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Commit 023b6557 authored by Alexander Rose's avatar Alexander Rose
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viewer, option to load files without adding visuals

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src/mol-plugin/state/actions/data-format.ts
+ 7
− 3
View file @ 023b6557
...@@ -103,25 +103,28 @@ export class DataFormatRegistry<D extends PluginStateObject.Data.Binary | Plugin ...@@ -103,25 +103,28 @@ export class DataFormatRegistry<D extends PluginStateObject.Data.Binary | Plugin
} }
} }
export type DataFormatBuilderOptions = { visuals: boolean }
export interface DataFormatProvider<D extends PluginStateObject.Data.Binary | PluginStateObject.Data.String> { export interface DataFormatProvider<D extends PluginStateObject.Data.Binary | PluginStateObject.Data.String> {
label: string label: string
description: string description: string
stringExtensions: string[] stringExtensions: string[]
binaryExtensions: string[] binaryExtensions: string[]
isApplicable(info: FileInfo, data: string | Uint8Array): boolean isApplicable(info: FileInfo, data: string | Uint8Array): boolean
getDefaultBuilder(ctx: PluginContext, data: StateBuilder.To<D>, state?: State): Task<void> getDefaultBuilder(ctx: PluginContext, data: StateBuilder.To<D>, options: DataFormatBuilderOptions, state?: State): Task<void>
} }
// //
export const OpenFile = StateAction.build({ export const OpenFile = StateAction.build({
display: { name: 'Open File', description: 'Load a file and create its default visual' }, display: { name: 'Open File', description: 'Load a file and optionally create its default visuals' },
from: PluginStateObject.Root, from: PluginStateObject.Root,
params: (a, ctx: PluginContext) => { params: (a, ctx: PluginContext) => {
const { extensions, options } = ctx.dataFormat.registry const { extensions, options } = ctx.dataFormat.registry
return { return {
file: PD.File({ accept: Array.from(extensions).map(e => `.${e}`).join(',')}), file: PD.File({ accept: Array.from(extensions).map(e => `.${e}`).join(',')}),
format: PD.Select('auto', options), format: PD.Select('auto', options),
visuals: PD.Boolean(true, { description: 'Add default visuals' }),
} }
} }
})(({ params, state }, ctx: PluginContext) => Task.create('Open File', async taskCtx => { })(({ params, state }, ctx: PluginContext) => Task.create('Open File', async taskCtx => {
...@@ -140,8 +143,9 @@ export const OpenFile = StateAction.build({ ...@@ -140,8 +143,9 @@ export const OpenFile = StateAction.build({
const provider = params.format === 'auto' ? ctx.dataFormat.registry.auto(info, dataStateObject) : ctx.dataFormat.registry.get(params.format) const provider = params.format === 'auto' ? ctx.dataFormat.registry.auto(info, dataStateObject) : ctx.dataFormat.registry.get(params.format)
const b = state.build().to(data.ref); const b = state.build().to(data.ref);
const options = { visuals: params.visuals }
// need to await the 2nd update the so that the enclosing Task finishes after the update is done. // need to await the 2nd update the so that the enclosing Task finishes after the update is done.
await provider.getDefaultBuilder(ctx, b, state).runInContext(taskCtx) await provider.getDefaultBuilder(ctx, b, options, state).runInContext(taskCtx)
})); }));
// //
......
src/mol-plugin/state/actions/shape.ts
+ 6
− 4
View file @ 023b6557
...@@ -10,7 +10,7 @@ import { Task } from '../../../mol-task'; ...@@ -10,7 +10,7 @@ import { Task } from '../../../mol-task';
import { FileInfo } from '../../../mol-util/file-info'; import { FileInfo } from '../../../mol-util/file-info';
import { PluginStateObject } from '../objects'; import { PluginStateObject } from '../objects';
import { StateTransforms } from '../transforms'; import { StateTransforms } from '../transforms';
import { DataFormatProvider } from './data-format'; import { DataFormatProvider, DataFormatBuilderOptions } from './data-format';
export const PlyProvider: DataFormatProvider<any> = { export const PlyProvider: DataFormatProvider<any> = {
label: 'PLY', label: 'PLY',
...@@ -20,11 +20,13 @@ export const PlyProvider: DataFormatProvider<any> = { ...@@ -20,11 +20,13 @@ export const PlyProvider: DataFormatProvider<any> = {
isApplicable: (info: FileInfo, data: string) => { isApplicable: (info: FileInfo, data: string) => {
return info.ext === 'ply' return info.ext === 'ply'
}, },
getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.String>, state: State) => { getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.String>, options: DataFormatBuilderOptions, state: State) => {
return Task.create('PLY default builder', async taskCtx => { return Task.create('PLY default builder', async taskCtx => {
const tree = data.apply(StateTransforms.Data.ParsePly) let tree: StateBuilder.To<any> = data.apply(StateTransforms.Data.ParsePly)
.apply(StateTransforms.Model.ShapeFromPly) .apply(StateTransforms.Model.ShapeFromPly)
.apply(StateTransforms.Representation.ShapeRepresentation3D) if (options.visuals) {
tree = tree.apply(StateTransforms.Representation.ShapeRepresentation3D)
}
await state.updateTree(tree).runInContext(taskCtx) await state.updateTree(tree).runInContext(taskCtx)
}) })
} }
......
src/mol-plugin/state/actions/structure.ts
+ 7
− 7
View file @ 023b6557
...@@ -13,7 +13,7 @@ import { StateTransforms } from '../transforms'; ...@@ -13,7 +13,7 @@ import { StateTransforms } from '../transforms';
import { Download } from '../transforms/data'; import { Download } from '../transforms/data';
import { StructureRepresentation3DHelpers } from '../transforms/representation'; import { StructureRepresentation3DHelpers } from '../transforms/representation';
import { CustomModelProperties, StructureSelection, CustomStructureProperties } from '../transforms/model'; import { CustomModelProperties, StructureSelection, CustomStructureProperties } from '../transforms/model';
import { DataFormatProvider, guessCifVariant } from './data-format'; import { DataFormatProvider, guessCifVariant, DataFormatBuilderOptions } from './data-format';
import { FileInfo } from '../../../mol-util/file-info'; import { FileInfo } from '../../../mol-util/file-info';
import { Task } from '../../../mol-task'; import { Task } from '../../../mol-task';
import { StructureElement } from '../../../mol-model/structure'; import { StructureElement } from '../../../mol-model/structure';
...@@ -29,10 +29,10 @@ export const MmcifProvider: DataFormatProvider<any> = { ...@@ -29,10 +29,10 @@ export const MmcifProvider: DataFormatProvider<any> = {
if (info.ext === 'cif' || info.ext === 'bcif') return guessCifVariant(info, data) !== 'dscif' if (info.ext === 'cif' || info.ext === 'bcif') return guessCifVariant(info, data) !== 'dscif'
return false return false
}, },
getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, state: State) => { getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, options: DataFormatBuilderOptions, state: State) => {
return Task.create('mmCIF default builder', async taskCtx => { return Task.create('mmCIF default builder', async taskCtx => {
const traj = createModelTree(data, 'cif'); const traj = createModelTree(data, 'cif');
await state.updateTree(createStructureTree(ctx, traj, false)).runInContext(taskCtx) await state.updateTree(options.visuals ? createStructureTree(ctx, traj, false) : traj).runInContext(taskCtx)
}) })
} }
} }
...@@ -45,10 +45,10 @@ export const PdbProvider: DataFormatProvider<any> = { ...@@ -45,10 +45,10 @@ export const PdbProvider: DataFormatProvider<any> = {
isApplicable: (info: FileInfo, data: string) => { isApplicable: (info: FileInfo, data: string) => {
return info.ext === 'pdb' || info.ext === 'ent' return info.ext === 'pdb' || info.ext === 'ent'
}, },
getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.String>, state: State) => { getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.String>, options: DataFormatBuilderOptions, state: State) => {
return Task.create('PDB default builder', async taskCtx => { return Task.create('PDB default builder', async taskCtx => {
const traj = createModelTree(data, 'pdb'); const traj = createModelTree(data, 'pdb');
await state.updateTree(createStructureTree(ctx, traj, false)).runInContext(taskCtx) await state.updateTree(options.visuals ? createStructureTree(ctx, traj, false) : traj).runInContext(taskCtx)
}) })
} }
} }
...@@ -61,10 +61,10 @@ export const GroProvider: DataFormatProvider<any> = { ...@@ -61,10 +61,10 @@ export const GroProvider: DataFormatProvider<any> = {
isApplicable: (info: FileInfo, data: string) => { isApplicable: (info: FileInfo, data: string) => {
return info.ext === 'gro' return info.ext === 'gro'
}, },
getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.String>, state: State) => { getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.String>, options: DataFormatBuilderOptions, state: State) => {
return Task.create('GRO default builder', async taskCtx => { return Task.create('GRO default builder', async taskCtx => {
const traj = createModelTree(data, 'gro'); const traj = createModelTree(data, 'gro');
await state.updateTree(createStructureTree(ctx, traj, false)).runInContext(taskCtx) await state.updateTree(options.visuals ? createStructureTree(ctx, traj, false) : traj).runInContext(taskCtx)
}) })
} }
} }
......
src/mol-plugin/state/actions/volume.ts
+ 19
− 11
View file @ 023b6557
...@@ -16,7 +16,7 @@ import { PluginStateObject } from '../objects'; ...@@ -16,7 +16,7 @@ import { PluginStateObject } from '../objects';
import { StateTransforms } from '../transforms'; import { StateTransforms } from '../transforms';
import { Download } from '../transforms/data'; import { Download } from '../transforms/data';
import { VolumeRepresentation3DHelpers } from '../transforms/representation'; import { VolumeRepresentation3DHelpers } from '../transforms/representation';
import { DataFormatProvider, guessCifVariant } from './data-format'; import { DataFormatProvider, guessCifVariant, DataFormatBuilderOptions } from './data-format';
export const Ccp4Provider: DataFormatProvider<any> = { export const Ccp4Provider: DataFormatProvider<any> = {
label: 'CCP4/MRC/BRIX', label: 'CCP4/MRC/BRIX',
...@@ -26,11 +26,13 @@ export const Ccp4Provider: DataFormatProvider<any> = { ...@@ -26,11 +26,13 @@ export const Ccp4Provider: DataFormatProvider<any> = {
isApplicable: (info: FileInfo, data: Uint8Array) => { isApplicable: (info: FileInfo, data: Uint8Array) => {
return info.ext === 'ccp4' || info.ext === 'mrc' || info.ext === 'map' return info.ext === 'ccp4' || info.ext === 'mrc' || info.ext === 'map'
}, },
getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.Binary>, state: State) => { getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.Binary>, options: DataFormatBuilderOptions, state: State) => {
return Task.create('CCP4/MRC/BRIX default builder', async taskCtx => { return Task.create('CCP4/MRC/BRIX default builder', async taskCtx => {
const tree = data.apply(StateTransforms.Data.ParseCcp4) let tree: StateBuilder.To<any> = data.apply(StateTransforms.Data.ParseCcp4)
.apply(StateTransforms.Volume.VolumeFromCcp4) .apply(StateTransforms.Volume.VolumeFromCcp4)
.apply(StateTransforms.Representation.VolumeRepresentation3D) if (options.visuals) {
tree = tree.apply(StateTransforms.Representation.VolumeRepresentation3D)
}
await state.updateTree(tree).runInContext(taskCtx) await state.updateTree(tree).runInContext(taskCtx)
}) })
} }
...@@ -44,11 +46,13 @@ export const Dsn6Provider: DataFormatProvider<any> = { ...@@ -44,11 +46,13 @@ export const Dsn6Provider: DataFormatProvider<any> = {
isApplicable: (info: FileInfo, data: Uint8Array) => { isApplicable: (info: FileInfo, data: Uint8Array) => {
return info.ext === 'dsn6' || info.ext === 'brix' return info.ext === 'dsn6' || info.ext === 'brix'
}, },
getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.Binary>, state: State) => { getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.Binary>, options: DataFormatBuilderOptions, state: State) => {
return Task.create('DSN6/BRIX default builder', async taskCtx => { return Task.create('DSN6/BRIX default builder', async taskCtx => {
const tree = data.apply(StateTransforms.Data.ParseDsn6) let tree: StateBuilder.To<any> = data.apply(StateTransforms.Data.ParseDsn6)
.apply(StateTransforms.Volume.VolumeFromDsn6) .apply(StateTransforms.Volume.VolumeFromDsn6)
.apply(StateTransforms.Representation.VolumeRepresentation3D) if (options.visuals) {
tree = tree.apply(StateTransforms.Representation.VolumeRepresentation3D)
}
await state.updateTree(tree).runInContext(taskCtx) await state.updateTree(tree).runInContext(taskCtx)
}) })
} }
...@@ -62,7 +66,7 @@ export const DscifProvider: DataFormatProvider<any> = { ...@@ -62,7 +66,7 @@ export const DscifProvider: DataFormatProvider<any> = {
isApplicable: (info: FileInfo, data: Uint8Array | string) => { isApplicable: (info: FileInfo, data: Uint8Array | string) => {
return guessCifVariant(info, data) === 'dscif' ? true : false return guessCifVariant(info, data) === 'dscif' ? true : false
}, },
getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, state: State) => { getDefaultBuilder: (ctx: PluginContext, data: StateBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>, options: DataFormatBuilderOptions, state: State) => {
return Task.create('DensityServer CIF default builder', async taskCtx => { return Task.create('DensityServer CIF default builder', async taskCtx => {
const cifBuilder = data.apply(StateTransforms.Data.ParseCif) const cifBuilder = data.apply(StateTransforms.Data.ParseCif)
const cifStateObject = await state.updateTree(cifBuilder).runInContext(taskCtx) const cifStateObject = await state.updateTree(cifBuilder).runInContext(taskCtx)
...@@ -72,11 +76,15 @@ export const DscifProvider: DataFormatProvider<any> = { ...@@ -72,11 +76,15 @@ export const DscifProvider: DataFormatProvider<any> = {
if (blocks.length === 1) { if (blocks.length === 1) {
tree = b tree = b
.apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: blocks[0].header }) .apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: blocks[0].header })
.apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 0.3 }, 'uniform', { value: ColorNames.teal })) if (options.visuals) {
tree = tree.apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 0.3 }, 'uniform', { value: ColorNames.teal }))
}
} else if (blocks.length === 2) { } else if (blocks.length === 2) {
tree = b tree = b
.apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: blocks[0].header }) .apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: blocks[0].header })
.apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 0.3 }, 'uniform', { value: ColorNames.blue })) if (options.visuals) {
tree = tree.apply(StateTransforms.Representation.VolumeRepresentation3D, VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(1.5), alpha: 0.3 }, 'uniform', { value: ColorNames.blue }))
}
const vol = tree.to(cifBuilder.ref) const vol = tree.to(cifBuilder.ref)
.apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: blocks[1].header }) .apply(StateTransforms.Volume.VolumeFromDensityServerCif, { blockHeader: blocks[1].header })
const posParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(3), alpha: 0.3 }, 'uniform', { value: ColorNames.green }) const posParams = VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface', { isoValue: VolumeIsoValue.relative(3), alpha: 0.3 }, 'uniform', { value: ColorNames.green })
...@@ -199,5 +207,5 @@ const DownloadDensity = StateAction.build({ ...@@ -199,5 +207,5 @@ const DownloadDensity = StateAction.build({
} }
const b = state.build().to(data.ref); const b = state.build().to(data.ref);
await provider.getDefaultBuilder(ctx, b, state).runInContext(taskCtx) await provider.getDefaultBuilder(ctx, b, { visuals: true }, state).runInContext(taskCtx)
})); }));
\ No newline at end of file
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