molstar
Version:
A comprehensive macromolecular library.
129 lines (128 loc) • 7.27 kB
JavaScript
"use strict";
/**
* Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Adam Midlik <midlik@gmail.com>
*/
Object.defineProperty(exports, "__esModule", { value: true });
exports.VolsegLatticeSegmentationData = void 0;
const volume_1 = require("../../mol-model/volume");
const volume_representation_params_1 = require("../../mol-plugin-state/helpers/volume-representation-params");
const transforms_1 = require("../../mol-plugin-state/transforms");
const data_1 = require("../../mol-plugin-state/transforms/data");
const misc_1 = require("../../mol-plugin-state/transforms/misc");
const volume_2 = require("../../mol-plugin-state/transforms/volume");
const commands_1 = require("../../mol-plugin/commands");
const color_1 = require("../../mol-util/color");
const entry_root_1 = require("./entry-root");
const global_state_1 = require("./global-state");
const GROUP_TAG = 'lattice-segmentation-group';
const SEGMENT_VISUAL_TAG = 'lattice-segment-visual';
const DEFAULT_SEGMENT_COLOR = color_1.Color.fromNormalizedRgb(0.8, 0.8, 0.8);
class VolsegLatticeSegmentationData {
constructor(rootData) {
this.entryData = rootData;
}
async loadSegmentation() {
var _a, _b, _c;
const hasLattices = this.entryData.metadata.raw.grid.segmentation_lattices.segmentation_lattice_ids.length > 0;
if (hasLattices) {
const url = this.entryData.api.latticeUrl(this.entryData.source, this.entryData.entryId, 0, entry_root_1.BOX, entry_root_1.MAX_VOXELS);
let group = (_a = this.entryData.findNodesByTags(GROUP_TAG)[0]) === null || _a === void 0 ? void 0 : _a.transform.ref;
if (!group) {
const newGroupNode = await this.entryData.newUpdate().apply(misc_1.CreateGroup, { label: 'Segmentation', description: 'Lattice' }, { tags: [GROUP_TAG], state: { isCollapsed: true } }).commit();
group = newGroupNode.ref;
}
const segmentLabels = this.entryData.metadata.allSegments.map(seg => ({ id: seg.id, label: seg.biological_annotation.name ? `<b>${seg.biological_annotation.name}</b>` : '' }));
const volumeNode = await this.entryData.newUpdate().to(group)
.apply(data_1.Download, { url, isBinary: true, label: `Segmentation Data: ${url}` })
.apply(data_1.ParseCif)
.apply(volume_2.VolumeFromSegmentationCif, { blockHeader: 'SEGMENTATION_DATA', segmentLabels: segmentLabels, ownerId: this.entryData.ref })
.commit();
const volumeData = volumeNode.data;
const segmentation = volume_1.Volume.Segmentation.get(volumeData);
const segmentIds = Array.from((_b = segmentation === null || segmentation === void 0 ? void 0 : segmentation.segments.keys()) !== null && _b !== void 0 ? _b : []);
await this.entryData.newUpdate().to(volumeNode)
.apply(transforms_1.StateTransforms.Representation.VolumeRepresentation3D, (0, volume_representation_params_1.createVolumeRepresentationParams)(this.entryData.plugin, volumeData, {
type: 'segment',
typeParams: { tryUseGpu: (_c = global_state_1.VolsegGlobalStateData.getGlobalState(this.entryData.plugin)) === null || _c === void 0 ? void 0 : _c.tryUseGpu },
color: 'volume-segment',
colorParams: { palette: this.createPalette(segmentIds) },
}), { tags: [SEGMENT_VISUAL_TAG] }).commit();
}
}
createPalette(segmentIds) {
const colorMap = new Map();
for (const segment of this.entryData.metadata.allSegments) {
const color = color_1.Color.fromNormalizedArray(segment.colour, 0);
colorMap.set(segment.id, color);
}
if (colorMap.size === 0)
return undefined;
for (const segid of segmentIds) {
colorMap.get(segid);
}
const colors = segmentIds.map(segid => { var _a; return (_a = colorMap.get(segid)) !== null && _a !== void 0 ? _a : DEFAULT_SEGMENT_COLOR; });
return { name: 'colors', params: { list: { kind: 'set', colors: colors } } };
}
async updateOpacity(opacity) {
const reprs = this.entryData.findNodesByTags(SEGMENT_VISUAL_TAG);
const update = this.entryData.newUpdate();
for (const s of reprs) {
update.to(s).update(transforms_1.StateTransforms.Representation.VolumeRepresentation3D, p => { p.type.params.alpha = opacity; });
}
return await update.commit();
}
makeLoci(segments) {
var _a;
const vis = this.entryData.findNodesByTags(SEGMENT_VISUAL_TAG)[0];
if (!vis)
return undefined;
const repr = (_a = vis.obj) === null || _a === void 0 ? void 0 : _a.data.repr;
const wholeLoci = repr.getAllLoci()[0];
if (!wholeLoci || !volume_1.Volume.Segment.isLoci(wholeLoci))
return undefined;
return { loci: volume_1.Volume.Segment.Loci(wholeLoci.volume, segments), repr: repr };
}
async highlightSegment(segment) {
const segmentLoci = this.makeLoci([segment.id]);
if (!segmentLoci)
return;
this.entryData.plugin.managers.interactivity.lociHighlights.highlight(segmentLoci, false);
}
async selectSegment(segment) {
if (segment === undefined || segment < 0)
return;
const segmentLoci = this.makeLoci([segment]);
if (!segmentLoci)
return;
this.entryData.plugin.managers.interactivity.lociSelects.select(segmentLoci, false);
}
/** Make visible the specified set of lattice segments */
async showSegments(segments) {
var _a;
const repr = this.entryData.findNodesByTags(SEGMENT_VISUAL_TAG)[0];
if (!repr)
return;
const selectedSegment = this.entryData.currentState.value.selectedSegment;
const mustReselect = segments.includes(selectedSegment) && !((_a = repr.params) === null || _a === void 0 ? void 0 : _a.values.type.params.segments.includes(selectedSegment));
const update = this.entryData.newUpdate();
update.to(repr).update(transforms_1.StateTransforms.Representation.VolumeRepresentation3D, p => { p.type.params.segments = segments; });
await update.commit();
if (mustReselect) {
await this.selectSegment(this.entryData.currentState.value.selectedSegment);
}
}
async setTryUseGpu(tryUseGpu) {
const visuals = this.entryData.findNodesByTags(SEGMENT_VISUAL_TAG);
for (const visual of visuals) {
const oldParams = visual.transform.params;
if (oldParams.type.params.tryUseGpu === !tryUseGpu) {
const newParams = { ...oldParams, type: { ...oldParams.type, params: { ...oldParams.type.params, tryUseGpu: tryUseGpu } } };
const update = this.entryData.newUpdate().to(visual.transform.ref).update(newParams);
await commands_1.PluginCommands.State.Update(this.entryData.plugin, { state: this.entryData.plugin.state.data, tree: update, options: { doNotUpdateCurrent: true } });
}
}
}
}
exports.VolsegLatticeSegmentationData = VolsegLatticeSegmentationData;