Package com.compomics.util.gui.parameters.identification.search

Class SequenceDbDetailsDialog

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Dialog

javax.swing.JDialog

com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible, RootPaneContainer, WindowConstants

public class SequenceDbDetailsDialog
extends JDialog

This dialog displays information about a sequence database.

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

Modifier and Type	Field	Description
static final String	lastFolderKey	The key to use to store FASTA files paths.
static final int	SAMPLE_BATCH_SIZE	The batch size of proteins to sample.

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 java.awt.image.ImageObserver

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

Fields inherited from interface javax.swing.WindowConstants

DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, EXIT_ON_CLOSE, HIDE_ON_CLOSE

Constructor Summary

Constructors

Constructor	Description
SequenceDbDetailsDialog(Dialog owner, Frame parent, String selectedFastaFile, FastaParameters fastaParameters, LastSelectedFolder lastSelectedFolder, boolean dbEditable, Image normalImange, Image waitingImage)	Creates a new SequenceDbDetailsDialog with a dialog as owner.
SequenceDbDetailsDialog(Frame parent, String selectedFastaFile, FastaParameters fastaParameters, LastSelectedFolder lastSelectedFolder, boolean dbEditable, Image normalImange, Image waitingImage)	Creates a new SequenceDbDetailsDialog.

Method Summary

Modifier and Type	Method	Description
FastaParameters	getFastaParameters()	Returns the FASTA parameters.
String	getLastSelectedFolder()	Returns the last selected folder.
String	getSelectedFastaFile()	Returns the selected FASTA file.
boolean	isCanceled()	Returns a boolean indicating whether the database selection was canceled by the user.
File	renameFastaFileName(File file)	Copies the content of the FASTA file to a new file and replaces any white space in the file name with '_' instead.
boolean	selectDB(boolean userCanDispose)	Allows the user to select a FASTA file, loads its information, and returns a boolean indicating whether the process loading was successful.

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, 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, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, requestFocusInWindow, resize, resize, revalidate, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setMaximumSize, setMixingCutoutShape, 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

Field Details

lastFolderKey

public static final String lastFolderKey

The key to use to store FASTA files paths.

See Also:

• Constant Field Values

SAMPLE_BATCH_SIZE

public static final int SAMPLE_BATCH_SIZE

The batch size of proteins to sample.

See Also:

• Constant Field Values

Constructor Details

SequenceDbDetailsDialog

public SequenceDbDetailsDialog(Dialog owner,
 Frame parent,
 String selectedFastaFile,
 FastaParameters fastaParameters,
 LastSelectedFolder lastSelectedFolder,
 boolean dbEditable,
 Image normalImange,
 Image waitingImage)

Creates a new SequenceDbDetailsDialog with a dialog as owner.

Parameters:

owner - the dialog owner

parent - the parent frame

selectedFastaFile - the selected FASTA file

fastaParameters - the parameters used to parse the FASTA file

lastSelectedFolder - the last selected folder

dbEditable - if the database is editable

normalImange - the normal icon

waitingImage - the waiting icon

SequenceDbDetailsDialog

public SequenceDbDetailsDialog(Frame parent,
 String selectedFastaFile,
 FastaParameters fastaParameters,
 LastSelectedFolder lastSelectedFolder,
 boolean dbEditable,
 Image normalImange,
 Image waitingImage)

Creates a new SequenceDbDetailsDialog.

Parameters:

parent - the parent frame

selectedFastaFile - the selected FASTA file

fastaParameters - the parameters used to parse the FASTA file

lastSelectedFolder - the last selected folder

dbEditable - if the database is editable

normalImange - the normal icon

waitingImage - the waiting icon

Method Details

getLastSelectedFolder

public String getLastSelectedFolder()

Returns the last selected folder.

Returns:

the last selected folder

selectDB

public boolean selectDB(boolean userCanDispose)

Allows the user to select a FASTA file, loads its information, and returns a boolean indicating whether the process loading was successful.

Parameters:

userCanDispose - if true, the dialog is closed if the user cancels the selection

Returns:

a boolean indicating whether a valid FASTA file was selected

renameFastaFileName

public File renameFastaFileName(File file)

Copies the content of the FASTA file to a new file and replaces any white space in the file name with '_' instead. Returns the new file, null if an error occurred.

Parameters:

file - the FASTA file to rename

Returns:

the renamed FASTA file

getSelectedFastaFile

public String getSelectedFastaFile()

Returns the selected FASTA file.

Returns:

the selected FASTA file

getFastaParameters

public FastaParameters getFastaParameters()

Returns the FASTA parameters.

Returns:

the FASTA parameters

isCanceled

public boolean isCanceled()

Returns a boolean indicating whether the database selection was canceled by the user.

Returns:

a boolean indicating whether the database selection was canceled by the user