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Spacing and formating changes - issue #30
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@ashrafabu
ashrafabu committed Jan 5, 2015
1 parent 066792b commit 9a81ef4
Showing 1 changed file with 9 additions and 33 deletions.
42 changes: 9 additions & 33 deletions js/neuron/model/NeuronModel.js
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Original file line number Diff line number Diff line change
Expand Up @@ -47,8 +47,7 @@ define( function( require ) {
var MODEL_WIDTH = 180; // In nanometers.
var PARTICLE_BOUNDS = new Shape.rect( -MODEL_WIDTH / 2, -MODEL_HEIGHT / 2, MODEL_WIDTH, MODEL_HEIGHT );

// Numbers of the various types of channels that are present on the
// membrane.
// Numbers of the various types of channels that are present on the membrane.
var NUM_GATED_SODIUM_CHANNELS = 20;
var NUM_GATED_POTASSIUM_CHANNELS = 20;
var NUM_SODIUM_LEAK_CHANNELS = 3;
Expand All @@ -68,11 +67,9 @@ define( function( require ) {

// Delay between the values in the HH model to the concentration readouts.
// This is needed to make sure that the concentration readouts don't
// change before visible potassium or sodium ions have crossed the
//membrane.
// change before visible potassium or sodium ions have crossed the membrane.
var CONCENTRATION_READOUT_DELAY = 0.001; // In seconds of sim time.


// Thresholds for determining whether an action potential should be
// considered to be in progress. These values relate to the rate of flow
// through the gated sodium, gated potassium, and combination of the
Expand All @@ -84,7 +81,6 @@ define( function( require ) {
var SODIUM_CURRENT_THRESH_FOR_ACTION_POTENTIAL = 0.001;
var LEAKAGE_CURRENT_THRESH_FOR_ACTION_POTENTIAL = 0.444;


// Rates at which concentration changes during action potential. These
// values combined with the conductance at each time step are used to
// calculate the concentration changes.
Expand Down Expand Up @@ -133,7 +129,6 @@ define( function( require ) {

thisModel.membraneChannels = new ObservableArray();
thisModel.hodgkinHuxleyModel = new ModifiedHodgkinHuxleyModel();

thisModel.crossSectionInnerRadius = (thisModel.axonMembrane.getCrossSectionDiameter() - thisModel.axonMembrane.getMembraneThickness()) / 2;
thisModel.crossSectionOuterRadius = (thisModel.axonMembrane.getCrossSectionDiameter() + thisModel.axonMembrane.getMembraneThickness()) / 2;

Expand All @@ -143,7 +138,6 @@ define( function( require ) {
thisModel.potassiumExteriorConcentration = NOMINAL_POTASSIUM_EXTERIOR_CONCENTRATION;

RecordAndPlaybackModel.call( thisModel, maxRecordPoints, {

// Notification Property that the setting for the visibility of the membrane
//potential chart has changed.
potentialChartVisible: DEFAULT_FOR_MEMBRANE_CHART_VISIBILITY,
Expand Down Expand Up @@ -173,18 +167,14 @@ define( function( require ) {
allowStepNavigation: false
} );


// Listen to the membrane for events that indicate that a traveling
// action potential has arrived at the location of the transverse
// cross section.
// action potential has arrived at the location of the transverse cross section.
thisModel.axonMembrane.travelingActionPotentialReachedCrossSectionProperty.lazyLink( function( reached ) {
// The action potential has arrived, so stimulate the model
// the simulates the action potential voltages and current
// flows.
// the simulates the action potential voltages and current flows.
if ( reached ) {
thisModel.hodgkinHuxleyModel.stimulate();
}

} );

function addInitialChannels() {
Expand All @@ -202,8 +192,7 @@ define( function( require ) {
var sodiumLeakChansAdded = 0;
var potassiumLeakChansAdded = 0;

// Add some of each type so that they are visible at the top portion
// of the membrane.
// Add some of each type so that they are visible at the top portion of the membrane.
if ( NUM_SODIUM_LEAK_CHANNELS > 0 ) {
thisModel.addChannel( MembraneChannelTypes.SODIUM_LEAKAGE_CHANNEL, angle );
sodiumLeakChansAdded++;
Expand Down Expand Up @@ -234,12 +223,14 @@ define( function( require ) {
var potassiumLeakUrgency = NUM_POTASSIUM_LEAK_CHANNELS / potassiumLeakChansAdded;
var sodiumLeakUrgency = NUM_SODIUM_LEAK_CHANNELS / sodiumLeakChansAdded;
var channelTypeToAdd = null;
if ( gatedSodiumUrgency >= gatedPotassiumUrgency && gatedSodiumUrgency >= potassiumLeakUrgency && gatedSodiumUrgency >= sodiumLeakUrgency ) {
if ( gatedSodiumUrgency >= gatedPotassiumUrgency && gatedSodiumUrgency >= potassiumLeakUrgency &&
gatedSodiumUrgency >= sodiumLeakUrgency ) {
// Add a gated sodium channel.
channelTypeToAdd = MembraneChannelTypes.SODIUM_GATED_CHANNEL;
gatedSodiumChansAdded++;
}
else if ( gatedPotassiumUrgency > gatedSodiumUrgency && gatedPotassiumUrgency >= potassiumLeakUrgency && gatedPotassiumUrgency >= sodiumLeakUrgency ) {
else if ( gatedPotassiumUrgency > gatedSodiumUrgency && gatedPotassiumUrgency >= potassiumLeakUrgency &&
gatedPotassiumUrgency >= sodiumLeakUrgency ) {
// Add a gated potassium channel.
channelTypeToAdd = MembraneChannelTypes.POTASSIUM_GATED_CHANNEL;
gatedPotassiumChansAdded++;
Expand Down Expand Up @@ -277,7 +268,6 @@ define( function( require ) {
thisModel.allowStepNavigation = true;
}
} );

this.reset(); // This does initialization
}

Expand Down Expand Up @@ -333,7 +323,6 @@ define( function( require ) {
// the model causes notifications to be sent out continuously.
if ( Math.abs( this.membranePotential - this.hodgkinHuxleyModel.getMembraneVoltage() ) > MEMBRANE_POTENTIAL_CHANGE_THRESHOLD ) {
this.membranePotential = this.hodgkinHuxleyModel.getMembraneVoltage();

}

// Update the stimulus lockout state.
Expand Down Expand Up @@ -493,7 +482,6 @@ define( function( require ) {
concentrationChanged = true;
}
if ( concentrationChanged ) {

this.concentrationChangedProperty.set( true ); // Trigger concentrationReadout change
}

Expand Down Expand Up @@ -651,7 +639,6 @@ define( function( require ) {
thisModel.transientParticles.remove( newParticle );
}
} );

return newParticle;
},

Expand Down Expand Up @@ -695,12 +682,10 @@ define( function( require ) {
newParticle = this.createBackgroundParticle( particleType );
newParticle.setOpaqueness( FOREGROUND_PARTICLE_DEFAULT_OPAQUENESS );
captureZone.assignNewParticleLocation( newParticle );

}
},

/**
*
* @returns {Shape}
*/
getParticleMotionBounds: function() {
Expand Down Expand Up @@ -729,7 +714,6 @@ define( function( require ) {
// per unit area.
var multiplier = Math.max( Math.random(), Math.random() );
var distance = (this.crossSectionInnerRadius - particle.getRadius() * 2) * multiplier;

particle.setPosition( distance * Math.cos( angle ), distance * Math.sin( angle ) );
},

Expand All @@ -742,7 +726,6 @@ define( function( require ) {
* @return {boolean}
*/
isActionPotentialInProgress: function() {

return this.axonMembrane.getTravelingActionPotential() ||
Math.abs( this.hodgkinHuxleyModel.get_k_current() ) > POTASSIUM_CURRENT_THRESH_FOR_ACTION_POTENTIAL ||
Math.abs( this.hodgkinHuxleyModel.get_na_current() ) > SODIUM_CURRENT_THRESH_FOR_ACTION_POTENTIAL ||
Expand Down Expand Up @@ -810,8 +793,6 @@ define( function( require ) {
else {
// Currently NOT locked out, see if that should change.
var backwards = this.getTime() - this.getMaxRecordedTime() <= 0;


if ( this.isActionPotentialInProgress() || (this.isPlayback() && backwards) ) {
this.setStimulusLockout( true );
}
Expand Down Expand Up @@ -945,7 +926,6 @@ define( function( require ) {
self.backgroundParticles.remove( newParticle );
}
} );

return newParticle;
},

Expand All @@ -964,7 +944,6 @@ define( function( require ) {
*/
addChannel: function( membraneChannelType, angle ) {
var membraneChannel = MembraneChannelFactory.createMembraneChannel( membraneChannelType, this, this.hodgkinHuxleyModel );

var radius = this.axonMembrane.getCrossSectionDiameter() / 2;
var newLocation = new Vector2( radius * Math.cos( angle ), radius * Math.sin( angle ) );

Expand All @@ -981,7 +960,6 @@ define( function( require ) {
* stimulus (i.e. action potential) is currently locked out. This is done
* to prevent the situation where multiple action potentials are moving
* down the membrane at the same time.
*
* @return {boolean}
*/
isStimulusInitiationLockedOut: function() {
Expand Down Expand Up @@ -1041,7 +1019,6 @@ define( function( require ) {
},

/**
*
* @returns {number}
*/
getMembranePotential: function() {
Expand All @@ -1060,7 +1037,6 @@ define( function( require ) {
* @param {NeuronModelState} state
*/
setPlaybackState: function( state ) {

this.concentrationChanged = false;

// Set the membrane channel state.
Expand Down

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