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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
org.peace_tools.generic.GenericWizardPage
org.peace_tools.core.job.FiltersWizardPage
public class FiltersWizardPage
This class serves as an interactive page in a JobWizard. This page permits the user to provide the information about the filters to be used in the job. Filters are used to weed out ESTs with undesirable characteristics (biologically speaking) that negatively impact with the quality of clusters generated by PEACE. Currently the following two filters are available in the clustering engine (and are exposed by the GUI):
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JPanel |
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javax.swing.JPanel.AccessibleJPanel |
Nested classes/interfaces inherited from class javax.swing.JComponent |
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javax.swing.JComponent.AccessibleJComponent |
Nested classes/interfaces inherited from class java.awt.Container |
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java.awt.Container.AccessibleAWTContainer |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary | |
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private javax.swing.JCheckBox |
enableLCFilter
Check box to indicate if the Low Complexity (LC) filter must be enabled for this job. |
private javax.swing.JCheckBox |
enableLenFilter
Check box to indicate if the length filter must be enabled for this job. |
private static java.lang.String |
FILTER_LIST_MSG
A generic informational message that is displayed to the user if the string list in filterList is invalid. |
private javax.swing.JTextField |
filterList
A list of comma separated strings (over ATCG) that are used to generate dummy low complexity sequences for filtering out ESTs that have low complexity regions. |
private static java.lang.String |
INFO_MSG
A generic informational message that is displayed at the top of this wizard page to provide some additional information to the user. |
private javax.swing.JSpinner |
minLen
The minimum length of the EST associated with the length filter. |
private static long |
serialVersionUID
A serialization UID to keep the compiler happy. |
private JobWizard |
wizard
A reference to the wizard dialog that logically owns this page. |
Fields inherited from class javax.swing.JComponent |
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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 |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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FiltersWizardPage(JobWizard wizard)
The constructor. |
Method Summary | |
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void |
actionPerformed(java.awt.event.ActionEvent event)
Method to handle clicking of check boxes. |
private javax.swing.JPanel |
adjustCheckBox(javax.swing.JCheckBox cb,
java.lang.String cmd)
Helper method to correctly format, enhance, and layout a given check box. |
private javax.swing.JPanel |
createLCFilterPanels()
This is a helper method that is used to create the necessary information regarding the Low Complexity (LC) filter. |
private javax.swing.JPanel |
createLenFilterPanels()
This is a helper method that is used to create the necessary information regarding the length filter. |
protected java.util.ArrayList<Filter> |
getFilters()
This method is a convenience method that can be used to obtain a FilterList object containing information from this page. |
protected java.lang.String |
getSummary()
This method is a convenience method that can be used to obtain a String summarizing the filters setup for this job. |
boolean |
pageChanging(WizardDialog dialog,
int currPage,
int nextPage)
Method to veto a page change if filter string is invalid. |
Methods inherited from class org.peace_tools.generic.GenericWizardPage |
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getPage, getSubTitle, getTitle, pageChanged, setTitle |
Methods inherited from class javax.swing.JPanel |
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getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI |
Methods inherited from class javax.swing.JComponent |
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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, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, 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 |
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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 |
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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, transferFocusBackward, transferFocusUpCycle |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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private final JobWizard wizard
private javax.swing.JCheckBox enableLenFilter
private javax.swing.JSpinner minLen
private javax.swing.JCheckBox enableLCFilter
private javax.swing.JTextField filterList
private static final java.lang.String INFO_MSG
private static final java.lang.String FILTER_LIST_MSG
private static final long serialVersionUID
Constructor Detail |
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public FiltersWizardPage(JobWizard wizard)
wizard
- The wizard that logically owns this page.Method Detail |
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private javax.swing.JPanel adjustCheckBox(javax.swing.JCheckBox cb, java.lang.String cmd)
cb
- The check box to be formatted.cmd
- The action command to be set.
private javax.swing.JPanel createLenFilterPanels()
private javax.swing.JPanel createLCFilterPanels()
public void actionPerformed(java.awt.event.ActionEvent event)
actionPerformed
in interface java.awt.event.ActionListener
protected java.util.ArrayList<Filter> getFilters()
protected java.lang.String getSummary()
public boolean pageChanging(WizardDialog dialog, int currPage, int nextPage)
pageChanging
in interface WizardPage
pageChanging
in class GenericWizardPage
dialog
- The wizard dialog that is invoking this method.currPage
- The logical (zero-based) index of the current
page in the sequence of pages in the wizard.nextPage
- The logical (zero-based) index of the next
page that is going to be displayed.
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