apollo.gui.synteny
Class SyntenyPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  apollo.gui.synteny.SyntenyPanel

All Implemented Interfaces:

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

public class SyntenyPanel
extends javax.swing.JPanel
implements ReverseComplementListener

JPanel that holds szaps and link panels(if multi species). Just gets created once, and theres only one of them - Singleton? szaps and link panels get reset on every load - change that?

See Also:

Serialized Form

Nested Class Summary

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

protected static org.apache.log4j.Logger

logger

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, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

SyntenyPanel(java.util.Vector speciesPanels, java.util.Vector linkPanels, CompositeApolloFrame c)

Method Summary

void	_layoutPanels()
void	addLinkPanel(SyntenyLinkPanel linkPanel)
void	addPanel(StrandedZoomableApolloPanel ap)
void	applyLayout(misc.JIniFile iniFile, boolean updateBaseLocation)
boolean	areLinksShadedByPercId()
boolean	areOpaqueLinksUsed()
java.util.Vector	getLinkPanels()
java.awt.Dimension	getMinimumSize() Min size 0,0 - allow the user to shrink the syn panel down to 0
java.util.Vector	getPanels()
java.awt.Dimension	getPreferredSize()
StatusBar	getStatusBar()
boolean	handleReverseComplementEvent(ReverseComplementEvent evt)
void	print(java.io.File file, java.lang.String orientation, java.lang.String scale)
void	removePanel(StrandedZoomableApolloPanel ap)
void	saveLayout(misc.JIniFile iniFile)
void	setLockScrolling(boolean value)
void	setShadeByPercId(boolean value)
void	setStatusBar(StatusBar sb)
void	setUseOpaqueLinks(boolean value)
void	setVisible(boolean state)
void	zoomToSelection()

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, getNextFocusableComponent, getPopupLocation, 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, 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

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

SyntenyPanel

public SyntenyPanel(java.util.Vector speciesPanels,
                    java.util.Vector linkPanels,
                    CompositeApolloFrame c)

Method Detail

print

public void print(java.io.File file,
                  java.lang.String orientation,
                  java.lang.String scale)

saveLayout

public void saveLayout(misc.JIniFile iniFile)

applyLayout

public void applyLayout(misc.JIniFile iniFile,
                        boolean updateBaseLocation)

getPanels

public java.util.Vector getPanels()

getLinkPanels

public java.util.Vector getLinkPanels()

getPreferredSize

public java.awt.Dimension getPreferredSize()

Overrides:

getPreferredSize in class javax.swing.JComponent

getMinimumSize

public java.awt.Dimension getMinimumSize()

Min size 0,0 - allow the user to shrink the syn panel down to 0

Overrides:

getMinimumSize in class javax.swing.JComponent

addPanel

public void addPanel(StrandedZoomableApolloPanel ap)

removePanel

public void removePanel(StrandedZoomableApolloPanel ap)

addLinkPanel

public void addLinkPanel(SyntenyLinkPanel linkPanel)

handleReverseComplementEvent

public boolean handleReverseComplementEvent(ReverseComplementEvent evt)

Specified by:

handleReverseComplementEvent in interface ReverseComplementListener

setStatusBar

public void setStatusBar(StatusBar sb)

zoomToSelection

public void zoomToSelection()

getStatusBar

public StatusBar getStatusBar()

_layoutPanels

public void _layoutPanels()

setVisible

public void setVisible(boolean state)

Overrides:

setVisible in class javax.swing.JComponent

areOpaqueLinksUsed

public boolean areOpaqueLinksUsed()

areLinksShadedByPercId

public boolean areLinksShadedByPercId()

setUseOpaqueLinks

public void setUseOpaqueLinks(boolean value)

setShadeByPercId

public void setShadeByPercId(boolean value)

setLockScrolling

public void setLockScrolling(boolean value)