com.compomics.util.gui.spectrum
Class FragmentIonTable

java.lang.Object
  extended by java.awt.Component
      extended by java.awt.Container
          extended by javax.swing.JComponent
              extended by javax.swing.JTable
                  extended by com.compomics.util.gui.spectrum.FragmentIonTable
All Implemented Interfaces:
java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.event.CellEditorListener, javax.swing.event.ListSelectionListener, javax.swing.event.RowSorterListener, javax.swing.event.TableColumnModelListener, javax.swing.event.TableModelListener, javax.swing.Scrollable

public class FragmentIonTable
extends javax.swing.JTable

Creates a fragment ion table with the detected fragment ions. Either shows a traditional ion table with the theoretical fragment ions, or a novel version showing the intensities as bar charts for each ion type.

Author:
Harald Barsnes
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class javax.swing.JTable
javax.swing.JTable.AccessibleJTable, javax.swing.JTable.DropLocation, javax.swing.JTable.PrintMode
 
Nested classes/interfaces inherited from class javax.swing.JComponent
javax.swing.JComponent.AccessibleJComponent
 
Nested classes/interfaces inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Nested classes/interfaces inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy
 
Field Summary
 
Fields inherited from class javax.swing.JTable
AUTO_RESIZE_ALL_COLUMNS, AUTO_RESIZE_LAST_COLUMN, AUTO_RESIZE_NEXT_COLUMN, AUTO_RESIZE_OFF, AUTO_RESIZE_SUBSEQUENT_COLUMNS, autoCreateColumnsFromModel, autoResizeMode, cellEditor, cellSelectionEnabled, columnModel, dataModel, defaultEditorsByColumnClass, defaultRenderersByColumnClass, editingColumn, editingRow, editorComp, gridColor, preferredViewportSize, rowHeight, rowMargin, rowSelectionAllowed, selectionBackground, selectionForeground, selectionModel, showHorizontalLines, showVerticalLines, tableHeader
 
Fields inherited from class javax.swing.JComponent
accessibleContext, 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
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
FragmentIonTable(Peptide currentPeptide, java.util.ArrayList<java.util.ArrayList<IonMatch>> allAnnotations, java.util.ArrayList<MSnSpectrum> allSpectra, java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes, boolean singleCharge, boolean twoCharges)
          Creates a novel fragment ion table displaying bar charts with the intensity of each fragment ion type.
FragmentIonTable(Peptide currentPeptide, java.util.ArrayList<IonMatch> annotations, java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes, boolean singleCharge, boolean twoCharges)
          Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.
 
Method Summary
protected  javax.swing.table.JTableHeader createDefaultTableHeader()
           
 
Methods inherited from class javax.swing.JTable
addColumn, addColumnSelectionInterval, addNotify, addRowSelectionInterval, changeSelection, clearSelection, columnAdded, columnAtPoint, columnMarginChanged, columnMoved, columnRemoved, columnSelectionChanged, configureEnclosingScrollPane, convertColumnIndexToModel, convertColumnIndexToView, convertRowIndexToModel, convertRowIndexToView, createDefaultColumnModel, createDefaultColumnsFromModel, createDefaultDataModel, createDefaultEditors, createDefaultRenderers, createDefaultSelectionModel, createScrollPaneForTable, doLayout, editCellAt, editCellAt, editingCanceled, editingStopped, getAccessibleContext, getAutoCreateColumnsFromModel, getAutoCreateRowSorter, getAutoResizeMode, getCellEditor, getCellEditor, getCellRect, getCellRenderer, getCellSelectionEnabled, getColumn, getColumnClass, getColumnCount, getColumnModel, getColumnName, getColumnSelectionAllowed, getDefaultEditor, getDefaultRenderer, getDragEnabled, getDropLocation, getDropMode, getEditingColumn, getEditingRow, getEditorComponent, getFillsViewportHeight, getGridColor, getIntercellSpacing, getModel, getPreferredScrollableViewportSize, getPrintable, getRowCount, getRowHeight, getRowHeight, getRowMargin, getRowSelectionAllowed, getRowSorter, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getSelectedColumn, getSelectedColumnCount, getSelectedColumns, getSelectedRow, getSelectedRowCount, getSelectedRows, getSelectionBackground, getSelectionForeground, getSelectionModel, getShowHorizontalLines, getShowVerticalLines, getSurrendersFocusOnKeystroke, getTableHeader, getToolTipText, getUI, getUIClassID, getUpdateSelectionOnSort, getValueAt, initializeLocalVars, isCellEditable, isCellSelected, isColumnSelected, isEditing, isRowSelected, moveColumn, paramString, prepareEditor, prepareRenderer, print, print, print, print, print, processKeyBinding, removeColumn, removeColumnSelectionInterval, removeEditor, removeNotify, removeRowSelectionInterval, resizeAndRepaint, rowAtPoint, selectAll, setAutoCreateColumnsFromModel, setAutoCreateRowSorter, setAutoResizeMode, setCellEditor, setCellSelectionEnabled, setColumnModel, setColumnSelectionAllowed, setColumnSelectionInterval, setDefaultEditor, setDefaultRenderer, setDragEnabled, setDropMode, setEditingColumn, setEditingRow, setFillsViewportHeight, setGridColor, setIntercellSpacing, setModel, setPreferredScrollableViewportSize, setRowHeight, setRowHeight, setRowMargin, setRowSelectionAllowed, setRowSelectionInterval, setRowSorter, setSelectionBackground, setSelectionForeground, setSelectionMode, setSelectionModel, setShowGrid, setShowHorizontalLines, setShowVerticalLines, setSurrendersFocusOnKeystroke, setTableHeader, setUI, setUpdateSelectionOnSort, setValueAt, sizeColumnsToFit, sizeColumnsToFit, sorterChanged, tableChanged, unconfigureEnclosingScrollPane, updateUI, valueChanged
 
Methods inherited from class javax.swing.JComponent
addAncestorListener, 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, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, 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, 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, transferFocusBackward, 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, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, 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, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

FragmentIonTable

public FragmentIonTable(Peptide currentPeptide,
                        java.util.ArrayList<IonMatch> annotations,
                        java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes,
                        boolean singleCharge,
                        boolean twoCharges)
Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.

Parameters:
currentPeptide - the peptide to show the table for
annotations - the spectrum annotations (from SpectrumAnnotator)
currentFragmentIonTypes - the list of currently selected fragment ion types
singleCharge - if true, singly charge ions are included in the table
twoCharges - if true, doubly charged ions are included in the table

FragmentIonTable

public FragmentIonTable(Peptide currentPeptide,
                        java.util.ArrayList<java.util.ArrayList<IonMatch>> allAnnotations,
                        java.util.ArrayList<MSnSpectrum> allSpectra,
                        java.util.ArrayList<PeptideFragmentIon.PeptideFragmentIonType> currentFragmentIonTypes,
                        boolean singleCharge,
                        boolean twoCharges)
Creates a novel fragment ion table displaying bar charts with the intensity of each fragment ion type. If more than one spectrum annotation set is provided the bars show the average intensities.

Parameters:
currentPeptide - the peptide to show the table for
allAnnotations - the spectrum annotations (from SpectrumAnnotator)
allSpectra - the list of spectra
currentFragmentIonTypes - the list of currently selected fragment ion types
singleCharge - if true, singly charge ions are included in the table
twoCharges - if true, doubly charged ions are included in the table
Method Detail

createDefaultTableHeader

protected javax.swing.table.JTableHeader createDefaultTableHeader()
Overrides:
createDefaultTableHeader in class javax.swing.JTable


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