Package eu.isas.peptideshaker.gui.pride

Class PrideReshakeGUI

java.lang.Object

java.awt.Component

java.awt.Container

java.awt.Window

java.awt.Frame

javax.swing.JFrame

eu.isas.peptideshaker.gui.pride.PrideReshakeGUI

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible, RootPaneContainer, WindowConstants

public class PrideReshakeGUI
extends JFrame

Frame for talking to the PRIDE Archive web service to select projects for reshaking.

Author:

Harald Barsnes, Marc Vaudel

See Also:

• Serialized Form

Nested Class Summary

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

JFrame.AccessibleJFrame

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

Frame.AccessibleAWTFrame

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.JFrame

accessibleContext, rootPane, rootPaneCheckingEnabled

Fields inherited from class java.awt.Frame

CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR

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
PrideReshakeGUI(PeptideShakerGUI peptideShakerGUI)	Creates a new PrideReShakeGUI frame.
PrideReshakeGUI(PeptideShakerGUI peptideShakerGUI, String pxAccession, boolean privateData)	Creates a new PrideReShakeGUI frame.

Method Summary

Modifier and Type	Method	Description
boolean	asMgf(uk.ac.ebi.pride.jaxb.model.Spectrum spectrum, BufferedWriter bw)	Writes the given spectrum to the buffered writer.
void	downloadPrideDatasets(String aWorkingFolder, ArrayList<String> selectedSpectrumFileLinks, ArrayList<String> selectedFileNames, String selectedSearchSettingsFileLink, String database, String aSpecies, ArrayList<Integer> fileSizes)	Download and convert a PRIDE project.
String	getCurrentPxAccession()	Returns the current PX accession number.
String	getCurrentSpeciesList()	Returns the list of species for the currently selected assay or project.
JTable	getFilesTable()	Returns the files table.
String	getPassword()	Returns the current password.
PeptideShakerGUI	getPeptideShakerGUI()	Returns a reference to the main GUI.
JTable	getProjectsTable()	Returns the projects table.
HashMap<String,ArrayList<String>>	getReshakeableFiles()	Returns the list of reshakable file types.
HashMap<String,ArrayList<String>>	getSearchSettingsFiles()	Returns the list of files that search settings can be extracted from.
String	getUserName()	Returns the current user name.
void	setCurrentFilterValues(String[] currentFilterValues, boolean assaysGreaterThanFiler)	Set the current filter values.
void	showProjectFilterRemovalOption(boolean show)	Show/hide the clear projects filters option.
void	updateProjectTableSelection()	Updates the project table selection.

Methods inherited from class javax.swing.JFrame

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

Methods inherited from class java.awt.Frame

addNotify, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setBackground, setCursor, setExtendedState, setMaximizedBounds, setMenuBar, setOpacity, setResizable, setShape, setState, setTitle, setUndecorated

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, hide, isActive, isAlwaysOnTop, isAlwaysOnTopSupported, isAutoRequestFocus, isFocusableWindow, isFocusCycleRoot, isFocused, isLocationByPlatform, isOpaque, isShowing, isValidateRoot, pack, paint, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, reshape, setAlwaysOnTop, setAutoRequestFocus, setBounds, setBounds, setCursor, setFocusableWindowState, setFocusCycleRoot, setIconImages, setLocation, setLocation, setLocationByPlatform, setLocationRelativeTo, setMinimumSize, setModalExclusionType, setSize, setSize, setType, setVisible, show, toBack, 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, 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

Methods inherited from interface java.awt.MenuContainer

getFont, postEvent

Constructor Details

PrideReshakeGUI

public PrideReshakeGUI(PeptideShakerGUI peptideShakerGUI)

Creates a new PrideReShakeGUI frame.

Parameters:

peptideShakerGUI - the PeptideShakerGUI parent

PrideReshakeGUI

public PrideReshakeGUI(PeptideShakerGUI peptideShakerGUI,
 String pxAccession,
 boolean privateData)

Creates a new PrideReShakeGUI frame.

Parameters:

peptideShakerGUI - the PeptideShakerGUI parent

pxAccession - the PX accession to display

privateData - if true, the private data login screen is displayed

Method Details

getProjectsTable

public JTable getProjectsTable()

Returns the projects table.

Returns:

the projects table

getPeptideShakerGUI

public PeptideShakerGUI getPeptideShakerGUI()

Returns a reference to the main GUI.

Returns:

a reference to the main GUI

downloadPrideDatasets

public void downloadPrideDatasets(String aWorkingFolder,
 ArrayList<String> selectedSpectrumFileLinks,
 ArrayList<String> selectedFileNames,
 String selectedSearchSettingsFileLink,
 String database,
 String aSpecies,
 ArrayList<Integer> fileSizes)

Download and convert a PRIDE project.

Parameters:

aWorkingFolder - the working folder

selectedSpectrumFileLinks - the selected spectrum files

selectedFileNames - the file names of the selected spectrum files

selectedSearchSettingsFileLink - the selected search settings file, can be null

database - the database

aSpecies - the current species

fileSizes - the file sizes

asMgf

public boolean asMgf(uk.ac.ebi.pride.jaxb.model.Spectrum spectrum,
 BufferedWriter bw)
              throws IOException

Writes the given spectrum to the buffered writer.

Parameters:

spectrum - the spectrum

bw - the buffered writer

Returns:

true of the spectrum could be converted to mgf

Throws:

IOException - thrown if a problem occurs when writing to the file

showProjectFilterRemovalOption

public void showProjectFilterRemovalOption(boolean show)

Show/hide the clear projects filters option.

Parameters:

show - if the option is to be shown or not

updateProjectTableSelection

public void updateProjectTableSelection()

Updates the project table selection.

setCurrentFilterValues

public void setCurrentFilterValues(String[] currentFilterValues,
 boolean assaysGreaterThanFiler)

Set the current filter values.

Parameters:

currentFilterValues - the current filter values

assaysGreaterThanFiler - the assays greater than filter

getFilesTable

public JTable getFilesTable()

Returns the files table.

Returns:

the files table

getCurrentPxAccession

public String getCurrentPxAccession()

Returns the current PX accession number. Null if no project is selected.

Returns:

the current PX accession number

getReshakeableFiles

public HashMap<String,ArrayList<String>> getReshakeableFiles()

Returns the list of reshakable file types.

Returns:

the reshakeableFiles

getSearchSettingsFiles

public HashMap<String,ArrayList<String>> getSearchSettingsFiles()

Returns the list of files that search settings can be extracted from.

Returns:

the searchSettingsFiles

getCurrentSpeciesList

public String getCurrentSpeciesList()

Returns the list of species for the currently selected assay or project. Null if no assay or project is currently selected.

Returns:

the list of species for the currently selected assay or project

getUserName

public String getUserName()

Returns the current user name.

Returns:

the userName

getPassword

public String getPassword()

Returns the current password.

Returns:

the password