apollo.analysis.filter
Class BlastFilterPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  apollo.analysis.filter.FilterPanel
                      apollo.analysis.filter.BlastFilterPanel

All Implemented Interfaces:

FilterPanelI, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class BlastFilterPanel
extends FilterPanel

See Also:

Serialized Form

Nested Class Summary

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 javax.swing.JTextField	compress_threshold
protected javax.swing.JPanel	filterConfigurationPanel
protected javax.swing.JComboBox	length_units
protected javax.swing.JCheckBox	limit_coverage
protected javax.swing.JTextField	max_coverage
protected javax.swing.JTextField	min_coincidence
protected javax.swing.JTextField	min_expect
protected javax.swing.JTextField	min_identity
protected javax.swing.JTextField	min_length
protected javax.swing.JTextField	min_score
protected javax.swing.JCheckBox	queryIsGenomic Before, query==genomic was the default.
protected javax.swing.JCheckBox	remove_lowinfo
protected javax.swing.JCheckBox	remove_shadows
protected javax.swing.JCheckBox	remove_twilight
protected javax.swing.JButton	showFilterConfiguration
protected javax.swing.JCheckBox	split_dups
protected javax.swing.JCheckBox	split_frames
protected javax.swing.JCheckBox	split_HSPs
protected javax.swing.JCheckBox	use_coincidence
protected javax.swing.JCheckBox	use_expect
protected javax.swing.JCheckBox	use_identity
protected javax.swing.JToggleButton	use_length
protected javax.swing.JCheckBox	use_score
protected javax.swing.JTextField	word_size

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

BlastFilterPanel(java.awt.Color bg_color)

Method Summary

protected void	buildGUI()
java.util.Properties	getProperties() add on the hit-information to the query-information already in there.
void	setInputs(AnalysisInput inputs) add on the hit-information to the query-information already in there.
void	setProperties(java.util.Properties properties) This contains the properties stored in the adapter history, which are read when the adapter is created.

Methods inherited from class apollo.analysis.filter.FilterPanel

getAnalysisPanel, setAnalysisPanel

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

filterConfigurationPanel

protected javax.swing.JPanel filterConfigurationPanel

showFilterConfiguration

protected javax.swing.JButton showFilterConfiguration

min_expect

protected javax.swing.JTextField min_expect

use_expect

protected javax.swing.JCheckBox use_expect

min_score

protected javax.swing.JTextField min_score

use_score

protected javax.swing.JCheckBox use_score

min_identity

protected javax.swing.JTextField min_identity

use_identity

protected javax.swing.JCheckBox use_identity

min_length

protected javax.swing.JTextField min_length

length_units

protected javax.swing.JComboBox length_units

use_length

protected javax.swing.JToggleButton use_length

min_coincidence

protected javax.swing.JTextField min_coincidence

use_coincidence

protected javax.swing.JCheckBox use_coincidence

max_coverage

protected javax.swing.JTextField max_coverage

limit_coverage

protected javax.swing.JCheckBox limit_coverage

word_size

protected javax.swing.JTextField word_size

compress_threshold

protected javax.swing.JTextField compress_threshold

remove_lowinfo

protected javax.swing.JCheckBox remove_lowinfo

remove_twilight

protected javax.swing.JCheckBox remove_twilight

remove_shadows

protected javax.swing.JCheckBox remove_shadows

split_frames

protected javax.swing.JCheckBox split_frames

split_dups

protected javax.swing.JCheckBox split_dups

split_HSPs

protected javax.swing.JCheckBox split_HSPs

queryIsGenomic

protected javax.swing.JCheckBox queryIsGenomic

Before, query==genomic was the default. Now query != genomic is the default.

Constructor Detail

BlastFilterPanel

public BlastFilterPanel(java.awt.Color bg_color)

Method Detail

buildGUI

protected void buildGUI()

getProperties

public java.util.Properties getProperties()

add on the hit-information to the query-information already in there.

Specified by:

getProperties in interface FilterPanelI

Overrides:

getProperties in class FilterPanel

setProperties

public void setProperties(java.util.Properties properties)

This contains the properties stored in the adapter history, which are read when the adapter is created. They will populate the history-comboboxes etc.

Specified by:

setProperties in interface FilterPanelI

Overrides:

setProperties in class FilterPanel

setInputs

public void setInputs(AnalysisInput inputs)

add on the hit-information to the query-information already in there.

Specified by:

setInputs in interface FilterPanelI

Overrides:

setInputs in class FilterPanel