com.compomics.util.gui.parameters.identification_parameters.algorithm_settings

Class XTandemSettingsDialog

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Dialog

javax.swing.JDialog

com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.XTandemSettingsDialog

All Implemented Interfaces:

AlgorithmSettingsDialog, ImageObserver, MenuContainer, Serializable, Accessible, RootPaneContainer, WindowConstants

public class XTandemSettingsDialog
extends JDialog
implements AlgorithmSettingsDialog

Dialog for the X!Tandem specific settings.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Nested Class Summary

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

JDialog.AccessibleJDialog

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

Dialog.AccessibleAWTDialog, Dialog.ModalExclusionType, Dialog.ModalityType

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

Window.AccessibleAWTWindow, Window.Type

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 inherited from class javax.swing.JDialog

accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Dialog

DEFAULT_MODALITY_TYPE

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

Constructor and Description
XTandemSettingsDialog(Dialog owner, Frame parent, XtandemParameters xtandemParameters, PtmSettings modificationProfile, double fragmentIonMassAccuracyInDa, boolean editable) Creates new form XtandemParametersDialog with a dialog as owner.
XTandemSettingsDialog(Frame parent, XtandemParameters xtandemParameters, PtmSettings modificationProfile, double fragmentIonMassAccuracyInDa, boolean editable) Creates new form XtandemParametersDialog with a frame as owner.

Method Summary

Modifier and Type	Method and Description
XtandemParameters	getInput() Returns the user selection as X!tandem parameters object.
PtmSettings	getModificationProfile() Returns the modification profile corresponding to the input by the user.
IdentificationAlgorithmParameter	getParameters() Returns the parameters as set by the user.
boolean	isCancelled() Indicates whether the user canceled the editing.
boolean	modProfileEdited() Returns true if the user edited the modification profile.
boolean	validateInput(boolean showMessage) Inspects the parameters validity.

Methods inherited from class javax.swing.JDialog

addImpl, createRootPane, dialogInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getGraphics, getJMenuBar, getLayeredPane, getRootPane, getTransferHandler, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, repaint, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, setTransferHandler, update

Methods inherited from class java.awt.Dialog

addNotify, getModalityType, getTitle, hide, isModal, isResizable, isUndecorated, setBackground, setModal, setModalityType, setOpacity, setResizable, setShape, setTitle, setUndecorated, setVisible, show, toBack

Methods inherited from class java.awt.Window

addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBackground, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getIconImages, getInputContext, getListeners, getLocale, getModalExclusionType, getMostRecentFocusOwner, getOpacity, getOwnedWindows, getOwner, getOwnerlessWindows, getShape, getToolkit, getType, getWarningString, getWindowFocusListeners, getWindowListeners, getWindows, getWindowStateListeners, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeNotify, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImage, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, toFront

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setName, setPreferredSize, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Constructor Detail

XTandemSettingsDialog

public XTandemSettingsDialog(Frame parent,
                             XtandemParameters xtandemParameters,
                             PtmSettings modificationProfile,
                             double fragmentIonMassAccuracyInDa,
                             boolean editable)

Creates new form XtandemParametersDialog with a frame as owner.

Parameters:

parent - the parent frame

xtandemParameters - the X!Tandem parameters

modificationProfile - the modification profile of the search

fragmentIonMassAccuracyInDa - the fragment ion mass accuracy of the mass spectrometer

editable - boolean indicating whether the settings can be edited by the user

XTandemSettingsDialog

public XTandemSettingsDialog(Dialog owner,
                             Frame parent,
                             XtandemParameters xtandemParameters,
                             PtmSettings modificationProfile,
                             double fragmentIonMassAccuracyInDa,
                             boolean editable)

Creates new form XtandemParametersDialog with a dialog as owner.

Parameters:

owner - the dialog owner

parent - the parent frame

xtandemParameters - the X!Tandem parameters

modificationProfile - the modification profile of the search

fragmentIonMassAccuracyInDa - the fragment ion mass accuracy of the mass spectrometer

editable - boolean indicating whether the settings can be edited by the user

Method Detail

isCancelled

public boolean isCancelled()

Description copied from interface: AlgorithmSettingsDialog

Indicates whether the user canceled the editing.

Specified by:

isCancelled in interface AlgorithmSettingsDialog

Returns:

true if cancel was pressed

getParameters

public IdentificationAlgorithmParameter getParameters()

Description copied from interface: AlgorithmSettingsDialog

Returns the parameters as set by the user.

Specified by:

getParameters in interface AlgorithmSettingsDialog

Returns:

the parameters as set by the user

getInput

public XtandemParameters getInput()

Returns the user selection as X!tandem parameters object.

Returns:

the user selection

getModificationProfile

public PtmSettings getModificationProfile()

Returns the modification profile corresponding to the input by the user.

Returns:

the modification profile corresponding to the input by the user

modProfileEdited

public boolean modProfileEdited()

Returns true if the user edited the modification profile. Note that it only checks if the user has made changed to the selection, not if the end result is different or not.

Returns:

true if the user edited the modification profile

validateInput

public boolean validateInput(boolean showMessage)

Inspects the parameters validity.

Parameters:

showMessage - if true an error messages are shown to the users

Returns:

a boolean indicating if the parameters are valid