lore-engine - npm Package Compare versions

Comparing version 1.0.0 to 1.0.1

gulpfile.js

@@ -23,2 +23,4 @@ var fs = require('fs');
     'src/Core/Effect.js',
+    'src/Core/Tree.js',
+    'src/Core/Graph.js',
     'src/Controls/ControlsBase.js',
@@ -25,0 +27,0 @@ 'src/Controls/OrbitalControls.js',

package.json

 {
   "name": "lore-engine",
-  "version": "1.0.0",
+  "version": "1.0.1",
   "description": "A WebGL based 3D data visualization engine.",
@@ -12,9 +12,9 @@ "main": "./dist/lore.js",
   },
-  "repository": "git+https://github.com/daenuprobst/smilesDrawer.git",
+  "repository": "git+https://github.com/reymond-group/lore.git",
   "author": "Daniel Probst, Reymond Group, University of Bern",
   "license": "MIT",
   "bugs": {
-    "url": "https://github.com/daenuprobst/lore/issues"
+    "url": "https://github.com/reymond-group/lore/issues"
   },
-  "homepage": "https://github.com/daenuprobst/lore#readme",
+  "homepage": "https://github.com/reymond-group/lore#readme",
   "dependencies": {},
@@ -21,0 +21,0 @@ "devDependencies": {

README.md

 ![Lore](https://github.com/reymond-group/lore/blob/master/logo.png?raw=true)
+
+If you use this code or application, please cite the original paper published by Bioinformatics: [10.1093/bioinformatics/btx760](http://dx.doi.org/10.1093/bioinformatics/btx760)
+
 # Lore
@@ -17,3 +20,2 @@ Current Version: 1.0.0 ([Starbreaker](https://www.youtube.com/watch?v=nr8pgN195Zw))
 
-
 Browsing the SureChEMBL database (containing > 12 million datapoints): [Faerun](http://faerun.gdb.tools).
@@ -23,2 +25,9 @@
 
+
+### Installation
+You can either download or clone this repository and use the JavaScript file in the dist folder, or you can use yarn to install the package lore-engine:
+```bash
+yarn add lore-engine
+```
+
 ### Building Lore
@@ -25,0 +34,0 @@ If you decide not to use the ready-to-go scripts in `dist`, you can (edit and) build the project by running:

src/Cameras/CameraBase.js

@@ -81,2 +81,3 @@ /**
         viewMatrix.invert();
+        console.log(viewMatrix.toString());
         this.viewMatrix = viewMatrix;
@@ -83,0 +84,0 @@ this.isViewMatrixStale = true;

src/Cameras/OrthographicCamera.js

@@ -51,3 +51,3 @@ /**
         let bottom = y - height;
-
+        
         this.projectionMatrix.setOrthographic(left, right, top, bottom, this.near, this.far);
@@ -54,0 +54,0 @@ this.isProjectionMatrixStale = true;

src/Cameras/PerspectiveCamera.js

@@ -14,2 +14,7 @@ /** A class representing an perspective camera. */
         this.type = 'Lore.PerspectiveCamera';
+
+        // TODO: There shouldn't be a zoom here. The problem is, that the orbital controls
+        // and also the point helper and zoom rely on it. However, for the perspective camera,
+        // zooming is achieved by adjusting the fov. 
+        this.zoom = 1.0;
         this.fov = fov;
@@ -39,4 +44,4 @@ this.aspect = aspect;
     updateViewport(width, height) {
-        this.aspect = width / height;
+      this.aspect = width / height;
     }
 }

src/Controls/OrbitalControls.js

@@ -34,3 +34,3 @@ /**
         this.scale = 0.95;
-
+        
         this.camera.position = new Lore.Vector3f(radius, radius, radius);
@@ -37,0 +37,0 @@ this.camera.updateProjectionMatrix();

src/Core/Color.js

@@ -124,2 +124,19 @@ /**
     /**
+     * Converts HSL to RGB.
+     * 
+     * @static
+     * @param {Number} h The hue component.
+     * @param {Number} s The saturation component.
+     * @param {Number} l The lightness component.
+     * @returns {String} A hex string representing the color (#RRGGBB).
+     */
+    static hslToHex(h, s, l) {
+      let [r, g, b] = Lore.Color.hslToRgb(h, s, l);
+      return '#' + [Math.round(r * 255), Math.round(g * 255), Math.round(b * 255)].map(e => {
+        const hex = e.toString(16);
+        return hex.length === 1 ? '0' + hex : hex
+      }).join('')
+    }
+
+    /**
      * Converts RGB to HSL.
@@ -126,0 +143,0 @@ *

src/Core/Geometry.js

@@ -13,106 +13,106 @@ /**
 Lore.Geometry = class Geometry extends Lore.Node {
-    constructor(name, gl, shader) {
-        super();
+  constructor(name, gl, shader) {
+      super();
 
-        this.type = 'Lore.Geometry';
-        this.name = name;
-        this.gl = gl;
-        this.shader = shader;
-        this.attributes = {};
-        this.drawMode = this.gl.POINTS;
-        this.isVisible = true;
-    }
+      this.type = 'Lore.Geometry';
+      this.name = name;
+      this.gl = gl;
+      this.shader = shader;
+      this.attributes = {};
+      this.drawMode = this.gl.POINTS;
+      this.isVisible = true;
+  }
 
-    addAttribute(name, data, length) {
-        this.attributes[name] = new Lore.Attribute(data, length, name);
-        this.attributes[name].createBuffer(this.gl, this.shader.program);
+  addAttribute(name, data, length) {
+      this.attributes[name] = new Lore.Attribute(data, length, name);
+      this.attributes[name].createBuffer(this.gl, this.shader.program);
 
-        return this;
-    }
+      return this;
+  }
 
-    updateAttribute(name, data) {
-        if (data) {
-            this.attributes[name].data = data;
-        }
+  updateAttribute(name, data) {
+      if (data) {
+          this.attributes[name].data = data;
+      }
 
-        this.attributes[name].update(this.gl);
+      this.attributes[name].update(this.gl);
 
-        return this;
-    }
+      return this;
+  }
 
-    getAttribute(name) {
-        return this.attributes[name];
-    }
+  getAttribute(name) {
+      return this.attributes[name];
+  }
 
-    removeAttribute(name) {
-        delete this.attributes[name];
+  removeAttribute(name) {
+      delete this.attributes[name];
 
-        return this;
-    }
+      return this;
+  }
 
-    setMode(drawMode) {
-        switch (drawMode) {
-        case Lore.DrawModes.points:
-            this.drawMode = this.gl.POINTS;
-            break;
-        case Lore.DrawModes.lines:
-            this.drawMode = this.gl.LINES;
-            break;
-        case Lore.DrawModes.lineStrip:
-            this.drawMode = this.gl.LINE_STRIP;
-            break;
-        case Lore.DrawModes.lineLoop:
-            this.drawMode = this.gl.LINE_LOOP;
-            break;
-        case Lore.DrawModes.triangles:
-            this.drawMode = this.gl.TRIANGLES;
-            break;
-        case Lore.DrawModes.triangleStrip:
-            this.drawMode = this.gl.TRIANGLE_STRIP;
-            break;
-        case Lore.DrawModes.triangleFan:
-            this.drawMode = this.gl.TRIANGLE_FAN;
-            break;
-        }
+  setMode(drawMode) {
+      switch (drawMode) {
+      case Lore.DrawModes.points:
+          this.drawMode = this.gl.POINTS;
+          break;
+      case Lore.DrawModes.lines:
+          this.drawMode = this.gl.LINES;
+          break;
+      case Lore.DrawModes.lineStrip:
+          this.drawMode = this.gl.LINE_STRIP;
+          break;
+      case Lore.DrawModes.lineLoop:
+          this.drawMode = this.gl.LINE_LOOP;
+          break;
+      case Lore.DrawModes.triangles:
+          this.drawMode = this.gl.TRIANGLES;
+          break;
+      case Lore.DrawModes.triangleStrip:
+          this.drawMode = this.gl.TRIANGLE_STRIP;
+          break;
+      case Lore.DrawModes.triangleFan:
+          this.drawMode = this.gl.TRIANGLE_FAN;
+          break;
+      }
 
-        return this;
-    }
+      return this;
+  }
 
-    size() {
-        // Is this ok? All attributes should have the same length ...
-        if (Object.keys(this.attributes).length > 0) {
-            return this.attributes[Object.keys(this.attributes)[0]].size;
-        }
+  size() {
+      // Is this ok? All attributes should have the same length ...
+      if (Object.keys(this.attributes).length > 0) {
+          return this.attributes[Object.keys(this.attributes)[0]].size;
+      }
 
-        return 0;
-    }
+      return 0;
+  }
 
-    draw(renderer) {
-        if (!this.isVisible) return;
+  draw(renderer) {
+      if (!this.isVisible) return;
 
-        for (let prop in this.attributes)
-            if (this.attributes[prop].stale) this.attributes[prop].update(this.gl);
+      for (let prop in this.attributes)
+          if (this.attributes[prop].stale) this.attributes[prop].update(this.gl);
 
-        this.shader.use();
+      this.shader.use();
 
-        // Update the modelView and projection matrices
-        if (renderer.camera.isProjectionMatrixStale) {
-            this.shader.uniforms.projectionMatrix.setValue(renderer.camera.getProjectionMatrix());
-        }
+      // Update the modelView and projection matrices
+      if (renderer.camera.isProjectionMatrixStale) {
+          this.shader.uniforms.projectionMatrix.setValue(renderer.camera.getProjectionMatrix());
+      }
 
-        if (renderer.camera.isViewMatrixStale) {
-            let modelViewMatrix = Lore.Matrix4f.multiply(renderer.camera.viewMatrix, this.modelMatrix);
-            this.shader.uniforms.modelViewMatrix.setValue(modelViewMatrix.entries);
-        }
+      if (renderer.camera.isViewMatrixStale) {
+          let modelViewMatrix = Lore.Matrix4f.multiply(renderer.camera.viewMatrix, this.modelMatrix);
+          this.shader.uniforms.modelViewMatrix.setValue(modelViewMatrix.entries);
+      }
 
-        this.shader.updateUniforms();
+      this.shader.updateUniforms();
 
-        // How exactly does the binding work??
-        // What will happen if I want to draw a second geometry?
-        for (let prop in this.attributes) {
-            this.attributes[prop].bind(this.gl);
-        }
+      // How exactly does the binding work??
+      // What will happen if I want to draw a second geometry?
+      for (let prop in this.attributes) {
+          this.attributes[prop].bind(this.gl);
+      }
 
-        this.gl.drawArrays(this.drawMode, 0, this.size());
-    }
+      this.gl.drawArrays(this.drawMode, 0, this.size());
+  }
 }

src/Core/Renderer.js

@@ -36,3 +36,3 @@ /**
         this.camera = new Lore.OrthographicCamera(this.getWidth() / -2, this.getWidth() / 2, this.getHeight() / 2, this.getHeight() / -2);
-        // this.camera = new Lore.PerspectiveCamera(45.0, this.getWidth() / this.getHeight());
+        // this.camera = new Lore.PerspectiveCamera(25.0, this.getWidth() / this.getHeight());
 
@@ -39,0 +39,0 @@ this.geometries = {};

src/Lore.js

@@ -55,6 +55,2 @@ /**
     
-    // Init UI
-    // var ui = new Lore.UI(canvas);
-    
-    // Start the 3D stuff
     var cc = Lore.Color.fromHex(this.opts.clearColor);
@@ -61,0 +57,0 @@

src/Math/ProjectionMatrix.js

@@ -56,3 +56,3 @@ /** A class representing a projection matrix */
         let range = near - far;
-        let tanHalfFov = Math.tan(Lore.Utils.DEG2RAD * fov / 2.0);
+        let tanHalfFov = Math.tan(Lore.Utils.DEG2RAD * 0.5 * fov);
         
@@ -65,2 +65,5 @@ let top = near * tanHalfFov;
         let bottom = top - height;
+        // let bottom = -top;
+        // let right = top * aspect;
+        // let left = -right;
 
@@ -72,3 +75,3 @@ let x = 2.0 * near / (right - left);
         let b = (top + bottom) / (top - bottom);
-        let c = (far + near) / (far - near);
+        let c = -(far + near) / (far - near);
         let d = -2 * far * near / (far - near);
@@ -75,0 +78,0 @@

src/Math/Statistics.js

 /** A helper class containing statistics methods. */
 Lore.Statistics = class Statistics {
     /**
+     * Transposes an array of arrays (2d array).
+     
+     * @param {Array} arr The 2d array to be transposed.
+     * @returns {Array} The transpose of the 2d array.
+     */
+    static transpose2dArray(arr) {
+      return arr[0].map((col, i) => arr.map(row => row[i]));
+    }
+
+    /**
      * Returns a normally distributed (pseudo) random number.
@@ -5,0 +15,0 @@ *

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Improved metrics

Total package byte prevSize

43895620

increased by1.72%

Number of package files

176

increased by9.32%

Lines of code

32262

increased by79.1%

Number of lines in readme file

126

increased by7.69%

No dependency changes