change "transparency" to "opacity"

index.html

@@ -304,7 +304,7 @@ <h1></h1>
         slide: function(event, ui) {
 
           pv.forEach(function(go) {
-            go.setTransparency(1.0 - ui.value/100. , go);
+            go.setOpacity(1.0 - ui.value/100. , go);
           });
           pv.requestRedraw();
         }

src/scene.js

@@ -351,12 +351,12 @@ LineGeom.prototype.colorBy = function(colorFunc, view) {
   console.timeEnd('LineGeom.colorBy');
 };
 
-LineGeom.prototype.setTransparency = function(val, view) {
-  console.time('LineGeom.setTransparency');
+LineGeom.prototype.setOpacity = function(val, view) {
+  console.time('LineGeom.setOpacity');
   this._ready = false;
   view = view || this.structure();
-  this._vertAssoc.setTransparency(val, view);
-  console.timeEnd('LineGeom.setTransparency');
+  this._vertAssoc.setOpacity(val, view);
+  console.timeEnd('LineGeom.setOpacity');
 };
 
 
@@ -369,7 +369,7 @@ LineGeom.prototype.setTransparency = function(val, view) {
 //
 // the vertex data is stored in the following format;
 //
-// Px Py Pz Nx Ny Nz Cr Cg Cb Id
+// Px Py Pz Nx Ny Nz Cr Cg Cb Ca Id
 //
 // , where P is the position, N the normal and C the color information
 // of the vertex.
@@ -485,12 +485,12 @@ MeshGeom.prototype.colorBy = function(colorFunc, view) {
   console.timeEnd('MeshGeom.colorBy');
 };
 
-MeshGeom.prototype.setTransparency = function(val, view) {
-  console.time('MeshGeom.setTransparency');
+MeshGeom.prototype.setOpacity = function(val, view) {
+  console.time('MeshGeom.setOpacity');
   this._ready = false;
   view = view || this.structure();
-  this._vertAssoc.setTransparency(val , view);
-  console.timeEnd('MeshGeom.setTransparency');
+  this._vertAssoc.setOpacity(val , view);
+  console.timeEnd('MeshGeom.setOpacity');
 };
 
 MeshGeom.prototype._drawVertArrays = function(cam, shader, indexedVertArrays, 

src/vert-assoc.js

@@ -76,13 +76,13 @@ AtomVertexAssoc.prototype.recolor = function(colorOp, view) {
   }
 };
 
-AtomVertexAssoc.prototype.setTransparency = function( val, view) {
+AtomVertexAssoc.prototype.setOpacity = function( val, view) {
   // apply the color to the actual interleaved vertex array.
   for (var i = 0; i < this._assocs.length; ++i) {
     var assoc = this._assocs[i];
     var va = assoc.vertexArray;
     for (var j = assoc.vertStart ; j < assoc.vertEnd; ++j) {
-      va.setTransparency(j, val);
+      va.setOpacity(j, val);
     }
   }
 };
@@ -159,13 +159,13 @@ TraceVertexAssoc.prototype.recolor = function(colorOp, view) {
 };
 
 
-TraceVertexAssoc.prototype.setTransparency = function( val, view) {
+TraceVertexAssoc.prototype.setOpacity = function( val, view) {
   // store the color in the actual interleaved vertex array.
   for (i = 0; i < this._assocs.length; ++i) {
     var assoc = this._assocs[i];
     var va = assoc.vertexArray;
     for (j = assoc.vertStart ; j < assoc.vertEnd; ++j) {
-      va.setTransparency(j, val);
+      va.setOpacity(j, val);
     }
   }
 

src/vertex-array-base.js

@@ -40,7 +40,7 @@ VertexArrayBase.prototype.setColor = function(index, r, g, b, a) {
   this._ready = false;
 };
 
-VertexArrayBase.prototype.setTransparency = function(index, a) {
+VertexArrayBase.prototype.setOpacity = function(index, a) {
   var colorStart = index * this._FLOATS_PER_VERT + this._COLOR_OFFSET;
   this._vertData[colorStart + 3] = a;
   this._ready = false;