org.biojava.spice.manypanel
Class BrowserPane

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  org.biojava.spice.manypanel.BrowserPane

All Implemented Interfaces:

Accessible, ChangeListener, DasSourceListener, EventListener, ImageObserver, MenuContainer, Serializable

public class BrowserPane

extends JPanel

implements DasSourceListener, ChangeListener

The main Container for the different sequence and alignment panels

Author:

Andreas Prlic

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class javax.swing.JPanel

JPanel.AccessibleJPanel

Nested classes inherited from class javax.swing.JComponent

JComponent.AccessibleJComponent

Nested classes inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

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

BrowserPane(String PDBCOORDSYS)
create a BrowserPane that only has a structure Panel

BrowserPane(String PDBCOORDSYS, String UNIPROTCOORDSYS, String ENSPCOORDSYS)
create a browserPane that has PDB, Uniprot and ENSP panels

Method Summary

void	addDasSourceListener(DasSourceListener li)
void	addEnspListener(ObjectListener li)
void	addEnspSequenceListener(SequenceListener li)
void	addEnspSpiceFeatureListener(SpiceFeatureListener li)
void	addPDBPositionListener(SequenceListener li)
void	addPDBSequenceListener(SequenceListener li)
void	addPDBSpiceFeatureListener(SpiceFeatureListener li)
void	addStructureListener(StructureListener li)
void	addUniProtListener(ObjectListener li)
void	addUniProtSequenceListener(SequenceListener li)
void	addUniProtSpiceFeatureListener(SpiceFeatureListener li)
void	clearDasSources()
void	clearDisplay()
void	clearListeners() removes all listeners
void	disableDasSource(DasSourceEvent dsEvent) a DAS source has been disabled
void	enableDasSource(DasSourceEvent dsEvent) a DAS source has been enabled
SpiceDasSource[]	getAlignmentServers(List sources, DasCoordinateSystem cs1, DasCoordinateSystem cs2) test if a server is a UniProt vs PDBresnum alignment server
AlignmentManager	getBottomAlignmentManager()
SequenceManager	getENSPManager()
SequenceListener[]	getPDBSequenceListener()
StructureListener[]	getStructureListener()
StructureManager	getStructureManager()
StructureRenderer	getStructureRenderer()
AlignmentManager	getTopAlignmentManager()
SequenceManager	getUPManager()
void	loadingFinished(DasSourceEvent ds) the loading of the features of this das source has finished
void	loadingStarted(DasSourceEvent ds) the features of this das source are being loaded
void	newDasSource(DasSourceEvent dsEvent) a new DAS source to be added
void	removeDasSource(DasSourceEvent dsEvent) remove a DAS source
void	removeEnspSequenceListener(SequenceListener li)
void	removeStructureListener(StructureListener li)
void	removeUniProtSequenceListener(SequenceListener li)
void	selectedDasSource(DasSourceEvent ds) a DAS source has been selected (in the GUI)
void	setDasSources(SpiceDasSource[] sources) set all das sources at once
void	setSeqSelection(int start, int end)
void	stateChanged(ChangeEvent e)
void	triggerLoadENSP(String enspCode)
void	triggerLoadStructure(String pdbcode)
void	triggerLoadUniProt(String accessionCode)

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addPropertyChangeListener, addPropertyChangeListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getGraphics, getHeight, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPreferredSize, getPropertyChangeListeners, getPropertyChangeListeners, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFont, setForeground, 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, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, 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, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, 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, processMouseEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, 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

BrowserPane

public BrowserPane(String PDBCOORDSYS)

create a BrowserPane that only has a structure Panel

Parameters:

PDBCOORDSYS -

BrowserPane

public BrowserPane(String PDBCOORDSYS,
                   String UNIPROTCOORDSYS,
                   String ENSPCOORDSYS)

create a browserPane that has PDB, Uniprot and ENSP panels

Parameters:

PDBCOORDSYS -

UNIPROTCOORDSYS -

ENSPCOORDSYS -

Method Detail

stateChanged

public void stateChanged(ChangeEvent e)

Specified by:

stateChanged in interface ChangeListener

disableDasSource

public void disableDasSource(DasSourceEvent dsEvent)

Description copied from interface: DasSourceListener

a DAS source has been disabled

Specified by:

disableDasSource in interface DasSourceListener

Parameters:

dsEvent -

enableDasSource

public void enableDasSource(DasSourceEvent dsEvent)

Description copied from interface: DasSourceListener

a DAS source has been enabled

Specified by:

enableDasSource in interface DasSourceListener

Parameters:

dsEvent -

removeDasSource

public void removeDasSource(DasSourceEvent dsEvent)

Description copied from interface: DasSourceListener

remove a DAS source

Specified by:

removeDasSource in interface DasSourceListener

Parameters:

dsEvent - an event

newDasSource

public void newDasSource(DasSourceEvent dsEvent)

Description copied from interface: DasSourceListener

a new DAS source to be added

Specified by:

newDasSource in interface DasSourceListener

Parameters:

dsEvent - an event

setDasSources

public void setDasSources(SpiceDasSource[] sources)

set all das sources at once

Parameters:

sources -

clearDasSources

public void clearDasSources()

selectedDasSource

public void selectedDasSource(DasSourceEvent ds)

Description copied from interface: DasSourceListener

a DAS source has been selected (in the GUI)

Specified by:

selectedDasSource in interface DasSourceListener

Parameters:

ds -

addPDBPositionListener

public void addPDBPositionListener(SequenceListener li)

addPDBSpiceFeatureListener

public void addPDBSpiceFeatureListener(SpiceFeatureListener li)

addUniProtSpiceFeatureListener

public void addUniProtSpiceFeatureListener(SpiceFeatureListener li)

addEnspSpiceFeatureListener

public void addEnspSpiceFeatureListener(SpiceFeatureListener li)

addStructureListener

public void addStructureListener(StructureListener li)

removeStructureListener

public void removeStructureListener(StructureListener li)

getStructureListener

public StructureListener[] getStructureListener()

addPDBSequenceListener

public void addPDBSequenceListener(SequenceListener li)

getPDBSequenceListener

public SequenceListener[] getPDBSequenceListener()

addUniProtListener

public void addUniProtListener(ObjectListener li)

addUniProtSequenceListener

public void addUniProtSequenceListener(SequenceListener li)

removeUniProtSequenceListener

public void removeUniProtSequenceListener(SequenceListener li)

addEnspListener

public void addEnspListener(ObjectListener li)

addEnspSequenceListener

public void addEnspSequenceListener(SequenceListener li)

removeEnspSequenceListener

public void removeEnspSequenceListener(SequenceListener li)

addDasSourceListener

public void addDasSourceListener(DasSourceListener li)

triggerLoadStructure

public void triggerLoadStructure(String pdbcode)

triggerLoadUniProt

public void triggerLoadUniProt(String accessionCode)

triggerLoadENSP

public void triggerLoadENSP(String enspCode)

getTopAlignmentManager

public AlignmentManager getTopAlignmentManager()

getBottomAlignmentManager

public AlignmentManager getBottomAlignmentManager()

clearDisplay

public void clearDisplay()

clearListeners

public void clearListeners()

removes all listeners

getStructureManager

public StructureManager getStructureManager()

getStructureRenderer

public StructureRenderer getStructureRenderer()

getUPManager

public SequenceManager getUPManager()

getENSPManager

public SequenceManager getENSPManager()

setSeqSelection

public void setSeqSelection(int start,
                            int end)

getAlignmentServers

public SpiceDasSource[] getAlignmentServers(List sources,
                                            DasCoordinateSystem cs1,
                                            DasCoordinateSystem cs2)

test if a server is a UniProt vs PDBresnum alignment server

Parameters:

sources -

cs1 -

cs2 -

Returns:

an array of SpiceDasSources

loadingFinished

public void loadingFinished(DasSourceEvent ds)

Description copied from interface: DasSourceListener

the loading of the features of this das source has finished

Specified by:

loadingFinished in interface DasSourceListener

Parameters:

ds -

loadingStarted

public void loadingStarted(DasSourceEvent ds)

Description copied from interface: DasSourceListener

the features of this das source are being loaded

Specified by:

loadingStarted in interface DasSourceListener

Parameters:

ds -