restructured the directories to meet PhET standards, see #29

js/neuron-main.js

@@ -7,8 +7,8 @@ define( function( require ) {
   'use strict';
 
   // modules
-  var NeuronProfiler = require( 'NEURON/neuron/NeuronProfiler' );
-  var NeuronScreen = require( 'NEURON/neuron/NeuronScreen' );
+  var NeuronProfiler = require( 'NEURON/neuron/common/NeuronProfiler' );
+  var NeuronScreen = require( 'NEURON/neuron/view/NeuronScreen' );
   var Sim = require( 'JOIST/Sim' );
   var SimLauncher = require( 'JOIST/SimLauncher' );
 

js/neuron/NeuronProfiler.js → js/neuron/common/NeuronProfiler.js

@@ -103,5 +103,6 @@ define( function( require ) {
       this.frameEndedTimes.length = 0;
       this.frameProcessingTimes.length = 0;
     }
+
   } );
 } );

js/neuron/model/AxonMembrane.js

@@ -15,7 +15,7 @@ define( function( require ) {
   var PropertySet = require( 'AXON/PropertySet' );
   var Vector2 = require( 'DOT/Vector2' );
   var Shape = require( 'KITE/Shape' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var TravelingActionPotential = require( 'NEURON/neuron/model/TravelingActionPotential' );
   var AxonMembraneState = require( 'NEURON/neuron/model/AxonMembraneState' );
   var Cubic = require( 'KITE/segments/Cubic' );

js/neuron/model/DualGateChannelTraversalMotionStrategy.js

@@ -18,12 +18,12 @@ define( function( require ) {
   var inherit = require( 'PHET_CORE/inherit' );
   var Vector2 = require( 'DOT/Vector2' );
   var MotionStrategy = require( 'NEURON/neuron/model/MotionStrategy' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var WanderAwayThenFadeMotionStrategy = require( 'NEURON/neuron/model/WanderAwayThenFadeMotionStrategy' );
   var TimedFadeAwayStrategy = require( 'NEURON/neuron/model/TimedFadeAwayStrategy' );
   var SpeedChangeLinearMotionStrategy = require( 'NEURON/neuron/model/SpeedChangeLinearMotionStrategy' );
   var LinearMotionStrategy = require( 'NEURON/neuron/model/LinearMotionStrategy' );
-  var MathUtils = require( 'NEURON/neuron/utils/MathUtils' );
+  var MathUtils = require( 'NEURON/neuron/common/MathUtils' );
 
   // Threshold at which particles will "bounce" back out of the channel
   // rather than traversing it.

js/neuron/model/ModifiedHodgkinHuxleyModel.js

@@ -19,7 +19,7 @@ define( function( require ) {
   // modules
   var inherit = require( 'PHET_CORE/inherit' );
   var DelayBuffer = require( 'NEURON/neuron/model/DelayBuffer' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
 
   /**
    * Amount of time used for each iteration of the model.  This is fixed, and when the model is stepped it breaks

js/neuron/model/NeuronModel.js

@@ -29,8 +29,8 @@ define( function( require ) {
   var SlowBrownianMotionStrategy = require( 'NEURON/neuron/model/SlowBrownianMotionStrategy' );
   var MembraneCrossingDirection = require( 'NEURON/neuron/model/MembraneCrossingDirection' );
   var TimedFadeInStrategy = require( 'NEURON/neuron/model/TimedFadeInStrategy' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
-  var MathUtils = require( 'NEURON/neuron/utils/MathUtils' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
+  var MathUtils = require( 'NEURON/neuron/common/MathUtils' );
 
   // Default configuration values.
   var DEFAULT_FOR_SHOW_ALL_IONS = true;

js/neuron/model/PotassiumGatedChannel.js

@@ -13,11 +13,11 @@ define( function( require ) {
   // modules
   var inherit = require( 'PHET_CORE/inherit' );
   var GatedChannel = require( 'NEURON/neuron/model/GatedChannel' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var PieSliceShapedCaptureZone = require( 'NEURON/neuron/model/PieSliceShapedCaptureZone' );
   var ParticleType = require( 'NEURON/neuron/model/ParticleType' );
   var MembraneCrossingDirection = require( 'NEURON/neuron/model/MembraneCrossingDirection' );
-  var MathUtils = require( 'NEURON/neuron/utils/MathUtils' );
+  var MathUtils = require( 'NEURON/neuron/common/MathUtils' );
   var MembraneChannelTypes = require( 'NEURON/neuron/model/MembraneChannelTypes' );
 
   // constants

js/neuron/model/PotassiumIon.js

@@ -13,7 +13,7 @@ define( function( require ) {
   var inherit = require( 'PHET_CORE/inherit' );
   var ParticleType = require( 'NEURON/neuron/model/ParticleType' );
   var Particle = require( 'NEURON/neuron/model/Particle' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
 
   /**
    * @constructor

js/neuron/model/PotassiumLeakageChannel.js

@@ -14,7 +14,7 @@ define( function( require ) {
   // modules
   var inherit = require( 'PHET_CORE/inherit' );
   var AbstractLeakChannel = require( 'NEURON/neuron/model/AbstractLeakChannel' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var PieSliceShapedCaptureZone = require( 'NEURON/neuron/model/PieSliceShapedCaptureZone' );
   var MembraneCrossingDirection = require( 'NEURON/neuron/model/MembraneCrossingDirection' );
   var ParticleType = require( 'NEURON/neuron/model/ParticleType' );

js/neuron/model/SodiumDualGatedChannel.js

@@ -14,12 +14,12 @@ define( function( require ) {
   // modules
   var inherit = require( 'PHET_CORE/inherit' );
   var GatedChannel = require( 'NEURON/neuron/model/GatedChannel' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var PieSliceShapedCaptureZone = require( 'NEURON/neuron/model/PieSliceShapedCaptureZone' );
   var MembraneCrossingDirection = require( 'NEURON/neuron/model/MembraneCrossingDirection' );
   var DualGateChannelTraversalMotionStrategy = require( 'NEURON/neuron/model/DualGateChannelTraversalMotionStrategy' );
   var ParticleType = require( 'NEURON/neuron/model/ParticleType' );
-  var MathUtils = require( 'NEURON/neuron/utils/MathUtils' );
+  var MathUtils = require( 'NEURON/neuron/common/MathUtils' );
   var MembraneChannelTypes = require( 'NEURON/neuron/model/MembraneChannelTypes' );
 
   var CHANNEL_HEIGHT = NeuronConstants.MEMBRANE_THICKNESS * 1.2; // In nanometers.

js/neuron/model/SodiumIon.js

@@ -12,7 +12,7 @@ define( function( require ) {
   var inherit = require( 'PHET_CORE/inherit' );
   var ParticleType = require( 'NEURON/neuron/model/ParticleType' );
   var Particle = require( 'NEURON/neuron/model/Particle' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
 
   /**
    *

js/neuron/model/SodiumLeakageChannel.js

@@ -14,9 +14,9 @@ define( function( require ) {
   // modules
   var inherit = require( 'PHET_CORE/inherit' );
   var Color = require( 'SCENERY/util/Color' );
-  var MathUtils = require( 'NEURON/neuron/utils/MathUtils' );
+  var MathUtils = require( 'NEURON/neuron/common/MathUtils' );
   var AbstractLeakChannel = require( 'NEURON/neuron/model/AbstractLeakChannel' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var PieSliceShapedCaptureZone = require( 'NEURON/neuron/model/PieSliceShapedCaptureZone' );
   var MembraneCrossingDirection = require( 'NEURON/neuron/model/MembraneCrossingDirection' );
   var ParticleType = require( 'NEURON/neuron/model/ParticleType' );

js/neuron/model/TraverseChannelAndFadeMotionStrategy.js

@@ -13,10 +13,10 @@ define( function( require ) {
   var inherit = require( 'PHET_CORE/inherit' );
   var Vector2 = require( 'DOT/Vector2' );
   var MotionStrategy = require( 'NEURON/neuron/model/MotionStrategy' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var WanderAwayThenFadeMotionStrategy = require( 'NEURON/neuron/model/WanderAwayThenFadeMotionStrategy' );
   var TimedFadeAwayStrategy = require( 'NEURON/neuron/model/TimedFadeAwayStrategy' );
-  var MathUtils = require( 'NEURON/neuron/utils/MathUtils' );
+  var MathUtils = require( 'NEURON/neuron/common/MathUtils' );
 
   /**
    *

js/neuron/model/WanderAwayThenFadeMotionStrategy.js

@@ -12,7 +12,7 @@ define( function( require ) {
   // modules
   var inherit = require( 'PHET_CORE/inherit' );
   var MotionStrategy = require( 'NEURON/neuron/model/MotionStrategy' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var TimedFadeAwayStrategy = require( 'NEURON/neuron/model/TimedFadeAwayStrategy' );
 
   // constants

js/neuron/view/MembraneChannelGateCanvasNode.js

@@ -17,7 +17,7 @@ define( function( require ) {
   var Shape = require( 'KITE/Shape' );
   var kite = require( 'KITE/kite' );
   var MembraneChannelTypes = require( 'NEURON/neuron/model/MembraneChannelTypes' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var Color = require( 'SCENERY/util/Color' );
 
   // utility function for drawing the shape that depicts the edge or side of a membrane channel

js/neuron/view/NeuronParticlesTexture.js

@@ -13,7 +13,7 @@ define( function( require ) {
   var Bounds2 = require( 'DOT/Bounds2' );
   var Color = require( 'SCENERY/util/Color' );
   var inherit = require( 'PHET_CORE/inherit' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var ParticleType = require( 'NEURON/neuron/model/ParticleType' );
   var Vector2 = require( 'DOT/Vector2' );
 

js/neuron/view/NeuronScreenView.js

@@ -17,7 +17,7 @@ define( function( require ) {
   var HBox = require( 'SCENERY/nodes/HBox' );
   var Vector2 = require( 'DOT/Vector2' );
   var Bounds2 = require( 'DOT/Bounds2' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var Matrix3 = require( 'DOT/Matrix3' );
   var Shape = require( 'KITE/Shape' );
   var Dimension2 = require( 'DOT/Dimension2' );
@@ -38,10 +38,10 @@ define( function( require ) {
   var ChargeSymbolsLayerNode = require( 'NEURON/neuron/view/ChargeSymbolsLayerNode' );
   var StepBackButton = require( 'SCENERY_PHET/buttons/StepBackButton' );
   var ZoomControl = require( 'NEURON/neuron/view/ZoomControl' );
-  var MembranePotentialChart = require( 'NEURON/neuron/chart/view/MembranePotentialChart' );
-  var IonsAndChannelsLegendPanel = require( 'NEURON/neuron/controlpanel/IonsAndChannelsLegendPanel' );
-  var AxonCrossSectionControlPanel = require( 'NEURON/neuron/controlpanel/AxonCrossSectionControlPanel' );
-  var SimSpeedControlPanel = require( 'NEURON/neuron/controlpanel/SimSpeedControlPanel' );
+  var MembranePotentialChart = require( 'NEURON/neuron/view/chart/MembranePotentialChart' );
+  var IonsAndChannelsLegendPanel = require( 'NEURON/neuron/view/controlpanel/IonsAndChannelsLegendPanel' );
+  var AxonCrossSectionControlPanel = require( 'NEURON/neuron/view/controlpanel/AxonCrossSectionControlPanel' );
+  var SimSpeedControlPanel = require( 'NEURON/neuron/view/controlpanel/SimSpeedControlPanel' );
   var PlayPauseButton = require( 'SCENERY_PHET/buttons/PlayPauseButton' );
   var StepButton = require( 'SCENERY_PHET/buttons/StepButton' );
   var Util = require( 'SCENERY/util/Util' );

js/neuron/view/ParticlesCanvasNode.js

@@ -15,7 +15,7 @@ define( function( require ) {
   var CanvasNode = require( 'SCENERY/nodes/CanvasNode' );
   var Color = require( 'SCENERY/util/Color' );
   var inherit = require( 'PHET_CORE/inherit' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var ParticleType = require( 'NEURON/neuron/model/ParticleType' );
 
   /**

js/neuron/view/ParticlesWebGLNode.js

@@ -16,7 +16,7 @@ define( function( require ) {
 
   // modules
   var inherit = require( 'PHET_CORE/inherit' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var NeuronParticlesTexture = require( 'NEURON/neuron/view/NeuronParticlesTexture' );
   var ParticleType = require( 'NEURON/neuron/model/ParticleType' );
   var ShaderProgram = require( 'SCENERY/util/ShaderProgram' );

js/neuron/chart/view/ChartCursor.js → js/neuron/view/chart/ChartCursor.js

@@ -17,7 +17,7 @@ define( function( require ) {
   var SimpleDragHandler = require( 'SCENERY/input/SimpleDragHandler' );
   var Util = require( 'DOT/Util' );
   var Rectangle = require( 'SCENERY/nodes/Rectangle' );
-  var GrippyIndentNode = require( 'NEURON/neuron/chart/view/GrippyIndentNode' );
+  var GrippyIndentNode = require( 'NEURON/neuron/view/chart/GrippyIndentNode' );
 
   // constants
   var WIDTH_PROPORTION = 0.013; // empirically determined

js/neuron/chart/view/MembranePotentialChart.js → js/neuron/view/chart/MembranePotentialChart.js

@@ -24,12 +24,12 @@ define( function( require ) {
   // modules
   var inherit = require( 'PHET_CORE/inherit' );
   var Bounds2 = require( 'DOT/Bounds2' );
-  var ChartCursor = require( 'NEURON/neuron/chart/view/ChartCursor' );
-  var DataLineCanvasNode = require( 'NEURON/neuron/chart/view/DataLineCanvasNode' );
+  var ChartCursor = require( 'NEURON/neuron/view/chart/ChartCursor' );
+  var DataLineCanvasNode = require( 'NEURON/neuron/view/chart/DataLineCanvasNode' );
   var dot = require( 'DOT/dot' );
   var HBox = require( 'SCENERY/nodes/HBox' );
   var ModelViewTransform2 = require( 'PHETCOMMON/view/ModelViewTransform2' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var Node = require( 'SCENERY/nodes/Node' );
   var Panel = require( 'SUN/Panel' );
   var Path = require( 'SCENERY/nodes/Path' );
@@ -54,8 +54,7 @@ define( function( require ) {
   var MAX_PANEL_WIDTH = 554;
   var MIN_DISTANCE_SQUARED_BETWEEN_POINTS = 0.01;
 
-  // This value sets the frequency of chart updates, which helps to reduce
-  // the processor consumption.
+  // This value sets the frequency of chart updates, which helps to reduce the processor consumption.
   var UPDATE_PERIOD = NeuronConstants.DEFAULT_ACTION_POTENTIAL_CLOCK_DT; // In seconds of sim time (not wall time)
 
   /**

js/neuron/controlpanel/AxonCrossSectionControlPanel.js → js/neuron/view/controlpanel/AxonCrossSectionControlPanel.js

@@ -12,7 +12,7 @@ define( function( require ) {
   // modules
   var CheckBox = require( 'SUN/CheckBox' );
   var inherit = require( 'PHET_CORE/inherit' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var Panel = require( 'SUN/Panel' );
   var PhetFont = require( 'SCENERY_PHET/PhetFont' );
   var Text = require( 'SCENERY/nodes/Text' );

js/neuron/controlpanel/IonsAndChannelsLegendPanel.js → js/neuron/view/controlpanel/IonsAndChannelsLegendPanel.js

@@ -23,7 +23,7 @@ define( function( require ) {
   var PhetFont = require( 'SCENERY_PHET/PhetFont' );
   var ModelViewTransform2 = require( 'PHETCOMMON/view/ModelViewTransform2' );
   var MembraneChannelNode = require( 'NEURON/neuron/view/MembraneChannelNode' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var ParticleNode = require( 'NEURON/neuron/view/ParticleNode' );
   var PotassiumGatedChannel = require( 'NEURON/neuron/model/PotassiumGatedChannel' );
   var SodiumLeakageChannel = require( 'NEURON/neuron/model/SodiumLeakageChannel' );

js/neuron/controlpanel/SimSpeedControlPanel.js → js/neuron/view/controlpanel/SimSpeedControlPanel.js

@@ -11,7 +11,7 @@ define( function( require ) {
 
   // modules
   var inherit = require( 'PHET_CORE/inherit' );
-  var NeuronConstants = require( 'NEURON/neuron/NeuronConstants' );
+  var NeuronConstants = require( 'NEURON/neuron/common/NeuronConstants' );
   var Panel = require( 'SUN/Panel' );
   var VerticalAquaRadioButtonGroup = require( 'SUN/VerticalAquaRadioButtonGroup' );
   var Text = require( 'SCENERY/nodes/Text' );