gata.plotter
Class AlignPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  gata.plotter.AlignPanel

All Implemented Interfaces:

javax.accessibility.Accessible, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable

public class AlignPanel

extends javax.swing.JPanel

Author:

Nix Panel holding the DNA box-line-box alignment

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Field Summary

Fields inherited from class javax.swing.JComponent

TOOL_TIP_TEXT_KEY, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

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

AlignPanel(GATAParams params)

Method Summary

static void	createShapes(Alignment[] alignments, double refX, double refY, double compX, double compY, double ntLenBig, double C, double D)
int	getAlignFrameHeight()
int	getAlignFrameWidth()
Alignment[]	getAlignments()
int	getHeightBuffImage()
javax.swing.JViewport	getViewPort()
Alignment[]	getVisableAlignments()
int	getWidthBuffImage()
void	makeAllShapes(int width, int height)
java.awt.image.BufferedImage	makeBufferedImage(double scale, boolean saveVisible) Generates a BufferedImage from the panel.
void	makeVisableAlignments() Resets an array of visable alignments
void	paintComponent(java.awt.Graphics g)
void	redrawGlyphPanel(AnnoSpecParams asp)
void	setAlignFrameWidth(int i)
void	setConsole(Console console)
void	setDrawCompBox(boolean drawCompBox)
void	setMaxScore(double max)
void	setMinScore(double min)
void	setPresenceOfGFFs()
void	setToolsRef(ToolsFrame aTF)
void	setViewPort(javax.swing.JViewport viewport)
void	zoom(int zScalar)

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, 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, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, 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, paintImmediately, paintImmediately, print, printAll, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removePropertyChangeListener, removePropertyChangeListener, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, 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, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, 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, remove, remove, removeAll, removeContainerListener, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setLayout, transferFocusBackward, transferFocusDownCycle, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, createImage, createImage, createVolatileImage, createVolatileImage, dispatchEvent, enable, 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, 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

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

AlignPanel

public AlignPanel(GATAParams params)

Method Detail

setToolsRef

public void setToolsRef(ToolsFrame aTF)

setPresenceOfGFFs

public void setPresenceOfGFFs()

zoom

public void zoom(int zScalar)

makeBufferedImage

public java.awt.image.BufferedImage makeBufferedImage(double scale,
                                                      boolean saveVisible)

Generates a BufferedImage from the panel. Can be scaled or cropped to visible.

redrawGlyphPanel

public void redrawGlyphPanel(AnnoSpecParams asp)

makeAllShapes

public void makeAllShapes(int width,
                          int height)

createShapes

public static void createShapes(Alignment[] alignments,
                                double refX,
                                double refY,
                                double compX,
                                double compY,
                                double ntLenBig,
                                double C,
                                double D)

paintComponent

public void paintComponent(java.awt.Graphics g)

makeVisableAlignments

public void makeVisableAlignments()

Resets an array of visable alignments

setMinScore

public void setMinScore(double min)

setMaxScore

public void setMaxScore(double max)

setConsole

public void setConsole(Console console)

getVisableAlignments

public Alignment[] getVisableAlignments()

setViewPort

public void setViewPort(javax.swing.JViewport viewport)

setAlignFrameWidth

public void setAlignFrameWidth(int i)

getAlignFrameHeight

public int getAlignFrameHeight()

getAlignFrameWidth

public int getAlignFrameWidth()

getHeightBuffImage

public int getHeightBuffImage()

getWidthBuffImage

public int getWidthBuffImage()

getViewPort

public javax.swing.JViewport getViewPort()

setDrawCompBox

public void setDrawCompBox(boolean drawCompBox)

getAlignments

public Alignment[] getAlignments()