don't overwrite alpha channel when setting selection

select.js

@@ -30,7 +30,7 @@ viewer.options('selectionColor', '#f00');
 
 pv.io.fetchPdb('/pdbs/1crn.pdb', function(s) {
   viewer.on('viewerReady', function() {
-    var go = viewer.lineTrace('crambin', s, { showRelated: '1'});
+    var go = viewer.cartoon('crambin', s, { showRelated: '1'});
     go.setSelection(go.select({rnumRange : [15,20]}));
     viewer.autoZoom();
   });

src/geom.js

@@ -280,13 +280,33 @@ var buildRotation = (function() {
 ;
 })();
 
+// linearly interpolates the array of values and returns it as an Float32Array
+function interpolateScalars(values, num) {
+  var out = new Float32Array(num*(values.length-1) + 1);
+  var index = 0;
+  var bf = 0.0, af = 0.0;
+  var delta = 1/num;
+  for (var i = 0; i < values.length-1; ++i) {
+    bf = values[i];
+    af = values[i + 1];
+    for (var j = 0; j < num; ++j) {
+      var t = delta * j;
+      out[index+0] = bf*(1-t)+af*t;
+      index+=1;
+    }
+  }
+  out[index+0] = af;
+  return out;
+}
+
 return {
   signedAngle : signedAngle,
   axisRotation : axisRotation,
   ortho : ortho,
   diagonalizer : diagonalizer,
   catmullRomSpline : catmullRomSpline,
   cubicHermiteInterpolate : cubicHermiteInterpolate,
+  interpolateScalars : interpolateScalars,
   catmullRomSplineNumPoints : catmullRomSplineNumPoints,
   Sphere : Sphere,
   buildRotation : buildRotation

src/gfx/vert-assoc.js

@@ -19,7 +19,7 @@
 // DEALINGS IN THE SOFTWARE.
 
 define(
-  ['../color'], function(color) {
+  ['../color', '../geom'], function(color, geom) {
 
 "use strict";
 
@@ -226,32 +226,32 @@ TraceVertexAssoc.prototype = {
   },
 
   setSelection : function(view) {
-    var colorData = [];
+    var selData = [];
     var i, j;
     var traces = this._structure.backboneTraces();
     for (i = 0; i < traces.length; ++i) {
       // get current residue colors
-      var data = this._perResidueColors[i];
+      var data = new Float32Array(this._perResidueColors[i].length);
       var index = 0;
       var trace = traces[i];
       for (j = 0; j < trace.length(); ++j) {
         var selected = view.containsResidue(trace.residueAt(j)) ? 1.0 : 0.0;
-        data[index + 3] = selected;
-        index+=4;
+        data[index] = selected;
+        index+=1;
       }
       if (this._interpolation > 1) {
-        colorData.push(color.interpolateColor(data, this._interpolation));
+        selData.push(geom.interpolateScalars(data, this._interpolation));
       } else {
-        colorData.push(data);
+        selData.push(data);
       }
     }
 
     // store the color in the actual interleaved vertex array.
     for (i = 0; i < this._assocs.length; ++i) {
       var assoc = this._assocs[i];
       var ai = assoc.slice;
-      var newColors = colorData[assoc.traceIndex];
-      var a = newColors[ai*4+3];
+      var sel = selData[assoc.traceIndex];
+      var a = sel[ai];
       var va = assoc.vertexArray;
       for (j = assoc.vertStart ; j < assoc.vertEnd; ++j) {
         va.setSelected(j, a);