de.unibi.techfak.jpredictor.gui
Class MainPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  de.unibi.techfak.jpredictor.gui.MainPanel

All Implemented Interfaces:

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

public class MainPanel
extends javax.swing.JPanel
implements java.awt.event.ActionListener

The main panel for the GUI, usable in a frame or window or in an applett.

See Also:

Serialized Form

Nested Class Summary

(package private) class

MainPanel.ActionThread The thread for doing searching and scoring.

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

javax.swing.JPanel.AccessibleJPanel

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

javax.swing.JComponent.AccessibleJComponent

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	bCutoffCalc
(package private) javax.swing.JButton	bMotifMaker The global action buttons.
(package private) javax.swing.JButton	bNegBrowse
(package private) javax.swing.JButton	bNegSet
(package private) javax.swing.JButton	bOutBrowse
(package private) javax.swing.JButton	bPosBrowse
(package private) javax.swing.JButton	bPosSet
(package private) javax.swing.JButton	bScoreSequ
(package private) javax.swing.JButton	bSearchMotifs
(package private) javax.swing.JButton	bSequBrowse
(package private) javax.swing.JButton	bSequSet Some global buttons for sequences.
(package private) java.lang.String[]	buttonTexts The text for the buttons.
(package private) javax.swing.JButton	bWeightMotifs
(package private) javax.swing.JCheckBox	cbAppend
(package private) javax.swing.JCheckBox	cbGraphOutput
(package private) javax.swing.JCheckBox	cbLengthNorm
(package private) javax.swing.JCheckBox	cbMotifOcc
(package private) javax.swing.JCheckBox	cbNegFile
(package private) javax.swing.JCheckBox	cbOverwrite
(package private) javax.swing.JCheckBox	cbPosFile
(package private) javax.swing.JCheckBox	cbSelectMulti
(package private) javax.swing.JCheckBox	cbSelectSingle
(package private) javax.swing.JCheckBox	cbSequFile Checkboxes.
(package private) javax.swing.JCheckBox	cbTextOutput
protected ICommunicator	comm The saved communicator, used to 'talk' to the operator, what means, doing all settings and gettings through it.
(package private) static java.lang.String	ERROR The string "Error" for varios uses.
(package private) javax.swing.JFileChooser	fileChooser The file chooser used in this window, its always used the same filechooser when browsing for files.
(package private) javax.swing.JMenuBar	menuBar Global setting whether a menu is already created or not.
protected MotifMaker	motifMaker The motif maker to be used by this class.
(package private) MotifCheckTree	motifTree The tree of motifs in a panel.
protected Operator	op The saved operator, which performs all tasks on the sequences by using the motifs.
(package private) java.awt.Window	parent The parent of this panel.
(package private) static java.lang.String	PASTED_SEQU The string which is shown in the file text fields, when a sequence was pasted instead of a set filename.
(package private) TextInsertDialog	sequenceInput The input form for the sequences.
(package private) javax.swing.JTextArea	taError The text area for the error messages.
(package private) javax.swing.JTextArea	taOutput The text area for the output.
(package private) javax.swing.JTextField	tfCutoff
(package private) javax.swing.JTextField	tfNegFile
(package private) javax.swing.JTextField	tfOutFile
(package private) javax.swing.JTextField	tfPosFile
(package private) javax.swing.JTextField	tfSequFile The textfields.
(package private) javax.swing.JTextField	tfWindowShift
(package private) javax.swing.JTextField	tfWindowWidth

Fields inherited from class javax.swing.JComponent

accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

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, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

MainPanel(java.awt.Window parent, ICommunicator comm, Operator op)
Simple constructor.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e) Handles the events thrown when a button is pressed.
private void	createJMenuBar(MouseOverHintManager hints) Creates a JMenu for this panel which may be added to any frame or dialog, preferably to the parent of this panel.
private javax.swing.JPanel	getInputOutputForm(MouseOverHintManager hints) Creates and returns the panel for the sequence motif
javax.swing.JMenuBar	getJMenuBar() After constructing this class the menu bar can be obtained.
private javax.swing.JPanel	getSettingsForm(MouseOverHintManager hints) Creates and returns the panel for the settings
private void	putCommunicatorToForms() Stores all information from the static communicator associated with this class in the main windows input forms.
private boolean	putFormsToCommunicator(boolean output) Stores all information from the main windows input forms in the static communicator associated with this class.

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, 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, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Field Detail

comm

protected ICommunicator comm

The saved communicator, used to 'talk' to the operator, what means, doing all settings and gettings through it. Given to and set by the constructor.

op

protected Operator op

The saved operator, which performs all tasks on the sequences by using the motifs. Set by the constructor.

PASTED_SEQU

static final java.lang.String PASTED_SEQU

The string which is shown in the file text fields, when a sequence was pasted instead of a set filename.

See Also:

Constant Field Values

ERROR

static final java.lang.String ERROR

The string "Error" for varios uses.

See Also:

Constant Field Values

motifMaker

protected MotifMaker motifMaker

The motif maker to be used by this class. Should only be instanciated if it is null.

parent

java.awt.Window parent

The parent of this panel. If it is an applet it is null.

buttonTexts

java.lang.String[] buttonTexts

The text for the buttons.

bSequSet

javax.swing.JButton bSequSet

Some global buttons for sequences.

bPosSet

javax.swing.JButton bPosSet

bNegSet

javax.swing.JButton bNegSet

bSequBrowse

javax.swing.JButton bSequBrowse

bPosBrowse

javax.swing.JButton bPosBrowse

bNegBrowse

javax.swing.JButton bNegBrowse

bOutBrowse

javax.swing.JButton bOutBrowse

bCancel

javax.swing.JButton bCancel

bMotifMaker

javax.swing.JButton bMotifMaker

The global action buttons.

bSearchMotifs

javax.swing.JButton bSearchMotifs

bWeightMotifs

javax.swing.JButton bWeightMotifs

bScoreSequ

javax.swing.JButton bScoreSequ

bCutoffCalc

javax.swing.JButton bCutoffCalc

tfSequFile

javax.swing.JTextField tfSequFile

The textfields.

tfPosFile

javax.swing.JTextField tfPosFile

tfNegFile

javax.swing.JTextField tfNegFile

tfOutFile

javax.swing.JTextField tfOutFile

tfWindowWidth

javax.swing.JTextField tfWindowWidth

tfWindowShift

javax.swing.JTextField tfWindowShift

tfCutoff

javax.swing.JTextField tfCutoff

cbSequFile

javax.swing.JCheckBox cbSequFile

Checkboxes.

cbPosFile

javax.swing.JCheckBox cbPosFile

cbNegFile

javax.swing.JCheckBox cbNegFile

cbLengthNorm

javax.swing.JCheckBox cbLengthNorm

cbMotifOcc

javax.swing.JCheckBox cbMotifOcc

cbAppend

javax.swing.JCheckBox cbAppend

cbOverwrite

javax.swing.JCheckBox cbOverwrite

cbTextOutput

javax.swing.JCheckBox cbTextOutput

cbGraphOutput

javax.swing.JCheckBox cbGraphOutput

cbSelectSingle

javax.swing.JCheckBox cbSelectSingle

cbSelectMulti

javax.swing.JCheckBox cbSelectMulti

taOutput

javax.swing.JTextArea taOutput

The text area for the output.

taError

javax.swing.JTextArea taError

The text area for the error messages.

motifTree

MotifCheckTree motifTree

The tree of motifs in a panel.

fileChooser

javax.swing.JFileChooser fileChooser

The file chooser used in this window, its always used the same filechooser when browsing for files. This garantees, that the user works always in the directory he changed into for the first time.

sequenceInput

TextInsertDialog sequenceInput

The input form for the sequences.

menuBar

javax.swing.JMenuBar menuBar

Global setting whether a menu is already created or not. Per default menuBar is set in the constructor. If not, it is null and no menu will be drawn.

Constructor Detail

MainPanel

public MainPanel(java.awt.Window parent,
                 ICommunicator comm,
                 Operator op)

Simple constructor. Inits the panel and all components. The communicator and the operator are used to build up certain components, just like the tree of available motifs. If the communicator contains no motif list it is created and inserted.

If the parent is not a window (frame or dialog, which is disposable), set it to null, which means, that no "Close"-button is shown and the parent is not disposed.

Parameters:

parent - The parent of the panel.

comm - The communicator interface.

op - An operator for calling the specified tasks.

Method Detail

getJMenuBar

public javax.swing.JMenuBar getJMenuBar()

After constructing this class the menu bar can be obtained. Calling this method will cause the created menu bar to be returned.

Returns:

The menu bar how it was build while class construction.

createJMenuBar

private void createJMenuBar(MouseOverHintManager hints)

Creates a JMenu for this panel which may be added to any frame or dialog, preferably to the parent of this panel. Should be the last to be called after the file chooser was set.

Parameters:

hints - The manager to register the hints.

getInputOutputForm

private javax.swing.JPanel getInputOutputForm(MouseOverHintManager hints)

Creates and returns the panel for the sequence motif

Parameters:

hints - The manager to register the hints.

Returns:

A panel with all components.

getSettingsForm

private javax.swing.JPanel getSettingsForm(MouseOverHintManager hints)

Creates and returns the panel for the settings

Parameters:

hints - The manager to register the hints.

Returns:

Returns a panel.

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.

putCommunicatorToForms

private void putCommunicatorToForms()

Stores all information from the static communicator associated with this class in the main windows input forms.

putFormsToCommunicator

private boolean putFormsToCommunicator(boolean output)

Stores all information from the main windows input forms in the static communicator associated with this class. Prints proper error messages to comm.err(), if wished Corrects wrong input (e.g. for windowWidth and windowShift) with the previous set one.

Parameters:

output - Decides whether error output should be written to comm.err()

Returns:

true iff all forms could be recognized properly, false otherwise.

See Also:

ICommunicator.err()