apollo.dataadapter.synteny
Class SyntenyComparaAdapterGUI

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.bdgp.swing.AbstractDataAdapterUI
                      apollo.dataadapter.synteny.SyntenyComparaAdapterGUI

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, org.bdgp.io.DataAdapterUI

public class SyntenyComparaAdapterGUI
extends org.bdgp.swing.AbstractDataAdapterUI

I am loaded into the 'compara' tab of the synteny adapter, and drive the loading of compara data.

See Also:

Serialized Form

Nested Class Summary

class	SyntenyComparaAdapterGUI.DnaAlignTypesButtonActionListener
class	SyntenyComparaAdapterGUI.FullPanelListener Launches the FullEnsjSyntenyPanel when the "view panel" button is hit.
class	SyntenyComparaAdapterGUI.ShowDataSourceConfigurationActionListener Space saver - Toggles the data source chooser to be visible/not.

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
static java.lang.String	PATTERN

Fields inherited from class org.bdgp.swing.AbstractDataAdapterUI

driver

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

SyntenyComparaAdapterGUI(org.bdgp.io.IOOperation op)

Method Summary

protected void	buildGUI()
java.util.Properties	createStateInformation() add on the hit-information to the query-information already in there.
java.lang.Object	doOperation(java.lang.Object values) The method that actually performs the data adapter operation (presumably by delegating to a data adapter).
org.bdgp.io.DataAdapter	getDataAdapter()
java.util.Properties	getProperties() Returns the state of the database config panel, pretty much.
void	setDataAdapter(org.bdgp.io.DataAdapter adapter) Sets the data adapter for this UI.
void	setInput(java.lang.Object input) This SNEAKY method is invoked by the CompositeAdapter after it's created this adapter as a child.
void	setProperties(java.util.Properties properties) This contains the properties stored in the adapter history, which are read when the adapter is created.

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

logger

protected static final org.apache.log4j.Logger logger

PATTERN

public static final java.lang.String PATTERN

See Also:

Constant Field Values

Constructor Detail

SyntenyComparaAdapterGUI

public SyntenyComparaAdapterGUI(org.bdgp.io.IOOperation op)

Method Detail

buildGUI

protected void buildGUI()

createStateInformation

public java.util.Properties createStateInformation()
                                            throws ApolloAdapterException

add on the hit-information to the query-information already in there.

Throws:

ApolloAdapterException

setInput

public void setInput(java.lang.Object input)

This SNEAKY method is invoked by the CompositeAdapter after it's created this adapter as a child.

This is invoked by the SyntenyMenu after the user has chosen a synteny region.

If the input is a HashMap, we use it to set values into the chromosome and high/low text fields.

If the input is an AbstractDataAdapterUI instance, then we are being told that this input is our 'parent'. We will set this parent on ourselves

WHY IS THIS METHOD OVERUSED?

(1) It is part of the standard AbstractDataAdapterUI interface,so I can use it without having to create an interface like "composable" with a get/setParent() method.

(2) I should move the other functionality in here to the setProperties() method.

Specified by:

setInput in interface org.bdgp.io.DataAdapterUI

Overrides:

setInput in class org.bdgp.swing.AbstractDataAdapterUI

setProperties

public void setProperties(java.util.Properties properties)

This contains the properties stored in the adapter history, which are read when the adapter is created. They will populate the history-comboboxes etc.

It also contains the NAMES of the query and hit species - note that these properties live in the style file for the synteny adapter. They are added onto the history-file properties passed into this adapter by the SyntenyAdapterGUI class.

getProperties

public java.util.Properties getProperties()

Returns the state of the database config panel, pretty much.

doOperation

public java.lang.Object doOperation(java.lang.Object values)
                             throws ApolloAdapterException

Description copied from interface: org.bdgp.io.DataAdapterUI

The method that actually performs the data adapter operation (presumably by delegating to a data adapter). The input and outputs to this method are entirely dependant on the operation the data adapter is supposed to perform. The input or output of this method may be null.

Throws:

ApolloAdapterException

setDataAdapter

public void setDataAdapter(org.bdgp.io.DataAdapter adapter)

Description copied from interface: org.bdgp.io.DataAdapterUI

Sets the data adapter for this UI. Since the UI provides it's own implementation of the IOOperation via the {link #doOperation(Object)}, the DataAdapterUI can decide whether or not to actually use the DataAdapter to perform the operation. However, a correct implementation of this interface will use the DataAdapter given in setDataAdapter.

Specified by:

setDataAdapter in interface org.bdgp.io.DataAdapterUI

Overrides:

setDataAdapter in class org.bdgp.swing.AbstractDataAdapterUI

getDataAdapter

public org.bdgp.io.DataAdapter getDataAdapter()