper/index.ts | 6 +-
src/mol-data/db/column.ts | 16 ++--
src/mol-data/generic/linked-list.ts | 4 +-
.../util/_spec/interval-iterator.spec.ts | 4 +-
src/mol-geo/geometry/text/font-atlas.ts | 10 +-
src/mol-geo/primitive/box.ts | 31 +++----
src/mol-geo/primitive/dodecahedron.ts | 32 +++----
src/mol-geo/util/marching-cubes/builder.ts | 2 +-
src/mol-io/reader/common/text/column/token.ts | 10 +-
src/mol-math/linear-algebra/3d.ts | 6 +-
src/mol-math/linear-algebra/3d/quat.ts | 14 +--
.../structure/pdb/assembly.ts | 22 ++---
.../computed/interactions/hydrogen-bonds.ts | 15 ++-
src/mol-model-props/rcsb/graphql/types.ts | 92 +++++++++----------
.../representations/assembly-symmetry-axes.ts | 2 +-
.../structure/model/properties/common.ts | 5 +-
.../structure/carbohydrates/compute.ts | 8 +-
.../structure/structure/element/stats.ts | 16 ++--
.../state/representation/structure/preset.ts | 2 +-
src/mol-plugin/state/snapshots.ts | 4 +-
.../state/transforms/representation.ts | 2 +-
src/mol-repr/structure/units-visual.ts | 4 +-
src/mol-script/language/expression.ts | 2 +-
src/mol-script/runtime/query/table.ts | 3 -
src/mol-state/state/builder.ts | 4 +-
src/mol-state/tree/transient.ts | 4 +-
src/mol-task/execution/observable.ts | 2 +-
src/mol-task/util/scheduler.ts | 50 +++++-----
src/mol-theme/label.ts | 1 -
src/servers/model/local.ts | 39 ++++----
src/servers/model/server.ts | 12 +--
src/servers/model/utils/fetch-props-pdbe.ts | 8 +-
src/servers/volume/common/binary-schema.ts | 9 +-
src/servers/volume/server/algebra/box.ts | 4 -
.../volume/server/algebra/coordinate.ts | 6 --
src/servers/volume/server/query/data-model.ts | 4 -
src/servers/volume/server/query/identify.ts | 6 +-
src/servers/volume/server/web-api.ts | 8 +-
src/servers/volume/server/web-schema.ts | 2 +-
42 files changed, 236 insertions(+), 263 deletions(-)
diff --git a/src/apps/basic-wrapper/superposition.ts b/src/apps/basic-wrapper/superposition.ts
index 6197fbc42..13e487af0 100644
--- a/src/apps/basic-wrapper/superposition.ts
+++ b/src/apps/basic-wrapper/superposition.ts
@@ -50,16 +50,16 @@ export function buildStaticSuperposition(ctx: PluginContext, src: SuperpositionT
export const StaticSuperpositionTestData: SuperpositionTestInput = [
{ pdbId: '1aj5', auth_asym_id: 'A', matrix: Mat4.identity() },
- { pdbId: '1df0', auth_asym_id: 'B', matrix: Mat4.ofRows(
- [[0.406, 0.879, 0.248, -200.633],
- [0.693, -0.473, 0.544, 73.403],
- [0.596, -0.049, -0.802, -14.209],
- [0, 0, 0, 1]] )},
- { pdbId: '1dvi', auth_asym_id: 'A', matrix: Mat4.ofRows(
- [[-0.053, -0.077, 0.996, -45.633],
- [-0.312, 0.949, 0.057, -12.255],
- [-0.949, -0.307, -0.074, 53.562],
- [0, 0, 0, 1]] )}
+ { pdbId: '1df0', auth_asym_id: 'B', matrix: Mat4.ofRows([
+ [0.406, 0.879, 0.248, -200.633],
+ [0.693, -0.473, 0.544, 73.403],
+ [0.596, -0.049, -0.802, -14.209],
+ [0, 0, 0, 1]] )},
+ { pdbId: '1dvi', auth_asym_id: 'A', matrix: Mat4.ofRows([
+ [-0.053, -0.077, 0.996, -45.633],
+ [-0.312, 0.949, 0.057, -12.255],
+ [-0.949, -0.307, -0.074, 53.562],
+ [0, 0, 0, 1]] )}
];
export async function dynamicSuperpositionTest(ctx: PluginContext, src: string[], comp_id: string) {
diff --git a/src/apps/chem-comp-bond/create-table.ts b/src/apps/chem-comp-bond/create-table.ts
index ba5410086..84091a6d6 100644
--- a/src/apps/chem-comp-bond/create-table.ts
+++ b/src/apps/chem-comp-bond/create-table.ts
@@ -226,8 +226,8 @@ const CCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif'
const PVCD_URL = 'http://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif'
const parser = new argparse.ArgumentParser({
- addHelp: true,
- description: 'Create a cif file with one big table of all chem_comp_bond entries from the CCD and PVCD.'
+ addHelp: true,
+ description: 'Create a cif file with one big table of all chem_comp_bond entries from the CCD and PVCD.'
});
parser.addArgument('out', {
help: 'Generated file output path.'
diff --git a/src/apps/structure-info/volume.ts b/src/apps/structure-info/volume.ts
index bb337fb80..c3780e97c 100644
--- a/src/apps/structure-info/volume.ts
+++ b/src/apps/structure-info/volume.ts
@@ -77,8 +77,8 @@ async function run(url: string, meshFilename: string) {
}
const parser = new argparse.ArgumentParser({
-addHelp: true,
-description: 'Info about VolumeData from mol-model module'
+ addHelp: true,
+ description: 'Info about VolumeData from mol-model module'
});
parser.addArgument([ '--emdb', '-e' ], {
help: 'EMDB id, for example 8116',
diff --git a/src/examples/proteopedia-wrapper/index.ts b/src/examples/proteopedia-wrapper/index.ts
index 6ff75c437..640739eda 100644
--- a/src/examples/proteopedia-wrapper/index.ts
+++ b/src/examples/proteopedia-wrapper/index.ts
@@ -160,9 +160,9 @@ class MolStarProteopediaWrapper {
root.delete(StateElements.WaterVisual);
} else {
root.applyOrUpdate(StateElements.WaterVisual, StateTransforms.Representation.StructureRepresentation3D,
- StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
- (style.water && style.water.kind) || 'ball-and-stick',
- (style.water && style.water.coloring), structure, { alpha: 0.51 }));
+ StructureRepresentation3DHelpers.getDefaultParamsWithTheme(this.plugin,
+ (style.water && style.water.kind) || 'ball-and-stick',
+ (style.water && style.water.coloring), structure, { alpha: 0.51 }));
}
}
diff --git a/src/mol-data/db/column.ts b/src/mol-data/db/column.ts
index 997f26e4e..3bb3fe1f3 100644
--- a/src/mol-data/db/column.ts
+++ b/src/mol-data/db/column.ts
@@ -290,14 +290,14 @@ function arrayColumn<T extends Column.Schema>({ array, schema, valueKind }: Colu
return ret;
}
: isTyped
- ? params => ColumnHelpers.typedArrayWindow(array, params) as any as ReadonlyArray<T>
- : params => {
- const { start, end } = ColumnHelpers.getArrayBounds(rowCount, params);
- if (start === 0 && end === array.length) return array as ReadonlyArray<T['T']>;
- const ret = new (params && typeof params.array !== 'undefined' ? params.array : (array as any).constructor)(end - start) as any;
- for (let i = 0, _i = end - start; i < _i; i++) ret[i] = array[start + i];
- return ret;
- },
+ ? params => ColumnHelpers.typedArrayWindow(array, params) as any as ReadonlyArray<T>
+ : params => {
+ const { start, end } = ColumnHelpers.getArrayBounds(rowCount, params);
+ if (start === 0 && end === array.length) return array as ReadonlyArray<T['T']>;
+ const ret = new (params && typeof params.array !== 'undefined' ? params.array : (array as any).constructor)(end - start) as any;
+ for (let i = 0, _i = end - start; i < _i; i++) ret[i] = array[start + i];
+ return ret;
+ },
areValuesEqual: (rowA, rowB) => array[rowA] === array[rowB]
}
}
diff --git a/src/mol-data/generic/linked-list.ts b/src/mol-data/generic/linked-list.ts
index 3f5422699..fbea58bd8 100644
--- a/src/mol-data/generic/linked-list.ts
+++ b/src/mol-data/generic/linked-list.ts
@@ -90,14 +90,14 @@ class LinkedListImpl<T> implements LinkedList<T> {
if (node.previous !== null) {
node.previous.next = node.next;
}
- else if (/*first == item*/ node.previous === null) {
+ else if (/* first == item*/ node.previous === null) {
this.first = node.next;
}
if (node.next !== null) {
node.next.previous = node.previous;
}
- else if (/*last == item*/ node.next === null) {
+ else if (/* last == item*/ node.next === null) {
this.last = node.previous;
}
diff --git a/src/mol-data/util/_spec/interval-iterator.spec.ts b/src/mol-data/util/_spec/interval-iterator.spec.ts
index 078d63a3c..c2dabf885 100644
--- a/src/mol-data/util/_spec/interval-iterator.spec.ts
+++ b/src/mol-data/util/_spec/interval-iterator.spec.ts
@@ -7,12 +7,12 @@
import { Interval, OrderedSet, SortedArray } from '../../int';
import { IntervalIterator } from '../interval-iterator';
- describe('interval', () => {
+describe('interval', () => {
function testIterator(name: string, interval: Interval, set: OrderedSet, expectedValues: { index: number[], start: number[], end: number[]}) {
it(`iterator, ${name}`, () => {
const intervalIt = new IntervalIterator(interval, set)
const { index, start, end } = expectedValues
-
+
let i = 0
while (intervalIt.hasNext) {
const segment = intervalIt.move()
diff --git a/src/mol-geo/geometry/text/font-atlas.ts b/src/mol-geo/geometry/text/font-atlas.ts
index 7ad994593..44e2b0547 100644
--- a/src/mol-geo/geometry/text/font-atlas.ts
+++ b/src/mol-geo/geometry/text/font-atlas.ts
@@ -24,11 +24,11 @@ export type FontVariant = 'normal' | 'small-caps'
export type FontWeight = 'normal' | 'bold'
export const FontAtlasParams = {
- fontFamily: PD.Select('sans-serif', [['sans-serif', 'Sans Serif'], ['monospace', 'Monospace'], ['serif', 'Serif'], ['cursive', 'Cursive']] as [FontFamily, string][]),
- fontQuality: PD.Select(3, [[0, 'lower'], [1, 'low'], [2, 'medium'], [3, 'high'], [4, 'higher']]),
- fontStyle: PD.Select('normal', [['normal', 'Normal'], ['italic', 'Italic'], ['oblique', 'Oblique']] as [FontStyle, string][]),
- fontVariant: PD.Select('normal', [['normal', 'Normal'], ['small-caps', 'Small Caps']] as [FontVariant, string][]),
- fontWeight: PD.Select('normal', [['normal', 'Normal'], ['bold', 'Bold']] as [FontWeight, string][]),
+ fontFamily: PD.Select('sans-serif', [['sans-serif', 'Sans Serif'], ['monospace', 'Monospace'], ['serif', 'Serif'], ['cursive', 'Cursive']] as [FontFamily, string][]),
+ fontQuality: PD.Select(3, [[0, 'lower'], [1, 'low'], [2, 'medium'], [3, 'high'], [4, 'higher']]),
+ fontStyle: PD.Select('normal', [['normal', 'Normal'], ['italic', 'Italic'], ['oblique', 'Oblique']] as [FontStyle, string][]),
+ fontVariant: PD.Select('normal', [['normal', 'Normal'], ['small-caps', 'Small Caps']] as [FontVariant, string][]),
+ fontWeight: PD.Select('normal', [['normal', 'Normal'], ['bold', 'Bold']] as [FontWeight, string][]),
}
export type FontAtlasParams = typeof FontAtlasParams
export type FontAtlasProps = PD.Values<FontAtlasParams>
diff --git a/src/mol-geo/primitive/box.ts b/src/mol-geo/primitive/box.ts
index a677d94a1..da8c23981 100644
--- a/src/mol-geo/primitive/box.ts
+++ b/src/mol-geo/primitive/box.ts
@@ -61,23 +61,20 @@ export function PerforatedBox() {
let boxCage: Cage
export function BoxCage() {
if (!boxCage) {
- boxCage = createCage(
- [
- 0.5, 0.5, -0.5, // bottom
- -0.5, 0.5, -0.5,
- -0.5, -0.5, -0.5,
- 0.5, -0.5, -0.5,
- 0.5, 0.5, 0.5, // top
- -0.5, 0.5, 0.5,
- -0.5, -0.5, 0.5,
- 0.5, -0.5, 0.5
- ],
- [
- 0, 4, 1, 5, 2, 6, 3, 7, // sides
- 0, 1, 1, 2, 2, 3, 3, 0, // bottom base
- 4, 5, 5, 6, 6, 7, 7, 4 // top base
- ]
- )
+ boxCage = createCage([
+ 0.5, 0.5, -0.5, // bottom
+ -0.5, 0.5, -0.5,
+ -0.5, -0.5, -0.5,
+ 0.5, -0.5, -0.5,
+ 0.5, 0.5, 0.5, // top
+ -0.5, 0.5, 0.5,
+ -0.5, -0.5, 0.5,
+ 0.5, -0.5, 0.5
+ ], [
+ 0, 4, 1, 5, 2, 6, 3, 7, // sides
+ 0, 1, 1, 2, 2, 3, 3, 0, // bottom base
+ 4, 5, 5, 6, 6, 7, 7, 4 // top base
+ ])
}
return boxCage
}
\ No newline at end of file
diff --git a/src/mol-geo/primitive/dodecahedron.ts b/src/mol-geo/primitive/dodecahedron.ts
index d54ada78f..e88f34bc1 100644
--- a/src/mol-geo/primitive/dodecahedron.ts
+++ b/src/mol-geo/primitive/dodecahedron.ts
@@ -14,46 +14,46 @@ const b = 1 / t;
const c = 2 - t;
export const dodecahedronVertices: ReadonlyArray<number> = [
- c, 0, a, -c, 0, a, -b, b, b, 0, a, c, b, b, b,
- b, -b, b, 0, -a, c, -b, -b, b, c, 0, -a, -c, 0, -a,
+ c, 0, a, -c, 0, a, -b, b, b, 0, a, c, b, b, b,
+ b, -b, b, 0, -a, c, -b, -b, b, c, 0, -a, -c, 0, -a,
-b, -b, -b, 0, -a, -c, b, -b, -b, b, b, -b, 0, a, -c,
-b, b, -b, a, c, 0, -a, c, 0, -a, -c, 0, a, -c, 0
];
/** indices of pentagonal faces, groups of five */
export const dodecahedronFaces: ReadonlyArray<number> = [
- 4, 3, 2, 1, 0,
- 7, 6, 5, 0, 1,
+ 4, 3, 2, 1, 0,
+ 7, 6, 5, 0, 1,
12, 11, 10, 9, 8,
15, 14, 13, 8, 9,
14, 3, 4, 16, 13,
- 3, 14, 15, 17, 2,
+ 3, 14, 15, 17, 2,
11, 6, 7, 18, 10,
- 6, 11, 12, 19, 5,
- 4, 0, 5, 19, 16,
+ 6, 11, 12, 19, 5,
+ 4, 0, 5, 19, 16,
12, 8, 13, 16, 19,
15, 9, 10, 18, 17,
- 7, 1, 2, 17, 18
+ 7, 1, 2, 17, 18
];
const dodecahedronIndices: ReadonlyArray<number> = [ // pentagonal faces
- 4, 3, 2, 2, 1, 0, 4, 2, 0, // 4, 3, 2, 1, 0
- 7, 6, 5, 5, 0, 1, 7, 5, 1, // 7, 6, 5, 0, 1
+ 4, 3, 2, 2, 1, 0, 4, 2, 0, // 4, 3, 2, 1, 0
+ 7, 6, 5, 5, 0, 1, 7, 5, 1, // 7, 6, 5, 0, 1
12, 11, 10, 10, 9, 8, 12, 10, 8, // 12, 11, 10, 9, 8
15, 14, 13, 13, 8, 9, 15, 13, 9, // 15, 14, 13, 8, 9
14, 3, 4, 4, 16, 13, 14, 4, 13, // 14, 3, 4, 16, 13
- 3, 14, 15, 15, 17, 2, 3, 15, 2, // 3, 14, 15, 17, 2
+ 3, 14, 15, 15, 17, 2, 3, 15, 2, // 3, 14, 15, 17, 2
11, 6, 7, 7, 18, 10, 11, 7, 10, // 11, 6, 7, 18, 10
- 6, 11, 12, 12, 19, 5, 6, 12, 5, // 6, 11, 12, 19, 5
- 4, 0, 5, 5, 19, 16, 4, 5, 16, // 4, 0, 5, 19, 16
+ 6, 11, 12, 12, 19, 5, 6, 12, 5, // 6, 11, 12, 19, 5
+ 4, 0, 5, 5, 19, 16, 4, 5, 16, // 4, 0, 5, 19, 16
12, 8, 13, 13, 16, 19, 12, 13, 19, // 12, 8, 13, 16, 19
15, 9, 10, 10, 18, 17, 15, 10, 17, // 15, 9, 10, 18, 17
- 7, 1, 2, 2, 17, 18, 7, 2, 18, // 7, 1, 2, 17, 18
+ 7, 1, 2, 2, 17, 18, 7, 2, 18, // 7, 1, 2, 17, 18
];
const dodecahedronEdges: ReadonlyArray<number> = [
- 0, 1, 0, 4, 0, 5, 1, 2, 1, 7, 2, 3, 2, 17, 3, 4, 3, 14, 4, 16,
- 5, 6, 5, 19, 6, 7, 6, 11, 7, 18, 8, 9, 8, 12, 8, 13, 9, 10, 9, 15,
+ 0, 1, 0, 4, 0, 5, 1, 2, 1, 7, 2, 3, 2, 17, 3, 4, 3, 14, 4, 16,
+ 5, 6, 5, 19, 6, 7, 6, 11, 7, 18, 8, 9, 8, 12, 8, 13, 9, 10, 9, 15,
10, 11, 10, 18, 11, 12, 12, 19, 13, 14, 13, 16, 14, 15, 15, 17, 16, 19, 17, 18,
]
diff --git a/src/mol-geo/util/marching-cubes/builder.ts b/src/mol-geo/util/marching-cubes/builder.ts
index 4b728d8b2..fde7aea04 100644
--- a/src/mol-geo/util/marching-cubes/builder.ts
+++ b/src/mol-geo/util/marching-cubes/builder.ts
@@ -13,7 +13,7 @@ import { AllowedContours } from './tables';
import { LinesBuilder } from '../../geometry/lines/lines-builder';
import { Lines } from '../../geometry/lines/lines';
- export interface MarchinCubesBuilder<T> {
+export interface MarchinCubesBuilder<T> {
addVertex(x: number, y: number, z: number): number
addNormal(x: number, y: number, z: number): void
addGroup(group: number): void
diff --git a/src/mol-io/reader/common/text/column/token.ts b/src/mol-io/reader/common/text/column/token.ts
index 8a6a22d2d..df8ea949c 100644
--- a/src/mol-io/reader/common/text/column/token.ts
+++ b/src/mol-io/reader/common/text/column/token.ts
@@ -19,11 +19,11 @@ export function TokenColumn<T extends Column.Schema>(tokens: Tokens, schema: T):
const { valueType: type } = schema;
const value: Column<T['T']>['value'] =
- type === 'str'
- ? row => data.substring(indices[2 * row], indices[2 * row + 1])
- : type === 'int'
- ? row => fastParseInt(data, indices[2 * row], indices[2 * row + 1]) || 0
- : row => fastParseFloat(data, indices[2 * row], indices[2 * row + 1]) || 0;
+ type === 'str'
+ ? row => data.substring(indices[2 * row], indices[2 * row + 1])
+ : type === 'int'
+ ? row => fastParseInt(data, indices[2 * row], indices[2 * row + 1]) || 0
+ : row => fastParseFloat(data, indices[2 * row], indices[2 * row + 1]) || 0;
return {
schema: schema,
diff --git a/src/mol-math/linear-algebra/3d.ts b/src/mol-math/linear-algebra/3d.ts
index d6e70b131..8a4b938b0 100644
--- a/src/mol-math/linear-algebra/3d.ts
+++ b/src/mol-math/linear-algebra/3d.ts
@@ -29,6 +29,6 @@ export { Mat4, Mat3, Vec2, Vec3, Vec4, Quat, EPSILON }
export type Vec<T> =
T extends 4 ? Vec4 :
- T extends 3 ? Vec3 :
- T extends 2 ? Vec2 :
- number[]
\ No newline at end of file
+ T extends 3 ? Vec3 :
+ T extends 2 ? Vec2 :
+ number[]
\ No newline at end of file
diff --git a/src/mol-math/linear-algebra/3d/quat.ts b/src/mol-math/linear-algebra/3d/quat.ts
index 574f88abe..eaab0f5a6 100644
--- a/src/mol-math/linear-algebra/3d/quat.ts
+++ b/src/mol-math/linear-algebra/3d/quat.ts
@@ -184,11 +184,11 @@ namespace Quat {
cosom = ax * bx + ay * by + az * bz + aw * bw;
// adjust signs (if necessary)
if ( cosom < 0.0 ) {
- cosom = -cosom;
- bx = - bx;
- by = - by;
- bz = - bz;
- bw = - bw;
+ cosom = -cosom;
+ bx = - bx;
+ by = - by;
+ bz = - bz;
+ bw = - bw;
}
// calculate coefficients
if ( (1.0 - cosom) > 0.000001 ) {
@@ -258,7 +258,7 @@ namespace Quat {
out[0] = (m[5]-m[7])*fRoot;
out[1] = (m[6]-m[2])*fRoot;
out[2] = (m[1]-m[3])*fRoot;
- } else {
+ } else {
// |w| <= 1/2
let i = 0;
if ( m[4] > m[0] ) i = 1;
@@ -384,7 +384,7 @@ namespace Quat {
if (dot < -0.999999) {
Vec3.cross(rotTmpVec3, rotTmpVec3UnitX, a);
if (Vec3.magnitude(rotTmpVec3) < 0.000001)
- Vec3.cross(rotTmpVec3, rotTmpVec3UnitY, a);
+ Vec3.cross(rotTmpVec3, rotTmpVec3UnitY, a);
Vec3.normalize(rotTmpVec3, rotTmpVec3);
setAxisAngle(out, rotTmpVec3, Math.PI);
return out;
diff --git a/src/mol-model-formats/structure/pdb/assembly.ts b/src/mol-model-formats/structure/pdb/assembly.ts
index 02f6a989e..23931f271 100644
--- a/src/mol-model-formats/structure/pdb/assembly.ts
+++ b/src/mol-model-formats/structure/pdb/assembly.ts
@@ -202,18 +202,18 @@ export function parseMtrix(lines: Tokens, lineStart: number, lineEnd: number): C
const struct_ncs_oper_rows: { [P in keyof CifCategory.Fields<mmCIF_Schema['struct_ncs_oper']>]?: string }[] = [];
let id = 1;
for (const oper of matrices) {
- const row = {
- id: 'ncsop' + (id++),
- code: '.',
- details: '.'
- } as (typeof struct_ncs_oper_rows)[0] as any;
- for (let i = 0; i < 3; i++) {
- for (let j = 0; j < 3; j++) {
- row[`matrix[${i + 1}][${j + 1}]`] = '' + Mat4.getValue(oper, i, j);
- }
- row[`vector[${i + 1}]`] = '' + Mat4.getValue(oper, i, 3);
+ const row = {
+ id: 'ncsop' + (id++),
+ code: '.',
+ details: '.'
+ } as (typeof struct_ncs_oper_rows)[0] as any;
+ for (let i = 0; i < 3; i++) {
+ for (let j = 0; j < 3; j++) {
+ row[`matrix[${i + 1}][${j + 1}]`] = '' + Mat4.getValue(oper, i, j);
}
- struct_ncs_oper_rows.push(row);
+ row[`vector[${i + 1}]`] = '' + Mat4.getValue(oper, i, 3);
+ }
+ struct_ncs_oper_rows.push(row);
}
const struct_ncs_oper: CifCategory.SomeFields<mmCIF_Schema['struct_ncs_oper']> = {
diff --git a/src/mol-model-props/computed/interactions/hydrogen-bonds.ts b/src/mol-model-props/computed/interactions/hydrogen-bonds.ts
index 697b187e3..f6021978c 100644
--- a/src/mol-model-props/computed/interactions/hydrogen-bonds.ts
+++ b/src/mol-model-props/computed/interactions/hydrogen-bonds.ts
@@ -72,14 +72,13 @@ function addUnitHydrogenDonors(structure: Structure, unit: Unit.Atomic, builder:
for (let i = 0 as StructureElement.UnitIndex, il = elements.length; i < il; ++i) {
const element = typeSymbol(unit, i)
if ((
- // include both nitrogen atoms in histidine due to
- // their often ambiguous protonation assignment
- isHistidineNitrogen(unit, i)
- ) || (
- totalH[i] > 0 &&
- (element === Elements.N || element === Elements.O || element === Elements.S)
- )
- ) {
+ // include both nitrogen atoms in histidine due to
+ // their often ambiguous protonation assignment
+ isHistidineNitrogen(unit, i)
+ ) || (
+ totalH[i] > 0 &&
+ (element === Elements.N || element === Elements.O || element === Elements.S)
+ )) {
builder.add(FeatureType.HydrogenDonor, FeatureGroup.None, x[elements[i]], y[elements[i]], z[elements[i]], i)
}
}
diff --git a/src/mol-model-props/rcsb/graphql/types.ts b/src/mol-model-props/rcsb/graphql/types.ts
index e21766370..dc12d2cf5 100644
--- a/src/mol-model-props/rcsb/graphql/types.ts
+++ b/src/mol-model-props/rcsb/graphql/types.ts
@@ -12,77 +12,77 @@ export type Unrepresentable = any;
// ====================================================
export namespace AssemblySymmetry {
- export type Variables = {
- pdbId: string;
- };
+ export type Variables = {
+ pdbId: string;
+ };
- export type Query = {
- __typename?: "Query";
+ export type Query = {
+ __typename?: 'Query';
- entry: Maybe<Entry>;
- };
+ entry: Maybe<Entry>;
+ };
- export type Entry = {
- __typename?: "CoreEntry";
+ export type Entry = {
+ __typename?: 'CoreEntry';
- assemblies: Maybe<(Maybe<Assemblies>)[]>;
- };
+ assemblies: Maybe<(Maybe<Assemblies>)[]>;
+ };
- export type Assemblies = {
- __typename?: "CoreAssembly";
+ export type Assemblies = {
+ __typename?: 'CoreAssembly';
- pdbx_struct_assembly: Maybe<PdbxStructAssembly>;
+ pdbx_struct_assembly: Maybe<PdbxStructAssembly>;
- rcsb_struct_symmetry: Maybe<(Maybe<RcsbStructSymmetry>)[]>;
- };
+ rcsb_struct_symmetry: Maybe<(Maybe<RcsbStructSymmetry>)[]>;
+ };
- export type PdbxStructAssembly = {
- __typename?: "PdbxStructAssembly";
+ export type PdbxStructAssembly = {
+ __typename?: 'PdbxStructAssembly';
- id: string;
- };
+ id: string;
+ };
- export type RcsbStructSymmetry = {
- __typename?: "RcsbStructSymmetry";
+ export type RcsbStructSymmetry = {
+ __typename?: 'RcsbStructSymmetry';
- clusters: (Maybe<Clusters>)[];
+ clusters: (Maybe<Clusters>)[];
- kind: string;
+ kind: string;
- oligomeric_state: string;
+ oligomeric_state: string;
- rotation_axes: Maybe<(Maybe<RotationAxes>)[]>;
+ rotation_axes: Maybe<(Maybe<RotationAxes>)[]>;
- stoichiometry: (Maybe<string>)[];
+ stoichiometry: (Maybe<string>)[];
- symbol: string;
+ symbol: string;
- type: string;
- };
+ type: string;
+ };
- export type Clusters = {
- __typename?: "RcsbStructSymmetryClusters";
+ export type Clusters = {
+ __typename?: 'RcsbStructSymmetryClusters';
- avg_rmsd: Maybe<number>;
+ avg_rmsd: Maybe<number>;
- members: (Maybe<Members>)[];
- };
+ members: (Maybe<Members>)[];
+ };
- export type Members = {
- __typename?: "ClustersMembers";
+ export type Members = {
+ __typename?: 'ClustersMembers';
- asym_id: string;
+ asym_id: string;
- pdbx_struct_oper_list_ids: Maybe<(Maybe<string>)[]>;
- };
+ pdbx_struct_oper_list_ids: Maybe<(Maybe<string>)[]>;
+ };
- export type RotationAxes = {
- __typename?: "RcsbStructSymmetryRotationAxes";
+ export type RotationAxes = {
+ __typename?: 'RcsbStructSymmetryRotationAxes';
- start: (Maybe<number>)[];
+ start: (Maybe<number>)[];
- end: (Maybe<number>)[];
+ end: (Maybe<number>)[];
- order: Maybe<number>;
- };
+ order: Maybe<number>;
+ };
}
diff --git a/src/mol-model-props/rcsb/representations/assembly-symmetry-axes.ts b/src/mol-model-props/rcsb/representations/assembly-symmetry-axes.ts
index 1f6428c02..9f716ffd8 100644
--- a/src/mol-model-props/rcsb/representations/assembly-symmetry-axes.ts
+++ b/src/mol-model-props/rcsb/representations/assembly-symmetry-axes.ts
@@ -124,7 +124,7 @@ export function createAssemblySymmetryAxesMesh(ctx: VisualContext, structure: St
const cylinderProps = { radiusTop: radius, radiusBottom: radius }
const builderState = MeshBuilder.createState(256, 128, mesh)
- for (let i = 0, il = axes._rowCount; i < il; ++i) {
+ for (let i = 0, il = axes._rowCount; i < il; ++i) {
if (axes.symmetry_id.value(i) !== symmetryId) continue
const start = Tensor.toVec3(Vec3(), vectorSpace, axes.start.value(i))
diff --git a/src/mol-model/structure/model/properties/common.ts b/src/mol-model/structure/model/properties/common.ts
index 342018386..84809978a 100644
--- a/src/mol-model/structure/model/properties/common.ts
+++ b/src/mol-model/structure/model/properties/common.ts
@@ -24,10 +24,7 @@ export interface Entities {
export type ChemicalComponent = Table.Row<mmCIF_Schema['chem_comp']>
export type ChemicalComponentMap = ReadonlyMap<string, ChemicalComponent>
-export type MissingResidue = Table.Row<Pick<
- mmCIF_Schema['pdbx_unobs_or_zero_occ_residues'],
- 'polymer_flag' | 'occupancy_flag'
->>
+export type MissingResidue = Table.Row<Pick<mmCIF_Schema['pdbx_unobs_or_zero_occ_residues'], 'polymer_flag' | 'occupancy_flag'>>
export interface MissingResidues {
has(model_num: number, asym_id: string, seq_id: number): boolean
get(model_num: number, asym_id: string, seq_id: number): MissingResidue | undefined
diff --git a/src/mol-model/structure/structure/carbohydrates/compute.ts b/src/mol-model/structure/structure/carbohydrates/compute.ts
index 604497c22..e96051db5 100644
--- a/src/mol-model/structure/structure/carbohydrates/compute.ts
+++ b/src/mol-model/structure/structure/carbohydrates/compute.ts
@@ -61,10 +61,10 @@ function getAnomericCarbon(unit: Unit.Atomic, ringAtoms: ArrayLike<StructureElem
}
}
return (indexHasTwoOxygen !== -1 ? indexHasTwoOxygen
- : indexHasOxygenAndCarbon !== -1 ? indexHasOxygenAndCarbon
- : indexHasC1Name !== -1 ? indexHasC1Name
- : indexIsCarbon !== -1 ? indexIsCarbon
- : elements[ringAtoms[0]]) as ElementIndex
+ : indexHasOxygenAndCarbon !== -1 ? indexHasOxygenAndCarbon
+ : indexHasC1Name !== -1 ? indexHasC1Name
+ : indexIsCarbon !== -1 ? indexIsCarbon
+ : elements[ringAtoms[0]]) as ElementIndex
}
/** Return first non-empty label_alt_id or an empty string */
diff --git a/src/mol-model/structure/structure/element/stats.ts b/src/mol-model/structure/structure/element/stats.ts
index afd53a33a..fea5bc419 100644
--- a/src/mol-model/structure/structure/element/stats.ts
+++ b/src/mol-model/structure/structure/element/stats.ts
@@ -156,11 +156,11 @@ export namespace Stats {
const segments = Unit.isAtomic(unit)
? unit.model.atomicHierarchy.chainAtomSegments
- : Unit.isSpheres(unit)
- ? unit.model.coarseHierarchy.spheres.chainElementSegments
+ : Unit.isSpheres(unit)
+ ? unit.model.coarseHierarchy.spheres.chainElementSegments
: Unit.isGaussians(unit)
- ? unit.model.coarseHierarchy.gaussians.chainElementSegments
- : void 0;
+ ? unit.model.coarseHierarchy.gaussians.chainElementSegments
+ : void 0;
if (!segments) {
console.warn('StructureElement loci stats: unknown unit type');
@@ -198,11 +198,11 @@ export namespace Stats {
// all the elements have the same model since they are part of the same group so this is ok.
const segments = Unit.isAtomic(element.unit)
? element.unit.model.atomicHierarchy.chainAtomSegments
- : Unit.isSpheres(element.unit)
- ? element.unit.model.coarseHierarchy.spheres.chainElementSegments
+ : Unit.isSpheres(element.unit)
+ ? element.unit.model.coarseHierarchy.spheres.chainElementSegments
: Unit.isGaussians(element.unit)
- ? element.unit.model.coarseHierarchy.gaussians.chainElementSegments
- : void 0;
+ ? element.unit.model.coarseHierarchy.gaussians.chainElementSegments
+ : void 0;
if (!segments) {
console.warn('StructureElement loci stats: unknown unit type');
diff --git a/src/mol-plugin/state/representation/structure/preset.ts b/src/mol-plugin/state/representation/structure/preset.ts
index aad0c4d73..418cbb640 100644
--- a/src/mol-plugin/state/representation/structure/preset.ts
+++ b/src/mol-plugin/state/representation/structure/preset.ts
@@ -134,7 +134,7 @@ const coarseCapsid = StructureRepresentationProvider({
const params = StructureRepresentation3DHelpers.createParams(plugin, structure, {
repr: [
BuiltInStructureRepresentations['gaussian-surface'],
- () => ({ smoothness: 0.5, radiusOffset: 1, /*visuals: ['gaussian-surface-mesh']*/ })
+ () => ({ smoothness: 0.5, radiusOffset: 1, /* visuals: ['gaussian-surface-mesh']*/ })
]
});
diff --git a/src/mol-plugin/state/snapshots.ts b/src/mol-plugin/state/snapshots.ts
index a37ecf699..cf3ed0ec8 100644
--- a/src/mol-plugin/state/snapshots.ts
+++ b/src/mol-plugin/state/snapshots.ts
@@ -134,8 +134,8 @@ class PluginStateSnapshotManager extends PluginComponent<{
const current = snapshot.current
? snapshot.current
: snapshot.entries.length > 0
- ? snapshot.entries[0].snapshot.id
- : void 0;
+ ? snapshot.entries[0].snapshot.id
+ : void 0;
this.updateState({
current,
entries: entries.asImmutable(),
diff --git a/src/mol-plugin/state/transforms/representation.ts b/src/mol-plugin/state/transforms/representation.ts
index 448c7326d..bc8cb3058 100644
--- a/src/mol-plugin/state/transforms/representation.ts
+++ b/src/mol-plugin/state/transforms/representation.ts
@@ -63,7 +63,7 @@ namespace StructureRepresentation3DHelpers {
}
export function createParams<R extends RepresentationProvider<Structure, any, any>, C extends ColorTheme.Provider<any>, S extends SizeTheme.Provider<any>>(
- ctx: PluginContext, structure: Structure, params: {
+ ctx: PluginContext, structure: Structure, params: {
repr?: R | [R, (r: R, ctx: ThemeRegistryContext, s: Structure) => Partial<RepresentationProvider.ParamValues<R>>],
color?: C | [C, (c: C, ctx: ThemeRegistryContext) => Partial<ColorTheme.ParamValues<C>>],
size?: S | [S, (c: S, ctx: ThemeRegistryContext) => Partial<SizeTheme.ParamValues<S>>]
diff --git a/src/mol-repr/structure/units-visual.ts b/src/mol-repr/structure/units-visual.ts
index 0ebbde252..290088ede 100644
--- a/src/mol-repr/structure/units-visual.ts
+++ b/src/mol-repr/structure/units-visual.ts
@@ -211,8 +211,8 @@ export function UnitsVisual<G extends Geometry, P extends UnitsParams & Geometry
function _createGeometry(ctx: VisualContext, unit: Unit, structure: Structure, theme: Theme, props: PD.Values<P>, geometry?: G) {
return includesUnitKind(props.unitKinds, unit)
- ? createGeometry(ctx, unit, structure, theme, props, geometry)
- : createEmptyGeometry(geometry)
+ ? createGeometry(ctx, unit, structure, theme, props, geometry)
+ : createEmptyGeometry(geometry)
}
function lociIsSuperset(loci: Loci) {
diff --git a/src/mol-script/language/expression.ts b/src/mol-script/language/expression.ts
index 8fe5ac9b1..ba6f77367 100644
--- a/src/mol-script/language/expression.ts
+++ b/src/mol-script/language/expression.ts
@@ -15,7 +15,7 @@ namespace Expression {
export type Arguments = Expression[] | { [name: string]: Expression }
export interface Apply { readonly head: Expression, readonly args?: Arguments }
- export function Symbol(name: string): Symbol { return { name }; }
+ export function Symbol(name: string): Expression.Symbol { return { name }; }
export function Apply(head: Expression, args?: Arguments): Apply { return args ? { head, args } : { head }; }
export function isArgumentsArray(e?: Arguments): e is Expression[] { return !!e && Array.isArray(e); }
diff --git a/src/mol-script/runtime/query/table.ts b/src/mol-script/runtime/query/table.ts
index 75a9104a8..390e0c57a 100644
--- a/src/mol-script/runtime/query/table.ts
+++ b/src/mol-script/runtime/query/table.ts
@@ -169,7 +169,6 @@ const symbols = [
return (tested & test) === test;
}),
- ////////////////////////////////////
// Structure
// ============= TYPES ================
@@ -340,8 +339,6 @@ const symbols = [
D(MolScript.structureQuery.bondProperty.atomB, (ctx, xs) => ctx.atomicBond.b),
D(MolScript.structureQuery.bondProperty.length, (ctx, xs) => ctx.atomicBond.length),
-
- ////////////////////////////////////
// Internal
D(MolScript.internal.generator.bundleElement, function internal_generator_bundleElement(ctx, xs) { return bundleElementImpl(xs.groupedUnits(ctx), xs.ranges(ctx), xs.set(ctx)) }),
D(MolScript.internal.generator.bundle, function internal_generator_bundle(ctx, xs) { return bundleGenerator(xs.elements(ctx))(ctx) }),
diff --git a/src/mol-state/state/builder.ts b/src/mol-state/state/builder.ts
index 269322bce..4f88fdf9e 100644
--- a/src/mol-state/state/builder.ts
+++ b/src/mol-state/state/builder.ts
@@ -86,8 +86,8 @@ namespace StateBuilder {
const ref = typeof refOrCellOrSelector === 'string'
? refOrCellOrSelector
: StateObjectCell.is(refOrCellOrSelector)
- ? refOrCellOrSelector.transform.ref
- : refOrCellOrSelector.ref;
+ ? refOrCellOrSelector.transform.ref
+ : refOrCellOrSelector.ref;
return new To<StateObject, StateTransformer>(this.state, ref, this);
}
toRoot<A extends StateObject>() { return new To<A>(this.state, this.state.tree.root.ref, this); }
diff --git a/src/mol-state/tree/transient.ts b/src/mol-state/tree/transient.ts
index 6f99d5ad3..a401fa41a 100644
--- a/src/mol-state/tree/transient.ts
+++ b/src/mol-state/tree/transient.ts
@@ -182,8 +182,8 @@ class TransientTree implements StateTree {
return true;
}
- /** Calls Transform.definition.params.areEqual if available, otherwise uses shallowEqual to check if the params changed */
- setTags(ref: StateTransform.Ref, tags: string | string[] | undefined) {
+ /** Calls Transform.definition.params.areEqual if available, otherwise uses shallowEqual to check if the params changed */
+ setTags(ref: StateTransform.Ref, tags: string | string[] | undefined) {
ensurePresent(this.transforms, ref);
const transform = this.transforms.get(ref)!;
diff --git a/src/mol-task/execution/observable.ts b/src/mol-task/execution/observable.ts
index c4bed0acf..5ead08799 100644
--- a/src/mol-task/execution/observable.ts
+++ b/src/mol-task/execution/observable.ts
@@ -198,7 +198,7 @@ class ObservableRuntimeContext implements RuntimeContext {
this.updateProgress(progress);
// TODO: do the shouldNotify check here?
- if (!!dontNotify /*|| !shouldNotify(this.info, this.lastUpdatedTime)*/) return;
+ if (!!dontNotify /* || !shouldNotify(this.info, this.lastUpdatedTime)*/) return;
notifyObserver(this.info, this.lastUpdatedTime);
diff --git a/src/mol-task/util/scheduler.ts b/src/mol-task/util/scheduler.ts
index b06021425..94cbb531e 100644
--- a/src/mol-task/util/scheduler.ts
+++ b/src/mol-task/util/scheduler.ts
@@ -10,7 +10,7 @@
* MIT license.
*/
-declare var WorkerGlobalScope: any;
+declare const WorkerGlobalScope: any;
function createImmediateActions() {
const global: any = (function () {
const _window = typeof window !== 'undefined' && window;
@@ -29,15 +29,15 @@ function createImmediateActions() {
let registerImmediate: ((handle: number) => void);
function setImmediate(callback: Callback, ...args: any[]) {
- // Callback can either be a function or a string
- if (typeof callback !== 'function') {
- callback = new Function('' + callback) as Callback;
- }
- // Store and register the task
- const task = { callback: callback, args: args };
- tasksByHandle[nextHandle] = task;
- registerImmediate(nextHandle);
- return nextHandle++;
+ // Callback can either be a function or a string
+ if (typeof callback !== 'function') {
+ callback = new Function('' + callback) as Callback;
+ }
+ // Store and register the task
+ const task = { callback: callback, args: args };
+ tasksByHandle[nextHandle] = task;
+ registerImmediate(nextHandle);
+ return nextHandle++;
}
function clearImmediate(handle: number) {
@@ -48,21 +48,21 @@ function createImmediateActions() {
const callback = task.callback;
const args = task.args;
switch (args.length) {
- case 0:
- callback();
- break;
- case 1:
- callback(args[0]);
- break;
- case 2:
- callback(args[0], args[1]);
- break;
- case 3:
- callback(args[0], args[1], args[2]);
- break;
- default:
- callback.apply(undefined, args);
- break;
+ case 0:
+ callback();
+ break;
+ case 1:
+ callback(args[0]);
+ break;
+ case 2:
+ callback(args[0], args[1]);
+ break;
+ case 3:
+ callback(args[0], args[1], args[2]);
+ break;
+ default:
+ callback.apply(undefined, args);
+ break;
}
}
diff --git a/src/mol-theme/label.ts b/src/mol-theme/label.ts
index 63d4afdf7..bf7c30451 100644
--- a/src/mol-theme/label.ts
+++ b/src/mol-theme/label.ts
@@ -183,7 +183,6 @@ function _atomicElementLabel(location: StructureElement.Location<Unit.Atomic>, g
const compId = granularity === 'residue' && microHetCompIds.length > 1 ?
`(${microHetCompIds.join('|')})` : comp_id
-
const label: string[] = []
switch (granularity) {
diff --git a/src/servers/model/local.ts b/src/servers/model/local.ts
index 9661d90c6..772c9dafd 100644
--- a/src/servers/model/local.ts
+++ b/src/servers/model/local.ts
@@ -12,26 +12,25 @@ console.log(`Mol* ModelServer (${Version}), (c) 2018 Mol* authors`);
console.log(``);
let exampleWorkload: LocalInput = [{
- input: 'c:/test/quick/1tqn.cif',
- output: 'c:/test/quick/localapi/1tqn_full.cif',
- query: 'full', // same as defined in Api/Queries
- }, {
- input: 'c:/test/quick/1tqn.cif',
- output: 'c:/test/quick/localapi/1tqn_full.bcif',
- query: 'full',
- params: {}
- }, {
- input: 'c:/test/quick/1cbs_updated.cif',
- output: 'c:/test/quick/localapi/1cbs_ligint.cif',
- query: 'residueInteraction', // action is case sensitive
- params: { atom_site: { label_comp_id: 'REA' }, radius: 5 }
- }, {
- input: 'c:/test/quick/1cbs_updated.cif', // multiple files that are repeated will only be parsed once
- output: 'c:/test/quick/localapi/1cbs_ligint.bcif',
- query: 'residueInteraction',
- params: { atom_site: { label_comp_id: 'REA' } } // parameters are just a JSON version of the query string
- }
-];
+ input: 'c:/test/quick/1tqn.cif',
+ output: 'c:/test/quick/localapi/1tqn_full.cif',
+ query: 'full', // same as defined in Api/Queries
+}, {
+ input: 'c:/test/quick/1tqn.cif',
+ output: 'c:/test/quick/localapi/1tqn_full.bcif',
+ query: 'full',
+ params: {}
+}, {
+ input: 'c:/test/quick/1cbs_updated.cif',
+ output: 'c:/test/quick/localapi/1cbs_ligint.cif',
+ query: 'residueInteraction', // action is case sensitive
+ params: { atom_site: { label_comp_id: 'REA' }, radius: 5 }
+}, {
+ input: 'c:/test/quick/1cbs_updated.cif', // multiple files that are repeated will only be parsed once
+ output: 'c:/test/quick/localapi/1cbs_ligint.bcif',
+ query: 'residueInteraction',
+ params: { atom_site: { label_comp_id: 'REA' } } // parameters are just a JSON version of the query string
+}];
if (process.argv.length !== 3) {
diff --git a/src/servers/model/server.ts b/src/servers/model/server.ts
index aed74869c..4dde6c496 100644
--- a/src/servers/model/server.ts
+++ b/src/servers/model/server.ts
@@ -31,12 +31,12 @@ function setupShutdown() {
console.log();
setTimeout(() => {
- /*if (WebApi.ApiState.pendingQueries > 0) {
- WebApi.ApiState.shutdownOnZeroPending = true;
- } else*/ {
- ConsoleLogger.log('Server', `Shut down due to timeout.`);
- process.exit(0);
- }
+ // if (WebApi.ApiState.pendingQueries > 0) {
+ // WebApi.ApiState.shutdownOnZeroPending = true;
+ // } else {
+ ConsoleLogger.log('Server', `Shut down due to timeout.`);
+ process.exit(0);
+ // }
}, tMs);
}
}
diff --git a/src/servers/model/utils/fetch-props-pdbe.ts b/src/servers/model/utils/fetch-props-pdbe.ts
index da6a1d326..047a95531 100644
--- a/src/servers/model/utils/fetch-props-pdbe.ts
+++ b/src/servers/model/utils/fetch-props-pdbe.ts
@@ -71,13 +71,13 @@ async function process() {
const data = Object.create(null);
for (let ee of e.entries) {
- const query = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${ee}`);
- try {
+ const query = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry/${ee}`);
+ try {
if (query.status === 200) data[ee] = (await query.json())[ee] || { };
else console.error(ee, query.status);
- } catch (e) {
+ } catch (e) {
console.error(ee, '' + e);
- }
+ }
}
// const query = await fetch(`https://www.ebi.ac.uk/pdbe/api/validation/residuewise_outlier_summary/entry`, { method: 'POST', body });
// console.log(query.status);
diff --git a/src/servers/volume/common/binary-schema.ts b/src/servers/volume/common/binary-schema.ts
index 96c35c681..8fb875e57 100644
--- a/src/servers/volume/common/binary-schema.ts
+++ b/src/servers/volume/common/binary-schema.ts
@@ -12,18 +12,17 @@ import { SimpleBuffer } from '../../../mol-io/common/simple-buffer';
export type Bool = { kind: 'bool' }
export type Int = { kind: 'int' }
export type Float = { kind: 'float' }
-export type String = { kind: 'string' }
+export type Str = { kind: 'string' }
export type Array = { kind: 'array', element: Element }
export type Prop = { element: Element, prop: string }
export type Obj = { kind: 'object', props: Prop[] }
-// tslint:disable-next-line:array-type
-export type Element = Bool | Int | Float | String | Array | Obj
+export type Element = Bool | Int | Float | Str | Array | Obj
export const bool: Bool = { kind: 'bool' };
export const int: Int = { kind: 'int' };
export const float: Float = { kind: 'float' };
-export const str: String = { kind: 'string' };
-// tslint:disable-next-line:array-type
+export const str: Str = { kind: 'string' };
+
export function array(element: Element): Array { return { kind: 'array', element }; }
export function obj<T>(schema: ((keyof T) | Element)[][]): Obj {
return {
diff --git a/src/servers/volume/server/algebra/box.ts b/src/servers/volume/server/algebra/box.ts
index d604156ff..8f0e5e252 100644
--- a/src/servers/volume/server/algebra/box.ts
+++ b/src/servers/volume/server/algebra/box.ts
@@ -11,9 +11,7 @@ export interface Cartesian extends Box<Coords.Cartesian> { }
export interface Fractional extends Box<Coords.Fractional> { }
export interface Grid<K> extends Box<Coords.Grid<K>> { }
-///////////////////////////////////////////
// CONVERSIONS
-///////////////////////////////////////////
export function cartesianToFractional(box: Cartesian, spacegroup: SpacegroupCell): Fractional {
const { a: l, b: r } = box;
@@ -54,9 +52,7 @@ export function expandGridBox<K>(box: Grid<K>, by: number) {
}
}
-///////////////////////////////////////////
// MISC
-///////////////////////////////////////////
export function shift<C extends Coords.Coord<S>, S extends Coords.Space>(box: Box<C>, offset: C): Box<C> {
return { a: Coords.add(box.a, offset), b: Coords.add(box.b, offset) } as Box<C>;
diff --git a/src/servers/volume/server/algebra/coordinate.ts b/src/servers/volume/server/algebra/coordinate.ts
index 01ac3e5ba..4c8bc5703 100644
--- a/src/servers/volume/server/algebra/coordinate.ts
+++ b/src/servers/volume/server/algebra/coordinate.ts
@@ -31,9 +31,7 @@ export interface Cartesian extends Coord<Space.Cartesian> { }
export interface Fractional extends Coord<Space.Fractional> { }
export interface Grid<K> extends Coord<Space.Grid> { domain: GridDomain<K> }
-///////////////////////////////////////////
// CONSTRUCTORS
-///////////////////////////////////////////
export function domain<K>(kind: K, info: GridInfo): GridDomain<K> {
const sc = info.sampleCount;
@@ -71,9 +69,7 @@ export function clone<C extends (Coord<Space> | Grid<any>)>(a: C): C {
return withCoord(a, a[0], a[1], a[2]);
}
-///////////////////////////////////////////
// CONVERSIONS
-///////////////////////////////////////////
export function cartesianToFractional(a: Cartesian, spacegroup: SpacegroupCell): Fractional {
const coord = Helpers.transform(a, spacegroup.toFractional);
@@ -98,9 +94,7 @@ export function gridToFractional<K>(a: Grid<K>): Fractional {
return coord;
}
-///////////////////////////////////////////
// MISC
-///////////////////////////////////////////
export function clampGridToSamples<K>(a: Grid<K>): Grid<K> {
const { sampleCount } = a.domain;
diff --git a/src/servers/volume/server/query/data-model.ts b/src/servers/volume/server/query/data-model.ts
index a5552a3d1..95d77403c 100644
--- a/src/servers/volume/server/query/data-model.ts
+++ b/src/servers/volume/server/query/data-model.ts
@@ -14,9 +14,7 @@ import { SpacegroupCell } from '../../../../mol-math/geometry';
import { FileHandle } from '../../../../mol-io/common/file-handle';
import { TypedArrayValueArray } from '../../../../mol-io/common/typed-array';
-//////////////////////////////////////
// DATA
-//////////////////////////////////////
export interface Sampling {
index: number,
@@ -39,9 +37,7 @@ export interface BlockData {
values: TypedArrayValueArray
}
-//////////////////////////////////////
// QUERY
-//////////////////////////////////////
export type QueryOutputStream = Writer & { end: () => void }
diff --git a/src/servers/volume/server/query/identify.ts b/src/servers/volume/server/query/identify.ts
index a0189a95b..85b276c30 100644
--- a/src/servers/volume/server/query/identify.ts
+++ b/src/servers/volume/server/query/identify.ts
@@ -9,7 +9,7 @@
import * as Coords from '../algebra/coordinate'
import * as Box from '../algebra/box'
import * as Data from './data-model'
-//import { FastMap } from '../utils/collections'
+// import { FastMap } from '../utils/collections'
/** Find a list of unique blocks+offsets that overlap with the query region. */
export default function findUniqueBlocks(data: Data.DataContext, sampling: Data.Sampling, queryBox: Box.Fractional) {
@@ -56,7 +56,7 @@ function overlapMultiplierRange(a: number, b: number, u: number, v: number): num
/**
* Finds that list of "unit" offsets (in fractional space) so that
- * shift(box, offset) has non-empty interaction with the region
+ * shift(box, offset) has non-empty interaction with the region
* described in the give domain.
*/
function findDataOverlapTranslationList(box: Box.Fractional, domain: Coords.GridDomain<'Data'>): Translations {
@@ -106,7 +106,7 @@ function findUniqueBlocksOffset(data: Data.DataContext, sampling: Data.Sampling,
const blockDomain = sampling.blockDomain;
- // this gets the "3d range" of block indices that contain data that overlaps
+ // this gets the "3d range" of block indices that contain data that overlaps
// with the query region.
//
// Clamping the data makes sure we avoid silly rounding errors (hopefully :))
diff --git a/src/servers/volume/server/web-api.ts b/src/servers/volume/server/web-api.ts
index 6aab235be..8b8d1a165 100644
--- a/src/servers/volume/server/web-api.ts
+++ b/src/servers/volume/server/web-api.ts
@@ -54,10 +54,10 @@ function getMapFileFn() {
const map = new Function('type', 'id', 'interpolate', [
'id = id.toLowerCase()',
'switch (type.toLowerCase()) {',
- ...ServerConfig.idMap.map(mapping => {
- const [type, path] = mapping
- return ` case '${type}': return interpolate('${path}', { id });`
- }),
+ ...ServerConfig.idMap.map(mapping => {
+ const [type, path] = mapping
+ return ` case '${type}': return interpolate('${path}', { id });`
+ }),
' default: return void 0;',
'}'
].join('\n'))
diff --git a/src/servers/volume/server/web-schema.ts b/src/servers/volume/server/web-schema.ts
index 05c743af2..fe7bc7db8 100644
--- a/src/servers/volume/server/web-schema.ts
+++ b/src/servers/volume/server/web-schema.ts
@@ -10,7 +10,7 @@ import { LimitsConfig, ServerConfig } from '../config';
export function getSchema() {
function detail(i: number) {
- return `${i} (${Math.round(100 * LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel[i] / 1000 / 1000) / 100 }M voxels)`;
+ return `${i} (${Math.round(100 * LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel[i] / 1000 / 1000) / 100 }M voxels)`;
}
const detailMax = LimitsConfig.maxOutputSizeInVoxelCountByPrecisionLevel.length - 1;
const sources = ServerConfig.idMap.map(m => m[0])
--
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