spectrophotometer
Class Spectrophotometer

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Panel
              java.applet.Applet
                  edu.davidson.tools.SApplet
                      spectrophotometer.Spectrophotometer

All Implemented Interfaces:

edu.davidson.tools.SDataSource, edu.davidson.tools.SStepable, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class Spectrophotometer
extends edu.davidson.tools.SApplet
implements edu.davidson.tools.SStepable, edu.davidson.tools.SDataSource

Simulation of a spectrophotometer. The simulation employs a particulate model for light, which is represented as photons (small balls) traveling from the light source to the detector. While passing through the cell, there is a chance the photons will be absorbed.

Applet Parameters

BGColor : background color (uses #FFFFFF notation)
Concentration : analyte concentration in mole/L (default 0.00100)
ControlPosition : position of the controls, 0=North, 1=East, 2=South, 3=West (default 2)
Dt : simulation time increment (fps = 1/Dt) (default 0.010)
Intensity : light source intensity in photons/sec (default 10)
IsReady : JavaScript variable set to true when this applet has loaded and initialized LiquidColor : color of liquid in cell (uses #FFFFFF notation)
MolarAbsorptivity : analyte molar absorptivity in L/(mole cm) (default 199)
PathLength : cell path length in cm (default 1.00)
PixelsPerCM : pixels per cm in the display (default 33)
ShowControls : true to show controls (default)
Speed : speed of photons (default 50 pixels/sec)
Wavelength : wavelength of light in nm, used to set photon color (default 400)

Version:

2.0, September 2008

Author:

David N. Blauch

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.BaselineResizeBehavior

Field Summary

Fields inherited from class edu.davidson.tools.SApplet

clock, dataConnections, dataListeners, dataSources, lock

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Spectrophotometer()

Method Summary

void	destroy()
java.lang.String	getAppletInfo()
java.awt.Color	getColor(double val) Returns the color associated with the specified wavelength.
edu.davidson.tools.SApplet	getOwner() Gets the owner of the data source.
java.lang.String	getParameter(java.lang.String key, java.lang.String def)
java.lang.String[][]	getParameterInfo()
double	getTime() Gets the current timer time.
double[][]	getVariables() Gets the values of the variables for SDataSource. element [0][0] is the time as provided by the timer, which might be disabled element [0][1] is the number of photons emitted by the light source element [0][2] is the number of photons detected by the detector element [0][3] is the intensity (photons/sec), which is zero if the timer is off element [0][4] is the transmittance, which is zero if the timer is off element [0][5] is the absorbance, which is zero if the timer is off The transmittance and absorbance are determined using the reference intensity, if it is defined; otherwise the source intensity is used.
java.lang.String[]	getVarStrings() Returns an array of the variable names supplied by this SDataSource. t is the simulation time in seconds s is the number of photons emitted by the source d is the number of photons that have reached the detector I is the measured photon intensity T is the measured transmittance A is the measured absorbance
void	init()
void	paint(java.awt.Graphics g)
void	resetSimulation() Resets the simulation.
void	setAutoTimer(boolean val) If true, the timer is automatically started when the first photon reaches the detector.
void	setBackgroundColor(java.lang.String rgb) Sets the background color of the applet.
void	setBackgroundScattering(double val) Sets the probability of background scattering when a photon encounters the cell walls
void	setConcentration(double val) Sets the concentration of the absorbing species
void	setIntensity(double val) Sets the source intensity, the rate at which photons are emitted from the light source.
void	setLiquidColor(java.lang.String rgb) Sets the color of the liquid in the cell.
void	setMolarAbsorptivity(double val) Sets the molar absorptivity of the absorbing species
void	setOwner(edu.davidson.tools.SApplet owner) Sets the owner for the SDataSource.
void	setPathLength(double val) Sets the cell path length.
void	setPhotonRadius(int val) Sets the radius of the photons.
void	setPixelsPerCM(int val) Sets the number of pixels per centimeter.
void	setReferenceIntensity(double val) Sets the reference intensity.
void	setScalingFactor(double val) Sets the scaling factor.
void	setSpeed(double val) Sets the speed with which a photon moves across the screen.
void	setTimeIncrement(double val) Sets the simulation time increment, the time between points in the simulation.
void	setWavelength(double val) Sets the wavelength of the photons.
void	start()
void	startSimulation() Starts the simulation by starting the clock.
void	startTimer() Starts the timer.
void	step(double dt, double tm) Calculates state of system at each step in the simulation.
void	stop()
void	stopSimulation() Stops the simulation.
void	stopTimer() Stops the timer.
void	useCell(boolean val) Determines whether the cell is used in the simulation

Methods inherited from class edu.davidson.tools.SApplet

addDataListener, addDataSource, cleanupDataConnections, clearAllData, clearData, deleteDataConnection, deleteDataConnections, forward, getClockID, getClockTime, getDataConnectionFromDL, getDataConnectionFromDS, getDataFromDS, getDataListener, getDataListener, getDataSource, getDataSource, getID, getRunningID, getSourceData, getSourceVariables, isAutoRefresh, isClockRunning, makeDataConnection, pause, removeDataListener, removeDataSource, reset, reverse, setAutoRefresh, setClockContinous, setClockCycle, setClockOneShot, setClockTime, setConnectionBlock, setConnectionListener, setConnectionSmoothing, setConnectionSource, setConnectionStride, setDefault, setDt, setExternalClock, setFPS, setRunningID, setRunningID, setTimeContinuous, setTimeCycle, setTimeOneShot, startClock, stepClock, stepTime, stepTimeBack, stepTimeForward, stopClock, updateDataConnection, updateDataConnections

Methods inherited from class java.applet.Applet

getAccessibleContext, getAppletContext, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, isActive, newAudioClip, play, play, resize, resize, setStub, showStatus

Methods inherited from class java.awt.Panel

addNotify

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, remove, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, setLayout, transferFocusBackward, transferFocusDownCycle, update, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, dispatchEvent, enable, enable, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocusInWindow, reshape, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface edu.davidson.tools.SDataSource

getID

Constructor Detail

Spectrophotometer

public Spectrophotometer()

Method Detail

destroy

public void destroy()

Overrides:

destroy in class edu.davidson.tools.SApplet

getAppletInfo

public java.lang.String getAppletInfo()

Overrides:

getAppletInfo in class java.applet.Applet

getColor

public java.awt.Color getColor(double val)

Returns the color associated with the specified wavelength. The wavelength must lie between 380 and 780 nm.

Parameters:

val - wavelength in nanometers

getOwner

public edu.davidson.tools.SApplet getOwner()

Gets the owner of the data source.

Specified by:

getOwner in interface edu.davidson.tools.SDataSource

Returns:

owner of the data source, which is this applet

getParameter

public java.lang.String getParameter(java.lang.String key,
                                     java.lang.String def)

getParameterInfo

public java.lang.String[][] getParameterInfo()

Overrides:

getParameterInfo in class java.applet.Applet

getTime

public double getTime()

Gets the current timer time. This value is zero if the timer is not running or if a simulation is not running.

Returns:

time in seconds

getVariables

public double[][] getVariables()

Gets the values of the variables for SDataSource.
element [0][0] is the time as provided by the timer, which might be disabled
element [0][1] is the number of photons emitted by the light source
element [0][2] is the number of photons detected by the detector
element [0][3] is the intensity (photons/sec), which is zero if the timer is off
element [0][4] is the transmittance, which is zero if the timer is off
element [0][5] is the absorbance, which is zero if the timer is off
The transmittance and absorbance are determined using the reference intensity, if it is defined; otherwise the source intensity is used.

Specified by:

getVariables in interface edu.davidson.tools.SDataSource

Returns:

a one-by-three array

getVarStrings

public java.lang.String[] getVarStrings()

Returns an array of the variable names supplied by this SDataSource.
t is the simulation time in seconds
s is the number of photons emitted by the source
d is the number of photons that have reached the detector
I is the measured photon intensity
T is the measured transmittance
A is the measured absorbance

Specified by:

getVarStrings in interface edu.davidson.tools.SDataSource

paint

public void paint(java.awt.Graphics g)

Overrides:

paint in class java.awt.Container

resetSimulation

public void resetSimulation()

Resets the simulation. This method calls the stopSimulation() method and then clears the display.

setAutoTimer

public void setAutoTimer(boolean val)

If true, the timer is automatically started when the first photon reaches the detector. This procedure compensates for the time delay between emission of a photon (which increments the source count) and the detection of a photon (which increments the detector count). The timer is automatically started only once. Calling the setAutoTimer method again re-enables this option. Calling the resetSimulation method also re-enables this option.

See Also:

resetSimulation()

setBackgroundColor

public void setBackgroundColor(java.lang.String rgb)

Sets the background color of the applet.

Parameters:

rgb - this string is converted into a 24-bit integer that defines the color

setBackgroundScattering

public void setBackgroundScattering(double val)

Sets the probability of background scattering when a photon encounters the cell walls

Parameters:

val - probability (default 0.00)

setConcentration

public void setConcentration(double val)

Sets the concentration of the absorbing species

Parameters:

val - concentration in mole/L

setIntensity

public void setIntensity(double val)

Sets the source intensity, the rate at which photons are emitted from the light source.

Parameters:

val - intensity in photons per second

setLiquidColor

public void setLiquidColor(java.lang.String rgb)

Sets the color of the liquid in the cell.

Parameters:

rgb - this string is converted into a 24-bit integer that defines the color

setMolarAbsorptivity

public void setMolarAbsorptivity(double val)

Sets the molar absorptivity of the absorbing species

Parameters:

val - molar absorptivity in L/(mole cm)

setOwner

public void setOwner(edu.davidson.tools.SApplet owner)

Sets the owner for the SDataSource. (In this implementation, this method does not do anything.

Specified by:

setOwner in interface edu.davidson.tools.SDataSource

Parameters:

owner - owner of the data source

setPathLength

public void setPathLength(double val)

Sets the cell path length. The cell path length cannot be altered if a simulation is running.

Parameters:

val - cell path length in centimeters

setPhotonRadius

public void setPhotonRadius(int val)

Sets the radius of the photons.

Parameters:

val - photon radius in pixels

setPixelsPerCM

public void setPixelsPerCM(int val)

Sets the number of pixels per centimeter. The number of pixels per centimeter cannot be altered if a simulation is running.

Parameters:

val - number of pixels per centimeter

setReferenceIntensity

public void setReferenceIntensity(double val)

Sets the reference intensity. The reference intensity is the intensity observed in the absence of analyte (but the cell and solution are typically present). If no reference intensity is set or if a zero or negative value is supplied, the source intensity and background scattering is used to calculate the transmittance.

Parameters:

val - reference intensity in photons per second

setScalingFactor

public void setScalingFactor(double val)

Sets the scaling factor. The standard simulation operates with a scaling factor of zero. For scaling factors above zero, additional photons that are not displayed are added to the source and detector counts. If the intensity if 10/sec and the scaling factor is 9, the effective intensity is 10/sec (1+9) = 100/sec.

setSpeed

public void setSpeed(double val)

Sets the speed with which a photon moves across the screen.

Parameters:

val - speed in pixels per second

setTimeIncrement

public void setTimeIncrement(double val)

Sets the simulation time increment, the time between points in the simulation. The simulation is always set to run in real time.

Parameters:

val - time increment in seconds

setWavelength

public void setWavelength(double val)

Sets the wavelength of the photons. The wavelength is used to set the photon color. This is a visible spectrometer; the wavelength must lie between 380 and 780 nm.

Parameters:

val - wavelength in nanometers

start

public void start()

Overrides:

start in class java.applet.Applet

startSimulation

public void startSimulation()

Starts the simulation by starting the clock. No other conditions are altered. This method can be used to resume a simulation after the stop method has been called.

See Also:

SApplet.stopClock()

startTimer

public void startTimer()

Starts the timer. A simulation must be running for the timer to run. This method can also be used to reset the timer while it is running.

step

public void step(double dt,
                 double tm)

Calculates state of system at each step in the simulation. Called only by the clock.

Specified by:

step in interface edu.davidson.tools.SStepable

stop

public void stop()

Overrides:

stop in class java.applet.Applet

stopSimulation

public void stopSimulation()

Stops the simulation.

stopTimer

public void stopTimer()

Stops the timer.

useCell

public void useCell(boolean val)

Determines whether the cell is used in the simulation

init

public void init()

Overrides:

init in class java.applet.Applet