com.compomics.util.protein_sequences_manager.gui

Class SequenceDbDetailsDialog

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Dialog

javax.swing.JDialog

com.compomics.util.protein_sequences_manager.gui.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

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 and Description
static String	lastFolderKey The key to use to store FASTA files paths.

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
SequenceDbDetailsDialog(Dialog owner, Frame parent, LastSelectedFolder lastSelectedFolder, boolean dbEditable, Image normalImange, Image waitingImage) Creates a new SequenceDbDetailsDialog with a dialog as owner.
SequenceDbDetailsDialog(Frame parent, LastSelectedFolder lastSelectedFolder, boolean dbEditable, Image normalImange, Image waitingImage) Creates a new SequenceDbDetailsDialog.

Method Summary

Modifier and Type	Method and Description
void	generateTargetDecoyDatabase(File targetFile, ProgressDialogX progressDialog) Appends decoy sequences to the given target database file.
String	getLastSelectedFolder() Returns the last selected folder.
void	loadUserPreferences() Loads the user preferences.
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 db and loads its information.

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

Field Detail

lastFolderKey

public static final String lastFolderKey

The key to use to store FASTA files paths.

See Also:

Constant Field Values

Constructor Detail

SequenceDbDetailsDialog

public SequenceDbDetailsDialog(Dialog owner,
                               Frame parent,
                               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

lastSelectedFolder - the last selected folder

dbEditable - if the database is editable

normalImange - the normal icon

waitingImage - the waiting icon

SequenceDbDetailsDialog

public SequenceDbDetailsDialog(Frame parent,
                               LastSelectedFolder lastSelectedFolder,
                               boolean dbEditable,
                               Image normalImange,
                               Image waitingImage)

Creates a new SequenceDbDetailsDialog.

Parameters:

parent - the parent frame

lastSelectedFolder - the last selected folder

dbEditable - if the database is editable

normalImange - the normal icon

waitingImage - the waiting icon

Method Detail

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 db and loads its information.

Parameters:

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

Returns:

true if the selection was not canceled by the user or an error occurred

generateTargetDecoyDatabase

public void generateTargetDecoyDatabase(File targetFile,
                                        ProgressDialogX progressDialog)

Appends decoy sequences to the given target database file.

Parameters:

targetFile - the target database file

progressDialog - the progress dialog

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

loadUserPreferences

public void loadUserPreferences()

Loads the user preferences.