Merge branch 'master' of https://github.com/molstar/molstar into pick-atom

.eslintrc.json

@@ -54,7 +54,8 @@
         "no-multi-spaces": "error",
         "block-spacing": "error",
         "keyword-spacing": "off",
-        "space-before-blocks": "error"
+        "space-before-blocks": "error",
+        "semi-spacing": "error"
     },
     "overrides": [
         {

CHANGELOG.md

@@ -20,6 +20,7 @@ Note that since we don't clearly distinguish between a public and private interf
 - Add ``preferAtoms`` option to SelectLoci/HighlightLoci behaviors
 - Make the implicit atoms of bond visuals pickable
     - Add ``preferAtomPixelPadding`` to Canvas3dInteractionHelper
+- Add ``markerPriority`` option to Renderer (useful in combination with edges of marking pass)
 
 ## [v2.3.0] - 2021-09-06
 

src/mol-gl/renderable/schema.ts

@@ -161,6 +161,7 @@ export const GlobalUniformSchema = {
     uSelectColor: UniformSpec('v3'),
     uHighlightStrength: UniformSpec('f'),
     uSelectStrength: UniformSpec('f'),
+    uMarkerPriority: UniformSpec('i'),
 
     uXrayEdgeFalloff: UniformSpec('f'),
 

src/mol-gl/renderer.ts

@@ -81,6 +81,7 @@ export const RendererParams = {
     selectColor: PD.Color(Color.fromNormalizedRgb(0.2, 1.0, 0.1)),
     highlightStrength: PD.Numeric(0.7, { min: 0.0, max: 1.0, step: 0.1 }),
     selectStrength: PD.Numeric(0.7, { min: 0.0, max: 1.0, step: 0.1 }),
+    markerPriority: PD.Select(1, [[1, 'Highlight'], [2, 'Select']]),
 
     xrayEdgeFalloff: PD.Numeric(1, { min: 0.0, max: 3.0, step: 0.1 }),
 
@@ -274,6 +275,7 @@ namespace Renderer {
             uSelectColor: ValueCell.create(Color.toVec3Normalized(Vec3(), p.selectColor)),
             uHighlightStrength: ValueCell.create(p.highlightStrength),
             uSelectStrength: ValueCell.create(p.selectStrength),
+            uMarkerPriority: ValueCell.create(p.markerPriority),
 
             uXrayEdgeFalloff: ValueCell.create(p.xrayEdgeFalloff),
         };
@@ -670,6 +672,10 @@ namespace Renderer {
                     p.selectStrength = props.selectStrength;
                     ValueCell.update(globalUniforms.uSelectStrength, p.selectStrength);
                 }
+                if (props.markerPriority !== undefined && props.markerPriority !== p.markerPriority) {
+                    p.markerPriority = props.markerPriority;
+                    ValueCell.update(globalUniforms.uMarkerPriority, p.markerPriority);
+                }
 
                 if (props.xrayEdgeFalloff !== undefined && props.xrayEdgeFalloff !== p.xrayEdgeFalloff) {
                     p.xrayEdgeFalloff = props.xrayEdgeFalloff;

src/mol-gl/shader/chunks/apply-marker-color.glsl.ts

@@ -1,6 +1,6 @@
 export const apply_marker_color = `
-if (marker > 0.1) {
-    if (intMod(marker, 2.0) > 0.1) {
+if (marker > 0.0) {
+    if ((uMarkerPriority == 1 && marker != 2.0) || (uMarkerPriority != 1 && marker == 1.0)) {
         gl_FragColor.rgb = mix(gl_FragColor.rgb, uHighlightColor, uHighlightStrength);
         gl_FragColor.a = max(gl_FragColor.a, uHighlightStrength * 0.002); // for direct-volume rendering
     } else {

src/mol-gl/shader/chunks/common-frag-params.glsl.ts

@@ -23,6 +23,7 @@ uniform vec3 uHighlightColor;
 uniform vec3 uSelectColor;
 uniform float uHighlightStrength;
 uniform float uSelectStrength;
+uniform int uMarkerPriority;
 
 #if defined(dMarkerType_uniform)
     uniform float uMarker;

src/mol-math/linear-algebra/tensor.ts

@@ -109,7 +109,10 @@ export namespace Tensor {
                 set: (t, d, x) => t[d] = x,
                 add: (t, d, x) => t[d] += x,
                 dataOffset: (d) => d,
-                getCoords: (o, c) => { c[0] = o; return c as number[]; }
+                getCoords: (o, c) => {
+                    c[0] = o;
+                    return c as number[];
+                }
             };
             case 2: {
                 // column major
@@ -120,7 +123,11 @@ export namespace Tensor {
                         set: (t, i, j, x) => t[j * rows + i] = x,
                         add: (t, i, j, x) => t[j * rows + i] += x,
                         dataOffset: (i, j) => j * rows + i,
-                        getCoords: (o, c) => { c[0] = o % rows; c[1] = Math.floor(o / rows) ; return c as number[]; }
+                        getCoords: (o, c) => {
+                            c[0] = o % rows;
+                            c[1] = Math.floor(o / rows);
+                            return c as number[];
+                        }
                     };
                 }
                 if (ao[0] === 1 && ao[1] === 0) {
@@ -130,7 +137,11 @@ export namespace Tensor {
                         set: (t, i, j, x) => t[i * cols + j] = x,
                         add: (t, i, j, x) => t[i * cols + j] += x,
                         dataOffset: (i, j) => i * cols + j,
-                        getCoords: (o, c) => { c[0] = Math.floor(o / cols); c[1] = o % cols; return c as number[]; }
+                        getCoords: (o, c) => {
+                            c[0] = Math.floor(o / cols);
+                            c[1] = o % cols;
+                            return c as number[];
+                        }
                     };
                 }
                 throw new Error('bad axis order');

src/mol-model-formats/structure/pdb/secondary-structure.ts

@@ -102,7 +102,7 @@ export function parseHelix(lines: Tokens, lineStart: number, lineEnd: number): C
     const beg_auth_comp_id = CifField.ofStrings(helices.map(h => h.initResName));
 
     const end_auth_asym_id = CifField.ofStrings(helices.map(h => h.endChainID));
-    const end_auth_comp_id = CifField.ofStrings(helices.map(h => h.endResName));;
+    const end_auth_comp_id = CifField.ofStrings(helices.map(h => h.endResName));
 
     const struct_conf: CifCategory.Fields<mmCIF_Schema['struct_conf']> = {
         beg_label_asym_id: beg_auth_asym_id,

src/mol-model-props/computed/helix-orientation/helix-orientation.ts

@@ -127,7 +127,8 @@ export function calcHelixOrientation(model: Model): HelixOrientation {
         Vec3.fromArray(v2, centers, e3 - 6);
         Vec3.normalize(axis, Vec3.sub(axis, v1, v2));
         const eI = traceElementIndex[e];
-        Vec3.set(a1, x[eI], y[eI], z[eI]);Vec3.copy(vt, a1);
+        Vec3.set(a1, x[eI], y[eI], z[eI]);
+        Vec3.copy(vt, a1);
         Vec3.projectPointOnVector(vt, vt, axis, v1);
         Vec3.toArray(vt, centers, e3);
     }

src/mol-model/structure/structure/unit.ts

@@ -369,7 +369,7 @@ namespace Unit {
         readonly props: CoarseProperties;
 
         getChild(elements: StructureElement.Set): Unit {
-            if (elements.length === this.elements.length) return this as any as Unit /** lets call this an ugly temporary hack */;
+            if (elements.length === this.elements.length) return this as any as Unit; // lets call this an ugly temporary hack
             return createCoarse(this.id, this.invariantId, this.chainGroupId, this.traits, this.model, this.kind, elements, this.conformation, CoarseProperties());
         }
 
@@ -465,7 +465,7 @@ namespace Unit {
     export class Gaussians extends Coarse<Kind.Gaussians, CoarseGaussianConformation> { }
 
     function createCoarse<K extends Kind.Gaussians | Kind.Spheres>(id: number, invariantId: number, chainGroupId: number, traits: Traits, model: Model, kind: K, elements: StructureElement.Set, conformation: SymmetryOperator.ArrayMapping<ElementIndex>, props: CoarseProperties): K extends Kind.Spheres ? Spheres : Gaussians {
-        return new Coarse(id, invariantId, chainGroupId, traits, model, kind, elements, conformation, props) as any /** lets call this an ugly temporary hack */;
+        return new Coarse(id, invariantId, chainGroupId, traits, model, kind, elements, conformation, props) as any; // lets call this an ugly temporary hack
     }
 
     export function areSameChainOperatorGroup(a: Unit, b: Unit) {

src/mol-plugin-ui/controls/line-graph/line-graph-component.tsx

@@ -207,7 +207,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
 
         const updatedPoint = this.unNormalizePoint(Vec2.create(this.updatedX, this.updatedY));
         const points = this.state.points.filter((_, i) => i !== selected[0]);
-        points.push(updatedPoint);;
+        points.push(updatedPoint);
         points.sort((a, b) => {
             if (a[0] === b[0]) {
                 if (a[0] === 0) {
@@ -372,7 +372,7 @@ export class LineGraphComponent extends React.Component<any, LineGraphComponentS
         const data = points;
         const size = data.length;
 
-        for (let i = 0; i < size - 1;i++) {
+        for (let i = 0; i < size - 1; i++) {
             const x1 = data[i][0];
             const y1 = data[i][1];
             const x2 = data[i + 1][0];

src/mol-plugin-ui/sequence/sequence.tsx

@@ -153,7 +153,11 @@ export class Sequence<P extends SequenceProps> extends PluginUIComponent<P> {
     private getBackgroundColor(marker: number) {
         // TODO: make marker color configurable
         if (typeof marker === 'undefined') console.error('unexpected marker value');
-        return marker === 0 ? '' : marker % 2 === 0 ? 'rgb(51, 255, 25)' /* selected */ : 'rgb(255, 102, 153)' /* highlighted */;
+        return marker === 0
+            ? ''
+            : marker % 2 === 0
+                ? 'rgb(51, 255, 25)' // selected
+                : 'rgb(255, 102, 153)'; // highlighted
     }
 
     private getResidueClass(seqIdx: number, label: string) {

src/mol-util/marker-action.ts

@@ -68,11 +68,19 @@ export function applyMarkerAction(array: Uint8Array, set: OrderedSet, action: Ma
     if (Interval.is(set)) {
         const start = Interval.start(set);
         const end = Interval.end(set);
-        const view = new Uint32Array(array.buffer, 0, array.buffer.byteLength >> 2);
-
         const viewStart = (start + 3) >> 2;
         const viewEnd = viewStart + ((end - 4 * viewStart) >> 2);
 
+        if (viewEnd <= viewStart) {
+            // avoid edge cases with overlapping front/end intervals
+            for (let i = start; i < end; ++i) {
+                applyMarkerActionAtPosition(array, i, action);
+            }
+            return true;
+        }
+
+        const view = new Uint32Array(array.buffer, 0, array.buffer.byteLength >> 2);
+
         const frontStart = start;
         const frontEnd = Math.min(4 * viewStart, end);
         const backStart = Math.max(start, 4 * viewEnd);

src/mol-util/zip/bin.ts

@@ -92,7 +92,7 @@ export function sizeUTF8(str: string) {
     for (let ci = 0; ci < strl; ci++) {
         const code = str.charCodeAt(ci);
         if ((code & (0xffffffff - (1 << 7) + 1)) === 0) {
-            i++ ;
+            i++;
         } else if ((code & (0xffffffff - (1 << 11) + 1)) === 0) {
             i += 2;
         } else if ((code & (0xffffffff - (1 << 16) + 1)) === 0) {

src/servers/volume/config.ts

@@ -197,7 +197,7 @@ export function configureLocal() {
         description: VOLUME_SERVER_HEADER
     });
     parser.add_argument('--jobs', { help: `Path to a JSON file with job specification.`, required: false });
-    parser.add_argument('--jobsTemplate', { help: 'Print example template for jobs.json and exit.', required: false, nargs: 0 });;
+    parser.add_argument('--jobsTemplate', { help: 'Print example template for jobs.json and exit.', required: false, nargs: 0 });
     addJsonConfigArgs(parser);
     addLimitsArgs(parser);