diff --git a/src/mol-plugin/context.ts b/src/mol-plugin/context.ts
index 13f4d4480d7ee680983295cdb2b06d562c25d4ec..5895a6c6dfa731ed5240e2b9ff6423a6e6588ffe 100644
--- a/src/mol-plugin/context.ts
+++ b/src/mol-plugin/context.ts
@@ -30,6 +30,7 @@ import { PLUGIN_VERSION, PLUGIN_VERSION_DATE } from './version';
import { PluginLayout } from './layout';
import { List } from 'immutable';
import { StateTransformParameters } from './ui/state/common';
+import { DataFormatRegistry } from './state/actions/basic';
export class PluginContext {
private disposed = false;
@@ -87,6 +88,10 @@ export class PluginContext {
themeCtx: { colorThemeRegistry: ColorTheme.createRegistry(), sizeThemeRegistry: SizeTheme.createRegistry() } as ThemeRegistryContext
}
+ readonly dataFormat = {
+ registry: new DataFormatRegistry()
+ }
+
readonly customModelProperties = new CustomPropertyRegistry();
readonly customParamEditors = new Map<string, StateTransformParameters.Class>();
diff --git a/src/mol-plugin/state/actions/basic.ts b/src/mol-plugin/state/actions/basic.ts
index d06655c3da87f40e51b6a8c33cd6829db2734f5a..db954502b1e46603f0f8a64fc22ca81aa598c42b 100644
--- a/src/mol-plugin/state/actions/basic.ts
+++ b/src/mol-plugin/state/actions/basic.ts
@@ -6,7 +6,7 @@
*/
import { PluginContext } from 'mol-plugin/context';
-import { StateTree, Transformer } from 'mol-state';
+import { StateTree, Transformer, StateObject } from 'mol-state';
import { StateAction } from 'mol-state/action';
import { StateSelection } from 'mol-state/state/selection';
import { StateTreeBuilder } from 'mol-state/tree/builder';
@@ -15,7 +15,7 @@ import { PluginStateObject } from '../objects';
import { StateTransforms } from '../transforms';
import { Download } from '../transforms/data';
import { StructureRepresentation3DHelpers } from '../transforms/representation';
-import { getFileInfo, FileInput } from 'mol-util/file-info';
+import { getFileInfo, FileInfo } from 'mol-util/file-info';
import { Task } from 'mol-task';
// TODO: "structure/volume parser provider"
@@ -170,55 +170,128 @@ export const UpdateTrajectory = StateAction.build({
//
-const VolumeFormats = { 'ccp4': '', 'mrc': '', 'map': '', 'dsn6': '', 'brix': '', 'dscif': '' }
-type VolumeFormat = keyof typeof VolumeFormats
-
-function getVolumeData(format: VolumeFormat, b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>) {
- switch (format) {
- case 'ccp4': case 'mrc': case 'map':
- return b.apply(StateTransforms.Data.ParseCcp4).apply(StateTransforms.Model.VolumeFromCcp4);
- case 'dsn6': case 'brix':
- return b.apply(StateTransforms.Data.ParseDsn6).apply(StateTransforms.Model.VolumeFromDsn6);
- case 'dscif':
- return b.apply(StateTransforms.Data.ParseCif).apply(StateTransforms.Model.VolumeFromDensityServerCif);
+export class DataFormatRegistry<D extends PluginStateObject.Data.Binary | PluginStateObject.Data.String, M extends StateObject> {
+ private _list: { name: string, provider: DataFormatProvider<D, M> }[] = []
+ private _map = new Map<string, DataFormatProvider<D, M>>()
+
+ get default() { return this._list[0]; }
+ get types(): [string, string][] {
+ return this._list.map(e => [e.name, e.provider.label] as [string, string]);
}
-}
-function createVolumeTree(format: VolumeFormat, ctx: PluginContext, b: StateTreeBuilder.To<PluginStateObject.Data.Binary | PluginStateObject.Data.String>): StateTree {
- return getVolumeData(format, b)
- .apply(StateTransforms.Representation.VolumeRepresentation3D)
- // the parameters will be used automatically by the reconciler and the IsoValue object
- // will get the correct Stats object instead of the empty one
- // VolumeRepresentation3DHelpers.getDefaultParamsStatic(ctx, 'isosurface'))
- .getTree();
-}
+ constructor() {
+ this.add('ccp4', Ccp4Provider)
+ this.add('dsn6', Dsn6Provider)
+ this.add('dscif', DscifProvider)
+ };
+
+ add(name: string, provider: DataFormatProvider<D, M>) {
+ this._list.push({ name, provider })
+ this._map.set(name, provider)
+ }
+
+ remove(name: string) {
+ this._list.splice(this._list.findIndex(e => e.name === name), 1)
+ this._map.delete(name)
+ }
-function getFileFormat(format: VolumeFormat | 'auto', file: FileInput, data?: Uint8Array): VolumeFormat {
- if (format === 'auto') {
- const fileFormat = getFileInfo(file).ext
- if (fileFormat in VolumeFormats) {
- return fileFormat as VolumeFormat
+ auto(info: FileInfo, dataStateObject: D) {
+ for (let i = 0, il = this.list.length; i < il; ++i) {
+ const { provider } = this._list[i]
+ if (provider.isApplicable(info, dataStateObject.data)) return provider
+ }
+ throw new Error('no compatible data format provider available')
+ }
+
+ get(name: string): DataFormatProvider<D, M> {
+ if (this._map.has(name)) {
+ return this._map.get(name)!
} else {
- throw new Error('unsupported format')
+ throw new Error(`unknown data format name '${name}'`)
}
- } else {
- return format
+ }
+
+ get list() {
+ return this._list
+ }
+}
+
+interface DataFormatProvider<D extends PluginStateObject.Data.Binary | PluginStateObject.Data.String, M extends StateObject> {
+ label: string
+ description: string
+ fileExtensions: string[]
+ isApplicable(info: FileInfo, data: string | Uint8Array): boolean
+ getDefaultBuilder(b: StateTreeBuilder.To<D>): StateTreeBuilder.To<M>
+}
+
+const Ccp4Provider: DataFormatProvider<any, any> = {
+ label: 'CCP4/MRC/BRIX',
+ description: 'CCP4/MRC/BRIX',
+ fileExtensions: ['ccp4', 'mrc', 'map'],
+ isApplicable: (info: FileInfo, data: Uint8Array) => {
+ return info.ext === 'ccp4' || info.ext === 'mrc' || info.ext === 'map'
+ },
+ getDefaultBuilder: (b: StateTreeBuilder.To<PluginStateObject.Data.Binary>) => {
+ return b.apply(StateTransforms.Data.ParseCcp4)
+ .apply(StateTransforms.Model.VolumeFromCcp4)
+ .apply(StateTransforms.Representation.VolumeRepresentation3D)
+ }
+}
+
+const Dsn6Provider: DataFormatProvider<any, any> = {
+ label: 'DSN6/BRIX',
+ description: 'DSN6/BRIX',
+ fileExtensions: ['dsn6', 'brix'],
+ isApplicable: (info: FileInfo, data: Uint8Array) => {
+ return info.ext === 'dsn6' || info.ext === 'brix'
+ },
+ getDefaultBuilder: (b: StateTreeBuilder.To<PluginStateObject.Data.Binary>) => {
+ return b.apply(StateTransforms.Data.ParseDsn6)
+ .apply(StateTransforms.Model.VolumeFromDsn6)
+ .apply(StateTransforms.Representation.VolumeRepresentation3D)
}
}
+const DscifProvider: DataFormatProvider<any, any> = {
+ label: 'DensityServer CIF',
+ description: 'DensityServer CIF',
+ fileExtensions: ['cif'],
+ isApplicable: (info: FileInfo, data: Uint8Array) => {
+ return info.ext === 'cif'
+ },
+ getDefaultBuilder: (b: StateTreeBuilder.To<PluginStateObject.Data.Binary>) => {
+ return b.apply(StateTransforms.Data.ParseCif, { })
+ .apply(StateTransforms.Model.VolumeFromDensityServerCif)
+ .apply(StateTransforms.Representation.VolumeRepresentation3D)
+ }
+}
+
+//
+
+function getDataFormatExtensionsOptions(dataFormatRegistry: DataFormatRegistry<any, any>) {
+ const extensions: string[] = []
+ const options: [string, string][] = [['auto', 'Automatic']]
+ dataFormatRegistry.list.forEach(({ name, provider }) => {
+ extensions.push(...provider.fileExtensions)
+ options.push([ name, provider.label ])
+ })
+ return { extensions, options }
+}
+
export const OpenVolume = StateAction.build({
display: { name: 'Open Volume', description: 'Load a volume from file and create its default visual' },
from: PluginStateObject.Root,
- params: {
- file: PD.File({ accept: '.ccp4,.mrc,.map,.dsn6,.brix,.cif'}),
- isBinary: PD.Boolean(true),
- format: PD.Select('auto', [
- ['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['map', 'MAP'], ['dsn6', 'DSN6'], ['brix', 'BRIX'], ['dscif', 'densityServerCIF']
- ]),
+ params: (a, ctx: PluginContext) => {
+ const { extensions, options } = getDataFormatExtensionsOptions(ctx.dataFormat.registry)
+ return {
+ file: PD.File({ accept: extensions.map(e => `.${e}`).join(',')}),
+ format: PD.Select('auto', options),
+ isBinary: PD.Boolean(true), // TOOD should take selected format into account
+ }
}
})(({ params, state }, ctx: PluginContext) => Task.create('Open Volume', async taskCtx => {
- const dataTree = state.build().toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: true });
- const volumeData = await state.updateTree(dataTree).runInContext(taskCtx);
+ const data = state.build().toRoot().apply(StateTransforms.Data.ReadFile, { file: params.file, isBinary: params.isBinary });
+ const dataStateObject = await state.updateTree(data).runInContext(taskCtx);
// Alternative for more complex states where the builder is not a simple StateTreeBuilder.To<>:
/*
@@ -227,10 +300,11 @@ export const OpenVolume = StateAction.build({
const dataCell = state.select(dataRef)[0];
*/
- const format = getFileFormat(params.format, params.file, volumeData.data as Uint8Array);
- const volumeTree = state.build().to(dataTree.ref);
+ const provider = params.format === 'auto' ? ctx.dataFormat.registry.auto(getFileInfo(params.file), dataStateObject) : ctx.dataFormat.registry.get(params.format)
+ const b = state.build().to(data.ref);
+ const tree = provider.getDefaultBuilder(b).getTree()
// need to await the 2nd update the so that the enclosing Task finishes after the update is done.
- await state.updateTree(createVolumeTree(format, ctx, volumeTree)).runInContext(taskCtx);
+ await state.updateTree(tree).runInContext(taskCtx);
}));
export { DownloadDensity };
@@ -238,41 +312,40 @@ type DownloadDensity = typeof DownloadDensity
const DownloadDensity = StateAction.build({
from: PluginStateObject.Root,
display: { name: 'Download Density', description: 'Load a density from the provided source and create its default visual.' },
- params: {
- source: PD.MappedStatic('rcsb', {
- 'pdbe': PD.Group({
- id: PD.Text('1tqn', { label: 'Id' }),
- type: PD.Select('2fofc', [['2fofc', '2Fo-Fc'], ['fofc', 'Fo-Fc']]),
- }, { isFlat: true }),
- 'rcsb': PD.Group({
- id: PD.Text('1tqn', { label: 'Id' }),
- type: PD.Select('2fofc', [['2fofc', '2Fo-Fc'], ['fofc', 'Fo-Fc']]),
- }, { isFlat: true }),
- 'url': PD.Group({
- url: PD.Text(''),
- isBinary: PD.Boolean(true),
- format: PD.Select('auto', [
- ['auto', 'Automatic'], ['ccp4', 'CCP4'], ['mrc', 'MRC'], ['map', 'MAP'], ['dsn6', 'DSN6'], ['brix', 'BRIX'], ['dscif', 'densityServerCIF']
- ]),
- }, { isFlat: true })
- }, {
- options: [
- ['pdbe', 'PDBe X-ray maps'],
- ['rcsb', 'RCSB X-ray maps'],
- ['url', 'URL']
- ]
- })
+ params: (a, ctx: PluginContext) => {
+ const { options } = getDataFormatExtensionsOptions(ctx.dataFormat.registry)
+ return {
+ source: PD.MappedStatic('rcsb', {
+ 'pdbe': PD.Group({
+ id: PD.Text('1tqn', { label: 'Id' }),
+ type: PD.Select('2fofc', [['2fofc', '2Fo-Fc'], ['fofc', 'Fo-Fc']]),
+ }, { isFlat: true }),
+ 'rcsb': PD.Group({
+ id: PD.Text('1tqn', { label: 'Id' }),
+ type: PD.Select('2fofc', [['2fofc', '2Fo-Fc'], ['fofc', 'Fo-Fc']]),
+ }, { isFlat: true }),
+ 'url': PD.Group({
+ url: PD.Text(''),
+ isBinary: PD.Boolean(false),
+ format: PD.Select('auto', options),
+ }, { isFlat: true })
+ }, {
+ options: [
+ ['pdbe', 'PDBe X-ray maps'],
+ ['rcsb', 'RCSB X-ray maps'],
+ ['url', 'URL']
+ ]
+ })
+ }
}
-})(({ params, state }, ctx: PluginContext) => {
- const b = state.build();
+})(({ params, state }, ctx: PluginContext) => Task.create('Download Density', async taskCtx => {
const src = params.source;
let downloadParams: Transformer.Params<Download>;
- let format: VolumeFormat
+ let provider: DataFormatProvider<any, any>
switch (src.name) {
case 'url':
downloadParams = src.params;
- format = getFileFormat(src.params.format, src.params.url)
break;
case 'pdbe':
downloadParams = {
@@ -282,7 +355,6 @@ const DownloadDensity = StateAction.build({
isBinary: true,
label: `PDBe X-ray map: ${src.params.id}`
};
- format = 'ccp4'
break;
case 'rcsb':
downloadParams = {
@@ -292,11 +364,28 @@ const DownloadDensity = StateAction.build({
isBinary: true,
label: `RCSB X-ray map: ${src.params.id}`
};
- format = 'dsn6'
break;
default: throw new Error(`${(src as any).name} not supported.`);
}
- const data = b.toRoot().apply(StateTransforms.Data.Download, downloadParams);
- return state.updateTree(createVolumeTree(format, ctx, data));
-});
\ No newline at end of file
+ const data = state.build().toRoot().apply(StateTransforms.Data.Download, downloadParams);
+ const dataStateObject = await state.updateTree(data).runInContext(taskCtx);
+
+ switch (src.name) {
+ case 'url':
+ downloadParams = src.params;
+ provider = src.params.format === 'auto' ? ctx.dataFormat.registry.auto(getFileInfo(downloadParams.url), dataStateObject) : ctx.dataFormat.registry.get(src.params.format)
+ break;
+ case 'pdbe':
+ provider = ctx.dataFormat.registry.get('ccp4')
+ break;
+ case 'rcsb':
+ provider = ctx.dataFormat.registry.get('dsn6')
+ break;
+ default: throw new Error(`${(src as any).name} not supported.`);
+ }
+
+ const b = state.build().to(data.ref);
+ const tree = provider.getDefaultBuilder(b).getTree()
+ await state.updateTree(tree).runInContext(taskCtx);
+}));
\ No newline at end of file