Package eu.isas.peptideshaker.gui.tabpanels

Class ProteinStructurePanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

eu.isas.peptideshaker.gui.tabpanels.ProteinStructurePanel

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible

public class ProteinStructurePanel
extends JPanel

The Protein Structure tab.

Author:

Harald Barsnes, Yehia Farag

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	ProteinStructurePanel.JmolPanel	A simple class for displaying a Jmol viewer in a JPanel.

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

JPanel.AccessibleJPanel

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

JComponent.AccessibleJComponent

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.JComponent

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

accessibleContext, 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

Constructor Summary

Constructors

Constructor	Description
ProteinStructurePanel(PeptideShakerGUI peptideShakerGUI)	Creates a new ProteinPanel.

Method Summary

Modifier and Type	Method	Description
void	clearData()	Clear all the data.
void	displayResults()	Displays the results in the result tables.
long[]	getDisplayedPeptides()	Returns a list of keys of the displayed peptides.
long[]	getDisplayedProteins()	Returns a list of keys of the displayed proteins.
String	getPDBAccesionLink(String pdbAccession)	Returns the PDB accession number as a web link to the given structure at https://www.rcsb.org.
JTable	getPeptideTable()	Returns the peptide table.
JTable	getProteinTable()	Returns the protein table.
void	newItemSelection()	Provides to the PeptideShakerGUI instance the currently selected protein, peptide and PSM.
void	selfUpdating(boolean selfUpdating)	Deactivates the self updating tables.
void	showSparkLines(boolean showSparkLines)	Displays or hide sparklines in the tables.
void	spinModel(boolean spin)	Turns the spinning of the model on or off.
void	updateMainMatch(String mainMatch, int proteinInferenceType)	Update the main match for the given row in the protein table.
void	updateModelType()	Updates the model type if the Jmol structure is currently visible.
void	updateModificationColors()	Update the PTM color coding.
void	updatePeptideProteinInference(int proteinInferenceType)	Update the protein inference type for the currently selected peptide.
void	updateScores()	Hides or displays the score columns in the protein and peptide tables.
void	updateSelection(boolean scrollToVisible)	Update the selected protein and peptide.

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, getBaseline, getBaselineResizeBehavior, 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, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, 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, 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, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, 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, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

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

Constructor Details

ProteinStructurePanel

public ProteinStructurePanel(PeptideShakerGUI peptideShakerGUI)

Creates a new ProteinPanel.

Parameters:

peptideShakerGUI - the PeptideShaker main frame

Method Details

getDisplayedProteins

public long[] getDisplayedProteins()

Returns a list of keys of the displayed proteins.

Returns:

a list of keys of the displayed proteins

getDisplayedPeptides

public long[] getDisplayedPeptides()

Returns a list of keys of the displayed peptides.

Returns:

a list of keys of the displayed peptides

displayResults

public void displayResults()

Displays the results in the result tables.

updateModelType

public void updateModelType()

Updates the model type if the Jmol structure is currently visible.

showSparkLines

public void showSparkLines(boolean showSparkLines)

Displays or hide sparklines in the tables.

Parameters:

showSparkLines - boolean indicating whether sparklines shall be displayed or hidden

getPDBAccesionLink

public String getPDBAccesionLink(String pdbAccession)

Returns the PDB accession number as a web link to the given structure at https://www.rcsb.org.

Parameters:

pdbAccession - the PDB accession number

Returns:

the PDB accession web link

updateMainMatch

public void updateMainMatch(String mainMatch,
 int proteinInferenceType)

Update the main match for the given row in the protein table.

Parameters:

mainMatch - the protein match to use

proteinInferenceType - the protein inference group type

spinModel

public void spinModel(boolean spin)

Turns the spinning of the model on or off.

Parameters:

spin - if true the spinning is turned on.

getProteinTable

public JTable getProteinTable()

Returns the protein table.

Returns:

the protein table

getPeptideTable

public JTable getPeptideTable()

Returns the peptide table.

Returns:

the peptide table

updateScores

public void updateScores()

Hides or displays the score columns in the protein and peptide tables.

updateModificationColors

public void updateModificationColors()

Update the PTM color coding.

updatePeptideProteinInference

public void updatePeptideProteinInference(int proteinInferenceType)

Update the protein inference type for the currently selected peptide.

Parameters:

proteinInferenceType - the protein inference type

updateSelection

public void updateSelection(boolean scrollToVisible)

Update the selected protein and peptide.

Parameters:

scrollToVisible - if true the table also scrolls to make the selected row visible

newItemSelection

public void newItemSelection()

Provides to the PeptideShakerGUI instance the currently selected protein, peptide and PSM.

clearData

public void clearData()

Clear all the data.

selfUpdating

public void selfUpdating(boolean selfUpdating)

Deactivates the self updating tables.

Parameters:

selfUpdating - boolean indicating whether the tables should update their content