apollo.dataadapter.analysis
Class AnalysisPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  apollo.dataadapter.analysis.AnalysisPanel

All Implemented Interfaces:

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

public class AnalysisPanel
extends javax.swing.JPanel

This is only used by AnalysisAdapterGUI. It was an inner class of it, but it seems to have outgrown innerclassness, so I broke it out into its own class AnalysisPanel class represents a panel within the JTabbedPane For now this is hardwired with one JComboBox to get input from change later if have different kinds of panels

See Also:

Serialized Form

Nested Class Summary

class	AnalysisPanel.displayTierItemListener Where will the blast analysis results appear, name that tier.
class	AnalysisPanel.fileItemListener Which file contains the analysis results

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 CurationSet	curation
protected static java.lang.String	DEFAULT_TIER
protected static java.lang.String	DEFAULT_TYPE
protected javax.swing.JComboBox	displayTierBox
protected javax.swing.JComboBox	displayTypeBox
protected static java.lang.String	file_prop
protected javax.swing.JComboBox	fileBox
protected AnalysisFilterI	filter
protected FilterPanel	filterPanel
protected static java.lang.String	offset_label
javax.swing.JTextField	offsetField
protected AnalysisAdapterGUI	parent
protected AnalysisParserI	parser
protected static java.lang.String	seq_label
protected static java.lang.String	seq_prop
protected javax.swing.JTextField	seqField
protected static java.lang.String	tier_label
protected static java.lang.String	type_label

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

Method Summary

protected void	addDisplayComponents() Default display type entry component is JComboBox
protected void	addToPanel(javax.swing.JComponent comp)
protected void	buildGUI()
protected java.lang.String	getCurrentFile()
protected AnalysisInput	getCurrentInput() Fills in the data structure with all of the values that the user has selected
protected java.lang.String	getCurrentSeq()
protected java.lang.String	getCurrentTier()
AnalysisFilterI	getFilter()
DataInputType	getInputType()
protected short	getMaxHistoryLength()
AnalysisParserI	getParser()
java.util.Properties	getProperties() Puts the size of history and all the history items into Properties prop
void	initTiersList(java.lang.String tier)
void	initTypesList(java.lang.String tier)
protected boolean	isNewCuration()
protected void	recordCurrentFileProperties()
protected java.lang.String	recordCurrentTierProperties() Puts currently selected item at top of history list
protected void	setFileProperties(java.lang.String file)
protected void	setInputs(AnalysisInput in)
void	setProperties(java.util.Properties combinedProperties) Walk each property we've been handed.
protected void	setTierProperties(java.lang.String tier)

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

fileBox

protected javax.swing.JComboBox fileBox

seqField

protected javax.swing.JTextField seqField

displayTierBox

protected javax.swing.JComboBox displayTierBox

displayTypeBox

protected javax.swing.JComboBox displayTypeBox

offsetField

public javax.swing.JTextField offsetField

parent

protected AnalysisAdapterGUI parent

curation

protected CurationSet curation

seq_label

protected static java.lang.String seq_label

tier_label

protected static java.lang.String tier_label

type_label

protected static java.lang.String type_label

file_prop

protected static java.lang.String file_prop

seq_prop

protected static java.lang.String seq_prop

offset_label

protected static java.lang.String offset_label

DEFAULT_TYPE

protected static java.lang.String DEFAULT_TYPE

DEFAULT_TIER

protected static java.lang.String DEFAULT_TIER

parser

protected AnalysisParserI parser

filter

protected AnalysisFilterI filter

filterPanel

protected FilterPanel filterPanel

Method Detail

getParser

public AnalysisParserI getParser()

getFilter

public AnalysisFilterI getFilter()

getMaxHistoryLength

protected short getMaxHistoryLength()

setInputs

protected void setInputs(AnalysisInput in)

isNewCuration

protected boolean isNewCuration()

getCurrentFile

protected java.lang.String getCurrentFile()

getCurrentSeq

protected java.lang.String getCurrentSeq()

getCurrentTier

protected java.lang.String getCurrentTier()

getCurrentInput

protected AnalysisInput getCurrentInput()

Fills in the data structure with all of the values that the user has selected

getInputType

public DataInputType getInputType()

buildGUI

protected void buildGUI()

addDisplayComponents

protected void addDisplayComponents()

Default display type entry component is JComboBox

addToPanel

protected void addToPanel(javax.swing.JComponent comp)

getProperties

public java.util.Properties getProperties()

Puts the size of history and all the history items into Properties prop

recordCurrentTierProperties

protected java.lang.String recordCurrentTierProperties()

Puts currently selected item at top of history list

recordCurrentFileProperties

protected void recordCurrentFileProperties()

initTiersList

public void initTiersList(java.lang.String tier)

initTypesList

public void initTypesList(java.lang.String tier)

setProperties

public void setProperties(java.util.Properties combinedProperties)

Walk each property we've been handed. Strip off the analysis name at the front of the property, and gather the properties into analysis-specific groups.

Add to these properties the configuration information in the analysis

Call setProperties() on each analysis' adapter panel, passing in the specific groups we've gathered.

setTierProperties

protected void setTierProperties(java.lang.String tier)

setFileProperties

protected void setFileProperties(java.lang.String file)