Update dependencies and fix lint issues

epam · Sep 25, 2020 · 3b2eee7 · 3b2eee7
1 parent 1331f7a
commit 3b2eee7
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Showing 36 changed files with 2,030 additions and 2,087 deletions.
diff --git a/packages/lib/demo/scripts/ui/Menu.js b/packages/lib/demo/scripts/ui/Menu.js
@@ -218,7 +218,6 @@ Menu.prototype._fillSelectionColorCombo = function (paletteID) {
   });
 };
 
-
 Menu.prototype._fillCombo = function (type, name, path, entityList) {
   const self = this;
   const frag = document.createDocumentFragment();
@@ -316,7 +315,6 @@ Menu.prototype._initReprListItemListeners = function (index) {
 
   reprList.find(`.panel:eq(${index}) input[type=checkbox]`).bootstrapSwitch();
 
-
   reprList.find(`.panel:eq(${index}) .panel-heading .btn-visible`).on('click', () => {
     reprList.find(`.panel:eq(${index}) .panel-heading .btn-visible`).hide();
     reprList.find(`.panel:eq(${index}) .panel-heading .btn-invisible`).show();
@@ -868,7 +866,6 @@ Menu.prototype._init = function () {
   self._xs = self._isXS();
   $(`${self._menuId} [data-value="${self._curPanelID}"]`).toggleClass('active');
 
-
   $(`${self._menuId} [data-toggle=miew-main-menu]`).on('click', function () {
     const state = this.getAttribute('data-state');
     if (state === 'on') {
@@ -1570,7 +1567,6 @@ function getAltLocNames(viewer) {
   return visual ? visual.getComplex().getAltLocNames() : 0;
 }
 
-
 Menu.prototype._initSelectionPanel = function () {
   const self = this;
   const selectionPanel = $(`${self._menuId} [data-panel-type=miew-menu-panel-selection]`);

diff --git a/packages/lib/demo/styles/main.scss b/packages/lib/demo/styles/main.scss
@@ -282,6 +282,7 @@ $selection-panel-row-height: 42px;
     margin-bottom: 0;
     // border-color: #aaa;
     // border-radius: 0;
+
     border: none;
     background-color: #eee;
     height: 100%;

diff --git a/packages/lib/package.json b/packages/lib/package.json
@@ -135,6 +135,7 @@
     "jquery": "3.4.1",
     "jquery.terminal": "=2.1.0",
     "jsdoc": "^3.6.3",
+    "lerna": "^3.21.0",
     "mini-css-extract-plugin": "^0.9.0",
     "mkdirp": "^1.0.3",
     "mocha": "^7.1.2",

diff --git a/packages/lib/src/ComplexVisual.js b/packages/lib/src/ComplexVisual.js
@@ -214,7 +214,6 @@ class ComplexVisual extends Visual {
     return { desc, index, status: '' };
   }
 
-
   /**
    * Get representation (not just description) by index.
    * @param {number=} index - Zero-based index, up to {@link Miew#repCount()}. Defaults to the current one.

diff --git a/packages/lib/src/ComplexVisualEdit.js b/packages/lib/src/ComplexVisualEdit.js
@@ -184,7 +184,6 @@ class ComplexComponentEditor extends ComplexEditor {
   }
 }
 
-
 class ComplexFragmentEditor extends ComplexEditor {
   constructor(complexVisual) {
     super();
@@ -379,7 +378,6 @@ class ComplexFragmentEditor extends ComplexEditor {
   }
 }
 
-
 export default {
   ComponentEditor: ComplexComponentEditor,
   FragmentEditor: ComplexFragmentEditor,

diff --git a/packages/lib/src/Miew-cli.js b/packages/lib/src/Miew-cli.js
@@ -76,7 +76,6 @@ class RepresentationMap {
   }
 }
 
-
 const representationsStorage = new RepresentationMap();
 
 function keyRemap(key) {
@@ -270,7 +269,6 @@ class CLIUtils {
 }
 // repIndexOrRepMap could be RepresentationMap or index
 
-
 const utilFunctions = new CLIUtils();
 
 function CreateObjectPair(a, b) {

diff --git a/packages/lib/src/Miew.js b/packages/lib/src/Miew.js
@@ -2255,7 +2255,6 @@ Miew.prototype._onLoad = function (dataSource, opts) {
     this._opts._objects = null;
   }
 
-
   if (dataSource.id === 'Complex') {
     const complex = dataSource;
 
@@ -2487,7 +2486,6 @@ Miew.prototype.rebuild = function () {
   Promise.all(rebuildActions).then(() => {
     self._spinner.stop();
 
-
     self._needRender = true;
 
     self._refreshTitle();

diff --git a/packages/lib/src/Visual.js b/packages/lib/src/Visual.js
@@ -28,5 +28,4 @@ class Visual extends gfxutils.RCGroup {
   }
 }
 
-
 export default Visual;
diff --git a/packages/lib/src/chem/AromaticLoopsMarker.js b/packages/lib/src/chem/AromaticLoopsMarker.js
@@ -11,7 +11,6 @@ const cAromaticAtoms = [
   // Element.ByName.S.number,
 ];
 
-
 /** Conditions for bonds:
    *   - Cross product with each subsequent bond to add is collinear and point to the same direction
    *   - Each pair of a adjacent bonds belong to not more than one cycle

diff --git a/packages/lib/src/gfx/CSS2DObject.js b/packages/lib/src/gfx/CSS2DObject.js
@@ -50,5 +50,4 @@ class CSS2DObject extends THREE.Object3D {
   }
 }
 
-
 export default CSS2DObject;
diff --git a/packages/lib/src/gfx/FrameInfo.js b/packages/lib/src/gfx/FrameInfo.js
@@ -308,7 +308,6 @@ class FrameInfo {
     return vec;
   }
 
-
   getResidues() {
     if (this._cachedResidues) {
       return this._residues;

diff --git a/packages/lib/src/gfx/Representation.js b/packages/lib/src/gfx/Representation.js
@@ -34,7 +34,6 @@ class Representation {
     this.setMode(mode);
   }
 
-
   markAtoms(complex) {
     this.count = complex.markAtoms(this.selector, 1 << this.index);
     this.needsRebuild = true;

diff --git a/packages/lib/src/gfx/VolumeMesh.js b/packages/lib/src/gfx/VolumeMesh.js
@@ -401,7 +401,6 @@ class VolumeMesh extends THREE.Mesh {
     const matrixWorldToLocal = VolumeMesh._matrixWorldToLocal;
     const clipPlane = VolumeMesh._clipPlane;
 
-
     this._updateIsoLevel();
 
     // get clip plane in local space
@@ -429,5 +428,4 @@ class VolumeMesh extends THREE.Mesh {
   }
 }
 
-
 export default VolumeMesh;
diff --git a/packages/lib/src/gfx/colorers/ConditionalColorer.js b/packages/lib/src/gfx/colorers/ConditionalColorer.js
@@ -1,7 +1,6 @@
 import Colorer from './Colorer';
 import selectors from '../../chem/selectors';
 
-
 /**
  * Create new colorer.
  *

diff --git a/packages/lib/src/gfx/geometries/ContactSurface.js b/packages/lib/src/gfx/geometries/ContactSurface.js
@@ -40,13 +40,11 @@ function AVHash(posRad, min, max, maxDistance) {
 
   const jkDim = jDim * kDim;
 
-
   /* Get cellID for cartesian x,y,z */
   const cellID = function (x, y, z) {
     return (((hashFunc(x, minX) * jDim) + hashFunc(y, minY)) * kDim) + hashFunc(z, minZ);
   };
 
-
   /* Initial building, could probably be optimized further */
   const preHash = [];
   let i;
@@ -188,7 +186,6 @@ function ContactSurface(packedArrays, boundaries, params, _indexList) {
   let atomMap = null;
   let visibilitySelector = null;
 
-
   // grid indices -> xyz coords
   let gridx;
   let gridy;
@@ -241,7 +238,6 @@ function ContactSurface(packedArrays, boundaries, params, _indexList) {
       atomMap = [];
     }
 
-
     gridx = utils.allocateTyped(Float32Array, dim[0]);
     gridy = utils.allocateTyped(Float32Array, dim[1]);
     gridz = utils.allocateTyped(Float32Array, dim[2]);
@@ -402,7 +398,6 @@ function ContactSurface(packedArrays, boundaries, params, _indexList) {
             const dx = gridx[ix] - ax;
             const d2 = dzy2 + dx * dx;
 
-
             if (d2 < ar2) {
               const w = Math.exp(-d2 * sigma2Inv);
               const cIdx = idx * 3;

diff --git a/packages/lib/src/gfx/geometries/CylinderBufferGeometry.js b/packages/lib/src/gfx/geometries/CylinderBufferGeometry.js
@@ -18,7 +18,6 @@ class CylinderBufferGeometry extends THREE.BufferGeometry {
     const thetaStart = 0;
     const thetaLength = 2 * Math.PI;
 
-
     this.type = 'CylinderBufferGeometry';
 
     this.parameters = {
@@ -108,7 +107,6 @@ class CylinderBufferGeometry extends THREE.BufferGeometry {
         normals.setXYZ(currVtxIdx, 0, 1, 0);
         uvs.setXY(currVtxIdx, 1, 1);
 
-
         const nextTVtx = startTIdx + ((fTIdx + 1) % radialSegments);
         indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, currVtxIdx, nextTVtx, lastIdx);
         currFaceIdx++;
@@ -134,7 +132,6 @@ class CylinderBufferGeometry extends THREE.BufferGeometry {
         normals.setXYZ(currVtxIdx, 0, -1, 0);
         uvs.setXY(currVtxIdx, 0, 0);
 
-
         const nextBVtx = startBIdx + ((fBIdx + 1) % radialSegments);
         indices.setXYZ(currFaceIdx * PTS_PER_TRIANGLE, nextBVtx, currVtxIdx, lastBIdx);
         currFaceIdx++;

diff --git a/packages/lib/src/gfx/geometries/IsoSurface.js b/packages/lib/src/gfx/geometries/IsoSurface.js
@@ -249,7 +249,6 @@ class IsoSurface {
       triangles[j] = new Triangle();
     }
 
-
     let appendVertex;
     const self = this;
     const positions = this._position;

diff --git a/packages/lib/src/gfx/geometries/IsosurfaceBuildNormals.js b/packages/lib/src/gfx/geometries/IsosurfaceBuildNormals.js
@@ -89,7 +89,6 @@ class IsosurfaceBuildNormals {
     } // for (i)
     // maxAtomsRefs = numAtoms * MAX_ATOMS_IN_SINGLE_VOXEL;
 
-
     this._voxelList = utils.allocateTyped(Int32Array, side3);
     const atomsList = [];
     atomsList.length = maxAtomsRefs;

diff --git a/packages/lib/src/gfx/geometries/RaycastableBufferGeometry.js b/packages/lib/src/gfx/geometries/RaycastableBufferGeometry.js
@@ -15,17 +15,14 @@ class RaycastableBufferGeometry extends THREE.BufferGeometry {
 
   static _vC = new THREE.Vector3();
 
-
   static _uvA = new THREE.Vector2();
 
   static _uvB = new THREE.Vector2();
 
   static _uvC = new THREE.Vector2();
 
-
   static _barycoord = new THREE.Vector3();
 
-
   static _intersectionPoint = new THREE.Vector3();
 
   uvIntersection(point, p1, p2, p3, uv1, uv2, uv3) {

diff --git a/packages/lib/src/gfx/geometries/SSIsosurfaceGeometry.js b/packages/lib/src/gfx/geometries/SSIsosurfaceGeometry.js
@@ -314,7 +314,6 @@ class SSIsosurfaceGeometry extends IsoSurfaceGeometry {
           cube.pointsValuesLinear[indPointValues + 6 * 3 + 1] += vCellStep.y;
           cube.pointsValuesLinear[indPointValues + 7 * 3 + 1] += vCellStep.y;
 
-
           // now current cell has intersections (from -x to +x) on some cube edges
           const indValues = indPointValues + 24;
           for (let i = 0; i < cNumVerts; ++i) {
@@ -437,7 +436,6 @@ class SSIsosurfaceGeometry extends IsoSurfaceGeometry {
     return atomT[letter * 2];
   }
 
-
   /**
    * Calculate values for marching cube grid points
    * positive values are outside sphere, negative - is inside

diff --git a/packages/lib/src/gfx/geometries/Simple2CCylindersGeometry.js b/packages/lib/src/gfx/geometries/Simple2CCylindersGeometry.js
@@ -8,7 +8,6 @@ const centerPos = new THREE.Vector3();
 const tmpVector = new THREE.Vector3();
 const normMtx = new THREE.Matrix3();
 
-
 class Simple2CCylindersGeometry extends ChunkedObjectsGeometry {
   constructor(instanceCount, polyComplexity) {
     const cylGeometry = new THREE.CylinderBufferGeometry(1, 1, 1.0, Math.max(3, polyComplexity), 2, true);
@@ -20,7 +19,6 @@ class Simple2CCylindersGeometry extends ChunkedObjectsGeometry {
     this._tmpVector = utils.allocateTyped(Float32Array, chunkSize * VEC_SIZE);
   }
 
-
   setItem(itemIdx, botPos, topPos, itemRad) {
     const chunkSize = this._chunkSize;
     const firstOffset = chunkSize * 2 * itemIdx * VEC_SIZE;
@@ -63,7 +61,6 @@ class Simple2CCylindersGeometry extends ChunkedObjectsGeometry {
     this._normals.set(tmpArray, secondOffset);
   }
 
-
   setColor(itemIdx, colorVal1, colorVal2) {
     const first = 2 * itemIdx;
     super.setColor(first, colorVal1);

diff --git a/packages/lib/src/gfx/geometries/ThickLinesGeometry.js b/packages/lib/src/gfx/geometries/ThickLinesGeometry.js
@@ -167,5 +167,4 @@ class ThickLinesGeometry extends THREE.BufferGeometry {
   }
 }
 
-
 export default ThickLinesGeometry;
diff --git a/packages/lib/src/gfx/geometries/TwoColorLinesGeometry.js b/packages/lib/src/gfx/geometries/TwoColorLinesGeometry.js
@@ -5,7 +5,6 @@ import Simple2CCylindersGeometry from './Simple2CCylindersGeometry';
 const COLLISION_RAD = 0.3;
 const tmpVector = new THREE.Vector3();
 
-
 class TwoColorLinesGeometry extends LinesGeometry {
   constructor(segmentsCount) {
     super(segmentsCount * 2);

diff --git a/packages/lib/src/gfx/gfxutils.js b/packages/lib/src/gfx/gfxutils.js
@@ -67,7 +67,6 @@ THREE.WebGLRenderer.prototype.renderScreenQuad = (function () {
   const _camera = new THREE.OrthographicCamera(-0.5, 0.5, 0.5, -0.5, -10000, 10000);
   _camera.position.z = 100;
 
-
   return function (material) {
     _quad.material = material;
     this.render(_scene, _camera);
@@ -122,7 +121,6 @@ THREE.WebGLRenderer.prototype.renderScreenQuadFromTex = (function () {
     transparent: true,
   });
 
-
   return function (srcTex, opacity) {
     _material.uniforms.srcTex.value = srcTex;
     _material.transparent = (opacity < 1.0);
@@ -137,7 +135,6 @@ THREE.WebGLRenderer.prototype.renderScreenQuadFromTexWithDistortion = (function
     fragmentShader: fragmentScreenQuadFromTexWithDistortion,
   });
 
-
   return function (srcTex, coef) {
     _material.uniforms.srcTex.value = srcTex;
     _material.uniforms.coef.value = coef;

diff --git a/packages/lib/src/gfx/modes/Mode.js b/packages/lib/src/gfx/modes/Mode.js
@@ -30,7 +30,6 @@ class Mode {
     this.opts = _.merge(utils.deriveDeep(this.settings.now.modes[this.id], true), opts);
   }
 
-
   /**
    * Get mode identification, probably with options.
    * @returns {string|Array} Mode identifier string ({@link Mode#id}) or two-element array containing both mode

diff --git a/packages/lib/src/gfx/modes/groups/AromaticGroup.js b/packages/lib/src/gfx/modes/groups/AromaticGroup.js
@@ -35,7 +35,6 @@ class AromaticGroup extends AtomsGroup {
       currVector.subVectors(currPos, center);
       const upDir = currVector.clone().cross(prevVector).normalize();
 
-
       for (; i < n; ++i) {
         const omega = prevVector.angleTo(currVector);
         tmpDir[i] = _slerp(omega, prevVector, currVector, 0.5).normalize();

diff --git a/packages/lib/src/gfx/palettes/Palette.js b/packages/lib/src/gfx/palettes/Palette.js
@@ -18,7 +18,6 @@ function lerpColor(c1, c2, alpha) {
   return (r << 16) | (g << 8) | b;
 }
 
-
 class Palette {
   constructor(name, id) {
     this.name = name || 'Custom';
@@ -283,7 +282,6 @@ _.assign(Palette.prototype, {
   },
 });
 
-
 const { namedColorsArray, namedColors } = Palette.prototype;
 
 for (let i = 0, { length } = namedColorsArray; i < length; ++i) {

diff --git a/packages/lib/src/io/parsers/CCP4Parser.js b/packages/lib/src/io/parsers/CCP4Parser.js
@@ -63,7 +63,6 @@ class Ccp4Model extends VolumeModel {
     xyz2crs[crs2xyz[2] - 1] = 2; // section
   }
 
-
   _setOrigins() {
     const [xaxis, yaxis, zaxis] = this._getAxis();
     this._setAxisIndices();

diff --git a/packages/lib/src/io/parsers/CIFParser.js b/packages/lib/src/io/parsers/CIFParser.js
@@ -186,7 +186,6 @@ class CIFParser extends Parser {
     return complex;
   }
 
-
   /**
    * Extract metadata
    * @param complex structure to fill
@@ -470,7 +469,6 @@ class CIFParser extends Parser {
     }
   }
 
-
   /**
    * Extract biological assemblies information from CIF structure and fill complex
    * @param {Complex} complex