de.unibi.techfak.jpredictor.gui
Class CutoffCalculator

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Dialog
                  javax.swing.JDialog
                      de.unibi.techfak.jpredictor.gui.CutoffCalculator

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.FocusListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants

public class CutoffCalculator
extends javax.swing.JDialog
implements java.awt.event.ActionListener, java.awt.event.FocusListener

A dialog for calculating the cutoff for scoring a genomic sequence. The user might enter an E-value and a genome length and with the motifs from the main window the number of bands for all possible cutoffs is calculated. All result are shown in a TextInsertDialog as well are send via the communicators output stream.

See Also:

TextInsertDialog, ICommunicator.out(), Serialized Form

Nested Class Summary

(package private) class

CutoffCalculator.CutoffCalcThread The class that performs the cutoff calculation

Nested classes/interfaces inherited from class javax.swing.JDialog

javax.swing.JDialog.AccessibleJDialog

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

java.awt.Dialog.AccessibleAWTDialog

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

java.awt.Window.AccessibleAWTWindow

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

java.awt.Container.AccessibleAWTContainer

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

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

(package private) javax.swing.JButton	bCancel
(package private) javax.swing.JButton	bExit The buttons.
(package private) javax.swing.JButton	bGetDistr
(package private) javax.swing.JButton	bStartCalc
(package private) java.lang.String[]	buttonTexts The text of all buttons
protected ICommunicator	comm The communicator which holds all settings.
(package private) char[]	generatingCharacters The characters used to generate the random sequences.
(package private) double[]	generatingDistribution The probabilities for the single characters.
protected IOperator	op The operator to perform the operations through.
(package private) java.awt.Window	owner The parent of this JDialog.
(package private) CutoffCalculator.CutoffCalcThread	t The thread how it was started.
(package private) javax.swing.JTextField	tfCutoff
(package private) javax.swing.JTextField	tfEValue the textfields
(package private) javax.swing.JTextField	tfProgress
(package private) javax.swing.JTextField	tfSampleSize
(package private) javax.swing.JTextField	tfSequLen

Fields inherited from class javax.swing.JDialog

accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

CutoffCalculator(java.awt.Dialog owner, ICommunicator comm)
Constructor, that takes a motif list, which is used to initialize the listing window.

CutoffCalculator(java.awt.Frame owner, ICommunicator comm)
Constructor, that takes a motif list, which is used to initialize the listing window.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) Handles the events thrown when a button is pressed.
protected void	createAndShowGUI() Creates the GUI.
(package private) void	evalueChanged() Reacts on E-value changes made by the user in the corresponding text field.
void	focusGained(java.awt.event.FocusEvent e)
void	focusLost(java.awt.event.FocusEvent e)
protected void	init(ICommunicator commold) Init the class.
static void	main(java.lang.String[] args) The main program

Methods inherited from class javax.swing.JDialog

addImpl, createRootPane, dialogInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.awt.Dialog

addNotify, getTitle, hide, isModal, isResizable, isUndecorated, setModal, setResizable, setTitle, setUndecorated, show

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, finalize, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, isActive, isAlwaysOnTop, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setAlwaysOnTop, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationByPlatform, setLocationRelativeTo, toBack, toFront

Methods inherited from class java.awt.Container

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

Methods inherited from class java.awt.Component

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

Methods inherited from class java.lang.Object

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

Field Detail

owner

java.awt.Window owner

The parent of this JDialog.

buttonTexts

java.lang.String[] buttonTexts

The text of all buttons

comm

protected ICommunicator comm

The communicator which holds all settings.

op

protected IOperator op

The operator to perform the operations through.

bExit

javax.swing.JButton bExit

The buttons.

bCancel

javax.swing.JButton bCancel

bStartCalc

javax.swing.JButton bStartCalc

bGetDistr

javax.swing.JButton bGetDistr

tfEValue

javax.swing.JTextField tfEValue

the textfields

tfSequLen

javax.swing.JTextField tfSequLen

tfSampleSize

javax.swing.JTextField tfSampleSize

tfProgress

javax.swing.JTextField tfProgress

tfCutoff

javax.swing.JTextField tfCutoff

generatingCharacters

char[] generatingCharacters

The characters used to generate the random sequences.

generatingDistribution

double[] generatingDistribution

The probabilities for the single characters. It is used when the random sequences are generated. It is set in the constructor, either the communicators background distribution or as { 0.283, 0.217, 0.217, 0.283 }.

t

CutoffCalculator.CutoffCalcThread t

The thread how it was started.

Constructor Detail

CutoffCalculator

public CutoffCalculator(java.awt.Frame owner,
                        ICommunicator comm)

Constructor, that takes a motif list, which is used to initialize the listing window.

Parameters:

owner - The parent frame.

comm - The communicator to get all settings from.

CutoffCalculator

public CutoffCalculator(java.awt.Dialog owner,
                        ICommunicator comm)

Constructor, that takes a motif list, which is used to initialize the listing window.

Parameters:

owner - The parent dialog.

comm - The communicator to get all settings from. correct directory is set.

Method Detail

init

protected void init(ICommunicator commold)

Init the class.

Parameters:

commold - The communicator to get all settings from. correct directory is set.

createAndShowGUI

protected void createAndShowGUI()

Creates the GUI.

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

Handles the events thrown when a button is pressed. Must not be called from others than the event dispatching thread due to unintended behaviour.

Specified by:

actionPerformed in interface java.awt.event.ActionListener

Parameters:

e - The event description.

main

public static void main(java.lang.String[] args)

The main program

Parameters:

args - Runtime arguments, parameters

focusGained

public void focusGained(java.awt.event.FocusEvent e)

Specified by:

focusGained in interface java.awt.event.FocusListener

focusLost

public void focusLost(java.awt.event.FocusEvent e)

Specified by:

focusLost in interface java.awt.event.FocusListener

evalueChanged

void evalueChanged()

Reacts on E-value changes made by the user in the corresponding text field. Set the sample size using the formula

 samplesize = 100 * 10 ^ -log(evalue)