More cleanup and review tags. Part of code review, see #29.

js/neuron/model/CaptureZone.js

@@ -1,7 +1,7 @@
 // Copyright 2002-2011, University of Colorado
 /**
- * Base class for "Capture Zones", which are essentially two dimensional
- * spaces where particles can be captured.
+ * Abstract base class for "Capture Zones", which are essentially two dimensional spaces where particles can be
+ * captured.
  *
  *@author John Blanco
  *@author Sharfudeen Ashraf (for Ghent University)

js/neuron/model/DelayBuffer.js

@@ -1,10 +1,10 @@
 // Copyright 2002-2011, University of Colorado
 /**
- * This class is a delay buffer that allows information to be put into it
- * and then extracted based on the amount of time in the past that a value
- * is needed.
+ * This class is a delay buffer that allows information to be put into it and then extracted based on the amount of
+ * time in the past that a value is needed.
  *
- * NOTE: If this turns out to be useful for other applications, it should be generalized.
+ * NOTE: This seems like it might be useful in other simulations.  If this turns out to be true, it will need some
+ * work to generalize.
  *
  * @author John Blanco
  * @author Sharfudeen Ashraf (for Ghent University)

js/neuron/model/DualGateChannelTraversalMotionStrategy.js

@@ -1,13 +1,12 @@
 //  Copyright 2002-2014, University of Colorado Boulder
 /**
- * A motion strategy for traversing through a dual-gate channel, meaning one
+ * A motion strategy for traversing through a dual-gated channel, meaning one
  * that has a gate and an inactivation level.
  * <p/>
  * This strategy makes several assumptions about the nature of the dual-gate
  * channel and how it is portrayed.  These assumptions depend both on the
  * model representation and the view representation of the dual-gated channel.
- * If changes are made to either, this class would need to be revised to
- * handle them.
+ * If changes are made to either, this class may need to be revised.
  *
  * @author John Blanco
  * @author Sharfudeen Ashraf (for Ghent University)
@@ -179,12 +178,12 @@ define( function( require ) {
     },
 
     /**
-     * @param xPos
-     * @param yPos
-     * @param travelsalPoint (object literal with x and y properties)
+     * @param posX
+     * @param posY
+     * @param traversalPoint (object literal with x and y properties)
      */
-    distanceBetweenPosAndTraversalPoint: function( posX, posY, travelsalPoint ) {
-      return  MathUtils.distanceBetween( posX, posY, travelsalPoint.x, travelsalPoint.y );
+    distanceBetweenPosAndTraversalPoint: function( posX, posY, traversalPoint ) {
+      return  MathUtils.distanceBetween( posX, posY, traversalPoint.x, traversalPoint.y );
     },
 
     moveBasedOnCurrentVelocity: function( movable, dt ) {
@@ -197,7 +196,8 @@ define( function( require ) {
      * this channel.
      *
      * @param channel
-     * @param startingLocation
+     * @param startingLocationX
+     * @param startingLocationY
      * @return
      */
     createTraversalPoints: function( channel, startingLocationX, startingLocationY ) {

js/neuron/model/GatedChannel.js

@@ -1,7 +1,7 @@
 // Copyright 2002-2011, University of Colorado
 /**
- * Base class for gated membrane channels, i.e. channels that can open and
- * close.
+ * Base class for gated membrane channels, i.e. channels that open and close.
+ *
  * @author John Blanco
  * @author Sharfudeen Ashraf (for Ghent University)
  */

js/neuron/model/MembraneChannel.js

@@ -1,7 +1,7 @@
 // Copyright 2002-2011, University of Colorado
 /**
- * Abstract base class for membrane channels, which represent any channel
- * through which atoms can go through to cross a membrane.
+ * Abstract base class for membrane channels, which represent any channel through which atoms can go through to cross a
+ * membrane.
  *
  * @author John Blanco
  * @author Sharfudeen Ashraf (for Ghent University)
@@ -45,16 +45,15 @@ define( function( require ) {
       representationChanged: false // All the channel states are  updated at once at the end stepInTime.This was done for performance reasons.
     } );
 
-    //position of the channel
+    // position of the channel
     this.centerLocation = new Vector2();
     // Variable that defines how open the channel is.Valid range is 0 to 1, 0 means fully closed, 1 is fully open.
     this.openness = 0;
     // Variable that defines how inactivated the channel is, which is distinct from openness.
     // Valid range is 0 to 1, 0 means completely active, 1 is completely inactive.
     this.inactivationAmt = 0;
 
-    // Reference to the model that contains that particles that will be moving
-    // through this channel.
+    // Reference to the model that contains that particles that will be moving through this channel.
     thisChannel.modelContainingParticles = modelContainingParticles;
     thisChannel.rotationalAngle = 0; // In radians.
     // Size of channel only, i.e. where the atoms pass through.