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@@ -8,16 +8,16 @@ import { Download, ParseCif } from '../../mol-plugin-state/transforms/data';
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import { CustomModelProperties, CustomStructureProperties, ModelFromTrajectory, StructureComponent, StructureFromModel, TrajectoryFromMmCif, TrajectoryFromPDB, TransformStructureConformation } from '../../mol-plugin-state/transforms/model';
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import { StructureRepresentation3D } from '../../mol-plugin-state/transforms/representation';
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import { PluginContext } from '../../mol-plugin/context';
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-import { StateBuilder, StateObjectSelector } from '../../mol-state';
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+import { StateObjectSelector } from '../../mol-state';
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import { canonicalJsonString } from '../../mol-util/json';
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+import { MolViewSpec } from './behavior';
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+import { setCamera, setCanvas, setFocus } from './camera';
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import { MVSAnnotationsProvider } from './components/annotation-prop';
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import { MVSAnnotationStructureComponent } from './components/annotation-structure-component';
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import { MVSAnnotationTooltipsProvider } from './components/annotation-tooltips-prop';
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import { CustomLabelProps, CustomLabelRepresentationProvider } from './components/custom-label/representation';
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import { CustomTooltipsProvider } from './components/custom-tooltips-prop';
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-import { MolViewSpec } from './behavior';
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-import { setCamera, setCanvas, setFocus } from './camera';
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-import { AnnotationFromSourceKind, AnnotationFromUriKind, LoadingActions, collectAnnotationReferences, collectAnnotationTooltips, collectInlineTooltips, colorThemeForNode, componentFromXProps, componentPropsFromSelector, isPhantomComponent, labelFromXProps, loadTree, makeNearestReprMap, representationProps, structureProps, transformProps } from './load-helpers';
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+import { AnnotationFromSourceKind, AnnotationFromUriKind, LoadingActions, UpdateTarget, collectAnnotationReferences, collectAnnotationTooltips, collectInlineTooltips, colorThemeForNode, componentFromXProps, componentPropsFromSelector, isPhantomComponent, labelFromXProps, loadTree, makeNearestReprMap, representationProps, structureProps, transformProps } from './load-helpers';
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import { MVSData } from './mvs-data';
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import { ParamsOfKind, SubTreeOfKind, validateTree } from './tree/generic/tree-schema';
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import { convertMvsToMolstar, mvsSanityCheck } from './tree/molstar/conversion';
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@@ -26,22 +26,27 @@ import { MVSTreeSchema } from './tree/mvs/mvs-tree';
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/** Load a MolViewSpec (MVS) tree into the Mol* plugin.
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- * If `options.deletePrevious`, remove all objects in the current Mol* state; otherwise add to the current state.
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+ * If `options.replaceExisting`, remove all objects in the current Mol* state; otherwise add to the current state.
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* If `options.sanityChecks`, run some sanity checks and print potential issues to the console. */
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-export async function loadMVS(plugin: PluginContext, data: MVSData, options: { deletePrevious?: boolean, sanityChecks?: boolean } = {}) {
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- // console.log(`MVS tree (v${data.version}):\n${treeToString(data.root)}`);
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- validateTree(MVSTreeSchema, data.root, 'MVS');
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- if (options.sanityChecks) mvsSanityCheck(data.root);
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- const molstarTree = convertMvsToMolstar(data.root);
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- // console.log(`Converted MolStar tree:\n${treeToString(molstarTree)}`);
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- validateTree(MolstarTreeSchema, molstarTree, 'Converted Molstar');
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- await loadMolstarTree(plugin, molstarTree, options);
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+export async function loadMVS(plugin: PluginContext, data: MVSData, options: { replaceExisting?: boolean, sanityChecks?: boolean } = {}) {
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+ try {
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+ // console.log(`MVS tree (v${data.version}):\n${treeToString(data.root)}`);
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+ validateTree(MVSTreeSchema, data.root, 'MVS');
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+ if (options.sanityChecks) mvsSanityCheck(data.root);
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+ const molstarTree = convertMvsToMolstar(data.root);
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+ // console.log(`Converted MolStar tree:\n${treeToString(molstarTree)}`);
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+ validateTree(MolstarTreeSchema, molstarTree, 'Converted Molstar');
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+ await loadMolstarTree(plugin, molstarTree, options);
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+ } catch (err) {
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+ plugin.log.error(`${err}`);
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+ throw err;
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+ }
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}
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/** Load a `MolstarTree` into the Mol* plugin.
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- * If `deletePrevious`, remove all objects in the current Mol* state; otherwise add to the current state. */
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-async function loadMolstarTree(plugin: PluginContext, tree: MolstarTree, options?: { deletePrevious?: boolean }) {
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+ * If `replaceExisting`, remove all objects in the current Mol* state; otherwise add to the current state. */
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+async function loadMolstarTree(plugin: PluginContext, tree: MolstarTree, options?: { replaceExisting?: boolean }) {
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const mvsExtensionLoaded = plugin.state.hasBehavior(MolViewSpec);
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if (!mvsExtensionLoaded) throw new Error('MolViewSpec extension is not loaded.');
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@@ -72,66 +77,67 @@ export interface MolstarLoadingContext {
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/** Loading actions for loading a `MolstarTree`, per node kind. */
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const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext> = {
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- root(update: StateBuilder.Root, msParent: StateObjectSelector, node: MolstarNode<'root'>, context: MolstarLoadingContext): StateObjectSelector {
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+ root(updateParent: UpdateTarget, node: MolstarNode<'root'>, context: MolstarLoadingContext): UpdateTarget {
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context.nearestReprMap = makeNearestReprMap(node);
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- return msParent;
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+ return updateParent;
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},
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- download(update: StateBuilder.Root, msParent: StateObjectSelector, node: MolstarNode<'download'>): StateObjectSelector {
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- return update.to(msParent).apply(Download, {
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+ download(updateParent: UpdateTarget, node: MolstarNode<'download'>): UpdateTarget {
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+ return UpdateTarget.apply(updateParent, Download, {
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url: node.params.url,
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isBinary: node.params.is_binary,
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- }).selector;
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+ });
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},
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- parse(update: StateBuilder.Root, msParent: StateObjectSelector, node: MolstarNode<'parse'>): StateObjectSelector | undefined {
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+ parse(updateParent: UpdateTarget, node: MolstarNode<'parse'>): UpdateTarget | undefined {
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const format = node.params.format;
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if (format === 'cif') {
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- return update.to(msParent).apply(ParseCif, {}).selector;
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+ return UpdateTarget.apply(updateParent, ParseCif, {});
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} else if (format === 'pdb') {
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- return msParent;
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+ return updateParent;
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} else {
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console.error(`Unknown format in "parse" node: "${format}"`);
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return undefined;
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}
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},
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- trajectory(update: StateBuilder.Root, msParent: StateObjectSelector, node: MolstarNode<'trajectory'>): StateObjectSelector | undefined {
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+ trajectory(updateParent: UpdateTarget, node: MolstarNode<'trajectory'>): UpdateTarget | undefined {
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const format = node.params.format;
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if (format === 'cif') {
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- return update.to(msParent).apply(TrajectoryFromMmCif, {
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+ return UpdateTarget.apply(updateParent, TrajectoryFromMmCif, {
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blockHeader: node.params.block_header ?? '', // Must set to '' because just undefined would get overwritten by createDefaults
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blockIndex: node.params.block_index ?? undefined,
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- }).selector;
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+ });
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} else if (format === 'pdb') {
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- return update.to(msParent).apply(TrajectoryFromPDB, {}).selector;
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+ return UpdateTarget.apply(updateParent, TrajectoryFromPDB, {});
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} else {
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console.error(`Unknown format in "trajectory" node: "${format}"`);
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return undefined;
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}
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},
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- model(update: StateBuilder.Root, msParent: StateObjectSelector, node: SubTreeOfKind<MolstarTree, 'model'>, context: MolstarLoadingContext): StateObjectSelector {
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+ model(updateParent: UpdateTarget, node: SubTreeOfKind<MolstarTree, 'model'>, context: MolstarLoadingContext): UpdateTarget {
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const annotations = collectAnnotationReferences(node, context);
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- return update.to(msParent)
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- .apply(ModelFromTrajectory, {
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- modelIndex: node.params.model_index,
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- })
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- .apply(CustomModelProperties, {
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- properties: {
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- [MVSAnnotationsProvider.descriptor.name]: { annotations }
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- },
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- autoAttach: [
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- MVSAnnotationsProvider.descriptor.name
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- ],
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- }).selector;
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+ const model = UpdateTarget.apply(updateParent, ModelFromTrajectory, {
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+ modelIndex: node.params.model_index,
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+ });
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+ UpdateTarget.apply(model, CustomModelProperties, {
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+ properties: {
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+ [MVSAnnotationsProvider.descriptor.name]: { annotations }
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+ },
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+ autoAttach: [
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+ MVSAnnotationsProvider.descriptor.name
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+ ],
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+ });
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+ return model;
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},
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- structure(update: StateBuilder.Root, msParent: StateObjectSelector, node: SubTreeOfKind<MolstarTree, 'structure'>, context: MolstarLoadingContext): StateObjectSelector {
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+ structure(updateParent: UpdateTarget, node: SubTreeOfKind<MolstarTree, 'structure'>, context: MolstarLoadingContext): UpdateTarget {
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const props = structureProps(node);
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- let result: StateObjectSelector = update.to(msParent).apply(StructureFromModel, props).selector;
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+ const struct = UpdateTarget.apply(updateParent, StructureFromModel, props);
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+ let transformed = struct;
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for (const t of transformProps(node)) {
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- result = update.to(result).apply(TransformStructureConformation, t).selector;
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+ transformed = UpdateTarget.apply(transformed, TransformStructureConformation, t); // applying to the result of previous transform, to get the correct transform order
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}
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const annotationTooltips = collectAnnotationTooltips(node, context);
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const inlineTooltips = collectInlineTooltips(node, context);
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if (annotationTooltips.length + inlineTooltips.length > 0) {
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- update.to(result).apply(CustomStructureProperties, {
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+ UpdateTarget.apply(struct, CustomStructureProperties, {
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properties: {
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[MVSAnnotationTooltipsProvider.descriptor.name]: { tooltips: annotationTooltips },
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[CustomTooltipsProvider.descriptor.name]: { tooltips: inlineTooltips },
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@@ -142,73 +148,73 @@ const MolstarLoadingActions: LoadingActions<MolstarTree, MolstarLoadingContext>
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],
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});
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}
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- return result;
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+ return struct;
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},
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tooltip: undefined, // No action needed, already loaded in `structure`
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tooltip_from_uri: undefined, // No action needed, already loaded in `structure`
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tooltip_from_source: undefined, // No action needed, already loaded in `structure`
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- component(update: StateBuilder.Root, msParent: StateObjectSelector, node: SubTreeOfKind<MolstarTree, 'component'>): StateObjectSelector | undefined {
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+ component(updateParent: UpdateTarget, node: SubTreeOfKind<MolstarTree, 'component'>): UpdateTarget | undefined {
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if (isPhantomComponent(node)) {
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- return msParent;
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+ return updateParent;
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}
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const selector = node.params.selector;
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- return update.to(msParent).apply(StructureComponent, {
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+ return UpdateTarget.apply(updateParent, StructureComponent, {
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type: componentPropsFromSelector(selector),
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label: canonicalJsonString(selector),
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nullIfEmpty: false,
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- }).selector;
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+ });
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},
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- component_from_uri(update: StateBuilder.Root, msParent: StateObjectSelector, node: SubTreeOfKind<MolstarTree, 'component_from_uri'>, context: MolstarLoadingContext): StateObjectSelector | undefined {
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+ component_from_uri(updateParent: UpdateTarget, node: SubTreeOfKind<MolstarTree, 'component_from_uri'>, context: MolstarLoadingContext): UpdateTarget | undefined {
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if (isPhantomComponent(node)) return undefined;
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const props = componentFromXProps(node, context);
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- return update.to(msParent).apply(MVSAnnotationStructureComponent, props).selector;
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+ return UpdateTarget.apply(updateParent, MVSAnnotationStructureComponent, props);
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},
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- component_from_source(update: StateBuilder.Root, msParent: StateObjectSelector, node: SubTreeOfKind<MolstarTree, 'component_from_source'>, context: MolstarLoadingContext): StateObjectSelector | undefined {
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+ component_from_source(updateParent: UpdateTarget, node: SubTreeOfKind<MolstarTree, 'component_from_source'>, context: MolstarLoadingContext): UpdateTarget | undefined {
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if (isPhantomComponent(node)) return undefined;
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const props = componentFromXProps(node, context);
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- return update.to(msParent).apply(MVSAnnotationStructureComponent, props).selector;
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+ return UpdateTarget.apply(updateParent, MVSAnnotationStructureComponent, props);
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},
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- representation(update: StateBuilder.Root, msParent: StateObjectSelector, node: MolstarNode<'representation'>, context: MolstarLoadingContext): StateObjectSelector {
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- return update.to(msParent).apply(StructureRepresentation3D, {
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+ representation(updateParent: UpdateTarget, node: MolstarNode<'representation'>, context: MolstarLoadingContext): UpdateTarget {
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+ return UpdateTarget.apply(updateParent, StructureRepresentation3D, {
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...representationProps(node.params),
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colorTheme: colorThemeForNode(node, context),
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- }).selector;
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+ });
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},
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color: undefined, // No action needed, already loaded in `structure`
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color_from_uri: undefined, // No action needed, already loaded in `structure`
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color_from_source: undefined, // No action needed, already loaded in `structure`
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- label(update: StateBuilder.Root, msParent: StateObjectSelector, node: MolstarNode<'label'>, context: MolstarLoadingContext): StateObjectSelector {
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+ label(updateParent: UpdateTarget, node: MolstarNode<'label'>, context: MolstarLoadingContext): UpdateTarget {
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const item: CustomLabelProps['items'][number] = {
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text: node.params.text,
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position: { name: 'selection', params: {} },
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};
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const nearestReprNode = context.nearestReprMap?.get(node);
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- return update.to(msParent).apply(StructureRepresentation3D, {
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+ return UpdateTarget.apply(updateParent, StructureRepresentation3D, {
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type: {
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name: CustomLabelRepresentationProvider.name,
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params: { items: [item] } satisfies Partial<CustomLabelProps>
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},
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colorTheme: colorThemeForNode(nearestReprNode, context),
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- }).selector;
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+ });
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},
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- label_from_uri(update: StateBuilder.Root, msParent: StateObjectSelector, node: MolstarNode<'label_from_uri'>, context: MolstarLoadingContext): StateObjectSelector {
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+ label_from_uri(updateParent: UpdateTarget, node: MolstarNode<'label_from_uri'>, context: MolstarLoadingContext): UpdateTarget {
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const props = labelFromXProps(node, context);
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- return update.to(msParent).apply(StructureRepresentation3D, props).selector;
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+ return UpdateTarget.apply(updateParent, StructureRepresentation3D, props);
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},
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- label_from_source(update: StateBuilder.Root, msParent: StateObjectSelector, node: MolstarNode<'label_from_source'>, context: MolstarLoadingContext): StateObjectSelector {
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+ label_from_source(updateParent: UpdateTarget, node: MolstarNode<'label_from_source'>, context: MolstarLoadingContext): UpdateTarget {
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const props = labelFromXProps(node, context);
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- return update.to(msParent).apply(StructureRepresentation3D, props).selector;
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+ return UpdateTarget.apply(updateParent, StructureRepresentation3D, props);
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},
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- focus(update: StateBuilder.Root, msParent: StateObjectSelector, node: MolstarNode<'focus'>, context: MolstarLoadingContext): StateObjectSelector {
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- context.focus = { kind: 'focus', focusTarget: msParent, params: node.params };
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- return msParent;
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+ focus(updateParent: UpdateTarget, node: MolstarNode<'focus'>, context: MolstarLoadingContext): UpdateTarget {
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+ context.focus = { kind: 'focus', focusTarget: updateParent.selector, params: node.params };
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+ return updateParent;
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},
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- camera(update: StateBuilder.Root, msParent: StateObjectSelector, node: MolstarNode<'camera'>, context: MolstarLoadingContext): StateObjectSelector {
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+ camera(updateParent: UpdateTarget, node: MolstarNode<'camera'>, context: MolstarLoadingContext): UpdateTarget {
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context.focus = { kind: 'camera', params: node.params };
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- return msParent;
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+ return updateParent;
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},
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- canvas(update: StateBuilder.Root, msParent: StateObjectSelector, node: MolstarNode<'canvas'>, context: MolstarLoadingContext): StateObjectSelector {
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+ canvas(updateParent: UpdateTarget, node: MolstarNode<'canvas'>, context: MolstarLoadingContext): UpdateTarget {
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context.canvas = node.params;
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- return msParent;
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+ return updateParent;
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},
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};
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midlik
