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'STRAP:multiple sequence alignments ' | ||||||||
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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
public class DialogDotPlot
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:
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JComponent |
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javax.swing.JComponent.AccessibleJComponent |
Nested classes/interfaces inherited from class java.awt.Component |
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java.awt.Component.BaselineResizeBehavior |
Field Summary | |
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static long |
BL2SEQ
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static long |
CB_HITS
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static java.lang.String |
CB_LAB_Trace
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static long |
NUCLEOTIDES
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Fields inherited from class charite.christo.ChPanel |
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KEY_REPRESENT_COMPONENT |
Fields inherited from class javax.swing.JComponent |
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TOOL_TIP_TEXT_KEY, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW |
Fields inherited from class java.awt.Component |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface charite.christo.Disposable |
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NONE |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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DialogDotPlot()
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DialogDotPlot(long options,
Protein pX,
Protein pY)
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Method Summary | |
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void |
addPoints(byte[] tX,
int startX,
boolean revX,
int fromX,
byte[] tY,
int startY,
boolean revY,
int fromY,
double score,
int[][] vHits)
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void |
dispose()
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javax.swing.JComponent |
getControlPanel(boolean real)
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byte[] |
getSeq(char X_or_Y)
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short[][] |
getValues(byte[] seqX,
char tX,
byte[] seqY,
char tY,
int w,
int h,
int[] weights)
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void |
handleEvent(StrapEvent ev)
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boolean |
isNucleotide(char X_or_Y)
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BA |
log()
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boolean |
paintHook(javax.swing.JComponent component,
java.awt.Graphics g,
boolean after)
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void |
processEv(java.awt.AWTEvent ev)
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void |
setBl2seq(int[][] data,
java.lang.Object hasCtrlPnl)
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Methods inherited from class charite.christo.strap.AbstractDialogJPanel |
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isDisposed, pTop |
Methods inherited from class javax.swing.JPanel |
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getAccessibleContext, getUI, getUIClassID, setUI, updateUI |
Methods inherited from class javax.swing.JComponent |
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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 |
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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 |
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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 |
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equals, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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public static final long BL2SEQ
public static final long CB_HITS
public static final long NUCLEOTIDES
public static final java.lang.String CB_LAB_Trace
Constructor Detail |
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public DialogDotPlot()
public DialogDotPlot(long options, Protein pX, Protein pY)
Method Detail |
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public void dispose()
dispose
in interface Disposable
dispose
in class AbstractDialogJPanel
public byte[] getSeq(char X_or_Y)
public boolean isNucleotide(char X_or_Y)
public void processEv(java.awt.AWTEvent ev)
processEv
in interface ProcessEv
EvAdapter
public void addPoints(byte[] tX, int startX, boolean revX, int fromX, byte[] tY, int startY, boolean revY, int fromY, double score, int[][] vHits)
public void setBl2seq(int[][] data, java.lang.Object hasCtrlPnl)
public short[][] getValues(byte[] seqX, char tX, byte[] seqY, char tY, int w, int h, int[] weights)
public final void handleEvent(StrapEvent ev)
handleEvent
in interface StrapListener
public boolean paintHook(javax.swing.JComponent component, java.awt.Graphics g, boolean after)
paintHook
in interface PaintHook
after
- This method is called once before and once after super.paintComponent.
public BA log()
public javax.swing.JComponent getControlPanel(boolean real)
getControlPanel
in interface HasControlPanel
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