apollo.dataadapter.synteny
Class SyntenyAdapterGUI

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

All Implemented Interfaces:

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

public class SyntenyAdapterGUI
extends org.bdgp.swing.AbstractDataAdapterUI

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 SyntenyAdapter	driver
protected static org.apache.log4j.Logger	logger
protected org.bdgp.io.IOOperation	op

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

SyntenyAdapterGUI(org.bdgp.io.IOOperation op, SyntenyAdapter adapter)

Method Summary

java.lang.Object	doOperation(java.lang.Object values) We need to post-process this composite curation set.
java.util.Map	getAdapterGUIs()
java.util.List	getAdapterLabelList()
protected org.bdgp.io.IOOperation	getOperation()
java.util.Properties	getProperties() Gather properties for each child adapter - prefix each gathered property with the name of the species (so, "myProp" -> "Homo_sapiens:myProp") and then glue all child Properties into one big Properties.
java.util.HashMap	getSharedData() Data common to all adapters should have a place to live - this is it.
void	setDataAdapter(org.bdgp.io.DataAdapter driver) This sets the SyntenyAdapter as the dataadapter for this GUI.
void	setInput(java.lang.Object input) This is called specifically by helpers (like the FullEnsJDBCSyntenyPanel) which need to set values directly into the widgets in its children.
void	setProperties(java.util.Properties combinedProperties) Walk each property we've been handed.

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

driver

protected SyntenyAdapter driver

op

protected org.bdgp.io.IOOperation op

Constructor Detail

SyntenyAdapterGUI

public SyntenyAdapterGUI(org.bdgp.io.IOOperation op,
                         SyntenyAdapter adapter)

Method Detail

setDataAdapter

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

This sets the SyntenyAdapter as the dataadapter for this GUI. We must propagate this relation down to the children, otherwise none of the GUI's in the child adapters will be connected to the child dataadapers.

Specified by:

setDataAdapter in interface org.bdgp.io.DataAdapterUI

Overrides:

setDataAdapter in class org.bdgp.swing.AbstractDataAdapterUI

setInput

public void setInput(java.lang.Object input)

This is called specifically by helpers (like the FullEnsJDBCSyntenyPanel) which need to set values directly into the widgets in its children. -- The point is that we get fed something (currently a SyntenyRegion) from the our invoker (currently the SyntenyMenu). We find the adapter gui's relevant to the chromosomes on the region and setInput on them, passing in a HashMap of text-field values relevant to each.

For instance, when given ranges on Human and Mouse, we will set the Human ranges on the Human adapter, the Mouse ranges on the Mouse adapter, and both ranges on the Human/Mouse adapter.

If we get called with anything other than a HashMap, we do nothing.

Specified by:

setInput in interface org.bdgp.io.DataAdapterUI

Overrides:

setInput in class org.bdgp.swing.AbstractDataAdapterUI

getProperties

public java.util.Properties getProperties()

Gather properties for each child adapter - prefix each gathered property with the name of the species (so, "myProp" -> "Homo_sapiens:myProp") and then glue all child Properties into one big Properties. Hand out!

setProperties

public void setProperties(java.util.Properties combinedProperties)

Walk each property we've been handed. Strip off the species name at the front of the property, and gather the properties into species-specific groups.

Add to these properties the configuration information in the synteny style file for this species (in particular, we'll throw in the query- and hit-species for the compara-adapters we load into the properties list)

Call setProperties() on each species' adapter, passing in the specific groups we've gathered.

doOperation

public java.lang.Object doOperation(java.lang.Object values)
                             throws org.bdgp.io.DataAdapterException

We need to post-process this composite curation set. Right now, protein homology information is being provided with no "extra" redundant information - namely, the positions of the homologous genes are no longer being stored with the gene pairs, but we have already retrieved these genes in the individual species' curation sets, so we will fill-in the feature pairs' position information with the gene info we already know. Changed this so it always returns a CompositeDataHolder now. Presently for gff and ensj it makes a composite cur set and then makes a comp data holder from that. Eventually they should just make a comp data holder from scratch.

Throws:

org.bdgp.io.DataAdapterException

getAdapterGUIs

public java.util.Map getAdapterGUIs()

getOperation

protected org.bdgp.io.IOOperation getOperation()

getAdapterLabelList

public java.util.List getAdapterLabelList()

getSharedData

public java.util.HashMap getSharedData()

Data common to all adapters should have a place to live - this is it.