apollo.gui.detailviewers.exonviewer
Class SelectableDNARenderer

java.lang.Object
  java.awt.Component
      java.awt.Container
          javax.swing.JComponent
              apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer
                  apollo.gui.detailviewers.exonviewer.SelectableDNARenderer

All Implemented Interfaces:

BaseRenderer, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable

public class SelectableDNARenderer
extends DefaultBaseRenderer

See Also:

Serialized Form

Nested Class Summary

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

protected int	exonColorIndex
protected int	transcriptColorIndex
protected java.awt.Color[][]	transcriptColorList

Fields inherited from class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer

c, CENTER_OUTLINE, LEFT_OUTLINE, metrics, NO_OUTLINE, pos, RIGHT_OUTLINE, seq, tier

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

SelectableDNARenderer(SeqAlignPanel baseEditor, int width, int height)

Method Summary

double[]	establishRange(SeqFeatureI sf, int pos, int tier, boolean use_set)
java.awt.Color	getBackgroundBoxColor()
java.awt.Color	getBackgroundLineColor()
java.awt.Component	getBaseRendererComponent(char base, int pos, int tier, SequenceI seq) Get component to be rendered, if pos outside of current range getFeatureAtPosition and reset currentRange, if feature is non null and not an instance of FeatureSetI then its an exon, and set isExon flag
java.awt.Color	getHatchColor()
java.awt.Color	getOutlineColor() Checks if selected or selected refs feature is the feature set at current pos, so an exon as well as a transcript will have an outline color
int	getOutlineType() Checks if selected or selected refs feature is the current feature set, so an exon as well as a transcript will have an outline type
java.awt.Color	getTextColor()
void	paint(java.awt.Graphics g)
void	paintNotify()
void	setSeqSelectColor(java.awt.Color in)
void	setTargetColor(java.awt.Color in)
void	setTargetPos(int pos, int tier)
void	setTier(int tier)

Methods inherited from class apollo.gui.detailviewers.exonviewer.DefaultBaseRenderer

getBrokenEdgeColor, init, setFont

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getAccessibleContext, 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, getUIClassID, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, paramString, 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, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update, updateUI

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

Field Detail

transcriptColorList

protected final java.awt.Color[][] transcriptColorList

transcriptColorIndex

protected int transcriptColorIndex

exonColorIndex

protected int exonColorIndex

Constructor Detail

SelectableDNARenderer

public SelectableDNARenderer(SeqAlignPanel baseEditor,
                             int width,
                             int height)

Method Detail

setTargetPos

public void setTargetPos(int pos,
                         int tier)

setTargetColor

public void setTargetColor(java.awt.Color in)

setSeqSelectColor

public void setSeqSelectColor(java.awt.Color in)

paintNotify

public void paintNotify()

Specified by:

paintNotify in interface BaseRenderer

Overrides:

paintNotify in class DefaultBaseRenderer

getBaseRendererComponent

public java.awt.Component getBaseRendererComponent(char base,
                                                   int pos,
                                                   int tier,
                                                   SequenceI seq)

Get component to be rendered, if pos outside of current range getFeatureAtPosition and reset currentRange, if feature is non null and not an instance of FeatureSetI then its an exon, and set isExon flag

Specified by:

getBaseRendererComponent in interface BaseRenderer

Overrides:

getBaseRendererComponent in class DefaultBaseRenderer

establishRange

public double[] establishRange(SeqFeatureI sf,
                               int pos,
                               int tier,
                               boolean use_set)

getHatchColor

public java.awt.Color getHatchColor()

Overrides:

getHatchColor in class DefaultBaseRenderer

getBackgroundBoxColor

public java.awt.Color getBackgroundBoxColor()

Overrides:

getBackgroundBoxColor in class DefaultBaseRenderer

getBackgroundLineColor

public java.awt.Color getBackgroundLineColor()

Overrides:

getBackgroundLineColor in class DefaultBaseRenderer

getTextColor

public java.awt.Color getTextColor()

Overrides:

getTextColor in class DefaultBaseRenderer

paint

public void paint(java.awt.Graphics g)

Overrides:

paint in class DefaultBaseRenderer

getOutlineType

public int getOutlineType()

Checks if selected or selected refs feature is the current feature set, so an exon as well as a transcript will have an outline type

Overrides:

getOutlineType in class DefaultBaseRenderer

getOutlineColor

public java.awt.Color getOutlineColor()

Checks if selected or selected refs feature is the feature set at current pos, so an exon as well as a transcript will have an outline color

Overrides:

getOutlineColor in class DefaultBaseRenderer

setTier

public void setTier(int tier)