org.emboss.jemboss.editor
Class ConsensusOptions

java.lang.Object
  extended byjava.awt.Component
      extended byjava.awt.Container
          extended byjava.awt.Window
              extended byjava.awt.Frame
                  extended byjavax.swing.JFrame
                      extended byorg.emboss.jemboss.editor.ConsensusOptions
All Implemented Interfaces:
javax.accessibility.Accessible, java.awt.image.ImageObserver, java.awt.MenuContainer, javax.swing.RootPaneContainer, java.io.Serializable, javax.swing.WindowConstants

public class ConsensusOptions
extends javax.swing.JFrame

Defines the options to be used in calculating a consensus

See Also:
Serialized Form

Nested Class Summary
 
Nested classes inherited from class javax.swing.JFrame
javax.swing.JFrame.AccessibleJFrame
 
Nested classes inherited from class java.awt.Frame
java.awt.Frame.AccessibleAWTFrame
 
Nested classes inherited from class java.awt.Window
java.awt.Window.AccessibleAWTWindow
 
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  TextFieldFloat caseFloat
          set the case
private  java.awt.Cursor cbusy
           
private  java.awt.Cursor cdone
           
private  GraphicSequenceCollection gsc
          graphic sequence collection
private  TextFieldInt idInt
          identity
private  javax.swing.JScrollPane jspSequence
           
private  Matrix mat
          scoring matrix
private  TextFieldFloat pluralFloat
          plurality
 
Fields inherited from class javax.swing.JFrame
accessibleContext, EXIT_ON_CLOSE, rootPane, rootPaneCheckingEnabled
 
Fields inherited from class java.awt.Frame
CROSSHAIR_CURSOR, DEFAULT_CURSOR, E_RESIZE_CURSOR, HAND_CURSOR, ICONIFIED, MAXIMIZED_BOTH, MAXIMIZED_HORIZ, MAXIMIZED_VERT, MOVE_CURSOR, N_RESIZE_CURSOR, NE_RESIZE_CURSOR, NORMAL, NW_RESIZE_CURSOR, S_RESIZE_CURSOR, SE_RESIZE_CURSOR, SW_RESIZE_CURSOR, TEXT_CURSOR, W_RESIZE_CURSOR, WAIT_CURSOR
 
Fields inherited from class java.awt.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 javax.swing.WindowConstants
DISPOSE_ON_CLOSE, DO_NOTHING_ON_CLOSE, HIDE_ON_CLOSE
 
Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
 
Constructor Summary
ConsensusOptions(javax.swing.JScrollPane jspSequence)
           
 
Method Summary
 float getCase()
          Get the minimum positive matches for a site to be made upper case in the consensus.
 int getIdentity()
          Get the minimum identical matches for a site to be included in the consensus.
 float getPlurality()
          Get the minimum positive match score for a site to be included in the consensus.
protected  void setCase(float caseValue)
          Set the minimum positive matches for a site to be made upper case in the consensus.
protected  void setGraphicSequenceCollection(GraphicSequenceCollection gsc)
          Set the graphic sequence collection
protected  void setMatrix(Matrix mat)
          Set the matrix to use
protected  void setPlurality(float plurality)
          Set the minimum positive match score for a site to be included in the consensus.
 
Methods inherited from class javax.swing.JFrame
addImpl, createRootPane, frameInit, getAccessibleContext, getContentPane, getDefaultCloseOperation, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isDefaultLookAndFeelDecorated, isRootPaneCheckingEnabled, paramString, processWindowEvent, remove, setContentPane, setDefaultCloseOperation, setDefaultLookAndFeelDecorated, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update
 
Methods inherited from class java.awt.Frame
addNotify, finalize, getCursorType, getExtendedState, getFrames, getIconImage, getMaximizedBounds, getMenuBar, getState, getTitle, isResizable, isUndecorated, remove, removeNotify, setCursor, setExtendedState, setIconImage, setMaximizedBounds, setMenuBar, setResizable, setState, setTitle, setUndecorated
 
Methods inherited from class java.awt.Window
addPropertyChangeListener, addPropertyChangeListener, addWindowFocusListener, addWindowListener, addWindowStateListener, applyResourceBundle, applyResourceBundle, createBufferStrategy, createBufferStrategy, dispose, getBufferStrategy, getFocusableWindowState, getFocusCycleRootAncestor, getFocusOwner, getFocusTraversalKeys, getGraphicsConfiguration, getInputContext, getListeners, getLocale, getMostRecentFocusOwner, getOwnedWindows, getOwner, getToolkit, getWarningString, getWindowFocusListeners, getWindowListeners, getWindowStateListeners, hide, isActive, isFocusableWindow, isFocusCycleRoot, isFocused, isShowing, pack, postEvent, processEvent, processWindowFocusEvent, processWindowStateEvent, removeWindowFocusListener, removeWindowListener, removeWindowStateListener, setCursor, setFocusableWindowState, setFocusCycleRoot, setLocationRelativeTo, show, toBack, toFront
 
Methods inherited from class java.awt.Container
add, add, add, add, add, addContainerListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalPolicy, getInsets, getLayout, getMaximumSize, getMinimumSize, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, remove, removeAll, removeContainerListener, setFocusTraversalKeys, setFocusTraversalPolicy, setFont, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isOpaque, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, resize, resize, setBackground, setBounds, setBounds, setComponentOrientation, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, setVisible, show, size, toString, transferFocus, transferFocusUpCycle
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface java.awt.MenuContainer
getFont, postEvent
 

Field Detail

pluralFloat

private TextFieldFloat pluralFloat
plurality


idInt

private TextFieldInt idInt
identity


caseFloat

private TextFieldFloat caseFloat
set the case


gsc

private GraphicSequenceCollection gsc
graphic sequence collection


mat

private Matrix mat
scoring matrix


cbusy

private java.awt.Cursor cbusy

cdone

private java.awt.Cursor cdone

jspSequence

private javax.swing.JScrollPane jspSequence
Constructor Detail

ConsensusOptions

public ConsensusOptions(javax.swing.JScrollPane jspSequence)
Method Detail

getPlurality

public float getPlurality()
Get the minimum positive match score for a site to be included in the consensus.


getCase

public float getCase()
Get the minimum positive matches for a site to be made upper case in the consensus.


getIdentity

public int getIdentity()
Get the minimum identical matches for a site to be included in the consensus.


setCase

protected void setCase(float caseValue)
Set the minimum positive matches for a site to be made upper case in the consensus. The float is rounded to 2 decimal places.


setGraphicSequenceCollection

protected void setGraphicSequenceCollection(GraphicSequenceCollection gsc)
Set the graphic sequence collection


setMatrix

protected void setMatrix(Matrix mat)
Set the matrix to use


setPlurality

protected void setPlurality(float plurality)
Set the minimum positive match score for a site to be included in the consensus. The float is rounded to 2 decimal places.