npm - molstar - Versions diffs - 2.3.9 → 2.4.0 - Mend

molstar 2.3.9 → 2.4.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (550) hide show

package/lib/commonjs/mol-repr/representation.js CHANGED Viewed

@@ -22,6 +22,8 @@ var util_1 = require("./util");
 var base_1 = require("../mol-geo/geometry/base");
 var visual_1 = require("./visual");
 var clipping_1 = require("../mol-theme/clipping");
+var set_1 = require("../mol-util/set");
+var util_2 = require("../mol-data/util");
 var RepresentationProvider;
 (function (RepresentationProvider) {
     function getDetaultParams(r, ctx, data) {
@@ -144,7 +146,7 @@ var Representation;
     Representation.updateState = updateState;
     Representation.StateBuilder = { create: createState, update: updateState };
     Representation.Empty = {
-        label: '', groupCount: 0, renderObjects: [], props: {}, params: {}, updated: new rxjs_1.Subject(), state: createState(), theme: theme_1.Theme.createEmpty(),
+        label: '', groupCount: 0, renderObjects: [], geometryVersion: -1, props: {}, params: {}, updated: new rxjs_1.Subject(), state: createState(), theme: theme_1.Theme.createEmpty(),
         createOrUpdate: function () { return mol_task_1.Task.constant('', undefined); },
         setState: function () { },
         setTheme: function () { },
@@ -152,10 +154,38 @@ var Representation;
         mark: function () { return false; },
         destroy: function () { }
     };
+    var GeometryState = /** @class */ (function () {
+        function GeometryState() {
+            this.curr = new Set();
+            this.next = new Set();
+            this._version = -1;
+        }
+        Object.defineProperty(GeometryState.prototype, "version", {
+            get: function () {
+                return this._version;
+            },
+            enumerable: false,
+            configurable: true
+        });
+        GeometryState.prototype.add = function (id, version) {
+            this.next.add((0, util_2.cantorPairing)(id, version));
+        };
+        GeometryState.prototype.snapshot = function () {
+            var _a;
+            if (!set_1.SetUtils.areEqual(this.curr, this.next)) {
+                this._version += 1;
+            }
+            _a = [this.next, this.curr], this.curr = _a[0], this.next = _a[1];
+            this.next.clear();
+        };
+        return GeometryState;
+    }());
+    Representation.GeometryState = GeometryState;
     function createMulti(label, ctx, getParams, stateBuilder, reprDefs) {
         var _this = this;
         var version = 0;
         var updated = new rxjs_1.Subject();
+        var geometryState = new GeometryState();
         var currentState = stateBuilder.create();
         var currentTheme = theme_1.Theme.createEmpty();
         var currentParams;
@@ -195,6 +225,7 @@ var Representation;
                 }
                 return renderObjects;
             },
+            get geometryVersion() { return geometryState.version; },
             get props() { return currentProps; },
             get params() { return currentParams; },
             createOrUpdate: function (props, data) {
@@ -216,16 +247,20 @@ var Representation;
                                 i = 0, il = reprList.length;
                                 _a.label = 1;
                             case 1:
-                                if (!(i < il)) return [3 /*break*/, 4];
+                                if (!(i < il)) return [3 /*break*/, 5];
                                 if (!(!visuals || visuals.includes(reprMap[i]))) return [3 /*break*/, 3];
                                 return [4 /*yield*/, reprList[i].createOrUpdate(currentProps, currentData).runInContext(runtime)];
                             case 2:
                                 _a.sent();
                                 _a.label = 3;
                             case 3:
+                                geometryState.add(i, reprList[i].geometryVersion);
+                                _a.label = 4;
+                            case 4:
                                 ++i;
                                 return [3 /*break*/, 1];
-                            case 4:
+                            case 5:
+                                geometryState.snapshot();
                                 updated.next(version++);
                                 return [2 /*return*/];
                         }
@@ -255,7 +290,7 @@ var Representation;
             setState: function (state) {
                 stateBuilder.update(currentState, state);
                 for (var i = 0, il = reprList.length; i < il; ++i) {
-                    reprList[i].setState(currentState);
+                    reprList[i].setState(state); // only set the new (partial) state
                 }
             },
             setTheme: function (theme) {
@@ -276,6 +311,7 @@ var Representation;
         var _this = this;
         var version = 0;
         var updated = new rxjs_1.Subject();
+        var geometryState = new GeometryState();
         var currentState = Representation.createState();
         var currentTheme = theme_1.Theme.createEmpty();
         var currentParams = param_definition_1.ParamDefinition.clone(base_1.BaseGeometry.Params);
@@ -285,6 +321,7 @@ var Representation;
             updated: updated,
             get groupCount() { return renderObject.values.uGroupCount.ref.value; },
             get renderObjects() { return [renderObject]; },
+            get geometryVersion() { return geometryState.version; },
             get props() { return currentProps; },
             get params() { return currentParams; },
             createOrUpdate: function (props) {
@@ -294,6 +331,8 @@ var Representation;
                 return mol_task_1.Task.create("Updating '".concat(label, "' representation"), function (runtime) { return (0, tslib_1.__awaiter)(_this, void 0, void 0, function () {
                     return (0, tslib_1.__generator)(this, function (_a) {
                         // TODO
+                        geometryState.add(0, renderObject.id);
+                        geometryState.snapshot();
                         updated.next(version++);
                         return [2 /*return*/];
                     });

package/lib/commonjs/mol-repr/representation.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/commonjs/mol-repr/shape/loci/orientation.d.ts CHANGED Viewed

@@ -10,7 +10,7 @@ export interface OrientationData {
     locis: StructureElement.Loci[];
 }
 export declare const OrientationParams: {
-    visuals: PD.MultiSelect<"axes" | "ellipsoid" | "box">;
+    visuals: PD.MultiSelect<"ellipsoid" | "axes" | "box">;
     color: PD.Color;
     scaleFactor: PD.Numeric;
     radiusScale: PD.Numeric;

package/lib/commonjs/mol-repr/shape/model/unitcell.d.ts CHANGED Viewed

@@ -14,8 +14,8 @@ interface UnitcellData {
 export declare const UnitcellParams: {
     cellColor: PD.Color;
     cellScale: PD.Numeric;
-    ref: PD.Select<"origin" | "model">;
-    attachment: PD.Select<"corner" | "center">;
+    ref: PD.Select<"model" | "origin">;
+    attachment: PD.Select<"center" | "corner">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;

package/lib/commonjs/mol-repr/shape/representation.js CHANGED Viewed

@@ -34,6 +34,7 @@ function ShapeRepresentation(getShape, geometryUtils, builder) {
     var renderObjects = [];
     var _renderObject;
     var _shape;
+    var geometryVersion = -1;
     var _theme = theme_1.Theme.createEmpty();
     var currentProps = param_definition_1.ParamDefinition.getDefaultValues(geometryUtils.Params); // TODO avoid casting
     var currentParams;
@@ -154,6 +155,9 @@ function ShapeRepresentation(getShape, geometryUtils, builder) {
                             geometryUtils.updateRenderableState(_renderObject.state, newProps);
                         }
                         currentProps = newProps;
+                        if (updateState.createGeometry || updateState.createNew) {
+                            geometryVersion += 1;
+                        }
                         // increment version
                         updated.next(version++);
                         return [2 /*return*/];
@@ -177,6 +181,7 @@ function ShapeRepresentation(getShape, geometryUtils, builder) {
         get state() { return _state; },
         get theme() { return _theme; },
         renderObjects: renderObjects,
+        get geometryVersion() { return geometryVersion; },
         updated: updated,
         createOrUpdate: createOrUpdate,
         getLoci: function (pickingId) {

package/lib/commonjs/mol-repr/shape/representation.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/commonjs/mol-repr/structure/complex-representation.js CHANGED Viewed

@@ -10,6 +10,7 @@ exports.ComplexRepresentation = void 0;
 var tslib_1 = require("tslib");
 var param_definition_1 = require("../../mol-util/param-definition");
 var representation_1 = require("./representation");
+var representation_2 = require("../representation");
 var structure_1 = require("../../mol-model/structure");
 var rxjs_1 = require("rxjs");
 var render_object_1 = require("../../mol-gl/render-object");
@@ -24,6 +25,7 @@ function ComplexRepresentation(label, ctx, getParams, visualCtor) {
     var version = 0;
     var webgl = ctx.webgl;
     var updated = new rxjs_1.Subject();
+    var geometryState = new representation_2.Representation.GeometryState();
     var materialId = (0, render_object_1.getNextMaterialId)();
     var renderObjects = [];
     var _state = representation_1.StructureRepresentationStateBuilder.create();
@@ -69,10 +71,14 @@ function ComplexRepresentation(label, ctx, getParams, visualCtor) {
                             setState(_state); // current state for new visual
                         // update list of renderObjects
                         renderObjects.length = 0;
-                        if (visual && visual.renderObject)
+                        if (visual && visual.renderObject) {
                             renderObjects.push(visual.renderObject);
+                            geometryState.add(visual.renderObject.id, visual.geometryVersion);
+                        }
+                        geometryState.snapshot();
                         // increment version
-                        updated.next(version++);
+                        version += 1;
+                        updated.next(version);
                         return [2 /*return*/];
                 }
             });
@@ -118,12 +124,12 @@ function ComplexRepresentation(label, ctx, getParams, visualCtor) {
         if (state.overpaint !== undefined && visual) {
             // Remap loci from equivalent structure to the current structure
             var remappedOverpaint = overpaint_1.Overpaint.remap(state.overpaint, _structure);
-            visual.setOverpaint(remappedOverpaint);
+            visual.setOverpaint(remappedOverpaint, webgl);
         }
         if (state.transparency !== undefined && visual) {
             // Remap loci from equivalent structure to the current structure
             var remappedTransparency = transparency_1.Transparency.remap(state.transparency, _structure);
-            visual.setTransparency(remappedTransparency);
+            visual.setTransparency(remappedTransparency, webgl);
         }
         if (state.clipping !== undefined && visual) {
             // Remap loci from equivalent structure to the current structure
@@ -155,6 +161,7 @@ function ComplexRepresentation(label, ctx, getParams, visualCtor) {
         get params() { return _params; },
         get state() { return _state; },
         get theme() { return _theme; },
+        get geometryVersion() { return geometryState.version; },
         renderObjects: renderObjects,
         updated: updated,
         createOrUpdate: createOrUpdate,

package/lib/commonjs/mol-repr/structure/complex-representation.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/lib/commonjs/mol-repr/structure/complex-visual.d.ts CHANGED Viewed

@@ -40,7 +40,7 @@ interface ComplexVisualGeometryBuilder<P extends StructureParams, G extends Geom
 }
 export declare function ComplexVisual<G extends Geometry, P extends StructureParams & Geometry.Params<G>>(builder: ComplexVisualGeometryBuilder<P, G>, materialId: number): ComplexVisual<P>;
 export declare const ComplexMeshParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -55,7 +55,7 @@ export interface ComplexMeshVisualBuilder<P extends ComplexMeshParams> extends C
 }
 export declare function ComplexMeshVisual<P extends ComplexMeshParams>(builder: ComplexMeshVisualBuilder<P>, materialId: number): ComplexVisual<P>;
 export declare const ComplexCylindersParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     sizeAspectRatio: PD.Numeric;
@@ -70,7 +70,7 @@ export interface ComplexCylindersVisualBuilder<P extends ComplexCylindersParams>
 }
 export declare function ComplexCylindersVisual<P extends ComplexCylindersParams>(builder: ComplexCylindersVisualBuilder<P>, materialId: number): ComplexVisual<P>;
 export declare const ComplexLinesParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     lineSizeAttenuation: PD.BooleanParam;
@@ -82,7 +82,7 @@ export interface ComplexLinesVisualBuilder<P extends ComplexLinesParams> extends
 }
 export declare function ComplexLinesVisual<P extends ComplexLinesParams>(builder: ComplexLinesVisualBuilder<P>, materialId: number): ComplexVisual<P>;
 export declare const ComplexTextParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
     sizeFactor: PD.Numeric;
     borderWidth: PD.Numeric;
@@ -111,7 +111,7 @@ export interface ComplexTextVisualBuilder<P extends ComplexTextParams> extends C
 }
 export declare function ComplexTextVisual<P extends ComplexTextParams>(builder: ComplexTextVisualBuilder<P>, materialId: number): ComplexVisual<P>;
 export declare const ComplexDirectVolumeParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
@@ -121,7 +121,7 @@ export declare const ComplexDirectVolumeParams: {
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{
@@ -144,7 +144,7 @@ export interface ComplexDirectVolumeVisualBuilder<P extends ComplexDirectVolumeP
 }
 export declare function ComplexDirectVolumeVisual<P extends ComplexDirectVolumeParams>(builder: ComplexDirectVolumeVisualBuilder<P>, materialId: number): ComplexVisual<P>;
 export declare const ComplexTextureMeshParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;

package/lib/commonjs/mol-repr/structure/complex-visual.js CHANGED Viewed

@@ -51,6 +51,7 @@ function ComplexVisual(builder, materialId) {
     var currentTheme = theme_1.Theme.createEmpty();
     var currentStructure;
     var geometry;
+    var geometryVersion = -1;
     var locationIt;
     var positionIt;
     function prepareUpdate(theme, props, structure) {
@@ -141,8 +142,10 @@ function ComplexVisual(builder, materialId) {
         currentProps = newProps;
         currentTheme = newTheme;
         currentStructure = newStructure;
-        if (newGeometry)
+        if (newGeometry) {
             geometry = newGeometry;
+            geometryVersion += 1;
+        }
     }
     function lociIsSuperset(loci) {
         if ((0, loci_1.isEveryLoci)(loci))
@@ -171,6 +174,7 @@ function ComplexVisual(builder, materialId) {
     return {
         get groupCount() { return locationIt ? locationIt.count : 0; },
         get renderObject() { return locationIt && locationIt.count ? renderObject : undefined; },
+        get geometryVersion() { return geometryVersion; },
         createOrUpdate: function (ctx, theme, props, structure) {
             if (props === void 0) { props = {}; }
             prepareUpdate(theme, props, structure || currentStructure);
@@ -210,11 +214,13 @@ function ComplexVisual(builder, materialId) {
         setTransform: function (matrix, instanceMatrices) {
             visual_1.Visual.setTransform(renderObject, matrix, instanceMatrices);
         },
-        setOverpaint: function (overpaint) {
-            visual_1.Visual.setOverpaint(renderObject, overpaint, lociApply, true);
+        setOverpaint: function (overpaint, webgl) {
+            var smoothing = { geometry: geometry, props: currentProps, webgl: webgl };
+            visual_1.Visual.setOverpaint(renderObject, overpaint, lociApply, true, smoothing);
         },
-        setTransparency: function (transparency) {
-            visual_1.Visual.setTransparency(renderObject, transparency, lociApply, true);
+        setTransparency: function (transparency, webgl) {
+            var smoothing = { geometry: geometry, props: currentProps, webgl: webgl };
+            visual_1.Visual.setTransparency(renderObject, transparency, lociApply, true, smoothing);
         },
         setClipping: function (clipping) {
             visual_1.Visual.setClipping(renderObject, clipping, lociApply, true);

package/lib/commonjs/mol-repr/structure/complex-visual.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/commonjs/mol-repr/structure/params.d.ts CHANGED Viewed

@@ -6,9 +6,9 @@
  */
 import { ParamDefinition as PD } from '../../mol-util/param-definition';
 import { UnitKind } from './visual/util/common';
-export declare function getUnitKindsParam(defaultValue: UnitKind[]): PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+export declare function getUnitKindsParam(defaultValue: UnitKind[]): PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
 export declare const StructureParams: {
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"atomic" | "spheres" | "gaussians">;
     includeParent: PD.BooleanParam;
 };
 export declare type StructureParams = typeof StructureParams;
@@ -89,7 +89,7 @@ export declare const StructureDirectVolumeParams: {
     renderMode: PD.Mapped<PD.NamedParams<PD.Normalize<{
         controlPoints: import("../../mol-math/linear-algebra/3d/vec2").Vec2[];
         list: {
-            kind: "interpolate" | "set";
+            kind: "set" | "interpolate";
             colors: import("../../mol-util/color/color").ColorListEntry[];
         };
     }>, "volume"> | PD.NamedParams<PD.Normalize<{