org.emboss.jemboss.editor
Class PlotConsensus

java.lang.Object
  extended byjava.awt.Component
      extended byjava.awt.Container
          extended byjavax.swing.JComponent
              extended byjavax.swing.JPanel
                  extended byorg.emboss.jemboss.editor.PlotConsensus
All Implemented Interfaces:
javax.accessibility.Accessible, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable

public class PlotConsensus
extends javax.swing.JPanel

Plot the average similarity. This is calculated by:

Av. Sim. = sum( Mij*wi + Mji*w2 ) / ( (Nseq*Wsize)*((Nseq-1)*Wsize) )

sum - over column*window size
M - matrix comparison table
i,j - wrt residue i or j
Nseq - no. of sequences in the alignment
Wsize - window size

See Also:
Serialized Form

Nested Class Summary
 
Nested classes inherited from class javax.swing.JPanel
javax.swing.JPanel.AccessibleJPanel
 
Nested classes inherited from class javax.swing.JComponent
javax.swing.JComponent.AccessibleJComponent
 
Nested classes inherited from class java.awt.Container
java.awt.Container.AccessibleAWTContainer
 
Nested classes inherited from class java.awt.Component
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy
 
Field Summary
private  int interval
          residue width
private  int numbins
          number of graph bins making up the seq length
private  float[] sumscore
          sum of scores for each column
private  GraphicSequenceCollection viewPane
          associated sequence panel
private  float ymax
          maximum y value
private  float ymin
          minimum y value
 
Fields inherited from class javax.swing.JPanel
 
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.Container
 
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
PlotConsensus(java.io.File matrixFile, java.util.Vector seqs, int winsize, int interval)
           
PlotConsensus(java.io.File matrixFile, java.util.Vector seqs, int winsize, int interval, GraphicSequenceCollection viewPane)
           
PlotConsensus(Matrix mat, java.util.Vector seqs, int winsize, int interval)
           
PlotConsensus(Matrix mat, java.util.Vector seqs, int winsize, int interval, GraphicSequenceCollection viewPane)
           
PlotConsensus(java.lang.String matrixJar, java.lang.String matrixFileName, java.util.Vector seqs, int winsize, int interval)
           
 
Method Summary
private  void createPlot(Matrix mat, java.util.Vector seqs, int winsize)
          Create the consensus plot
 int getMaxSequenceLength(java.util.Vector seqs)
          Check all sequences lengths and return length of the longest sequence
 java.lang.String getResidue(java.util.Vector seqs, int i, int k)
          Returns the residue of the sequence i at position k
 float getSequenceWeight(java.util.Vector seqs, int i)
          Returns the weight of sequence i
static void main(java.lang.String[] args)
           
 void paintComponent(java.awt.Graphics g)
          Override paintComponent to draw consensus plot
 void setInterval(int interval)
          Set the interval
 void setPlotSize()
          Set the consensus plot preferred size using the graph dimensions
 
Methods inherited from class javax.swing.JPanel
getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI
 
Methods inherited from class javax.swing.JComponent
addAncestorListener, addNotify, addPropertyChangeListener, addPropertyChangeListener, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getGraphics, getHeight, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPreferredSize, getPropertyChangeListeners, getPropertyChangeListeners, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isPreferredSizeSet, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFont, setForeground, 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, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, 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, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, 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, processMouseEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, 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
 

Field Detail

sumscore

private float[] sumscore
sum of scores for each column


numbins

private int numbins
number of graph bins making up the seq length


interval

private int interval
residue width


ymin

private float ymin
minimum y value


ymax

private float ymax
maximum y value


viewPane

private GraphicSequenceCollection viewPane
associated sequence panel

Constructor Detail

PlotConsensus

public PlotConsensus(java.io.File matrixFile,
                     java.util.Vector seqs,
                     int winsize,
                     int interval,
                     GraphicSequenceCollection viewPane)
Parameters:
matrixFile - scoring matrix file
seqs - vector of the Sequence objects
winsize - window size
interval - residue width
viewPane - graphical sequence view

PlotConsensus

public PlotConsensus(java.io.File matrixFile,
                     java.util.Vector seqs,
                     int winsize,
                     int interval)
Parameters:
matrixFile - scoring matrix file
seqs - vector of the Sequence objects
winsize - window size
interval - residue width

PlotConsensus

public PlotConsensus(java.lang.String matrixJar,
                     java.lang.String matrixFileName,
                     java.util.Vector seqs,
                     int winsize,
                     int interval)
Parameters:
matrixJar - jar file containing matrix
seqs - vector of the Sequence objects
winsize - window size
interval - residue width

PlotConsensus

public PlotConsensus(Matrix mat,
                     java.util.Vector seqs,
                     int winsize,
                     int interval,
                     GraphicSequenceCollection viewPane)
Parameters:
mat - scoring matrix
seqs - vector of the Sequence objects
winsize - window size
interval - residue width
viewPane - graphical sequence view

PlotConsensus

public PlotConsensus(Matrix mat,
                     java.util.Vector seqs,
                     int winsize,
                     int interval)
Parameters:
mat - scoring matrix
seqs - vector of the Sequence objects
winsize - window size
interval - residue width
Method Detail

createPlot

private void createPlot(Matrix mat,
                        java.util.Vector seqs,
                        int winsize)
Create the consensus plot

Parameters:
mat - scoring matrix
seqs - vector of the Sequence objects
winsize - window size

setPlotSize

public void setPlotSize()
Set the consensus plot preferred size using the graph dimensions


getResidue

public java.lang.String getResidue(java.util.Vector seqs,
                                   int i,
                                   int k)
Returns the residue of the sequence i at position k

Parameters:
seqs - vector of Sequence objects
i - sequence index
k - sequence position
Returns:
residue k from sequence i

getSequenceWeight

public float getSequenceWeight(java.util.Vector seqs,
                               int i)
Returns the weight of sequence i

Parameters:
seqs - vector of Sequence objects
i - sequence index
Returns:
sequence weight

getMaxSequenceLength

public int getMaxSequenceLength(java.util.Vector seqs)
Check all sequences lengths and return length of the longest sequence

Parameters:
seqs - vector of Sequence objects
Returns:
length of the longest sequence

paintComponent

public void paintComponent(java.awt.Graphics g)
Override paintComponent to draw consensus plot

Parameters:
g - graphics

setInterval

public void setInterval(int interval)
Set the interval

Parameters:
interval - interval

main

public static void main(java.lang.String[] args)