idare.subnetwork.internal.GUI

Class SubnetworkPropertiesSelectionGUI

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

idare.subnetwork.internal.GUI.SubnetworkPropertiesSelectionGUI

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible

public class SubnetworkPropertiesSelectionGUI
extends JPanel

A GUI for the selection of the properties for SubNetwork Generation.

Author:

Thomas Pfau

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel

JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field and Description
JComboBox<String>	colSelector
JComboBox<String>	layoutSelector

Fields inherited from class javax.swing.JComponent

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

accessibleContext, 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

Constructors

Constructor and Description
SubnetworkPropertiesSelectionGUI(Collection<String> AlgorithmNames, Vector<String> ColumnNames, org.cytoscape.model.CyNetwork network, NetworkViewSwitcher nvs, String IDCol) Generate the GUI for selection of Subnetwork generation properties

Method Summary

Modifier and Type	Method and Description
TableModel	createSubNetworkTableModel(org.cytoscape.model.CyNetwork network) Create the TableModel for the SubSystem Selection
Set<org.cytoscape.model.CyNode>	getNodesToDuplicate() Get the CyNode which should not link to other networks
Set<org.cytoscape.model.CyNode>	getNodesToRemove() Get All Nodes that are to be ignored in the SubNetwork Generation
Set<org.cytoscape.model.CyNode>	getNodesToSkip() Get the CyNode which should not link to other networks
SubNetworkProperties	getProperties() Get the Properties for the Subnetwork generation task as defined in this GUI
Vector<Object>	SubSystemsToGenerate() Get the selected SubSystems from the SubSystemSelector

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, getBaseline, getBaselineResizeBehavior, 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, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, 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, 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, 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, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

layoutSelector

public final JComboBox<String> layoutSelector

colSelector

public final JComboBox<String> colSelector

Constructor Detail

SubnetworkPropertiesSelectionGUI

public SubnetworkPropertiesSelectionGUI(Collection<String> AlgorithmNames,
                                        Vector<String> ColumnNames,
                                        org.cytoscape.model.CyNetwork network,
                                        NetworkViewSwitcher nvs,
                                        String IDCol)

Generate the GUI for selection of Subnetwork generation properties

Parameters:

AlgorithmNames - The Layout algorithms available to the generator

ColumnNames - The ColumnNames available for Subnetwork column selection

network - the CyNetwork to generate subnetworks for

nvs - the NetworkViewSwitcher Object to obtain present subnetworks from.

IDCol - The String Identifying the column used for the compound IDs

Method Detail

createSubNetworkTableModel

public TableModel createSubNetworkTableModel(org.cytoscape.model.CyNetwork network)
                                      throws NoNetworksToCreateException

Create the TableModel for the SubSystem Selection

Parameters:

network - - the CyNetworkSubsystems are created for

Returns:

A TableModel containing a list of potential Subnetworks

Throws:

NoNetworksToCreateException - if all selected networks are already created or none are equested.

SubSystemsToGenerate

public Vector<Object> SubSystemsToGenerate()

Get the selected SubSystems from the SubSystemSelector

Returns:

A Vector of all Objects which were selected

getNodesToRemove

public Set<org.cytoscape.model.CyNode> getNodesToRemove()

Get All Nodes that are to be ignored in the SubNetwork Generation

Returns:

A Set of CyNodes that are ignored for the subnetwork generation

getNodesToSkip

public Set<org.cytoscape.model.CyNode> getNodesToSkip()

Get the CyNode which should not link to other networks

Returns:

a Set of CyNodes that are not used to create links

getNodesToDuplicate

public Set<org.cytoscape.model.CyNode> getNodesToDuplicate()

Get the CyNode which should not link to other networks

Returns:

a Set of CyNodes that are not used to create links

getProperties

public SubNetworkProperties getProperties()

Get the Properties for the Subnetwork generation task as defined in this GUI

Returns:

The SubNetworkProperties to be used.