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java.lang.Object java.awt.Component java.awt.Container javax.swing.JComponent javax.swing.JPanel org.emboss.jemboss.editor.PlotConsensus
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
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 |
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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)
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PlotConsensus(java.io.File matrixFile,
java.util.Vector seqs,
int winsize,
int interval,
GraphicSequenceCollection viewPane)
|
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PlotConsensus(Matrix mat,
java.util.Vector seqs,
int winsize,
int interval)
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PlotConsensus(Matrix mat,
java.util.Vector seqs,
int winsize,
int interval,
GraphicSequenceCollection viewPane)
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PlotConsensus(java.lang.String matrixJar,
java.lang.String matrixFileName,
java.util.Vector seqs,
int winsize,
int interval)
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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 |
private float[] sumscore
private int numbins
private int interval
private float ymin
private float ymax
private GraphicSequenceCollection viewPane
Constructor Detail |
public PlotConsensus(java.io.File matrixFile, java.util.Vector seqs, int winsize, int interval, GraphicSequenceCollection viewPane)
matrixFile
- scoring matrix fileseqs
- vector of the Sequence objectswinsize
- window sizeinterval
- residue widthviewPane
- graphical sequence viewpublic PlotConsensus(java.io.File matrixFile, java.util.Vector seqs, int winsize, int interval)
matrixFile
- scoring matrix fileseqs
- vector of the Sequence objectswinsize
- window sizeinterval
- residue widthpublic PlotConsensus(java.lang.String matrixJar, java.lang.String matrixFileName, java.util.Vector seqs, int winsize, int interval)
matrixJar
- jar file containing matrixseqs
- vector of the Sequence objectswinsize
- window sizeinterval
- residue widthpublic PlotConsensus(Matrix mat, java.util.Vector seqs, int winsize, int interval, GraphicSequenceCollection viewPane)
mat
- scoring matrixseqs
- vector of the Sequence objectswinsize
- window sizeinterval
- residue widthviewPane
- graphical sequence viewpublic PlotConsensus(Matrix mat, java.util.Vector seqs, int winsize, int interval)
mat
- scoring matrixseqs
- vector of the Sequence objectswinsize
- window sizeinterval
- residue widthMethod Detail |
private void createPlot(Matrix mat, java.util.Vector seqs, int winsize)
mat
- scoring matrixseqs
- vector of the Sequence objectswinsize
- window sizepublic void setPlotSize()
public java.lang.String getResidue(java.util.Vector seqs, int i, int k)
seqs
- vector of Sequence objectsi
- sequence indexk
- sequence position
public float getSequenceWeight(java.util.Vector seqs, int i)
seqs
- vector of Sequence objectsi
- sequence index
public int getMaxSequenceLength(java.util.Vector seqs)
seqs
- vector of Sequence objects
public void paintComponent(java.awt.Graphics g)
g
- graphicspublic void setInterval(int interval)
interval
- intervalpublic static void main(java.lang.String[] args)
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