apollo.dataadapter.ensj19
Class AnnotationEnsJAdapterGUI

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.bdgp.swing.AbstractDataAdapterUI
                      apollo.dataadapter.ensj19.EnsJAdapterGUI
                          apollo.dataadapter.ensj19.AnnotationEnsJAdapterGUI

All Implemented Interfaces:

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

public class AnnotationEnsJAdapterGUI
extends EnsJAdapterGUI
implements ApolloDataAdapterGUI

See Also:

Serialized Form

Nested Class Summary

class	AnnotationEnsJAdapterGUI.DataSourceConfigInteractionListener If the user chooses a particular ensembl database from the default filechooser, we will update the other databases with our best guess (if we can find one) for the maps and variation databases.
class	AnnotationEnsJAdapterGUI.ShowAnnotationConfigurationActionListener Space saver - Toggles the annotation source chooser to be visible/not.
class	AnnotationEnsJAdapterGUI.ShowDataSourceConfigurationActionListener Space saver - Toggles the data source chooser to be visible/not.
class	AnnotationEnsJAdapterGUI.ShowTypesActionListener Sets the Include Panel contained in the types panel to visible and re-packs the dialog - this makes it look like the dialog has expanded with those options

Nested classes/interfaces inherited from class apollo.dataadapter.ensj19.EnsJAdapterGUI

EnsJAdapterGUI.ChromosomeDropdownPopupListener, EnsJAdapterGUI.DataSourceChangeListener, EnsJAdapterGUI.DataTypeButton

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

Fields inherited from class apollo.dataadapter.ensj19.EnsJAdapterGUI

DEFAULT_CONFIG_FILE, locationPanel, logger

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

AnnotationEnsJAdapterGUI(org.bdgp.io.IOOperation op)

Method Summary

protected void	addDataChangeListenerToDataSourceConfigPanels()
protected void	buildGUI()
java.util.Properties	createStateInformation() We make sure (in addition to the superclass's setStateInfo) that we have added the names of the chosen annotation input and output files.
java.lang.Object	doOperation(java.lang.Object values) The method that actually performs the data adapter operation (presumably by delegating to a data adapter).
CompositeDataSourceConfigurationPanel	getDataConfigChooser()
java.util.Properties	getProperties() This method is run to capture the state of the GUI.
void	setInput(java.lang.Object input) If the input is a HashMap, and use it to set values into the chromosome and high/low text fields.
void	setProperties(java.util.Properties inputPassedIn) This is run by apollo to set the GUI state: it is run when the adapter is first started up, as well as when the user moves around or reloads data.

Methods inherited from class apollo.dataadapter.ensj19.EnsJAdapterGUI

buildIncludePanel, buildLocationPanel, createBorder, findFile, getChrAction, getChrButton, getChrDropdown, getChrStartEndList, getCloneFragmentButton, getCloneFragmentPanel, getDataAdapter, getDataTypeButtons, getEndTextBox, getInitialSettings, getLocationPanel, getLoggingFile, getOperation, getPrefixedProperties, getSelectedChr, getSelectedChrStartEnd, getSelectedCloneFragment, getSelectedEnd, getSelectedStableID, getSelectedStart, getStableIdButton, getStartTextBox, initialiseChromosomeDropdown, isChromosomeListInitialised, putPrefixedProperties, setDataAdapter, setDataTypeButtons, setLoggingFile, setSelectedStableId

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

Constructor Detail

AnnotationEnsJAdapterGUI

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

Method Detail

buildGUI

protected void buildGUI()

Overrides:

buildGUI in class EnsJAdapterGUI

createStateInformation

public java.util.Properties createStateInformation()
                                            throws ApolloAdapterException

We make sure (in addition to the superclass's setStateInfo) that we have added the names of the chosen annotation input and output files.

Specified by:

createStateInformation in interface ApolloDataAdapterGUI

Specified by:

createStateInformation in class EnsJAdapterGUI

Throws:

ApolloAdapterException

doOperation

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

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.

Specified by:

doOperation in interface org.bdgp.io.DataAdapterUI

Throws:

org.bdgp.io.DataAdapterException

setInput

public void setInput(java.lang.Object input)

If the input is a HashMap, and use it to set values into the chromosome and high/low text fields. If the input is a string, use it to set the logical species name. If the input is a composite adapter, set a handle to ourselves on that adapter (our parent), keyed by our logical species name.

Specified by:

setInput in interface org.bdgp.io.DataAdapterUI

Overrides:

setInput in class org.bdgp.swing.AbstractDataAdapterUI

getProperties

public java.util.Properties getProperties()

This method is run to capture the state of the GUI. It returns all GUI-state - the contents of the fields, as well as the history vectors in the fields.

It is run when the adapter gui has successfully read data once (to write out the history file, as well as keep state information to help with navigation)

In addition to the superclass method's work, this method writes out the annotation input/output file information and history, and the annotation's input/output server information and history

Specified by:

getProperties in interface org.bdgp.io.DataAdapterUI

Overrides:

getProperties in class EnsJAdapterGUI

Returns:

all of the history information for the drop-down lists.

setProperties

public void setProperties(java.util.Properties inputPassedIn)

This is run by apollo to set the GUI state: it is run when the adapter is first started up, as well as when the user moves around or reloads data.

I set the widgets to reflect the history fields passed in - the annotation file chooser histories, in addition to the superclass.

Specified by:

setProperties in interface org.bdgp.io.DataAdapterUI

Overrides:

setProperties in class EnsJAdapterGUI

getDataConfigChooser

public CompositeDataSourceConfigurationPanel getDataConfigChooser()

addDataChangeListenerToDataSourceConfigPanels

protected void addDataChangeListenerToDataSourceConfigPanels()