NeoBio (NeoBio API)

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## neobio.gui
Class NeoBio

    java.lang.Object
      |
      +--java.awt.Component
            |
            +--java.awt.Container
                  |
                  +--java.awt.Window
                        |
                        +--java.awt.Frame
                              |
                              +--javax.swing.JFrame
                                    |
                                    +--neobio.gui.NeoBio

All Implemented Interfaces:
  javax.accessibility.Accessible, java.awt.image.ImageObserver, java.awt.MenuContainer, javax.swing.RootPaneContainer, java.io.Serializable, javax.swing.WindowConstants

public class NeoBio
extends javax.swing.JFrame

This class is a simple GUI utility 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.JFrame
`javax.swing.JFrame.AccessibleJFrame`

Nested classes inherited from class java.awt.Frame
`java.awt.Frame.AccessibleAWTFrame`

Nested classes inherited from class java.awt.Window
`java.awt.Window.AccessibleAWTWindow`

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 javax.swing.JMenuItem` | `about_menuitem`
`private javax.swing.JButton` | `alignment_button`
`private javax.swing.JDesktopPane` | `desktop_pane`
`private javax.swing.JMenuItem` | `exit_menuitem`
`private javax.swing.JMenu` | `file_menu`
`private javax.swing.JToolBar` | `file_toolbar`
`private javax.swing.JMenu` | `help_menu`
`private javax.swing.JMenuBar` | `menu_bar`
`private javax.swing.JSeparator` | `mid_separator`
`private javax.swing.JMenuItem` | `new_alignment_item`
`private javax.swing.JPanel` | `toolbar_panel`

Fields inherited from class javax.swing.JFrame
`accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled`

Fields inherited from class java.awt.Frame
`CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR`

Fields inherited from class java.awt.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, HIDE_ON_CLOSE`

Fields inherited from interface java.awt.image.ImageObserver
`ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH`

Constructor Summary
`NeoBio()` Creates a new instance of a graphical interface.

Method Summary
`private void` | `aboutMenuItemActionPerformed(java.awt.event.ActionEvent e)`
`private void` | `exitForm()`
`private void` | `exitMenuItemActionPerformed(java.awt.event.ActionEvent e)`
`private void` | `initComponents()`
`static void` | `main(java.lang.String[] args)` Create and run a new interface.
`private void` | `newAlignmentActionPerformed(java.awt.event.ActionEvent e)`
`private void` | `pairwiseAlignment()`

Methods inherited from class javax.swing.JFrame
`addImpl, createRootPane, frameInit, 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.Frame
`addNotify, finalize, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setIconImage, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated`

Methods inherited from class java.awt.Window
`addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isFocusableWindow, isFocusCycleRoot, isFocused, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationRelativeTo, show, 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, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setFocusTraversalKeys, setFocusTraversalPolicy, 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, 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, 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, isOpaque, 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, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle`

Methods inherited from class java.lang.Object
`clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Methods inherited from interface java.awt.MenuContainer
`getFont, postEvent`

Field Detail

### file_menu

    private javax.swing.JMenu file_menu

### help_menu

    private javax.swing.JMenu help_menu

### menu_bar

    private javax.swing.JMenuBar menu_bar

### new_alignment_item

    private javax.swing.JMenuItem new_alignment_item

### exit_menuitem

    private javax.swing.JMenuItem exit_menuitem

### about_menuitem

    private javax.swing.JMenuItem about_menuitem

### mid_separator

    private javax.swing.JSeparator mid_separator

### file_toolbar

    private javax.swing.JToolBar file_toolbar

### toolbar_panel

    private javax.swing.JPanel toolbar_panel

### alignment_button

    private javax.swing.JButton alignment_button

### desktop_pane

    private javax.swing.JDesktopPane desktop_pane

Constructor Detail

### NeoBio

    public NeoBio()

  Creates a new instance of a graphical interface.

Method Detail

### initComponents

    private void initComponents()

### aboutMenuItemActionPerformed

    private void aboutMenuItemActionPerformed(java.awt.event.ActionEvent e)

### exitMenuItemActionPerformed

    private void exitMenuItemActionPerformed(java.awt.event.ActionEvent e)

### exitForm

    private void exitForm()

### newAlignmentActionPerformed

    private void newAlignmentActionPerformed(java.awt.event.ActionEvent e)

### pairwiseAlignment

    private void pairwiseAlignment()

### main

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

  Create and run a new interface. The main method takes no parameter from the command line.

  Parameters:
    `args` - command line arguments

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http://neobio.sourceforge.net
NeoBio is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. NeoBio is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with NeoBio; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.