gata.menu
Class GATAFrame

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Window
              java.awt.Frame
                  javax.swing.JFrame
                      gata.menu.GATAFrame

All Implemented Interfaces:

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

public class GATAFrame

extends javax.swing.JFrame

Author:

Nix Frame holding all of the menues for running the GATAPlotter App. Is also a container for the aligner panel and any glyph/annotation panels. Sort of ugly!

See Also:

Serialized Form

Field Summary

Fields inherited from class javax.swing.JFrame

EXIT_ON_CLOSE

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.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

GATAFrame(GATAParams gataParams)

Method Summary

javax.swing.JMenuItem	addScaleRuler(javax.swing.JMenu menu, java.lang.String label)
javax.swing.JMenuItem	addScaleTrackColors(javax.swing.JMenu menu)
javax.swing.JMenuItem	addShowHide(javax.swing.JMenu menu, java.lang.String label, boolean color)
javax.swing.JMenuItem	addShowHideLabel(javax.swing.JMenu menu, java.lang.String label)
javax.swing.JMenuItem	addShowHideWithPath(javax.swing.JMenu menu, java.lang.String label, java.lang.String path)
javax.swing.JMenuItem	addTrack(javax.swing.JMenu menu, java.lang.String label, boolean color)
void	colorizeGenericGlyphs(int colorizer) helper method, 0 = linear, 1 = log10, 2 = lnx, 3= reset to solid 4= log2
void	completeAnnotationMenu(boolean gffRefPres, boolean gffCompPres, AnnoSpecParams refParams, AnnoSpecParams compParams) must be called after the initial creation when the user has possibly loaded generic annotation
void	reallyRedrawAnnotationPanel(AnnoSpecParams asp)
void	redrawAlignPanel()
void	redrawAnnotationPanels() basically draws annotation twice, once to estimate the size, the second time for real
void	setAlignPanel(AlignPanel panel)
void	setCompAnnotation(Annotation a) needed to add later since annotation doesn't exist when ToolFrame is created
void	setCompGlyphPanel(GlyphPanel panel)
void	setRefAnnotation(Annotation a) needed to add later since annotation doesn't exist when ToolFrame is created
void	setRefGlyphPanel(GlyphPanel panel)
void	setWindowsVisibility(boolean setting) Add new windows/panels here to enable them to be shown or hidden in sync with the main frame

Methods inherited from class javax.swing.JFrame

getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, update

Methods inherited from class java.awt.Frame

addNotify, 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, 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, remove, removeAll, removeContainerListener, setFocusTraversalKeys, setFocusTraversalPolicy, setFont, transferFocusBackward, transferFocusDownCycle, 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, 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, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, 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

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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Constructor Detail

GATAFrame

public GATAFrame(GATAParams gataParams)

Method Detail

setRefAnnotation

public void setRefAnnotation(Annotation a)

needed to add later since annotation doesn't exist when ToolFrame is created

setCompAnnotation

public void setCompAnnotation(Annotation a)

needed to add later since annotation doesn't exist when ToolFrame is created

completeAnnotationMenu

public void completeAnnotationMenu(boolean gffRefPres,
                                   boolean gffCompPres,
                                   AnnoSpecParams refParams,
                                   AnnoSpecParams compParams)

must be called after the initial creation when the user has possibly loaded generic annotation

addShowHide

public javax.swing.JMenuItem addShowHide(javax.swing.JMenu menu,
                                         java.lang.String label,
                                         boolean color)

addScaleRuler

public javax.swing.JMenuItem addScaleRuler(javax.swing.JMenu menu,
                                           java.lang.String label)

addScaleTrackColors

public javax.swing.JMenuItem addScaleTrackColors(javax.swing.JMenu menu)

addShowHideWithPath

public javax.swing.JMenuItem addShowHideWithPath(javax.swing.JMenu menu,
                                                 java.lang.String label,
                                                 java.lang.String path)

addShowHideLabel

public javax.swing.JMenuItem addShowHideLabel(javax.swing.JMenu menu,
                                              java.lang.String label)

addTrack

public javax.swing.JMenuItem addTrack(javax.swing.JMenu menu,
                                      java.lang.String label,
                                      boolean color)

colorizeGenericGlyphs

public void colorizeGenericGlyphs(int colorizer)

helper method, 0 = linear, 1 = log10, 2 = lnx, 3= reset to solid 4= log2

redrawAlignPanel

public void redrawAlignPanel()

redrawAnnotationPanels

public void redrawAnnotationPanels()

basically draws annotation twice, once to estimate the size, the second time for real

reallyRedrawAnnotationPanel

public void reallyRedrawAnnotationPanel(AnnoSpecParams asp)

setAlignPanel

public void setAlignPanel(AlignPanel panel)

setCompGlyphPanel

public void setCompGlyphPanel(GlyphPanel panel)

setRefGlyphPanel

public void setRefGlyphPanel(GlyphPanel panel)

setWindowsVisibility

public void setWindowsVisibility(boolean setting)

Add new windows/panels here to enable them to be shown or hidden in sync with the main frame