org.emboss.jemboss.editor
Class PlotConsensus

java.lang.Object
  |
  +--java.awt.Component
        |
        +--java.awt.Container
              |
              +--javax.swing.JComponent
                    |
                    +--javax.swing.JPanel
                          |
                          +--org.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

See Also:
Serialized Form

Field Summary
private  int interval
           
private  int numbins
           
private  float[] sumscore
           
private  GraphicSequenceCollection viewPane
           
private  float ymax
           
private  float ymin
           
 
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)
           
 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)
           
 void setInterval(int interval)
           
 void setPlotSize()
           
 
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

numbins

private int numbins

interval

private int interval

ymin

private float ymin

ymax

private float ymax

viewPane

private GraphicSequenceCollection viewPane
Constructor Detail

PlotConsensus

public PlotConsensus(java.io.File matrixFile,
                     java.util.Vector seqs,
                     int winsize,
                     int interval,
                     GraphicSequenceCollection viewPane)

PlotConsensus

public PlotConsensus(java.io.File matrixFile,
                     java.util.Vector seqs,
                     int winsize,
                     int interval)

PlotConsensus

public PlotConsensus(java.lang.String matrixJar,
                     java.lang.String matrixFileName,
                     java.util.Vector seqs,
                     int winsize,
                     int interval)

PlotConsensus

public PlotConsensus(Matrix mat,
                     java.util.Vector seqs,
                     int winsize,
                     int interval,
                     GraphicSequenceCollection viewPane)

PlotConsensus

public PlotConsensus(Matrix mat,
                     java.util.Vector seqs,
                     int winsize,
                     int interval)
Method Detail

createPlot

private void createPlot(Matrix mat,
                        java.util.Vector seqs,
                        int winsize)

setPlotSize

public void setPlotSize()

getResidue

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


getSequenceWeight

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


getMaxSequenceLength

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


paintComponent

public void paintComponent(java.awt.Graphics g)
Overrides:
paintComponent in class javax.swing.JComponent

setInterval

public void setInterval(int interval)

main

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