neobio.gui
Class PairwiseAlignmentFrame

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--javax.swing.JComponent
                    |
                    +--javax.swing.JInternalFrame
                          |
                          +--neobio.gui.PairwiseAlignmentFrame

All Implemented Interfaces:

javax.accessibility.Accessible, java.awt.image.ImageObserver, java.awt.MenuContainer, javax.swing.RootPaneContainer, java.io.Serializable, javax.swing.WindowConstants

public class PairwiseAlignmentFrame

extends javax.swing.JInternalFrame

This class is the internal frame of NeoBio's graphical interface for computing pairwise sequence alignments using one of the the algorithms provided in the neobio.alignment package.

Author:

Sergio A. de Carvalho Jr.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class javax.swing.JInternalFrame

javax.swing.JInternalFrame.AccessibleJInternalFrame, javax.swing.JInternalFrame.JDesktopIcon

Nested classes inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes inherited from class java.awt.Component

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

Field Summary

private PairwiseAlignmentAlgorithm[]	algorithm
private javax.swing.JComboBox	algorithm_combo
private java.lang.String[]	algorithm_name
private javax.swing.JPanel	algorithm_panel
private javax.swing.JRadioButton	basic_button
private boolean	basic_scheme
private javax.swing.JRadioButton	file_button
private javax.swing.JFileChooser	find_dialog
private javax.swing.JButton	find_matrix_button
private javax.swing.JButton	find_output_button
private javax.swing.JButton	find_seq1_button
private javax.swing.JButton	find_seq2_button
private javax.swing.JTextField	gap_field
private javax.swing.JLabel	gap_label
private javax.swing.JPanel	input_panel
private javax.swing.JTextField	match_field
private javax.swing.JLabel	match_label
private javax.swing.JRadioButton	matrix_button
private javax.swing.JTextField	matrix_field
private javax.swing.JTextField	mismatch_field
private javax.swing.JLabel	mismatch_label
private javax.swing.JTextArea	output_area
private javax.swing.JTextField	output_field
private javax.swing.ButtonGroup	output_group
private javax.swing.JPanel	output_panel
private javax.swing.JTabbedPane	output_tab
private javax.swing.JPanel	output_tab_panel
private boolean	output_to_file
private java.awt.Frame	parent_frame
private javax.swing.JTextArea	progress_area
private javax.swing.JPanel	progress_tab_panel
private javax.swing.JButton	run_button
private javax.swing.ButtonGroup	scoring_group
private javax.swing.JPanel	scoring_panel
private javax.swing.JRadioButton	screen_button
private javax.swing.JTextField	seq1_field
private javax.swing.JLabel	seq1_label
private javax.swing.JTextField	seq2_field
private javax.swing.JLabel	seq2_label
private static int	window_number

Fields inherited from class javax.swing.JInternalFrame

closable, CONTENT_PANE_PROPERTY, desktopIcon, FRAME_ICON_PROPERTY, frameIcon, GLASS_PANE_PROPERTY, iconable, IS_CLOSED_PROPERTY, IS_ICON_PROPERTY, IS_MAXIMUM_PROPERTY, IS_SELECTED_PROPERTY, isClosed, isIcon, isMaximum, isSelected, LAYERED_PANE_PROPERTY, maximizable, MENU_BAR_PROPERTY, resizable, ROOT_PANE_PROPERTY, rootPane, rootPaneCheckingEnabled, title, TITLE_PROPERTY

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.Container

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

PairwiseAlignmentFrame(java.awt.Frame parent_frame)
Creates a new instance of the internal frame.

Method Summary

private void	add(javax.swing.JComponent a, javax.swing.JComponent b, java.awt.GridBagConstraints c, int x, int y)
private void	checkRunButtonStatus()
private void	findMatrixButtonActionPerformed()
private void	findOutputButtonActionPerformed()
private void	findSeq1ButtonActionPerformed()
private void	findSeq2ButtonActionPerformed()
private void	initComponents()
private void	outputOptionStateChanged()
private void	runButtonActionPerformed()
private void	schemeOptionStateChanged()
private void	showError(java.lang.String message)

Methods inherited from class javax.swing.JInternalFrame

addImpl, addInternalFrameListener, createRootPane, dispose, doDefaultCloseAction, fireInternalFrameEvent, getAccessibleContext, getContentPane, getDefaultCloseOperation, getDesktopIcon, getDesktopPane, getFocusCycleRootAncestor, getFocusOwner, getFrameIcon, getGlassPane, getInternalFrameListeners, getJMenuBar, getLayer, getLayeredPane, getMenuBar, getMostRecentFocusOwner, getNormalBounds, getRootPane, getTitle, getUI, getUIClassID, getWarningString, isClosable, isClosed, isFocusCycleRoot, isIcon, isIconifiable, isMaximizable, isMaximum, isResizable, isRootPaneCheckingEnabled, isSelected, moveToBack, moveToFront, pack, paintComponent, paramString, remove, removeInternalFrameListener, reshape, restoreSubcomponentFocus, setClosable, setClosed, setContentPane, setDefaultCloseOperation, setDesktopIcon, setFocusCycleRoot, setFrameIcon, setGlassPane, setIcon, setIconifiable, setJMenuBar, setLayer, setLayer, setLayeredPane, setLayout, setMaximizable, setMaximum, setMenuBar, setNormalBounds, setResizable, setRootPane, setRootPaneCheckingEnabled, setSelected, setTitle, setUI, show, toBack, toFront, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addPropertyChangeListener, addPropertyChangeListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getGraphics, getHeight, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPreferredSize, getPropertyChangeListeners, getPropertyChangeListeners, getRegisteredKeyStrokes, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFont, setForeground, 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, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, setFocusTraversalKeys, setFocusTraversalPolicy, 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, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, 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, processMouseEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Field Detail

window_number

private static int window_number

parent_frame

private java.awt.Frame parent_frame

input_panel

private javax.swing.JPanel input_panel

scoring_panel

private javax.swing.JPanel scoring_panel

algorithm_panel

private javax.swing.JPanel algorithm_panel

output_panel

private javax.swing.JPanel output_panel

progress_tab_panel

private javax.swing.JPanel progress_tab_panel

output_tab_panel

private javax.swing.JPanel output_tab_panel

seq1_field

private javax.swing.JTextField seq1_field

seq2_field

private javax.swing.JTextField seq2_field

matrix_field

private javax.swing.JTextField matrix_field

output_field

private javax.swing.JTextField output_field

match_field

private javax.swing.JTextField match_field

mismatch_field

private javax.swing.JTextField mismatch_field

gap_field

private javax.swing.JTextField gap_field

progress_area

private javax.swing.JTextArea progress_area

output_area

private javax.swing.JTextArea output_area

find_seq1_button

private javax.swing.JButton find_seq1_button

find_seq2_button

private javax.swing.JButton find_seq2_button

find_output_button

private javax.swing.JButton find_output_button

find_matrix_button

private javax.swing.JButton find_matrix_button

run_button

private javax.swing.JButton run_button

algorithm_combo

private javax.swing.JComboBox algorithm_combo

output_tab

private javax.swing.JTabbedPane output_tab

screen_button

private javax.swing.JRadioButton screen_button

file_button

private javax.swing.JRadioButton file_button

basic_button

private javax.swing.JRadioButton basic_button

matrix_button

private javax.swing.JRadioButton matrix_button

scoring_group

private javax.swing.ButtonGroup scoring_group

output_group

private javax.swing.ButtonGroup output_group

seq1_label

private javax.swing.JLabel seq1_label

seq2_label

private javax.swing.JLabel seq2_label

match_label

private javax.swing.JLabel match_label

mismatch_label

private javax.swing.JLabel mismatch_label

gap_label

private javax.swing.JLabel gap_label

find_dialog

private javax.swing.JFileChooser find_dialog

output_to_file

private boolean output_to_file

basic_scheme

private boolean basic_scheme

algorithm_name

private java.lang.String[] algorithm_name

algorithm

private PairwiseAlignmentAlgorithm[] algorithm

Constructor Detail

PairwiseAlignmentFrame

public PairwiseAlignmentFrame(java.awt.Frame parent_frame)

Creates a new instance of the internal frame.

Parameters:

parent_frame - the parent frame

Method Detail

initComponents

private void initComponents()

add

private void add(javax.swing.JComponent a,
                 javax.swing.JComponent b,
                 java.awt.GridBagConstraints c,
                 int x,
                 int y)

findSeq1ButtonActionPerformed

private void findSeq1ButtonActionPerformed()

findSeq2ButtonActionPerformed

private void findSeq2ButtonActionPerformed()

findMatrixButtonActionPerformed

private void findMatrixButtonActionPerformed()

findOutputButtonActionPerformed

private void findOutputButtonActionPerformed()

schemeOptionStateChanged

private void schemeOptionStateChanged()

outputOptionStateChanged

private void outputOptionStateChanged()

checkRunButtonStatus

private void checkRunButtonStatus()

runButtonActionPerformed

private void runButtonActionPerformed()

showError

private void showError(java.lang.String message)