apollo.gui.detailviewers.sequencealigner
Class MultiTierPanel

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              javax.swing.JPanel
                  apollo.gui.detailviewers.sequencealigner.MultiTierPanel

All Implemented Interfaces:

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

Direct Known Subclasses:

HomogeneousPanel, ReferencePanel, ReferencePanel

public class MultiTierPanel
extends javax.swing.JPanel
implements javax.swing.Scrollable, BaseScrollable

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel

javax.swing.JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

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.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

MultiTierPanel(FeaturePlaceFinder.Type type)

Method Summary

AbstractTierPanel	addFeature(SeqFeatureI feature)
AbstractTierPanel	addPanel(AbstractTierPanel panel) Adds a new
int	basePairToTierPosition(int basePair) Converts from base pair to tier position
boolean	canAddFeature(SeqFeatureI feature)
void	clear()
int	getBaseHeight()
int	getBaseWidth()
java.util.Collection<SeqFeatureI>	getFeatures()
int	getHigh(SeqFeatureI sf)
int	getLow(SeqFeatureI sf)
SeqFeatureI	getNextFeature(int p) Given a pixel position return the next feature
Orientation	getOrientation()
AbstractTierPanel	getPanel(int i)
java.util.List<AbstractTierPanel>	getPanels()
java.awt.Point	getPixelForPosition(int p)
int	getPositionForPixel(java.awt.Point p)
java.awt.Dimension	getPreferredScrollableViewportSize() These Are the methods needed to implement the Scrollable interface.
SeqFeatureI	getPrevFeature(int p) Given a pixel position return the previous feature
ReadingFrame	getReadingFrame()
SequenceI	getReferenceSequence()
BaseRendererI	getRenderer()
int	getScrollableBlockIncrement(java.awt.Rectangle visibleRect, int orientation, int direction)
boolean	getScrollableTracksViewportHeight()
boolean	getScrollableTracksViewportWidth()
int	getScrollableUnitIncrement(java.awt.Rectangle visibleRect, int orientation, int direction)
Strand	getStrand()
TierI	getTier(int i)
java.util.List<TierI>	getTiers()
SequenceType	getType()
int	getVisibleBase()
int	getVisibleBaseCount()
int	numTiers()
void	paint(java.awt.Graphics g)
int	pixelPositionToTierPosition(int p) Converts from pixel position to tier position
void	reformat(boolean isRecursive) calculate size of components, calculate size of self, add components
void	removePanel(AbstractTierPanel panel)
void	removeTier(TierI tier)
void	scrollToBase(int pos)
void	scrollToPosition(int pos) position is pixel position
void	setOrientation(Orientation o)
void	setReadingFrame(ReadingFrame rf)
void	setReferenceSequence(SequenceI s)
void	setRenderer(BaseRendererI r)
void	setStrand(Strand s)
void	switchOrientation()
void	switchStrand()
int	tierForPixel(java.awt.Point p)
int	tierPositionToBasePair(int position) Converts from tier position to base pair
int	tierPositionToPixelPosition(int p) Converts from tier position to pixel position

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, 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, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, 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, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, 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, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, 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

Constructor Detail

MultiTierPanel

public MultiTierPanel(FeaturePlaceFinder.Type type)

Method Detail

canAddFeature

public boolean canAddFeature(SeqFeatureI feature)

addFeature

public AbstractTierPanel addFeature(SeqFeatureI feature)

getFeatures

public java.util.Collection<SeqFeatureI> getFeatures()

addPanel

public AbstractTierPanel addPanel(AbstractTierPanel panel)

Adds a new

Parameters:

tier -

panel -

Returns:

getPanels

public java.util.List<AbstractTierPanel> getPanels()

getTiers

public java.util.List<TierI> getTiers()

removeTier

public void removeTier(TierI tier)

removePanel

public void removePanel(AbstractTierPanel panel)

numTiers

public int numTiers()

paint

public void paint(java.awt.Graphics g)

Overrides:

paint in class javax.swing.JComponent

reformat

public void reformat(boolean isRecursive)

calculate size of components, calculate size of self, add components

getTier

public TierI getTier(int i)

getPanel

public AbstractTierPanel getPanel(int i)

tierForPixel

public int tierForPixel(java.awt.Point p)

basePairToTierPosition

public int basePairToTierPosition(int basePair)

Converts from base pair to tier position

tierPositionToBasePair

public int tierPositionToBasePair(int position)

Converts from tier position to base pair

pixelPositionToTierPosition

public int pixelPositionToTierPosition(int p)

Converts from pixel position to tier position

tierPositionToPixelPosition

public int tierPositionToPixelPosition(int p)

Converts from tier position to pixel position

getStrand

public Strand getStrand()

getType

public SequenceType getType()

getPixelForPosition

public java.awt.Point getPixelForPosition(int p)

getPositionForPixel

public int getPositionForPixel(java.awt.Point p)

switchStrand

public void switchStrand()

setStrand

public void setStrand(Strand s)

getHigh

public int getHigh(SeqFeatureI sf)

getLow

public int getLow(SeqFeatureI sf)

getReferenceSequence

public SequenceI getReferenceSequence()

setReferenceSequence

public void setReferenceSequence(SequenceI s)

getReadingFrame

public ReadingFrame getReadingFrame()

setReadingFrame

public void setReadingFrame(ReadingFrame rf)

getOrientation

public Orientation getOrientation()

switchOrientation

public void switchOrientation()

setOrientation

public void setOrientation(Orientation o)

getRenderer

public BaseRendererI getRenderer()

setRenderer

public void setRenderer(BaseRendererI r)

clear

public void clear()

getBaseHeight

public int getBaseHeight()

getBaseWidth

public int getBaseWidth()

getNextFeature

public SeqFeatureI getNextFeature(int p)

Given a pixel position return the next feature

getPrevFeature

public SeqFeatureI getPrevFeature(int p)

Given a pixel position return the previous feature

getPreferredScrollableViewportSize

public java.awt.Dimension getPreferredScrollableViewportSize()

These Are the methods needed to implement the Scrollable interface.

Specified by:

getPreferredScrollableViewportSize in interface javax.swing.Scrollable

See Also:

Scrollable

getScrollableBlockIncrement

public int getScrollableBlockIncrement(java.awt.Rectangle visibleRect,
                                       int orientation,
                                       int direction)

Specified by:

getScrollableBlockIncrement in interface javax.swing.Scrollable

getScrollableTracksViewportHeight

public boolean getScrollableTracksViewportHeight()

Specified by:

getScrollableTracksViewportHeight in interface javax.swing.Scrollable

getScrollableTracksViewportWidth

public boolean getScrollableTracksViewportWidth()

Specified by:

getScrollableTracksViewportWidth in interface javax.swing.Scrollable

getScrollableUnitIncrement

public int getScrollableUnitIncrement(java.awt.Rectangle visibleRect,
                                      int orientation,
                                      int direction)

Specified by:

getScrollableUnitIncrement in interface javax.swing.Scrollable

getVisibleBase

public int getVisibleBase()

Specified by:

getVisibleBase in interface BaseScrollable

getVisibleBaseCount

public int getVisibleBaseCount()

Specified by:

getVisibleBaseCount in interface BaseScrollable

scrollToBase

public void scrollToBase(int pos)

Specified by:

scrollToBase in interface BaseScrollable

scrollToPosition

public void scrollToPosition(int pos)

position is pixel position