apollo.dataadapter.das2
Class DAS2AdapterGUI

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.bdgp.swing.AbstractDataAdapterUI
                      apollo.gui.GenericFileAdapterGUI
                          apollo.dataadapter.das2.DAS2AdapterGUI

All Implemented Interfaces:

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

public class DAS2AdapterGUI
extends GenericFileAdapterGUI
implements ApolloDataAdapterGUI

This actually constructs a completely different GUI for reading vs. writing. The version for reading from a DAS/2 server offers a pulldown list of known servers (currently hardcoded in apollo.cfg as DASServer; in the future, to be retrieved from registry), a list of sequence sources (organism + version), a list of chromosomes or segments, boxes for indicating the desired start/end, and (maybe this should go BEFORE the sequence sources list?) a list of previous selections (i.e. a history). There's also a box for Proxy settings and a "Change" button to change the proxy settings. In write mode, the GUI is much simpler, with a box for you to enter the filename. If you want a simpler way to test reading of DAS/2 features, you can call DAS2FeatureSaxParser from the command line with a filename argument for a file containing DAS2XML.

See Also:

Serialized Form

Nested Class Summary

class	DAS2AdapterGUI.DSNListener
class	DAS2AdapterGUI.HistoryListener
class	DAS2AdapterGUI.ProxyListener This listener gets fired when the user wants to set a Proxy Server for the session
class	DAS2AdapterGUI.ServerListener

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 DAS2Adapter	driver
protected DAS2AdapterGUI.DSNListener	dsn_listener
protected DAS2AdapterGUI.HistoryListener	history_listener
protected static org.apache.log4j.Logger	logger
static int	MAX_HISTORY_LENGTH
protected org.bdgp.io.IOOperation	op
protected DAS2AdapterGUI.ServerListener	server_listener

Fields inherited from class apollo.gui.GenericFileAdapterGUI

browseButton, filePaths, filter, panel, panel2, pathList, typeLabel

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

DAS2AdapterGUI()

DAS2AdapterGUI(org.bdgp.io.IOOperation op)

Method Summary

void	buildGUIForReading()
java.util.Properties	createStateInformation()
java.lang.Object	doOperation(java.lang.Object values) This is where the real work starts--we read the data or write it.
void	finishGUIForReading() Not currently used
java.util.Properties	getProperties() This must run after the server successfully finishes the doOperation() method - i.e.
DASDsn	getSelectedDSN() This returns an actual DASDsn - either the source id or the MapMaster attribute will give the URL of the annotated source.
java.lang.String	getSelectedHistory()
DASSegment	getSelectedSegment()
java.lang.String	getSelectedServer()
void	init()
void	setDataAdapter(org.bdgp.io.DataAdapter driver) Sets the data adapter for this UI.
void	setIOOperation(org.bdgp.io.IOOperation op) Breaking this out because it gets called separately if you want to save or load data during an already-running Apollo session
void	setProperties(java.util.Properties in) This gets called when Apollo starts up (and probably elsewhere as well) and is responsible for the initialisation of the listboxes.
protected void	setSelectedSegmentWithId(java.lang.String id, java.util.Vector model, javax.swing.JComboBox list)
protected void	setSelectedSourceWithId(java.lang.String id, java.util.Vector model, javax.swing.JComboBox list)
protected void	setSelection(java.lang.Object item, java.util.Vector model, javax.swing.JComboBox list) Sets the input model to be that of the list.
protected void	updateSegments()
protected void	updateVersionedSources()

Methods inherited from class apollo.gui.GenericFileAdapterGUI

attachListeners, browseFiles, buildGUI, fileBrowser, fileBrowser, getFileFilter, getPanel, getPathListWidth, getSelectedPath, initGUI, setFileFilter, setPathListWidth, validOperation

Methods inherited from class org.bdgp.swing.AbstractDataAdapterUI

setInput

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

MAX_HISTORY_LENGTH

public static final int MAX_HISTORY_LENGTH

See Also:

Constant Field Values

driver

protected DAS2Adapter driver

op

protected org.bdgp.io.IOOperation op

server_listener

protected DAS2AdapterGUI.ServerListener server_listener

dsn_listener

protected DAS2AdapterGUI.DSNListener dsn_listener

history_listener

protected DAS2AdapterGUI.HistoryListener history_listener

Constructor Detail

DAS2AdapterGUI

public DAS2AdapterGUI()

DAS2AdapterGUI

public DAS2AdapterGUI(org.bdgp.io.IOOperation op)

Method Detail

setIOOperation

public void setIOOperation(org.bdgp.io.IOOperation op)

Breaking this out because it gets called separately if you want to save or load data during an already-running Apollo session

init

public void init()

buildGUIForReading

public void buildGUIForReading()

setDataAdapter

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

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 GenericFileAdapterGUI

createStateInformation

public java.util.Properties createStateInformation()

Specified by:

createStateInformation in interface ApolloDataAdapterGUI

setProperties

public void setProperties(java.util.Properties in)

This gets called when Apollo starts up (and probably elsewhere as well) and is responsible for the initialisation of the listboxes.

Specified by:

setProperties in interface org.bdgp.io.DataAdapterUI

Overrides:

setProperties in class GenericFileAdapterGUI

getProperties

public java.util.Properties getProperties()

This must run after the server successfully finishes the doOperation() method - i.e. after a successful read. Copy the data from the server,dsn,entry point and range into a string, insert into the history dropdown. Then copy the contents of both dropdowns into the properies file, which you return.

-- of course, you omit any "choose..." prompts in the dropdowns when copying into the properties files.

One nice side-effect of the timing of this method is that unsuccessful url's don't seem to get copied into the history.

Specified by:

getProperties in interface org.bdgp.io.DataAdapterUI

Overrides:

getProperties in class GenericFileAdapterGUI

finishGUIForReading

public void finishGUIForReading()

Not currently used

getSelectedServer

public java.lang.String getSelectedServer()

getSelectedDSN

public DASDsn getSelectedDSN()

This returns an actual DASDsn - either the source id or the MapMaster attribute will give the URL of the annotated source.

getSelectedSegment

public DASSegment getSelectedSegment()

getSelectedHistory

public java.lang.String getSelectedHistory()

updateVersionedSources

protected void updateVersionedSources()

updateSegments

protected void updateSegments()

doOperation

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

This is where the real work starts--we read the data or write it.

Specified by:

doOperation in interface org.bdgp.io.DataAdapterUI

Throws:

org.bdgp.io.DataAdapterException

setSelection

protected void setSelection(java.lang.Object item,
                            java.util.Vector model,
                            javax.swing.JComboBox list)

Sets the input model to be that of the list. Additionally, if the input list contains the item, then select it. Otherwise, add it into the list.

setSelectedSourceWithId

protected void setSelectedSourceWithId(java.lang.String id,
                                       java.util.Vector model,
                                       javax.swing.JComboBox list)

setSelectedSegmentWithId

protected void setSelectedSegmentWithId(java.lang.String id,
                                        java.util.Vector model,
                                        javax.swing.JComboBox list)