charite.christo.strap
Class DialogDotPlot

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  charite.christo.ChPanel
                      charite.christo.strap.AbstractDialogJPanel
                          charite.christo.strap.DialogDotPlot

All Implemented Interfaces:

Disposable, HasControlPanel, PaintHook, ProcessEv, StrapListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible, javax.swing.Scrollable

public class DialogDotPlot
extends AbstractDialogJPanel
implements Disposable, HasControlPanel, StrapListener, PaintHook, ProcessEv

HELP A dot-plot is a correlogram of two sequence WIKI:Dot_plot_(bioinformatics). Each dot in the pane represents a pair of residues from either protein. The brightness of the dot is mainly determined by the similarity of both amino acids according to the blosum62 matrix. A number of positions up and downstream are taken into account with declining weight.

GUI-controls:

• Slider: The width of the low pass filter with Co-sinus weights.
• Slider: The brightness of the entire plot.
• Combo box: The proteins of the X axis and Y axis.
• Toggle CB:DialogDotPlot#CB_LAB_Trace: View the trace of the sequence alignment.

Anchor points:
Anchor points can be set by clicking into the pane and are marked in the multiple sequence alignment and the scrollbar. The idea is to chose an anchor point on a bright oblique line with high sequence similarity. Subsequently, one can introduce gaps into the proteins until the corresponding marks coincide in the multiple sequence alignment pane.

Periodicity Sequence periodicity becomes evident by more than one white oblique trace. See PDB:1g61 for an example.

Save ink while printing: JCOMPONENT:ChUtils#buttn(TOG_WHITE_BG)!

Related links: PUBMED:15724278 MOL_TOOLKIT:dnadot

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JComponent.AccessibleJComponent

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

java.awt.Component.BaselineResizeBehavior

Field Summary

static long	BL2SEQ
static long	CB_HITS
static java.lang.String	CB_LAB_Trace
static long	NUCLEOTIDES

Fields inherited from class charite.christo.ChPanel

KEY_REPRESENT_COMPONENT

Fields inherited from class javax.swing.JComponent

TOOL_TIP_TEXT_KEY, 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 charite.christo.Disposable

NONE

Fields inherited from interface java.awt.image.ImageObserver

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

Constructor Summary

DialogDotPlot()

DialogDotPlot(long options, Protein pX, Protein pY)

Method Summary

void	addPoints(byte[] tX, int startX, boolean revX, int fromX, byte[] tY, int startY, boolean revY, int fromY, double score, int[][] vHits)
void	dispose()
javax.swing.JComponent	getControlPanel(boolean real)
byte[]	getSeq(char X_or_Y)
short[][]	getValues(byte[] seqX, char tX, byte[] seqY, char tY, int w, int h, int[] weights)
void	handleEvent(StrapEvent ev)
boolean	isNucleotide(char X_or_Y)
BA	log()
boolean	paintHook(javax.swing.JComponent component, java.awt.Graphics g, boolean after)
void	processEv(java.awt.AWTEvent ev)
void	setBl2seq(int[][] data, java.lang.Object hasCtrlPnl)

Methods inherited from class charite.christo.strap.AbstractDialogJPanel

isDisposed, pTop

Methods inherited from class charite.christo.ChPanel

cp, getDndDateien, getMaximumSize, getPreferredScrollableViewportSize, getPreferredSize, getScrollableBlockIncrement, getScrollableTracksViewportHeight, getScrollableTracksViewportWidth, getScrollableUnitIncrement, getToolTipLocation, getToolTipText, getWhenPainted, invalidate, isAlreadyPainted, isEnabled, isShowing, isValidateRoot, paint, paintChildren, paintComponent, processEvent, removeAll

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMinimumSize, getNextFocusableComponent, getPopupLocation, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingTile, isRequestFocusEnabled, paintImmediately, paintImmediately, print, printAll, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, 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, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, remove, remove, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusBackward, transferFocusDownCycle, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, createImage, createImage, createVolatileImage, createVolatileImage, dispatchEvent, enable, enableInputMethods, 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, 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, postEvent, prepareImage, prepareImage, 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

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

BL2SEQ

public static final long BL2SEQ

See Also:

Constant Field Values

CB_HITS

public static final long CB_HITS

See Also:

Constant Field Values

NUCLEOTIDES

public static final long NUCLEOTIDES

See Also:

Constant Field Values

CB_LAB_Trace

public static final java.lang.String CB_LAB_Trace

See Also:

Constant Field Values

Constructor Detail

DialogDotPlot

public DialogDotPlot()

DialogDotPlot

public DialogDotPlot(long options,
                     Protein pX,
                     Protein pY)

Method Detail

dispose

public void dispose()

Specified by:

dispose in interface Disposable

Overrides:

dispose in class AbstractDialogJPanel

getSeq

public byte[] getSeq(char X_or_Y)

isNucleotide

public boolean isNucleotide(char X_or_Y)

processEv

public void processEv(java.awt.AWTEvent ev)

Specified by:

processEv in interface ProcessEv

See Also:

EvAdapter

addPoints

public void addPoints(byte[] tX,
                      int startX,
                      boolean revX,
                      int fromX,
                      byte[] tY,
                      int startY,
                      boolean revY,
                      int fromY,
                      double score,
                      int[][] vHits)

setBl2seq

public void setBl2seq(int[][] data,
                      java.lang.Object hasCtrlPnl)

getValues

public short[][] getValues(byte[] seqX,
                           char tX,
                           byte[] seqY,
                           char tY,
                           int w,
                           int h,
                           int[] weights)

handleEvent

public final void handleEvent(StrapEvent ev)

Specified by:

handleEvent in interface StrapListener

paintHook

public boolean paintHook(javax.swing.JComponent component,
                         java.awt.Graphics g,
                         boolean after)

Specified by:

paintHook in interface PaintHook

after - This method is called once before and once after super.paintComponent.

Returns:

means do not call super.paintComponent

log

public BA log()

getControlPanel

public javax.swing.JComponent getControlPanel(boolean real)

Specified by:

getControlPanel in interface HasControlPanel