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java.lang.Object | +--java.awt.Component | +--java.awt.Container | +--javax.swing.JComponent | +--javax.swing.JPanel | +--org.emboss.jemboss.editor.PlotConsensus
Field Summary | |
private int |
interval
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private int |
numbins
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private float[] |
sumscore
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private GraphicSequenceCollection |
viewPane
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private float |
ymax
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private float |
ymin
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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)
|
|
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)
|
|
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)
|
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)
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void |
paintComponent(java.awt.Graphics g)
|
void |
setInterval(int interval)
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void |
setPlotSize()
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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)
public PlotConsensus(java.io.File matrixFile, java.util.Vector seqs, int winsize, int interval)
public PlotConsensus(java.lang.String matrixJar, java.lang.String matrixFileName, java.util.Vector seqs, int winsize, int interval)
public PlotConsensus(Matrix mat, java.util.Vector seqs, int winsize, int interval, GraphicSequenceCollection viewPane)
public PlotConsensus(Matrix mat, java.util.Vector seqs, int winsize, int interval)
Method Detail |
private void createPlot(Matrix mat, java.util.Vector seqs, int winsize)
public void setPlotSize()
public java.lang.String getResidue(java.util.Vector seqs, int i, int k)
public float getSequenceWeight(java.util.Vector seqs, int i)
public int getMaxSequenceLength(java.util.Vector seqs)
public void paintComponent(java.awt.Graphics g)
paintComponent
in class javax.swing.JComponent
public void setInterval(int interval)
public static void main(java.lang.String[] args)
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